No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
TREECON for windows: A software package for the construction and drawing of evolutionary trees for the MICROSOFT Windows Environment
... Then, molecular identification was conducted using sequencing of the 16S rDNA gene analysis. Genomic DNA was isolated as described by [21] and the extracted DNA was quantified by NanoDrop 2000c (Thermoscientific, Waltham, MA, USA). The uni-Eng. ...
... Proc. 2024, 67, 60 3 of 9 versal primers 16S rRNA prokaryotes: 27f (5 ′ -AGAGTTTGATCCTGGCTCAG-3 ′ ) and 1492r (5 ′ -TACGGYTACCTTGTTACGACTT-3 ′ ) [21] were used for amplification of the 16S rDNA genes. ...
... The amplified DNA was purified as described by [21]. Sequencing of obtaining fragments was performed on an Applied Biosystems Genetic Analyzer automatic sequencer. ...
... Sequences accession numbers are indicated. The analysis was conducted by a neighborjoining method of the ssu rRNA gene using Treecon software [100] after ClustalW alignment of the sequences [101]. Bootstrap values lower than 75% are not displayed. ...
... Sequences accession numbers are indicated. The analysis was conducted by a neighbor-joining method of the ssu rRNA gene using Treecon software [100] after ClustalW alignment of the sequences [101]. Bootstrap values lower than 75% are not displayed. ...
Wild chimpanzee populations in West Africa (Pan troglodytes verus) have dramatically decreased as a direct consequence of anthropogenic activities and infectious diseases. Little information is currently available on the epidemiology, pathogenic significance, and zoonotic potential of protist species in wild chimpanzees. This study investigates the occurrence and genetic diversity of intestinal and blood protists as well as filariae in faecal samples (n = 234) from wild chimpanzees in the Dindefelo Community Nature Reserve, Senegal. PCR-based results revealed the presence of intestinal potential pathogens (Sarcocystis spp.: 11.5%; Giardia duodenalis: 2.1%; Cryptosporidium hominis: 0.9%), protist of uncertain pathogenicity (Blastocystis sp.: 5.6%), and commensal species (Entamoeba dispar: 18.4%; Troglodytella abrassarti: 5.6%). Entamoeba histolytica, Enterocytozoon bieneusi, and Balantioides coli were undetected. Blood protists including Plasmodium malariae (0.4%), Trypanosoma brucei (1.3%), and Mansonella perstans (9.8%) were also identified. Sanger sequencing analyses revealed host-adapted genetic variants within Blastocystis, but other parasitic pathogens (C. hominis, P. malariae, T. brucei, M. perstans) have zoonotic potential, suggesting that cross-species transmission between wild chimpanzees and humans is possible in areas where both species overlap. Additionally, we explored potential interactions between intestinal/blood protist species and seasonality and climate variables. Chimpanzees seem to play a more complex role on the epidemiology of pathogenic and commensal protist and nematode species than initially anticipated.
... Cluster analysis was conducted using the Treecon v.1.3b programme [33]. ...
Strawberry anthracnose is becoming more important from a scientific and economic standpoint. The Colletotrichum spp. pathogen complex includes C. fragariae, C. gloeosporioides and C. acutatum. The aim was to use microsatellite (SSR) markers to assess the genetic diversity of Colletotrichum species. We used seven SSR primer pairs previously developed for the C. acutatum (3) and C. gloeosporioides (4) species. To analyze the genetic diversity of C. fragariae, it was discovered that SSR primer pairs created for C. gloeosporioides were helpful. SSR molecular markers were used in this study for the first time to identify the species of C. fragariae. The average polymorphism information content (PIC) value across all SSR primer pairs was 0.72, making them all informative. The most informative SSR primers were CG22 and CG30, with PIC values of 0.83 and 0.82, respectively. We believe these primers are suitable for the genetic diversity analysis of C. fragariae species. Therefore, the SSR primer pairs CG20 and CG30 are suggested for the genetic investigation of C. acutatum and C. gloeosporioides. A higher incidence of Colletotrichum spp. polymorphism in Lithuania can be linked to adaptation to survival in our environment, according to this study’s findings on the number of alleles and the degree of genetic diversity, which are higher than the results reported in the literature.
... The DNA was isolated according to [9] and then treated with the Nan-oDrop 2000c Kit (Thermo Scientific). The universal primers of 16S rRNA prokaryotes were used for the amplification: 27f (5 ′ -AGAGTTTGATCCTGGCTCAG-3 ′ ) and 1492r (5 ′ -TACGGYTACCTTGTTACGACTT-3 ′ ) [13]. The sequencing of the resulting fragments was performed with the Applied Biosystems Genetic Analyzer automatic sequencer. ...
Autotrophic sulfur-oxidizing bacteria can play a key role in the metal bioleaching from low-grade sulfide-containing ores. The most commonly used bioleaching group is presented with acidophilic bacteria of the order Acidithiobacillales. We studied the diversity of bacteria in the arsenopyrite gold-bearing ore and also discovered a wide distribution of neutrophilic non-thermophilic bacteria Thermithiobacillus plumbiphilus in this ore, as well as its drainage and flotation concentrate. For the first time, T. plumbiphilus was isolated from the natural arsenic-containing mineral material. The first description of complete genome for the species T. plumbiphilus was also carried out and discovered genes providing the As resistance. Culturing the isolated strain T. plumbiphilus AAFK confirmed the found bacterial resistance to arsenite and cocadylate during the effective thiosulfate oxidation. Experiments on the arsenopyrite bioleaching showed that T. plumbiphilus AAFK can be used as an auxiliary bacterial culture capable of oxidizing reduced / intermediate sulfur compounds. The genetic basis of the T. plumbiphilus AAFK resistance to the arsenic compounds is discussed; the mechanisms are similar with the ones known for acidophilic thiobacilli. The biofilm formation is shown for the first time for T. plumbiphilus; presumably, it could provide some protection and immobilization of the cells. Structures of the T. plumbiphilus AAFK cells and their production of outer membrane vesicles are described and discussed.
... Genetic distances among the 15 single profiles plus the 6 reference cultivar profiles were estimated using Cluster analysis and Principal coordinates analysis (PCoA). Cluster analysis used Treecon 1.3 b software [28] to provide a UPGMA tree based on Nei and Li's [29] similarity matrix, with 1000 bootstraps over loci shown as a percentage value. The PCoA was carried out using GenAlEx 6.503 with a covariance matrix and data standardization to calculate the genetic distances among varieties. ...
The study of biodiversity is of fundamental importance in the context of environmental protection and eco-sustainable agriculture management. Its preservation has a key role and an extraordinary importance not only for the protection of potential gene pools, which is essential for selection and breeding programs, but also because local varieties are the expression of a territory and therefore reflect culture, knowledge, and tradition heritage. In this paper, 27 local cherry varieties collected in different areas of Sardinia were characterized and described from different perspectives, including pomology and genetics, using SSR markers. A complete framework on the biodiversity of cherry trees in Sardinia is presented, in order to support an objective assessment of different cultivar traits, namely those of agronomical interest, and to support the dissemination and conservation of the historical fruit tree cultivation heritage.
... Phenetic analyses were performed by unweighted pair group method with arithmetic mean (UPGMA) based on Nei and Li's (1979) distance using molecular evolutionary genetic analysis program TREECON (Version 1.3b, Van de Peer and De Wachter 1994) The reliability of the dendrogram was assessed by performing a bootstrap analysis at a 50% threshold with 1000 replications. ...
