Figure 3 - uploaded by Alireza Asem
Content may be subject to copyright.
Putative secondary structures of mitochondrial tRNAs determined in A. urmiana. Nucleotides in red color indicate anticodon sequences.
Source publication
In the previously published mitochondrial genome sequence of Artemia urmiana (NC_021382 [JQ975176]), the taxonomic status of the examined Artemia had not been determined, due to parthenogenetic populations coexisting with A. urmiana in Urmia Lake. Additionally, NC_021382 [JQ975176] has been obtained with pooled cysts of Artemia (0.25 g cysts consis...
Contexts in source publication
Context 1
... The shortest and longest tRNAs were tRNA-Ala, tRNA-Ley (59 bp), and tRNA-Ser 2 (67 bp), respectively (Figure 3). Diversity ...
Context 2
... highest and lowest values of AT percentage in tRNAs were detected in tRNA-Glu (80.3%) and tRNA-Ser1 (47.7%), respectively. The shortest and longest tRNAs were tRNA-Ala, tRNA-Ley (59 bp), and tRNA-Ser2 (67 bp), respectively (Figure 3). ...
Citations
... Allozymic and mtDNA studies show that all parthenogenetic populations arose from only one branch of an Old World sexual ancestor, possibly Artemia urmiana or Artemia salina (Browne 1992;Manaffar et al. 2011;Eimanifar et al. 2016). Asem et al. (2021) determined the evolutionary relationship and the genetic variation of bisexual and parthenogenetic Artemia using three mitochondrial and two nuclear markers, they find that the diploid parthenogenetic Artemia are closely related to Artemia urmiana and tetraploids share a common ancestor with Artemia sinica. With time, an unusually high degree of divergence has produced among populations because of considerable changes in environmental conditions, such as salinity and temperature which consequently generated variability in reproductive, lifespan and physiological traits, population size (Browne 1992;Eimanifar et al. 2020). ...
Morphological and reproductive characteristics of brine shrimp Artemia from two western Algerian populations (El Melah and Timimoun) were studied for the first time alongside the northwestern population (Bethioua). Sexual, survival, growth, and reproduction were recorded for each population raised under standardized culture conditions. The morphological results showed that Artemia from the Timimoun and El Melah populations are bisexual, while the Bethioua population is parthenogenetic. After 20 days at salinity of 80 PSU, higher survival rates were found for the El Melah (85.5%) and Timimoun (72.0%) populations, while the Bethouia population showed the lowest survival rate (30.2%). Total body lengths of naupliar stages of the parthenogenetic populations were significantly longer than those of the bisexual populations. The Bethouia population displayed the highest absolute growth rate resulting in the largest adults compared to the bisexual populations. El Melah and Timimoun females were significantly larger morphologically in seven of the nine morphological characteristics compared to their respective males. The Bethouia females had smaller total and abdominal lengths compared to the females from the bisexual populations. The bisexual strains were significantly different from the parthenogenetic population in 9 of the 11 reproductive characteristics. Bethouia females, however, had the highest offspring/day/female and longest post-reproductive period compared to bisexual females. The Timimoun population adapted reproductive strategies differently compared to the other two populations: a late maturity (21.6 days), and more offspring/females (65.1). The data from the study will help future management and potential development of the Algerian brine shrimp populations.
... Total genomic DNA was extracted from 30 mg of tissue using Genomic Animal DNA Isolation (Sangon Biotech Co., Kit NO. B518221, Shanghai, China) (Asem et al. 2021). A pairedend genomic library was arranged (10 GB; two pair reads: 150 bp) utilizing the Illumina HiSeq X-ten. ...
The complete mitochondrial genome (mitogenome) of the soft coral Sinularia acuta Manuputty and
van Ofwegen, 2007 was sequenced and annotated using Illumina next-generation sequencing (NGS).
The mitogenome of S. acuta was 18,730 bp in length and consisted of 14 protein-coding genes (PCGs),
two ribosomal RNA genes (rRNA), and only one transfer RNA gene (tRNA-Met). The base composition
was 30.18% A, 16.46% C, 19.35% G, and 34.00% T, with a total AþT content of 64.19%. The phylogenetic
analysis demonstrated a close evolutionary relationship among Sinularia acuta, Sinularia penghuensis,
and Sinularia maxima.
