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Acer is a large and important genus of woody plants most commonly encountered as small to large trees in urban landscapes. Considerable investigation has been devoted to addressing the taxonomy of maples, but little is known about genome sizes across the genus. Relatively more work has been conducted to determine chromosome numbers and ploidy of mo...
Citations
... Fraxinus americana (Wheeler, 1981)gerando sazonalmente condições semelhantes às encontradas no género Acer. Por fim, um estudo laboratorial com ramos podados mostrou que nos géneros testados (Fagus, Thuya, Betula, Acer), todos absorveram a seiva quando congelados e excretaram ao descongelar, exceto Acer que demonstrou o opostoexcretou seiva ao congelar (Johnson et al., 1987 (Contreras & Shearer, 2018); esta informação está amplamente disponível, contudo os genomas de Portugal carecem de estudo genético adicional (Gómez & Güemes, 2015;Leitch et al., 2019). ...
Este capítulo explora o potencial da seiva como produto florestal não lenhoso em Portugal, analisando espécies nativas como Acer pseudoplatanus e Betula pubescens. Com base em casos de sucesso internacionais e no mapeamento de áreas com maior aptidão bioclimática, o estudo destaca técnicas de extração, viabilidade económica e compatibilidade com usos múltiplos da floresta. O capítulo sublinha a relevância deste recurso inovador para diversificar o setor florestal português, promovendo sustentabilidade e valorização das florestas nativas.
... The base chromosome number of Acer is x = 13, with most maples investigated reported as diploid (2n = 2x = 26), and less than 10 species as polyploid (4x, 6x, 8x; Rice et al., 2015;Contreras & Shearer, 2018;http://ccdb.tau.ac.il/search/). ...
Accurate species delimitation is crucial for biodiversity conservation. The Acer series Campestria comprises four species, A. campestre, A. miyabei, A. miaotaiense and A. yangjuechi. To clarify controversies over the taxonomic status of the latter three endangered species, we performed phylogenomic, morphological and niche differentiation analyses in series Campestria. Our coalescent species tree of 544 and 77 single‐copy nuclear genes (SCNGs) supported series Campestria as monophyletic, with A. yangjuechi having the closest relationship with A. miaotaiense. However, in the plastome‐derived tree based on 64 protein coding sequences (CDS) the four species did not cluster together, and each of them grouped with some other sympatric Acer species. Given this nuclear‐cytoplasmic conflict, we hypothesize that A. yangjuechi have been subject to nuclear gene introgression and plastid (pt) capture involving another sympatric maple, i.e. A. amplum. Principal component analysis and machine learning based on morphological data could not separate A. yangjuechi and A. miaotaiense, but both could be clearly distinguished from A. miyabei. Moreover, the niche overlap tests of the two more widespread species, A. miyabei and A. miaotaiense, showed they clearly occupy distinct niches. Overall, we conclude that A. miyabei and A. miaotaiense are distinct species, while A. yangjuechi (endemic to Mt. Tianmu/East China) should be treated as a subspecies of A. miaotaiense. Our study points out that multiple lines of phylogenomic, morphological and ecological evidence prove highly useful in species delimitation. Additionally, our results should help to inform conservation measures for endangered species of the genus Acer/series Campestria in East Asia. This article is protected by copyright. All rights reserved.
... Studies have shown that fluorophores such as 4 0 ,6diamidino-2-phenylindole (DAPI) and mithramycin, which preferentially bind to AT and GC bps, respectively, can yield inaccurate estimates of genome size based on differing AT% and GC% between the sample and standard (Coleman et al., 1981;Ortega-Ortega et al., 2019). Although DAPI has been used to estimate the genome size of various plant species, intercalating fluorophores such as propidium iodide (PI) should be preferentially selected to yield more accurate estimates (Contreras and Shearer, 2018;Ortega-Ortega et al., 2019). ...