Terminalia superba and T. ivorensis are difficult to identify with morphological markers. Molecular characterization is very effective to correct the delimitation of timber species, especially when the discriminatory power of morphological markers is weak. In this study, four amplified fragment length polymorphism (AFLP) marker combinations were used to determine the taxonomic relationship among a total of 33 accessions of the genus Terminalia, consisting of two species, Terminalia ivorensis (12 accessions) and T. superba (21). The primer combinations produced a total of 740 fragments out of which 619 (83.6%) were polymorphic. Among all the primer combinations used, E-ACT/M-CTC was the most informative, which generated 11 unique markers for clear identification of the two species. The average polymorphic information content (PIC) ranged from 0.24 (E-ACT/M-CAT) to 0.28 (E-ACT/M-CTC) while the resolving power (RP) varied from 40.73 (E-AAC/M-CTA) to 63.76 (E-ACT/M-CTC). The genetic difference between the two species was significant (PhiPT = 0.610, p<0.001). All 33 accessions were delimited by both the UPGMA cluster and principal component analysis. Based on the results, it was concluded that E-ACT/M-CTC is the best among the marker combinations used for molecular study of the two tree species and used significantly to distinguish them. STRUCTURE analysis identified two accessions of Terminalia superba with alleles derived from T. ivorensis as well as revealed five putative hybrid accessions, which requires further genetic investigation to substantiate the finding.
... As needed, a Phylo-mLogo [96] display of the multiple sequence alignment was generated by writing a simple tree, aggregating clade-specific sets of seqs. Multiple sequence alignments were trimmed to eliminate sites with gaps or judged poorly informative in the Phylo-mLogo display, using Treecon [97]. Parsimony-informative sites were selected using Mega [98]. ...
The Lactobacillales (LB) stand apart among bacterial orders, using manganese (Mn) instead of iron to support their growth and swiftly ferment complex foods while acidifying their environment. The present work investigates whether a shift in the use of Mn could mark the origin of LB. Transmembrane carriers of the ubiquitous Slc11 family play key roles in LB physiology by catalyzing proton-dependent Mn import. In prior studies, the Slc11 clade found in LB (MntH Cb, MCb) showed both remarkable structural plasticity and highly efficient Mn uptake, and another Slc11 clade, MCg1, demonstrated divergent evolution coinciding with emergence of bacterial genera (e.g., Bordetella, Achromobacter). Herein, the Slc11 clade MCb is subdivided in sister groups: MCbie and MCbgut. MCbie derives directly from the Slc11 clade MCa, pointing an intermediate stage in the evolution of MCbgut. MCbie predominates in marine Bacillaceae, is more conserved than MCbgut, lacks the structural plasticity that typify MCbgut carriers, and responds differently to identical mutagenesis. Exchanging MCbie/MCbgut amino acid residues at sites that distinguish these clades showed conformation-dependent effects with both MCbie and MCbgut templates, and the 3D location of the targeted sites in the carrier structure together suggests that the mechanism to open the inner gate, and release Mn into the cytoplasm, differs between MCbie and MCbgut. Building on the established phylogeny for Enterococcus revealed that a pair of genes encoding MCbgut was present in the common ancestor of LB, as MCbgu1 and MCbgu2 templates exhibited distinct structural dynamics properties. These data are discussed when examining whether MCbgut+ LB could emerge in the upper gut of early vertebrates (ca. 540 mya), through genome contraction and evolution toward Mn-centrism, as they specialized as gastric aids favoring stomach establishment in jawed vertebrates through bi-directional communication with host nervous, endocrine and immune systems.
... ÑÎfl ÔÓÒÚÓÂÌËfl ‰ẨÓ" ‡ÏÏ˚ "ÂÌÂÚ˘ÂÒÍËı ‡Á΢ËÈ Ì ‡ ÓÒÌÓ‚Â RAPD-ÒÔÂÍÚÓ‚, ÔÓÎÛ˜ÂÌÌ˚ı Ò ÔÓÏÓ˘¸˛ ¯ÂÒÚË Ô ‡ÈÏÂÓ‚, ·˚Î ‡ ÒÓÒÚ ‡‚ÎÂÌ ‡ ·ËÌ ‡Ì ‡fl Ï ‡Úˈ ‡. èÓËÁ‚Ó‰ÌÛ˛ Ï ‡ÚËˆÛ ÔÓÔ ‡-Ì˚ı "ÂÌÂÚ˘ÂÒÍËı ‰ËÒÚ ‡ÌˆËÈ [17] ÍÎ ‡ÒÚÂËÁÓ‚ ‡ÎË Ò ÔÓÏÓ˘¸˛ ÔÓ" ‡ÏÏ˚ TREECON for Windows [18] Ò ËÒÔÓθÁÓ‚ ‡ÌËÂÏ ÏÂÚÓ‰ ‡ "·ÎËÊ ‡È¯Â"Ó ÒÓÒÂ-‰ ‡" (Neighbor-Joining). ç ‡‰ÂÊÌÓÒÚ¸ ‚ÂÚ‚ÎÂÌËfl ÓˆÂÌË‚ ‡Î ‡Ò¸ Ì ‡ ÓÒÌÓ‚ ‡ÌËË ‡Ò˜ÂÚÌÓ"Ó Ë̉ÂÍÒ ‡ ·ÛÚÒÚÂÔ ‡ (1000 ÂÔÎËÍ). ...
... Genetic distances were calculated for all Taraxacum accessions, according to Nei and Li (1979), followed by a dendrogram construction using the unweighted pair group method, with arithmetic average (UPGMA), using the Treecon ver. 3.1 software (Van de Peer and De Wachter 1994). Statistical support of the branches was tested with bootstrap analysis using 2000 replicates. ...
The dandelions from Taraxacum sect. Erythrosperma are taxonomically well distinguished and ecologically restricted to warm and sunlit habitats of steppes, dry and sandy grasslands, and distributed in temperate regions of Europe and Central Asia, with some being introduced to North America. Despite the long tradition of botanical research, the taxonomy and distribution of dandelions of T. sect. Erythrosperma is still underexplored in central Europe. In this paper, by combining traditional taxonomic studies supported by micromorphological, molecular and flow cytometry analyses as well as potential distribution modelling we shed light on taxonomical and phylogenetical relationships between members of T. sect. Erythrosperma in Poland. We also provide an identification key, species-checklist, detailed descriptions of morphology and occupated habitats as well as distribution maps for 14 Polish erythrosperms (T. bellicum, T. brachyglossum, T. cristatum, T. danubium, T. disseminatum, T. dissimile, T. lacistophyllum, T. parnassicum, T. plumbeum, T. proximum, T. sandomiriense, T. scanicum, T. tenuilobum, T. tortilobum). Finally, conservation assessments performed using the IUCN method and threat categories for all the examined species are proposed.
Wolanin M, Klichowska E, Jedrzejczyk I, Rewers M, Nobis M (2023) Taxonomy and distribution of Taraxacum sect. Erythrosperma (Asteraceae) in Poland. PhytoKeys 224: 1-88.
... The dendrogram was constructed using the Nei-Li [27] distance and UPGMA methods in the Treecon v.1.3b program [28]. ...
On the summit of a hill with a lack of humidity, and in usually stronger eroded midslope parts, crops thin out. Changing ecological conditions change the soil seed bank as well. The aim of this study was to examine changes in the seed bank size and number of species and the influence of seed surface characteristics on their spread in different-intensity agrophytocenoses under hilly relief conditions. This study included different parts of the hill (summit, midslope and footslope) in Lithuania. The southern exposition slope’s soil was slightly eroded Eutric Retisol (loamic). In spring and autumn, the seed bank was investigated at depths of 0–5 and 5–15 cm. Irrespective of the season, in the soil of permanent grassland, the seed number was 6.8 and 3.4 times smaller compared to those of cereal–grass crop rotation and crop rotation with black fallow. The highest number of seed species was determined in the footslope of the hill. Seeds with rough surfaces dominated on all parts of the hill, but the highest amount (on the average 69.6%) was determined on the summit of the hill. In autumn, a strong correlation was found between the total seed number and soil microbial carbon biomass (r = 0.841–0.922).