... The sequencing was performed by a single constructed library, pooled on Illumina HiSeq X-ten sequencing flow cell (Novogene, Tianjin, China). Sequence quality control and assembly followed Asem et al., (2021b). Sequencing information is included in Supplementary material Table S1. ...
... MK069595, Asem et al., 2019a) and A. urmiana (GenBank accession no. MN240408, Asem et al., 2021b), which consist of two ribosomal RNAs (rRNAs) and 13 protein-coding genes (PCGs). The analysis considered maximum likelihood (ML) in MEGA X (Kumar et al., 2018) and Bayesian inference (BI) as implemented in MrBayes 3.2.2 on XSEDE (Miller et al., 2010). ...
... Differences in control region demonstrate that it is not conserved in Asian Artemia species, and such differences may be relevant considering that this region controls the regulation and initiation of DNA replication and transcription (Geng et al., 2016). Its mutations can thus alter the expression and energy of mitogenomic activity (Coskun et al., 2003;Asem et al., 2021b), which may be effective in adaptation to particular sites. ...
Species of Artemia are regionally endemic branchiopod crustaceans composed of sexual species and parthenogenetic lineages, and represent an excellent model for studying adaptation and speciation to extreme and heterogeneous hypersaline environments. We tested hypotheses of whether populations from the Tibetan Plateau belong to A. tibetiana Abatzopoulos, Zhang & Sorgeloos,1998 and whether a population from Kazakhstan is a new species, using other Asian species of Artemia as outgroups. We conducted a multitrait phylogenetic study based on the complete mitogenome, mitochondrial (COI, 12S, 16S) and nuclear (microsatellites, ITS1) markers, and a suit of uni-and multivariate morphological traits. Our results led to the discovery of two new species, one from the Tibetan Plateau (Haiyan Lake) in China (Artemia sorgeloosi n. sp.) and a second from Kazakhstan (Artemia amati n. sp.). Our analysis demonstrate that A. tibetiana and A. amati n. sp. are monophyletic, whereas A. sorgeloosi n. sp., and A. tibetiana are polyphyletic. Evolutionary relationships based on mitochondrial and nSSR markers suggest that A. tibetiana may have arisen from a past hybridization event of a maternal ancestor of A. tibetiana with A. sorgeloosi n. sp. or its ancestor. We present the complete mitogenome of A. tibetiana, A. amati n. sp., and A. sorgeloosi n. sp. We also provide a novel taxonomic identification key based on morphology, emphasizing the phenotype as a necessary component of the species concept.
... Total genomic DNA was extracted with Genomic DNA Isolation Kit no. B518221 (Sangon Biotech Co., Shanghai, China) (Asem et al. 2021). ...
In this study, the complete mitochondrial genome (mitogenome) of Sinularia humilis van Ofwegen, 2008 was determined using next-generation sequencing (NGS) method. The mitogenome of S. humilis is 18,743 bp in length, containing 14 protein-coding genes (PCGs), two ribosomal RNAs (rRNA) and one tRNA (tRNA-Met), which has same gene order with other species of Sinularia. ATG was determined as start codon in all 14 PCGs. Eight TAG, five TAA, and one incomplete codons (T-) were found as stop codon. Phylogenetic analysis of the small number of available mitogenomes showed that S. humilis is closely related to Sinularia ceramensis and Sinularia peculiaris.
... In this genus Artemia spp have more or less similar morphological patterns and appearance. They were resolved through microscopic observations, morphometry, and assessment of life history, RAPD, RFLP (Baxevanis et al., 2005;Thirunavukkarasu et al., 2021a) and other valuable genetic tools like COXI, mtDNA, mtDNA control region, ITS1, 16S rRNA p26 (Asem et al., 2018(Asem et al., , 2021Thirunavukkarasu et al., 2021b). At present, innumerous data are available on molecular taxonomy of Artemia species, but there is hardly data on molecular identification of morphotypes in these species (Sheir et al., 2018;Asem et al., 2020). ...
... Mitochondrial markers have become an indispensable tool for molecular identification and drawing phylogenetic relationships (Teske, 2021;Asem et al., 2021;Kern et al., 2020). The mitochondrial ribosomal RNA gene is a successful marker for exploring relationships at circumspecific levels (Chan et al., 2020;Abdul-Manan et al., 2020;Barua et al., 2021). ...