... Figure 2 includes sample spectra of Salvia analyzed with each internal standard. For species with known ploidy, the DNA content of the nonreplicated genome (1Cx) was calculated by dividing the experimentally determined 2C value by ploidy (Contreras and Shearer, 2018). ...
Salvia is a genetically diverse genus in the Lamiaceae family, with hundreds of species distributed globally. With base chromosome numbers ranging from 6 to 19 and ploidy levels ranging from diploid to octoploid, the genus has been proposed to be subdivided based on molecular data rather than morphology. However, little is known about total DNA content across the genus. The DNA content of 141 Salvia genotypes were analyzed using flow cytometry. Samples of Salvia were stained with propidium iodide and compared with the internal standards Pisum sativum ‘Ctirad’ and Solanum lycopersicum ‘Stupické’ to generate estimations of DNA content. Holoploid 2C genome sizes of the analyzed Salvia ranged from 0.63 pg to 6.12 pg. DNA content showed a wide distribution across chromosome number, ploidy, and clade. The wide distribution of DNA content across the genus further indicates the diversity of Salvia and may be useful for future breeding efforts.
... Genome size is a taxonomically significant character that can vary both intraspecifically and intragenerically (Contreras and Shearer, 2018;Greilhuber, 1998;Ranney et al., 2007;Shearer and Ranney, 2013). Intraspecific variation can be due to reproductive isolation of populations, chromosomal variation, and heterochromatin polymorphisms (Greilhuber 1998). ...
... Intrageneric variation results from the ongoing processes of adaptation and evolution through which plants undergo whole genome duplication events and subsequent loss of genomic material (Bennetzen et al., 2005;Soltis et al., 2003). In addition to facilitating the effective development of breeding objectives and strategies, genome size data have been demonstrated as useful in clarifying taxonomy and nomenclature (Hembree et al., 2020;Ranney et al., 2007), screening interspecific hybrid seedlings (Galbraith et al., 2005;Parris et al., 2010;Shearer and Ranney, 2013), and determining ploidy (Contreras and Shearer, 2018;Roberts and Werner, 2016). ...
... Genome size and ploidy can be measured relatively quickly through the use of flow cytometry, evident in the growing body of horticultural crop surveys (Contreras and Shearer, 2018;Hembree et al., 2020;Jones et al., 2007;Parris et al., 2010;Roberts and Werner, 2016;Rothleutner et al., 2016;Rounsaville and Ranney, 2010;Shearer and Ranney, 2013). The two most common fluorochromes for measuring genome size are PI and DAPI. ...
Styrax L. is a genus of ≈130 species, many with horticultural traits of interest, though sparsely represented in cultivation. Previous studies reporting chromosome counts have established a base chromosome number of x = 8 and provided evidence of diploid, tetraploid, pentaploid, and hexaploid levels within the genus, including the more commonly cultivated Styrax japonicus Siebold & Zucc. being reported as pentaploid. Little has been reported relative to genome size within the Styracaceae. We conducted flow cytometry using fluorochromes propidium iodide (PI) and 4′,6-diamidino-2-phenylindole (DAPI) to estimate relative 2C genome size and ploidy of 47 accessions representing 15 species of Styrax and base composition of a subset of 9 accessions representing 6 species. Cytologic analysis of chromosomes was completed on Styrax confusus Hemsl. for ploidy calibration to genome size. Diploids, tetraploids, pentaploids, hexaploids, and octoploids were identified. Relative 2C genome size ranged from 1.38 to 6.61 pg. This survey confirms published ploidy for Styrax americanus Lam., Styrax obassia Siebold & Zucc., Styrax redivivus (Torr.) L.C.Wheeler (diploid), and S. japonicus (pentaploid); suggests alternate ploidy levels and/or ploidy series for Styrax grandifolius Aiton (diploid) and Styrax hookeri C.B.Clarke (octoploid); and establishes ploidy levels for Styrax glabrescens Benth., Styrax odoratissimus Champ. ex Benth., Styrax officinalis L., Styrax platanifolius Engelm. ex Torr., Styrax ramirezii Greenm., Styrax wilsonii Rehder (diploid), Styrax confusus, Styrax hemsleyanus Diels (tetraploid), and Styrax fortunei Hance (diploid and hexaploid).