... Множественное выравнивание нуклеотидных последовательностей осуществляли в программе Clustal Omega (http://www.ebi.ac.uk/Tools/msa/clustalo/), с последующим анализом результатов выравнивания при помощи программы GeneDoc 2.7 (https://genedoc.software.informer.com/2.7/). Для построения дендрограммы использовали программу TREECON (22). Производные аминокислотные последовательности были получены с помощью программы EditSeq (https://macdownload.informer.com/editseq/download/). Для поиска гомологов полученных последовательностей в базе данных NCBI использовали программу BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi). ...
... The sample was tested using the AMOVA package with the calculation of the population differentiation index using 1000 rounds of premutations (Chesnokov and Kosolapov, 2016). Based on the binary matrix, the genetic distance matrix according to Nei (D) was calculated and a dendrogram was constructed using the UPGMA method, reflecting the degree of similarity of the studied populations according to ISSR-PCR spectra using the Treecon 1.3b computer program with bootstrap support-100 pseudo replicas (Peer and Wachter, 1994). ...
... Sequence alignment including the corresponding sequences of the closest bacterial species was performed using CLUSTALW v 1.75 (Thompson et al., 1994). The phylogenetic trees of the strains studied were constructed using the neighbor-joining algorithm (Saitou and Nei, 1987) of the TREECONW software package ( Van de Peer and De Wachter, 1994) and the Maximum Likelihood algorithm of MEGA 11 v. 11.0.8. ...
... CDDP fingerprinting and transcript profiling procedures using the differential display technique were performed in at least two independent replications, and only reproducible CDDP or TDF bands were used to make a binary matrix for further analysis. Nei and Li [45] genetic distance-based UPGMA dendrograms were constructed using TREECON v. 1.3b software [46]. Homology searches for the sequenced polymorphic TDFs were performed using the BLAST algorithm [47] in the NCBI database. ...
Among the heavy metals (HMs), only cobalt induces a polymorphic response in Vicia faba plants, manifesting as chlorophyll morphoses and a ‘break-through’ effect resulting in the elevated accumulation of other HMs, which makes Co-pretreated broad bean plants an attractive model for investigating soil pollution by HMs. In this study, Co-sensitized V. faba plants were used to evaluate the long-term effect of residual industrial pollution by examining biochemical (H2O2, ascorbic acid, malondialdehyde, free proline, flavonoid, polyphenols, chlorophylls, carotenoids, superoxide dismutase) and molecular (conserved DNA-derived polymorphism and transcript-derived polymorphic fragments) markers after long-term exposure. HM-polluted soil induced a significantly higher frequency of chlorophyll morphoses and lower levels of nonenzymatic antioxidants in Co-pretreated V. faba plants. Both molecular markers effectively differentiated plants from polluted and control soils into distinct clusters, showing that HMs in mildly polluted soil are capable of inducing changes in DNA coding regions. These findings illustrate that strong background abiotic stressors (pretreatment with Co) can aid investigations of mild stressors (slight levels of soil pollution) by complementing each other in antioxidant content reduction and induction of DNA changes.
... Электрофоретический SDS-анализ (Laemmly, 1970) (Агафонов, Агафонова, 1992). Дендрограмма по полипептидным профилям построена методом UPGMA (Sneath, Sokal, 1973) с помощью программы TREECON (version 1.3b) ( Van de Peer, Wachter, 1994). ...
E.V. Shabanova, M.V. Emtseva, A.V. Agafonov
PHYLOGENETIC RELATIONSHIPS BETWEEN
THE CENTRAL ASIAN PERENNIAL GRASSES ELYMUS FEDTSCHENKOI,
E. NEVSKII AND E. PRAERUPTUS (POACEAE)
Central Siberian Botanical Garden SB RAS, Russia, 101, Zolotodolinskaya str., Novosibirsk, 630090, Russia;
ekobozeva87@mail.ru, emtsevamv@yandex.ru, agalex@mail.ru
Elymus fedtschenkoi, E. nevskii and E. praeruptus are three morphologically similar species traditionally assigned
to the informal “Elymus semicostatus group” and distributed in open habitats in the mountainous regions of Central
Asia, including the Russian Gorny Altai. There are no data on the finding of E. praeruptus within Russia to
date. The work provides a detailed analysis of the history of synonymy of the studied species. Their close relationship
is confirmed not only by morphological similarity, but also by the high numbers of bivalents per cell (10–12)
in meiosis in interspecific hybrids (Salomon, 1993). Analysis of the variability of endosperm proteins in individual
caryopses by SDS-electrophoresis showed the following: a) each of the three species has internal polymorphism,
which makes it possible to effectively study inter- and intrapopulation specificity even using non-viable
material; b) differences within the accessions of E. fedtschenkoi – E. nevskii are more pronounced with geographic
remoteness than depending on the formal species; c) the accessions E. praeruptus from Gissar-Alai had completely
unique sets of components, and the visual coincidence of the REM values with other accessions, in our
opinion, may be of a random nature. According to the revealed polymorphism of ISSR markers, E. fedtschenkoi
and E. nevskii have a distinct genetic similarity, while E. praeruptus is noticeably distant from this pair of species.
Probably, biotypes with the trait “long lemma’s awns” (up to 25 mm), attributed to E. fedtschenkoi s. str., together
with biotypes with the trait “short lemma’s awns” (1–6 mm), which are classified as E. nevskii s. str., should be attributed
to a unified complex E. nevskii s.l.
Key words: Elymus semicostatus group, SDS-electrophoresis, ISSR-markers.
For citation. Shabanova, E.V., Emtseva V.V., Agafonov A.V. Phylogenetic relationships between the Central
Asian perennial grasses Elymus fedtschenkoi, E. nevskii and E. praeruptus (Poaceae). Rastitel’nyj Mir Aziatskoj Rossii
= Flora and Vegetation of Asian Russia. 2021;14(4):265-276. DOI 10.15372/RMAR20210401.
... Genomic DNA was isolated from cells using the Fungal/Bacterial DNA Kit (Zymo Research, Irvine, CA, USA) according to the manufacturer's recommendation. The 16S rRNA gene was amplified by PCR using primers universal for 16S rRNA prokaryotes: 27f (5 -AGAGTTTGATCCTGGCTCAG-3 ) and 1492r (5 -TACGGYTACCTTGTTACGACTT-3 ) [17]. The amplified DNA was purified using the Zymoclean Gel DNA Recovery Kit (Zymo Research, Irvine, CA, USA). ...
Microbial interactions play an important role in natural habitat. The long-term coevolution of various species leads to the adaptation of certain types of microorganisms as well as to the formation of a wide variety of interactions such as competitive, antagonistic, pathogenic and parasitic relationships. The aim of this work is a comprehensive study of a new ultramicrobacterium Microbacterium lacticum str. F2E, isolated from perennial oil sludge, which is characterized by high antimicrobial activity and a unique ultrastructural organization of the cell envelope, which includes globular surface ultrastructures with a high negative charge. A previously undescribed mechanism for the antagonistic action of the F2E strain against the prey bacterium is proposed. This mechanism is based on the ability to preferentially capture essential microelements, in which charge interactions and the property of phosphate accumulation may play a significant role. The revealed type of intermicrobial interaction can probably be attributed to the non-contact type antagonistic action in the absence of any diffuse factor secreted by the antagonistic bacteria.
... The allele copy number of SNPs was scored using both the Data Acquisition & Data Analysis software DAx7.1 (Van Mierlo Software Consultancy) and manual scoring. For nucleotide diversity and phylogenetic analysis the consensus haplotype sequences were compared with one another and with S. lycopersicum-derived sequences using MEGA 4 (Tamura et al. 2007) and TREECON (Van de Peer and De Wachter 1994) software. Similarity between each pair of sequences was calculated on the basis of percentage identity and tree construction was performed using the Neighbor-joining method. ...
Key message
Association analysis resulted in the identification of specific StGWD alleles causing either an increase or decrease in starch phosphate content which was verified in diploid and tetraploid potato mapping populations.
