scholarly journals Genome survey sequencing of common vetch (Vicia sativa L.) and genetic diversity analysis of Chinese germplasm with genomic SSR markers

2021 ◽  
Author(s):  
Lin Ma ◽  
Xiao Wang ◽  
Min Yan ◽  
Fang Liu ◽  
Shuxing Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sequence Data ◽  
Gc Content ◽  
Vicia Sativa ◽  
Whole Genome ◽  
Common Vetch ◽  
High Genetic Diversity ◽  
Genome Survey ◽  
Genome Features ◽  
High Quality Sequence

Abstract Background Common vetch (Vicia sativa L.) is an annual legume with excellent suitability in cold and dry regions. Despite its great applied potential, the genomic information regarding common vetch currently remains unavailable. Methods and results In the present study, the whole genome survey of common vetch was performed using the next-generation sequencing (NGS). A total of 79.84 Gbp high quality sequence data were obtained and assembled into 3,754,145 scaffolds with an N50 length of 3556 bp. According to the K-mer analyses, the genome size, heterozygosity rate and GC content of common vetch genome were estimated to be 1568 Mbp, 0.4345 and 35%, respectively. In addition, a total of 76,810 putative simple sequence repeats (SSRs) were identified. Among them, dinucleotide was the most abundant SSR type (44.94%), followed by Tri- (35.82%), Tetra- (13.22%), Penta- (4.47%) and Hexanucleotide (1.54%). Furthermore, a total of 58,175 SSR primer pairs were designed and ten of them were validated in Chinese common vetch. Further analysis showed that Chinese common vetch harbored high genetic diversity and could be clustered into two main subgroups. Conclusion This is the first report about the genome features of common vetch, and the information will help to design whole genome sequencing strategies. The newly identified SSRs in this study provide basic molecular markers for germplasm characterization, genetic diversity and QTL mapping studies for common vetch.

scholarly journals Genome Survey Sequencing of Common Vetch (Vicia Sativa L.) and Genetic Diversity Analysis of Chinese Germplasm with Genomic SSR Markers

2021 ◽  
Author(s):  
lin ma ◽  
Xiao Wang ◽  
Min Yan ◽  
Fang Liu ◽  
Xuemin Wang
Keyword(s):  
Genetic Diversity ◽  
Sequence Data ◽  
Gc Content ◽  
Vicia Sativa ◽  
Whole Genome ◽  
Common Vetch ◽  
High Genetic Diversity ◽  
Genome Survey ◽  
Genome Features ◽  
High Quality Sequence

Abstract Common vetch (Vicia sativa L.) is an annual legume with excellent suitability in cold and dry regions. Despite its great applied potential, the genomic information regarding common vetch currently remains unavailable. In the present study, the whole genome survey of common vetch was performed using the next-generation sequencing (NGS). A total of 79.84 Gbp high quality sequence data were obtained and assembled into 3,754,145 scaffolds with an N50 length of 3,556 bp. According to the K-mer analyses, the genome size, heterozygosity rate and GC content of common vetch genome were estimated to be 1,568 Mbp, 0.4345% and 35%, respectively. In addition, a total of 76,810 putative simple sequence repeats (SSRs) were identified. Among them, dinucleotide was the most abundant SSR type (44.94%), followed by Tri- (35.82%), Tetra- (13.22%), Penta- (4.47%) and Hexanucleotide (1.54%). Furthermore, a total of 58,175 SSR primer pairs were designed and ten of them were validated in Chinese common vetch. Further analysis showed that Chinese common vetch harbored high genetic diversity and could be clustered into two main subgroups. This is the first report about the genome features of common vetch, and the information will help to design whole genome sequencing strategies. The newly identified SSRs in this study provide basic molecular markers for germplasm characterization, genetic diversity and QTL mapping studies for common vetch.

scholarly journals A First Insight into a Draft Genome of Silver Sillago (Sillago sihama) via Genome Survey Sequencing