... Acer negundo was similar with 61 Gb of PacBio data, an N50 of 17 kb (max read length 95 kb), and 223 Gb of Illumina PE data. Genome size estimation using short reads resulted in smaller than expected estimates (Contreras & Shearer, 2018;Leitch et al., 2019) at 636 and 319 Mb for A. saccharum and A. negundo, respectively ( Figure S1). DNA sequence read coverage was high, with long reads at 1119 and 1419 and short reads at 1809 and 2089 for A. saccharum and A. negundo, respectively (Table S1). ...
... BUSCO embryophyta scores were 97.4% complete with 5.6% duplicate, 0.9% fragmented, and 1.7% missing (Data S1). Earlier work based on low-coverage sequencing postulated higher GC content for both A. saccharum (Staton et al., 2015) and A. negundo in particular (Contreras & Shearer, 2018), but whole genome sequencing supports their place at the lower range among angiosperm plants (Tr avn ı cek et al., 2019). ...
Maples (the genus Acer) represent important and beloved forest, urban, and ornamental trees distributed throughout the Northern hemisphere. They exist in a diverse array of native ranges and distributions, across spectrums of tolerance or decline, and have varying levels of susceptibility to biotic and abiotic stress. Among Acer species, several stand out in their importance to economic interest. Here we report the first two chromosome-scale genomes for North American species, Acer negundo and Acer saccharum. Both assembled genomes contain scaffolds corresponding to 13 chromosomes, with A. negundo at a length of 442 Mb, N50 of 32 Mb and 30,491 genes, and A. saccharum at 626 Mb, N50 of 46 Mb, and 40,074 genes. No recent whole genome duplications were detected, though A. saccharum has local gene duplication and more recent bursts of transposable elements, as well as a large-scale translocation between two chromosomes. Genomic comparison revealed that A. negundo has a smaller genome with recent gene family evolution that is predominantly contracted and expansions that are potentially related to invasive tendencies and tolerance to abiotic stress. Examination of expression from RNA-Seq obtained from A. saccharum grown in long-term aluminum and calcium soil treatments at the Hubbard Brook Experimental Forest, provided insights into genes involved in aluminum stress response at the systemic level, as well as signs of compromised processes upon calcium deficiency, a condition contributing to maple decline.
... Flow cytometric analysis -For the first time, the genome size of five indigenous and endangered coffee species was estimated by flow cytometry using propidium iodide (PI) staining (Fig. 1a). Unlike DAPI which are considered as base-specific fluorochromes, PI is an intercalating dye without base specificity, and therefore many authors have suggested using PI for accurate estimation of genome size in various plant species including coffee (Asif et al. 2001;Noirot et al. 2002;Contreras and Shearer 2018;Zabka et al. 2018;Ortega et al. 2019). Irrespective of the time, all the FCM measurements between the replicated samples within the species revealed a CV of less than 5% (Table 1). ...
The nuclear 2C DNA content and ploidy level determination of five indigenous coffee species from India was carried out using flow cytometry and by assessing the stomatal characteristics. The nuclear DNA content (2C/pg) analyzed varied from 1.29 pg in Coffea wightiana Wall. ex Wight & Arn. to 1.48 pg in Coffea jenkinsii Hook.f. Based on the genome size, all five species were divided into two groups. The first group comprises Coffea travancorensis Wight & Arn and C. wightiana with lower genome size (2C DNA 1.29–1.30 pg), and the second group consists of Coffea bengalensis Roxb.ex Schult, Coffea khasiana (Korth.) Hook.f and C. jenkinsii with larger genome size (2C DNA 1.45–1.48 pg). The species included in the first group were inhabited in dry environmental conditions in contrast to the species included in the second group which was predominantly from mesic habitat. Among the stomatal characteristics, no significant variation in stomatal density was observed among the species, although stomatal guard cell length and stomatal chloroplast number recorded significant variation among some species. Based on flow cytometry and stomatal characteristics, all five endangered coffee species analyzed in the study were identified as diploids. The study revealed that stomatal guard cell length and stomatal chloroplast number could be fast, inexpensive, and reliable methods for determining the ploidy status of indigenous coffee species.