Abstract
Potatoes are grown for various purposes like French fries, table potatoes, crisps and for their starch. One of the most important aspects of potato starch is that it contains a high amount of phosphate ester groups which are considered to be important for providing improved functionalization after derivatization processes. Little is known about the variation in phosphate content as such in different potato varieties and thus we studied the genetic diversity for this trait. From other studies it was clear that the phosphate content is controlled by a quantitative trait locus (QTL) underlying the candidate gene α-Glucan Water Dikinase ( StGWD ) on chromosome 5. We performed direct amplicon sequencing of this gene by Sanger sequencing. Sequences of two StGWD amplicons from a global collection of 398 commercial cultivars and progenitor lines were used to identify 16 different haplotypes. By assigning tag SNPs to these haplotypes, each of the four alleles present in a cultivar could be deduced and linked to a phosphate content. A high value for intra-individual heterozygosity was observed ( Ho = 0.765). The average number of different haplotypes per individual ( Ai ) was 3.1. Pedigree analysis confirmed that the haplotypes are identical-by-descent (IBD) and offered insight in the breeding history of elite potato germplasm. Haplotypes originating from introgression of wild potato accessions carrying resistance genes could be traced. Furthermore, association analysis resulted in the identification of specific StGWD alleles causing either an increase or decrease in starch phosphate content varying from 12 nmol PO 4 /mg starch to 38 nmol PO 4 /mg starch. These allele effects were verified in diploid and tetraploid mapping populations and offer possibilities to breed and select for this trait.
... The matrices obtained were used to build phylogenetic trees. The trees were built by the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) [32] using Treecon 1.3b software [33]. To evaluate the confidence intervals of the trees, the bootstrap method with 100 samples was used [34]. ...
Simple Summary
Aggressive-invasive species often interact with native ones, thus considerably changing the biological communities, with ecological, economic, and even social effects. It is a challenge to evaluate the direction and the rate of microevolution in native and introduced populations. One of the ways to do this is to estimate the genetic diversity. An introduction often imposes a reduction in population size (genetic drift, bottleneck, founder effect), which has the potential to reduce genetic diversity. However, after a lag, the genetic diversity can be restored due to repeated invasions (multiply introductions), hybridization between individuals from two different subspecies or species in the invaded ranges, as well as during rapid genetic changes under selection pressures in the novel environment. The purpose of this study was to determine the level of genetic diversity in successful invasive species Lupinus polyphyllus Lindl. and Heracleum sosnowskyi Manden. from Russia and Ukraine, and whether it may be associated with the strategy of their further expansion.
Abstract
In our study, two aggressive-invasive species, Lupinus polyphyllus Lindl. and Heracleum sosnowskyi Manden. from Russia and Ukraine, were investigated. The success in naturalization of both species is associated with human activities, since they have been used in agriculture and floriculture and both have qualities such as environmental tolerance, high fertility and phenotypic plasticity. The purpose of this study was to determine the level of genetic diversity of both species. For Heracleum sosnowskyi Manden., genetic diversity was compared in invasive and native populations. For Lupinus polyphyllus Lindl., the genetic diversity was compared in variety, feral and invasive populations. A genetic diversity was formulated using RAPD, ISSR and REMAP. For Heracleum sosnowskyi Manden., the average genetic diversity within the invasive population was similar (0.432), but slightly less (0.502) than within the native Caucasian population. This may suggest the successful naturalization of invaders and almost complete reconstruction of their genetic diversity. For Lupinus polyphyllus Lindl., the genetic diversity for the invasive population was the highest, with an average of 0.294, while for variety, it was the lowest, with an average of 0.194. The feral population had an intermediate place with an average of 0.248, which could suggest an increase of diversity in the process of naturalization.
... Then, the quantity and quality of the DNA was determined by the biophotometer (Eppendorf, Germany). The 16S rRNA gene was amplified by following the standard method of Turner et al. (1999) using the universal primer pairs 8F (AGA GTT TGA TCC TGG CTC AG) and 1492R (GGT TAC CTT GTT ACG ACT T). The PCR products were excised from the Agarose purified using QIA quick gel extraction kit (QIAGEN, Germany) and sequenced (Macrogen, South Korea). ...
Recently, in India, the marine finfish culture is expanding rapidly without adequate knowledge and research information on the coastal and marine finfish disease epidemics. Therefore, for the benefit of farmers, this study was designed to find the prevalence of Vibriosis outbreaks in marine finfish farms. In this study, 167 moribund fishes that show outward symptoms of lethargy, popeye, pale gills, skin erosions, abdominal edema, or hemorrhagic spots on different parts of the body were collected from 26 marine finfish farms (Latescalcarifer, Rachycentroncanadum, and Trachinotus blochii) located in the states of Tamil Nadu, Andhra Pradesh, and Kerala, India. A total of 173 bacterial isolates were retrieved from all the fish samples, of which 144 isolates demonstrated a Vibrio-like character during biochemical and Vibriostatic 0/129 examinations. The phenotypic, 16s RNA gene sequencing and histopathological analysis confirm that the isolated bacterial strains were Vibriospecies. In the collected fish samples, the total prevalence of Vibrio species was 83.2% and the remaining 16.8% were other bacterial species. Among these bacteria, V. harveyi was the most predominant bacterium (34.1%) that cause infection in all the three fish species whereas Photobacteriumdamselae was found to be the least (2.9%) one.In the pathogenicity study, the highest mortality of 83% was observed after 168 h, when the seabass fingerling exposure to V.harveyiat 106 CFU/ml, and established similar clinical signs to the disease specimens of farmed fish. The in vitro antibacterial study confirms that the tested probiotic effectively inhibits the V. harveyiat 125µl (108 CFU/ml). The above results inspire further in-depth studies on the probiotic efficacy to control the V. harveyi in finfish farms.
Fungal endophytes were recovered from Tamarix nilotica (Tamaricaceae) roots and stems collected in Taif, Saudi Arabia. A total of 49 different taxa were identified. The overall colonization rate of root and stem segments was 30.6%. A total of 49 isolates were collected and categorized into 21 operational taxonomic units using the rRNA gene’s internal transcribed spacer region. The most prevalent species were Penicillium chrysogenum (16 isolates), Fungal sp. (12), and Alternaria alternata (10). Forty-nine isolates were investigated for antifungal activity against Fusarium solani and Rhizoctonia solani; all tested isolates showed antifungal activity against Fusarium solani, while 43 isolates showed antifungal activity against Rhizoctonia solani. The most potent antifungal agents against Fusarium solani and Rhizoctonia solani are Aspergillus ochraceus (2 isolates) and Penicillium chrysogenum (16 isolates). Endophytic isolates collected during this experiment were evaluated to produce amylase, cellulase, lipase, and protease enzymes. Among the strains examined for enzymatic potentials (4 enzymes), 26 strains (53% of the total strains) produce only one enzyme. Penicillium chrysogenum (TUPc2, 3, and 4) produced the highest amount of the four enzymes that were examined.
Grafting of vegetable crops is widely used in industrial vegetable growing in Asia and Western Europe. However, the influence of the genetic relationship of the scion and rootstock, the activity of peroxidase and the content of ascorbic acid in the components of the graft during inosculation period on graft survival has been poorly studied. The objects of the research are nine species of the pumpkin family (Cucurbitaceae). The polymorphism of 11 taxa was studied based on ISSR-PCR of genomic DNA. The record of survival rate of scion-rootstock combinations was conducted on the 10-th day. The activity of peroxidase was determined by the spectrophotometric method, the content of ascorbic acid was determined by Murri. Significant differences in survival rate were noted when grafting momordica into pumpkin rootstock variants: large-fruited (94.6 %) and nutmeg (67.1 %). In experiments with watermelon, melon and trichosanthes, the influence of the type of rootstock on the viability of the graft was not revealed. According to the ISSR spectra, the taxa were divided into two clusters; interspecific groupings of each clade were supported by average bootstrap values (from 26 to 100 %). A medium effect (r = 0.36) of the degree of genetic similarity of the scion with the rootstock on the survival rate of watermelon and a weak effect on the survival rate of melon, momordica and trichosanthes were revealed. The activity of peroxidase and the content of ascorbic acid in the grafting components in different scionrootstock combinations had a weak and moderate effect on plant survival, respectively. The survival rate of trichosanthes on various types of rootstocks strongly depended on the content of ascorbic acid (r = 0.7). Genetic relatedness, peroxidase activity, and ascorbic acid content had a weak or moderate effect on the survival rate of plants in scion-rootstock combinations.