We document morphology and genetic relatedness of morphotypes within the Artemia franciscana that has colonized Covelong saltern in Kelambakkam (South India). They exhibits high phenotypic plasticity and intra-population variation in a supposedly panmictic population. Morphometric analysis was carried out on 18 traits in males and 15 in females and subjected to multivariate analysis. Three types each in males (M1, M3 and M4) and females (F1, F2 and F3) were singled out. The axes in the plot explain 77.9% in males and 73.9% in females of the variation through discriminant function analysis. The sequence divergence of the population was evaluated through mtDNA (16S rRNA) and nDNA (p26 gene) markers. The substantial sequence divergence was observed between the morphotypes through nDNA and appearing sequence divergence was recognized by mtDNA. Likewise, phylogenetic analyses of maximum likelihood and Bayesian analysis through nDNA revealed a maximum similarities between M1, M4 with F1 & F2 and M3 with F3. Further, haplotype distribution of nDNA revealed unique haplotype between M1 and M4 with F1 and F2 morphotypes. This study thus confirms the occurrence of morphotypes with specific characteristics inside a seemingly homogeneous population.
... In particular, early publications of new mitogenomes have often suffered from a lack of sequence data available for comparison. Recent re-evaluations of previously published mitogenomes using next-generation sequencing (NGS) methods reveal a variety of errors in Gen-Bank sequences such as incorrect annotation of genes or incorrect attribution of partial sequences to the heavy or light strand (Prada & Boore, 2019, Asem et al. 2021). Avian mitogenomes have been shown to include numt sequences (up to 93% of one Falco peregrinus mitogenome) or to miss a large duplication block that was only detected using long-range polymerase chain reaction (PCR), for example in cranes (Skujina et al. 2017). ...
Online repositories of DNA sequences are a rich and indispensable source of comparative data for biodiversity research and taxonomic studies. Despite increasingly high data quality of published sequences and associated metadata, particular attention should be paid to taxonomic assignment of DNA sequences, in particular if voucher specimens were not available or could not be examined. In this study, two nearly identical mitogenomes of two distinctive plover species (Charadrius alexandrinus and C. placidus) were re‐analysed and compared to a comprehensive data set of DNA‐barcode sequences (cytochrome‐oxidase subunit 1, COI) for 55 shorebird species. Phylogenetic analysis separated the two plover species in two reciprocally monophyletic clades that differed by mean p‐distances of 11.5–14.7%, however the COI sequence from the C. placidus mitogenome was nested in the Kentish Plover clade (C. alexandrinus). A similar mismatch was found for another DNA‐barcode sequence from a C. mongolus mitogenome that clustered with one of two clades of C. leschenaultii in the COI tree. These results strongly suggest that to date two out of seven mitogenomes published for Charadriidae are not representative of the taxon names the respective Genbank entries were assigned to. Only a few DNA‐barcode sequences were associated with outdated taxonomy, others were suspected to be chimeric sequences. Thus, free access to digital sequence information is a key factor for steady improvement of data quality in online repositories via swarm intelligence of the scientific community.
Due to the lack of a taxonomic key for the identification of Artemia species, molecular markers have been increasingly used for phylogenetic studies. The mt COI marker is a regularly considered marker for the molecular systematics of Artemia populations. The proposed universal and specific primers have mostly failed to amplify the Artemia aff. sinica mt COI marker, and on the whole, the successfully amplified products of the PCR were inefficient, primarily through the representation of poly-peak or incomplete sequences. We presumed that if a forward primer could be developed regarding the joint regions of the last part of the previous gene (tRNA Tyr ) and the beginning of the target gene mt COI , the sequence could be relevant to the target-sequence of mt COI . Thus, here, we describe a new set of primers, which could be used to amplify the mt COI barcoding region of Artemia aff. sinica Cai, 1989, with a high performance of sequencing. The new primer set worked well also for other Artemia bisexual species, as well as for parthenogenetic populations. It is recommended that joint regions between the previous/next gene(s) and the target marker, could be aimed at when designing specific primers for other markers and taxa.