... DNA amount and ploidy level of each collected population were measured using an indirect approach by measuring the holoploid (2C) (Greilhuber et al. 2005) relative genome with a flow cytometer (Contreras and Shearer 2018;Doležel et al. 2007;Lattier et al. 2019;Rothleutner et al. 2016). Fifty seeds of each population were placed in 24 by 24 cm plastic trays and germinated in growth chambers set for 12 h of light with a temperature regime of 23/ 15 C. Plants were watered daily and fertilized once a week with a standard 20-20-20 fertilizer (Miracle-Gro® water-soluble, Scotts Company). ...
Italian ryegrass [Lolium perenne L. spp. multiflorum (Lam.) Husnot] is one of the most troublesome weeds worldwide. L. multiflorum is also a grass seed crop cultivated on 50,000 ha in Oregon, where both diploid and tetraploid cultivars are grown. A survey was conducted to understand the distribution, frequency, and susceptibility of L. multiflorum to selected herbicides used to control L. multiflorum. The herbicides selected were clethodim, glufosinate, glyphosate, mesosulfuron-methyl (mesosulfuron), paraquat, pinoxaden, pyroxsulam, quizalofop-P-ethyl (quizolafop), pronamide, flufenacet + metribuzin, and pyroxasulfone. The ploidy levels of the populations were also tested. A total of 150 fields were surveyed between 2017 and 2018, of which 75 (50%) had L. multiflorum present. Herbicide-resistant populations were documented in 88% of the 75 populations collected. The most frequent mechanisms of action were resistance to Acetyl-CoA carboxylase (ACCase), Acetolactate Synthase (ALS), 5-enolpyruvylshikimate-3-phosphate (EPSPs) inhibitors, and combinations thereof. Multiple and cross-resistance, found in 75% of the populations, were the most frequent patterns of resistance. Paraquat-resistant biotypes were confirmed in six orchard crop populations for the first time in Oregon. Herbicide resistance was spatially clustered, with most cases of resistance in the northern part of the surveyed area. ALS and ACCase resistant populations were prevalent in wheat (Triticum aestivum L.) fields. Multiple-resistance was positively correlated with plant density. Tetraploid feral populations were identified, but no cases of herbicide resistance were documented. This is the first survey of herbicide resistance and ploidy diversity in L. multiflorum in western Oregon. Resistant populations were present across the surveyed area, indicating that the problem is widespread.
... Furthermore, negative public perception and the cost of navigating regulatory approval is estimated to be in the tens of millions of dollars [8]. Ploidy manipulation to develop sterile triploids is relatively inexpensive and proven effective in many plant taxa. Inducing polyploids using chemical means, particularly the dinitroaniline herbicide, oryzalin, has become commonplace in woody plants including Acer [9][10][11]. Ploidy is the number of chromosome sets found in an organism and most organisms have two sets (diploids = 2x) but plants are capable of existing with more than two sets of chromosomes. ...
... Flow cytometry analysis of extracted nuclei stained with DAPI (4′,6-diamidino-2-phenylindole) was carried out according to Contreras and Shearer [10] with the modification that only one sample was used for parent and seedlings. ...
... Flow cytometry analysis of extracted nuclei stained with DAPI (4 ,6-diamidino-2-phenylindole) was carried out according to Contreras and Shearer [10] with the modification that only one sample was used for parent and seedlings. ...