The Trigonella species possess medicinal, nutraceutical and pharmaceutical properties due to the presence of many bioactive compounds. Its therapeutic effects are mostly valuable in medicine, cosmetics and the functional food industry. Correct genetic characterisation of plant material is needed to increase the potential of Trigonella species by breeding and conservation programs. The aim of this study was to develop a reliable marker system to support the morphological and phytochemical analysis in Trigonella taxonomic research, species identification and characterization as well as determination of the interspecific variation within this genus along with relationships between species. For this purpose, flow cytometry and SCoT molecular markers were combined. Flow cytometric analyses revealed that Trigonella species possess very small and small genomes. The range of genome sizes was from 1.10 to 5.76 pg/2C, with most species possessing very small genomes (< 2.8 pg/2C). In seeds of 14 species endopolyploid nuclei were detected. Flow cytometric analysis of genome size enabled quick identification of four out of 20 species, while combined with endopolyploidy detection in seeds, facilitated distinction of the next seven species. ScoT molecular markers helped to identify closely related species with similar genome size and cell cycle activity. Therefore, flow cytometry was proposed as the first-choice method for quick accession screening, while the more detailed genetic classification was obtained using SCoT molecular markers.
The Lactobacillales (LB) stand apart among bacterial orders, using manganese (Mn) instead of iron to support their growth and swiftly ferment complex foods while acidifying their environment. The present work investigates whether a shift in the use of Mn could mark the origin of LB. Transmembrane carriers of the ubiquitous Slc11 family play key roles in LB physiology by catalyzing proton-dependent Mn import. In prior studies, the Slc11 clade found in LB (MntH Cb, MCb) showed both remarkable structural plasticity and highly efficient Mn uptake, and another Slc11 clade, MCg1, demonstrated divergent evolution coinciding with emergence of bacterial genera (e.g., Bordetella, Achromobacter). Herein, Slc11 clade MCb is subdivided in sister groups: MCbie and MCbgut. MCbie derives directly from Slc11 clade MCa, pointing an intermediate stage in the evolution of MCbgut. MCbie predominates in marine Bacillaceae, is more conserved than MCbgut, lacks the structural plasticity that typify MCbgut carriers, and responds differently to identical mutagenesis. Exchanging MCbie/MCbgut amino acid residues at sites that distinguish these clades showed conformation-dependent effects with both MCbie and MCbgut templates and the 3D location of the targeted sites in the carrier structure together suggest the mechanism to open the inner gate, and release Mn into the cytoplasm, differs between MCbie and MCbgut. Building on the established phylogeny for Enterococcus revealed that a pair of genes encoding MCbgut was present in the common ancestor of LB, as MCbgu1 and MCbgu2 templates exhibit distinct structural dynamics properties. These data are discussed examining whether MCbgut+ LB could emerge in the upper gut of early vertebrates (ca. 540 mya), through genome contraction and evolution toward Mn-centrism, as they specialized as gastric aids favoring stomach establishment in jawed vertebrates through bi-directional communication with host nervous, endocrine and immune systems.
The breeding of remontant rose cultivars that are resistant to diseases and adverse conditions, with high decorative value and continuous flowering is the most important task during work with the gene pool of garden roses. Currently, intercultivar hybridization within a single garden group has largely outlived its usefulness. It is necessary to breed for highly decorative forms or cultivars that have outstanding resistance, morphological characters and patterns of seasonal rhythms, and use these plants as parental forms in further breeding. This study represents a comparative analysis of rose cultivars from two garden groups, Grandiflora (Gurzuf, Lezginka, Korallovy Syurpriz, Queen Elizabeth, Komsomolsky Ogonyok, Love) and Rosa Kordesii (Letniye Zvyozdy, Dortmund, Gutsulochka). These cultivars proved themselves during many years of testing in harsh climatic conditions. The objectives of the study were to determine the genetic relationship within the groups and to assign phenotypically different cultivars to one or another garden group. The analysis was carried out by morphological, phenological and ISSR markers. According to the phenological observations on the Grandiflora cultivars, Komsomolsky Ogonyok had later budding and flowering stages. Polymorphic data generated from the ISSR markers showed that this cultivar was the most distant from the others and formed a separate cluster on the dendrogram. A comparison of the morphological characters (flower diameter, number of petals, peduncle length, bush height) showed a significant difference ( p < 0.05) between Komsomolsky Ogonyok and the other Grandiflora cultivars. A dendrogram based on a molecular analysis showed a lack of close relationships between Komsomolsky Ogonyok and the Kordesii group, which formed a separate cluster. A pairwise comparison of the morphological characters in Komsomolsky Ogonyok with the Kordesii group revealed a significant ( p < 0.05) difference in three of the four characters studied. The exceptions were flower diameter when comparing with Dortmund and Letniye Zvyozdy and peduncle length when comparing with Gutsulochka. Although Komsomolsky Ogonyok has a pattern of seasonal development similar to Dortmund in the Kordesii group, the molecular analysis did not assign the former to this group of roses. The cultivars that have valuable characters that no average rose does and that are phenotypically different from such roses represent the most valuable breeding material.
The study aiming to clarify the taxonomic status of Primula mazurenkoae (Aleuritia section, Primulaceae) and determining the level of its genetic divergence in relation to the morphologically close P. farinosa was carried out. To study the genetic relationships between the closely related species, ISSR analysis was performed using five primers; 23 nucleotide sequences of nrITS region were obtained; 20 of them were revealed in the present study. Genetic analyses revealed a high level of variability in natural populations of P. mazurenkoae. Here we can conclude that the level of morphological similarity between P. mazurenkoae and P. farinosa correlates with the results of ISSR analysis and ITS nucleotide data obtained in the study.
Listeriosis is an infectious and fatal disease of domestic mammals and humans caused by Listeria monocytogenes (L. monocytogenes). This study discusses the prevalence, pathology, microbiology, and molecular characterization of reported encephalitic listeriosis cases in caprine and ovine species in the north of Oman between 2017 and 2019. Thirty suspected small ruminants (goats=20 and sheep=10) were reported from eight outbreaks in northern Oman during the 3 years. The overall morbidity, mortality, and case fatality in goats were 5.8%, 5.5%, and 95%, respectively, while in sheep, were 8.4%, 4.2%, and 50%, respectively. Animals under 12 months of age had a case fatality rate of 100% compared to 50% in animals older than one year. The clinical signs in all reported cases were fever, anorexia, deviated neck, and circling. Necropsied animals showed no significant gross lesions. Microscopically, microabscesses, hemorrhages, and perivascular cuffs were observed in the hindbrain along with positive immunostaining of intracellular L. monocytogens antigens in the mononuclear and polymorph nuclear cells. Two L. monocytogenes isolates (A4 and E7) from two goats had multiple antimicrobial-resistant indices scores of (0.5 and 0.3) respectively which is above the Krumperman permissible threshold (>0.2), indicating a high-risk source of contamination by the resistant antibiotics in the study area. Encephalitic listeriosis was further confirmed through the 16sRNA molecular characterization and phylogenetic analysis of the two listeria isolates. Here we report two multidrug-resistant L. monocytogens isolates from goats in Oman, which pose a serious public health threat to both humans and animals.Neweshy MS, 2023. Encephalitic listeriosis in small ruminants in Oman: pathophysiology, antimicrobial sensitivity, and molecular characterization. Pak Vet J. http://dx.
Der Gelbe Enzian (Gentiana lutea) und der Ungarische Enzian (Gentiana pannonica) gehören zu den montan bis subalpin verbreiteten Arten, welche im Harz nicht ursprünglich heimisch sind, sondern nach Anlage des Brockengartens im Jahr 1890 dort angepflanzt wurden. Nach erfolgreicher Etablierung unter den spezifischen klimatischen Bedingungen der Brockenkuppe konnten sich beide Enziane, wie ca. 30 weitere Gefäßpflanzenarten, über das Gartenareal hinaus ausbreiten und werden heute auch an verschiedenen Standorten auf der Kuppe gefunden. Kreuzungen von G. lutea und G. pannonica wurden schon von Wyneken (1938) beschrieben. Eine Distanzanalyse mittels molekularer Marker soll einen detaillierteren Einblick in das interspezifische Hybridisierungsgeschehen liefern. Diskutiert werden Fragen der 1890 eingeleiteten Florenverfälschung auf dem Bergplateau.
W pracy określono zmiany fenotypowe i genotypowe w pokoleniu M1 i M2 petunii (Petunia atkinsiana D. Don) odmiany Flash Red, wywołane azydkiem sodu (AS), siarczanem etylowo-metylowym (EMS), siarczanem metylowo-metylowym (MMS) i siarczan dietylowym (DES), w stężeniach: 0,5; 1,0; 1,5 i 2,0 mM. Do oceny zmian genotypowych na poziomie DNA wykorzystano technikę ISSR-PCR. Otrzymane w pokoleniach M1 i M2 u petunii zmiany to: nieregularne białe przebarwienia na płatkach korony, ciemniejsze żyłkowania, zmiany koloru kwiatów z czerwonego na różowy, jaśniejsze przebarwienia na liściach, zmiana pokroju rośliny (kształt rozety). Częstotliwość zmian zależała od zastosowanego mutagenu i jego stężenia w roztworze. W pokoleniu M1 największą częstotliwość zmian otrzymano stosując do indukowania mutacji EMS i MMS o stężeniu 1,5 i 2,0mM, w pokoleniu M2 — MMS, o stężeniu 2,0 mM.
Fusarium pseudograminearum is one of the major pathogens causing crown rot of wheat in the semi-arid and arid areas in Tunisia. In this study, the molecular diversity of 74 isolates of F. pseudograminearum representing three populations from Tunisia and a set of isolates from the world collection was investigated. The potential mycotoxin-producing ability was tested by PCR using primer pairs specific for the Tri3, Tri7 and Tri13 genes. Results indicated that all the isolates are potentially DON and ⁄ or 3-AcDON producers. The mating-type idiomorphs were identified using diagnostic PCR primer for MAT1-1 and MAT1-2. Both mating types were recovered from the same region and in some cases from the same field. Restriction analysis of the nuclear ribosomal DNA (nrDNA) intergenic spacer region (IGS) revealed 11 haplotypes, five of which were identified in the world collection. The analysis of population structure using the combined IGS and MAT data revealed that the total gene diversity (H T = 0.108) was mostly attributable to diversity within populations (H S = 0.102) and that the genetic differentiation among the four populations was low (G ST = 0.09). The analysis of molecular variance (amova amova) showed that 15% of the variability was between the Tunisian populations and the world collection. These findings indicate that quarantine measures should be in place to limit the introduction of new populations of F. pseudograminearum into Tunisia.
Flower development is the process leading from a reproductive meristem to a mature flower with fully developed floral organs. This multi-step process is complex and involves thousands of genes in intertwined regulatory pathways; navigating through the FLOR-ID website will give an impression of this complexity and of the astonishing amount of work that has been carried on the topic (Bouché et al., Nucleic Acids Res 44:D1167-D1171, 2016). Our understanding of flower development mostly comes from the model species Arabidopsis thaliana, but numerous other studies outside of Brassicaceae have helped apprehend the conservation of these mechanisms in a large evolutionary context (Moyroud and Glover, Curr Biol 27:R941-R951, 2017; Smyth, New Phytol 220:70-86, 2018; Soltis et al., Ann Bot 100:155-163, 2007). Integrating additional species and families to the research on this topic can only advance our understanding of flower development and its evolution.In this chapter, we review the contribution that the Solanaceae family has made to the comprehension of flower development. While many of the general features of flower development (i.e., the key molecular players involved in flower meristem identity, inflorescence architecture or floral organ development) are similar to Arabidopsis, our main objective in this chapter is to highlight the points of divergence and emphasize specificities of the Solanaceae. We will not discuss the large topics of flowering time regulation, inflorescence architecture and fruit development, and we will restrict ourselves to the mechanisms included in a time window after the floral transition and before the fertilization. Moreover, this review will not be exhaustive of the large amount of work carried on the topic, and the choices that we made to describe in large details some stories from the literature are based on the soundness of the functional work performed, and surely as well on our own preferences and expertise.First, we will give a brief overview of the Solanaceae family and some of its specificities. Then, our focus will be on the molecular mechanisms controlling floral organ identity, for which extended functional work in petunia led to substantial revisions to the famous ABC model. Finally, after reviewing some studies on floral organ initiation and growth, we will discuss floral organ maturation, using the examples of the inflated calyx of the Chinese lantern Physalis and petunia petal pigmentation.
Background. Rhaponticum carthamoides (Willd.) Iljin (Asteraceae) is a rare species for the Altai Republic (AR).
The purpose of this study was to characterize the genetic polymorphism of Rhaponticum carthamoides at the inter- and intrapopulation level in a comparative analysis for subsequent selection of seed samples from the genetically most heterogeneous natural populations of the AR for practical purposes.
Materials and methods. The species was studied for ISSR variability in five habitats in the AR. DNA from dried leaves of R. carthamoides was isolated using the STAB method. For testing seventeen ISSR primers were used, seven of which were selected as most informative ones.
Results and conclusion. The analysis showed that individual plants from five cenopopulations (CP) were distributed into three groups of similarity on the dendrogram. A separate clade was formed by plant samples from two CPs of the Katun Nature Reserve (KNR). Samples of one of those CPs grew on well-warmed southern slopes and exhibited a higher genetic heterogeneity than the others. The highest intrapopulation and interpopulation similarity in the distribution of DNA fragments was also found in two CPs from habitats with the smallest geographic distance from each other. Representatives of a separate population, least in size and number of individuals in the KNR, showed a high level of similarity in the distribution of DNA fragments. Significantly lower coefficients of genetic similarity with other CPs were found in plants from a small isolated CP from the Shavlinsky Protected Area. It can be assumed that one of the main reasons for the least genetic similarity of this population with others is its location in the immediate vicinity of the foothill at the pass to Achik (Ongudaysky District; absolute height: 2300 masl). This location can be a limiting factor for the exchange of genetic information with individuals from other populations.
Hellenia speciosa (J. Koenig) S. R. Dutta (Syn: Costus speciosus (J. Koenig) Sm.) is well known for its anti-diabetic properties and is in high demand for its steroidal sapogenin, diosgenin, which is used in the pharmaceutical industry for manufacturing steroidal drugs. The increasing demand for this plant has led to the depletion of its wild population. This study was conducted to reveal the genetic diversity of H. speciosa collected from various agro-ecological regions of India for use in devising conservational strategies, and cultivation and breeding programs. Twenty inter-simple sequence repeat markers yielded 304 products with 100% polymorphism demonstrating high genetic diversity. Nei′s gene diversity and Shannon information indexes were estimated among the populations as 0.19 ± 0.23 and 0.28 ± 0.25, respectively. High genetic differentiation (GST = 0.40) and low gene flow (Nm = 0.74) were observed, which corroborated with the analysis of molecular variance revealing maximum (86.75%) variance within populations. The unweighted pair group method with arithmetic mean analysis grouped all accessions into three major clusters. Principal component analysis showed that the first three components accounted for 30.66%, 4.54%, and 3.98% variation, respectively, and Bayesian clustering through structure showed the presence of two genetic population (K = 2). This study revealed high genetic diversity among the populations collected from high altitude compared to those from the plain. A positive but low correlation among genetic and geographic distances was obtained (r = 0.282, p < 0.0001). Identification of genetic diversity and intra population variation of a species are prime factors to take defined conservation strategies.