Maples are common street and shade trees throughout the temperate zone. They are widely used for their wide range of ornamental traits and adaptability, particularly to urban settings. Unfortunately, some species such as Acer tataricum ssp. ginnala (Amur maple) and A. platanoides (Norway maple) have escaped cultivation to become pests or in some cases threaten native flora. However, these species remain economically important and are still asked for by name. To ameliorate potential future ecological damage from additional escapes, we have been breeding for sterile forms using ploidy manipulation and backcrossing to develop triploids. We began with a series of experiments to develop tetraploids of Amur, Norway, and trident (A. buergerianum) maples. Treatment of seedlings at the cotyledon or first true leaf stage was successful in inducing tetraploids of each species. Mortality, cytochimeras, and tetraploids varied among species. After identifying tetraploids, they were field planted alongside diploid cultivars and seedlings, which served as pollinizers in open-pollination. Seedlings derived from open-pollinated tetraploids were generally found to be a high percentage triploids. Thus far, no Norway or trident maple triploids have flowered but after three years we observed five, 22, and 22 Amur maple triploids flowering over three respective years with no seedlings recovered to date. Further evaluation is required but our findings are encouraging that the triploids we have developed thus far will be sterile and provide new cultivars for nursery growers and land managers.
Acer palmatum is a deciduous shrub or small tree. It is a popular ornamental plant because of its beautiful leaves, which change colour in autumn. This study revealed 116 ApNAC genes within the genome of A. palmatum . These genes are unevenly distributed on the 13 chromosomes of A. palmatum . An analysis of the phylogenetic tree of Arabidopsis thaliana NAC family members revealed that ApNAC proteins could be divided into 16 subgroups. A comparison of ApNAC proteins with NAC genes from other species suggested their potential involvement in evolutionary processes. Studies suggest that tandem and segmental duplications may be key drivers of the expansion of the ApNAC gene family. Analysis of the transcriptomic data and qRT‒PCR results revealed significant upregulation of most ApNAC genes during autumn leaf senescence compared with their expression levels in summer leaves. Coexpression network analysis revealed that the expression profiles of 10 ApNAC genes were significantly correlated with those of 200 other genes, most of which are involved in plant senescence processes. In conclusion, this study contributes to elucidating the theoretical foundation of the ApNAC gene family and provides a valuable basis for future investigations into the role of NAC genes in regulating leaf senescence in woody ornamental plants.
Premise
Cytogenetic traits such as an organism's chromosome number and genome size are taxonomically critical as they are instrumental in defining angiosperm diversity. Variations in these traits can be traced to evolutionary processes such as polyploidization, although geographic variations across cytogenetic traits remain underexplored. In the pantropical monocot family Zingiberaceae (~1500 species), cytogenetic traits have been well documented; however, the role of these traits in shaping taxonomic diversity and biogeographic patterns of gingers is not known.
Methods
A time‐calibrated Bayesian phylogenetic tree was constructed for 290 taxa covering three of the four subfamilies in Zingiberaceae. We tested models of chromosome number and genome size evolution within the family and whether lineage age, taxonomic diversity, and distributional range explain the variations in the cytogenetic traits. Tests were carried out at two taxonomic ranks: within Zingiberaceae and within genus Hedychium using correlations, generalized linear models and phylogenetic least square models.
Results
The most frequent changes in chromosome number within Zingiberaceae were noted to be demi‐polyploidization and polyploidization (~57% of the time), followed by ascending dysploidy (~27%). The subfamily Zingiberoideae showed descending dysploidy at its base, while Alpinioideae showed polyploidization at its internal nodes. Although chromosome counts and genome sizes did not corroborate with each other, suggesting that they are not equivalent; higher chromosome number variations and higher genome size variations were associated with higher taxonomic diversity and wider biogeographic distribution.
Conclusions
Within Zingiberaceae, multiple incidences of polyploidization were discovered, and cytogenetic events appear to have reduced the genome sizes and increased taxonomic diversity, distributional ranges and invasiveness.