Due to the high value and economic importance of the plant Lycium (goji), its genome has been intensively studied in multidisciplinary research. In the present study, the structure and genetic relationships of 14 selected Lycium genotypes from different origins are presented. By using 18 random amplified polymorphic DNA (RAPD) decamers and 15 inter-simple sequence repeat (ISSR) primers, 200 and 183 loci were amplified, respectively. Among the amplified loci, 45.5–49.2% were polymorphic, and 6.5–7.6% were genotype-specific. Cluster and STRUCTURE analyses performed for RAPD and ISSR revealed the genetic relationships among the genotypes. The highly significant and positive value of the Mantel’s correlation coefficient calculated for the Jaccard similarity matrices of RAPD and ISSR confirmed the suitability of using both these methods separately in this type of study. The significant values of FST statistics obtained in AMOVA for ‘among’ and ‘within’ group analysis confirmed the diversity of genotypes not only between the designated groups but also within them. This diversity provides opportunities to select interesting genotypes and conduct further studies on identifying markers for marker-assisted selection.
Long-term pea callus cultures of different genotypes (mutants R-9 and W-1 and cultivar Viola) were used to regenerate plants (generation R 0 ). The regenerants displayed changes both in qualitative and in quantitative traits. The most dramatic morphological alterations and complete sterility were observed in regenerants of the cultivar Viola. To estimate the genetic differences, regenerants were compared with the original lines with the use of RAPD (random amplified polymorphic DNA) and ISSR (inter simple sequence repeat) analyses. The extent of divergence varied among regenerants and depended mostly on the original genotype. The genetic difference from the original line was no more than 1% in W-1 regenerants, 0.7–5.3% in R-9 regenerants, and 10– 15% in sterile regenerants of the cultivar Viola. The genetic variation of plants regenerated from a callus culture maintained for ten years did not exceed that of plants obtained from a culture maintained for two years.
Les roses à fleurs doubles attirent sélectionneurs et scientifiques depuis de nombreux siècles. L’analyse des taux de ségrégation et cartes génétiques indique que le passage de la fleur simple à la fleur double est dû à une seule mutation dominante située sur le chromosome 3. Cette mutation conduit à une conversion homéotique d’une partie des étamines en pétales, soulignant la possibilité que cette mutation impacte certains gènes du modèle ABC. Il y a quelques années, notre équipe a démontré que l’augmentation du nombre de pétales chez le rosier était corrélée à une restriction de l’expression de RcAGAMOUS (RcAG) vers le centre du méristème floral. Cependant, RcAG étant porté par le chromosome 5, il ne peut être le déterminant génétique de la fleur double. Il a donc été supposé que la mutation en cause se trouvait dans un gène intervenant en amont de RcAG.Récemment, nous avons séquencé, assemblé et publié le génome de Rosa chinensis cv ‘Old Blush’ un ancêtre des rosiers modernes qui produit déjà des fleurs doubles. L’assemblage, de très bonne qualité, nous a aidé à reconstruire la séquence des deux haplotypes de l'intervalle contenant la mutation liée à la fleur double. Nous avons identifié, parmi les 631 gènes de cet intervalle, un gène APETALA2-LIKE (RcAP2L) comme candidat plus que prometteur. En effet, il a été découvert que ce gène existait sous la forme de deux allèles, l’un d’entre eux contenant un grand élément transposable, donnant lieu à un allèle tronqué résistant à l’inhibition par miR172, appelé RcAP2LΔ172. Sachant que la surexpression d’un variant résistant au miR172 entraîne souvent la formation de pétales supplémentaires chez A. thaliana, j’ai démontré que la présence de ce variant corrèle avec le phénotype « fleur double » chez les rosiers d’origine chinoise. Enfin, alors qu’AP2 est capable d’inhiber l’expression d’AG en se liant directement à ses séquences régulatrices chez A. thaliana, j’ai confirmé la capacité des protéines codées par les deux allèles de RcAP2L à lier les séquences régulatrices de RcAG, in vitro. À partir de ces résultats, je propose donc un modèle pouvant expliquer la formation de fleurs doubles chez les rosiers chinois et peut-être d’autres Rosaceae, dans lesquelles la protéine RcAP2LΔ172 peut s’accumuler du fait de sa résistance au miR172 et restreindre davantage l’expression de RcAG au centre du méristème floral. Ainsi, la frontière entre les domaines A et C se trouve elle aussi déplacée vers le centre du méristème, ce qui induit la conversion des étamines en pétales.
Heavy metals can affect the morphology, physiology and evolution of plants. Asplenium viride is a diploid species, belonging to the largest genus of the cosmopolitan fern family Aspleniaceae, and occurring on various types of alkaline rocks. It is known to colonize sites with high concentrations of heavy metals, exhibiting changes in frond morphology. Microevolutionary processes, manifesting as changes in genome size and new genotype formation, can ultimately lead to the formation of new subspecies and speciation. This study aimed to evaluate the morphological and genetic diversity of A. viride, and to test for a potential correlation between variability and heavy metal concentration. Analysis of A. viride specimens, from one metalliferous site and five non-metalliferous localities, showed no apparent variation in genome size between plants from affected and non-affected sites. There was no significant correlation between genetic variability and heavy metal concentration. This was possibly due to intragametophytic selfing, caused by patchy habitats and subsequent founder effects, resulting from long-distance colonization by single spores.
Context
Preservation of genetic diversity of species is a pressing issue; in particular, the preservation of the gene pool of many rare and endangered plants is a priority. Species of the genus Crambe (family Brassicaceae) have potential in agriculture and bioremediation.
Aims
This study aims to assess the genetic diversity and DNA fingerprint of five rare species of the genus Crambe, and to develop the concept of a genetic passport for rare plants.
Methods
DNA fingerprinting was conducted via the inter simple sequence repeat (ISSR) method, using six ISSR primers. Hierarchical cluster analysis of the species was performed.
Key results
In total, 145 polymorphic loci were detected. The studied species formed two different clusters on genetic dendrogram analysis. The first cluster comprised two species, Crambe steveniana and C. tataria from a single subsection (Tatariae), forming a common clade. They were the most genetically close species with genetic similarity of 0.8431. The remaining three species (C. cordifolia, C. maritima, C. pinnatifida), from another subsection of Crambe, formed nodes from the general clade.
Conclusions
The findings allow plants to be genetically certified using our methods and informative ISSR primers for rare plants. We were able to propose a genetic formula identifying a species and present an example of a genetic passport for rare plants. The genetic structure of C. pinnatifida was investigated for the first time.
Implications
The present findings contribute to the systematics and critical investigation of rare plant species with genetic resource potential. A genetic passport could be used in the protection of copyright of agricultural varieties.
Due to its value and economic importance, the genome of Lonicera caerulea L. has been widely studied in various fields of science. In this study the genetic structure and relationships between 24 accessions of L. caerulea of different origins were assessed. A total of 692, 814, and 258 loci were amplified using 43 RAPD (random amplified polymorphic DNA), 40 ISSR (intersimple sequence repeat), and 20 R-ISSR (RAPD+ISSR) primers, respectively. Among the amplified loci, 66-78% were polymorphic and 12-20% were private. Selected R-ISSR sequences were detected in Lonicera japonica transcripts. Cluster and STRUCTURE analyses performed for each of the techniques revealed the existing differences and unknown similarities between the genotypes. The r-factor values calculated in the Mantel test indicated highly significant positive correlations between the Nei distance matrices, similar to the FST values (FST_RAPD=0.223, FST_ISSR=0.279, FST_R-ISSR=0.363) determined in the analysis of molecular variance. It was found that 78%, 72%, and 64% of the genetic variations were related to the differences observed within the populations, which suggest that the variations are mainly reflected in the differences among the genotypes. The principal coordinate analysis showed greater differences between the mean distances of the Lonicera genotype pair and the actual distances of the same pairs on the Nei matrix compared to multidimensional scaling. These differences were 45%, 56%, and 42% higher for RAPD, ISSR and R-ISSR, respectively.
Heavy metals can affect the morphology, physiology and evolution of plants. Asplenium viride is a diploid species, belonging to the largest genus of the cosmopolitan fern family Aspleniaceae, and occurring on various types of alkaline rocks. It is known to colonize sites with high concentrations of heavy metals, exhibiting changes in frond morphology. Microevolutionary processes, manifesting as changes in genome size and new genotype formation, can ultimately lead to the formation of new subspecies and speciation. This study aimed to evaluate the morphological and genetic diversity of A. viride , and to test for a potential correlation between variability and heavy metal concentration. Analysis of A. viride specimens, from one metalliferous site and five non-metalliferous localities, showed no apparent variation in genome size between plants from affected and non-affected sites. There was no significant correlation between genetic variability and heavy metal concentration. This was possibly due to intragametophytic selfing, caused by patchy habitats and subsequent founder effects, resulting from long-distance colonization by single spores.
Mentha is a complex genus encompassing many species as a consequence of their interspecific hybridization and polyploidy. Southeast Asian mints have been poorly distinguished though they are widely used for culinary and medical purposes. In this study, we have analyzed Southeast Asian mints and known varieties as well as a related Lamiaceae species (Nepeta sp.) using simple sequence repeat (SSR) markers and leaf morphology. Two types of mints were clearly distinguished based on their venation pattern and leaf shape index. We developed 12 SSR markers that allowed good amplification in the Mentha and another Lamiaceae species. In the SSR-based phylogram, the Mentha lines could be delimited into groups I-VI. The Southeast Asian mints divided into groups I and II, and the phylogram separated most of the available species, with groups I and II containing the known species M. × cordifolia and M. arvensis, respectively. The separation of the two groups was supported by a population structure analysis. The SSR markers developed in this study enabled the simultaneous classification of mints and will help improve our understanding of the genetic composition of known mint varieties and as yet unclassified Southeast Asian mints.
Heavy metals can affect the morphology, physiology and evolution of plants. Asplenium viride is a diploid species, belonging to the largest genus of the cosmopolitan fern family Aspleniaceae, and occurring on various types of alkaline rocks. It is known to colonize sites with high concentrations of heavy metals, exhibiting changes in frond morphology. Microevolutionary processes, manifesting as changes in genome size and new genotype formation, can ultimately lead to the formation of new subspecies and speciation. This study aimed to evaluate the morphological and genetic diversity of A. viride , and to test for a potential correlation between variability and heavy metal concentration. Analysis of A. viride specimens, from one metalliferous site and five non-metalliferous localities, showed no apparent variation in genome size between plants from affected and non-affected sites. There was no significant correlation between genetic variability and heavy metal concentration. This was possibly due to intragametophytic selfing, caused by patchy habitats and subsequent founder effects, resulting from long-distance colonization by single spores.
Norway maple (Acer platanoides L.) is a key species of broadleaved forests whose population genetics is poorly studied using modern genetic tools. We used ISSR analysis to explore genetic diversity and differentiation among 10 Russian populations on the eastern margin of the species range of distribution, and to compare the revealed patterns with the results of our population genetic studies of pedunculate oak (Quercus robur L.). In the first set comparatively high heterozygosity and allelic diversity were found (expected heterozygosity HE = 0.160 ± 0.033, number of alleles na = 1.440 ± 0.080, effective number of alleles ne = 1.271 ± 0.062) in comparison with strongly fragmented and geographically isolated small maple stands of the second set (HE = 0.083 ± 0.011, na = 1.281 ± 0.031, ne = 1.136 ± 0.019). A relatively high genetic differentiation among populations was detected (the proportion of the inter-population component of total genetic variation, GST = 0.558 ± 0.038). In the Cis-Urals, local groups of populations that are confined to the northern, middle and southern parts of the Urals were identified. On the contrary, the current significant fragmentation of the pedunculate oak distribution area in the same study area did not lead to any noticeable genetic differentiation among the majority of populations, the values of the population genetic diversity were very similar in different parts of the Southern Urals.
Kinship and genetic diversity determination among six rose varieties from the Grandiflora group were carried out using ISSR thechnics. The studied varities were divided into 3 clades: I) ‘Lezginka’, ‘Queen Elizabeth’ and ‘Koralovy surpriz’ varieties; II) ‘Gurzuf’ and ‘Love’ varieties; III) ‘Komsomolsky ogonek’ variety formed a separate branch. This division into clades was confirmed by a statistical comparison of morphometric characters. On the basis of the obtained data, it can be concluded that the analysis using the selected primer group is well-suited for differentiation rose varieties into groups, which makes it possible, for one thing, to determine the genetic distance between varieties, and for another, to use these data in the future by certification of the varieties promising by resistance characters to the continental climate conditions.
The study is based on the field experiment, carried out between 2009-2012 in Żyznów, in randomized blocks with 3 replications. The factors of experiment were, firstly the varieties of sweet potato: Carmen Rubin, Goldstar, White Triumph, and secondly the three various cultivation technologies: a) traditional farming method without protection, b) cultivation with use of PE-foil, c) cultivation with use of PP-non-woven fabric. The level of fertilization was kept on the constant level. The cultivation with use of protection caused brightening of the apical part, both the stolon parts, compared with the cultivated in traditional ways. The specific genetic features of different varieties of sweet potato were influencing the browning of flesh of cooked and raw potatoes.
In 2009–2011 there was investigated the effect of Asahi SL on crop and chemical composition of some potato cultivars: Denar, Irys, Satina. Studies were carried out in field experiment station in the central-eastern part of Polish on the soil of light loamy sand content. The experiment was set by the means of randomized sub-blocks in dependent system. The primary factors were: sub-blocks with Asahi SL; control group with distilled water. The secondary factors were three potato cultivars. Growth regulator Asahi SL contributed to the increase in the total yield and commercial tuber yield by modifying the structure. Asahi SL caused the increase of total and commercial crop of tubers as well as phenolic compounds content. The content of starch and vitamin C did not change, and levels of soluble, reductive sugars and sacharose decreased under this synthetic growth regulator influence. Among investigated varieties the most prolific was very early cultivar – Denar, the least prolific – middle early Satina. The highest levels of starch, soluble and reductive sugars as well as vitamin C was characterized Satina cultivar, the highest concentration of sacharose – Irys, and the phenolic compounds – Denar. The reaction of investigated varieties towards Asahi SL application – regarding the soluble, reductive sugars, sacharose, vitamin C and phenols – was differentiated . It was found positive interaction of this preparation with the crop and its quality. The most prolific cultivar appeared to be Denar, the richest in analyzed compounds – Satina.
A package of programs (run by a management program called TREECON) was developed for the construction and drawing of evolutionary
trees. The program MATRIX calculates dissimilarity values and can perform bootstrap analysis on nucleic acid sequences. TREE
implements different evolutionary tree constructing methods based on distance matrices. Because some of these methods produce
unrooted evolutionary trees, a program ROOT places a root on the tree. Finally, the program DRAW draws the evolutionary tree,
changes its size or topology, and produces drawings suitable for publication. Whereas MATRIX is suited only for nucleic acids,
the modules TREE, ROOT and DRAW are applicable to any kind of dissimilarity matrix. The programs run on IBM-compatible microcomputers
using the DOS operating system.
A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.