Animals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 756 ◽  
Author(s):  
Li ◽  
Tian ◽  
Huang ◽  
Lin ◽  
Wang ◽  
...  
Keyword(s):  
Sequence Data ◽  
Economic Value ◽  
Draft Genome ◽  
Gc Content ◽  
Dinucleotide Repeats ◽  
Dominant Form ◽  
Genome Survey ◽  
High Quality Sequence ◽  
Sillago Sihama ◽  
Next Generation Sequencing Ngs

Sillago sihama has high economic value and is one of the most attractive aquaculture species in China. Despite its economic importance, studies of its genome have barely been performed. In this study, we conducted a first genomic survey of S. sihama using next-generation sequencing (NGS). In total, 45.063 Gb of high-quality sequence data were obtained. For the 17-mer frequency distribution, the genome size was estimated to be 508.50 Mb. The sequence repeat ratio was calculated to be 21.25%, and the heterozygosity ratio was 0.92%. Reads were assembled into 1,009,363 contigs, with a N50 length of 1362 bp, and then into 814,219 scaffolds, with a N50 length of 2173 bp. The average Guanine and Cytosine (GC) content was 45.04%. Dinucleotide repeats (56.55%) were the dominant form of simple sequence repeats (SSR).

scholarly journals Genome Survey of Male and Female Spotted Scat (Scatophagus argus)

Animals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 1117 ◽  
Author(s):  
Yuanqing Huang ◽  
Dongneng Jiang ◽  
Ming Li ◽  
Umar Farouk Mustapha ◽  
Changxu Tian ◽  
...  
Keyword(s):  
Sequence Data ◽  
Economic Value ◽  
Gc Content ◽  
Dinucleotide Repeats ◽  
Dominant Form ◽  
Scatophagus Argus ◽  
Genome Survey ◽  
Male Genome ◽  
A Genome ◽  
High Quality Sequence

The spotted scat, Scatophagus argus, is a species of fish that is widely propagated within the Chinese aquaculture industry and therefore has significant economic value. Despite this, studies of its genome are severely lacking. In the present study, a genomic survey of S. argus was conducted using next-generation sequencing (NGS). In total, 55.699 GB (female) and 51.047 GB (male) of high-quality sequence data were obtained. Genome sizes were estimated to be 598.73 (female) and 597.60 (male) Mbp. The sequence repeat ratios were calculated to be 27.06% (female) and 26.99% (male). Heterozygosity ratios were 0.37% for females and 0.38% for males. Reads were assembled into 444,961 (female) and 453,459 (male) contigs with N50 lengths of 5,747 and 5,745 bp for females and males, respectively. The average guanine-cytosine (GC) content of the female genome was 41.78%, and 41.82% for the male. A total of 42,869 (female) and 43,283 (male) genes were annotated to the non-redundant (NR) and SwissProt databases. The female and male genomes contained 66.6% and 67.8% BUSCO core genes, respectively. Dinucleotide repeats were the dominant form of simple sequence repeats (SSR) observed in females (68.69%) and males (68.56%). Additionally, gene fragments of Dmrt1 were only observed in the male genome. This is the first report of a genome-wide characterization of S. argus.

scholarly journals Genomic characteristics and profile of microsatellite primers for Acanthogobius ommaturus by genome survey sequencing

2020 ◽  
Vol 40 (11) ◽  
Author(s):  
Bingjie Chen ◽  
Zhicheng Sun ◽  
Fangrui Lou ◽  
Tian-xiang Gao ◽  
Na Song
Keyword(s):  
Sequence Data ◽  
Gc Content ◽  
Dinucleotide Repeats ◽  
Genome Survey ◽  
Genome Wide ◽  
Sequencing Method ◽  
High Quality Sequence ◽  
Repeat Rate ◽  
Nucleotide Repeats ◽  
Distribution Frequency

Abstract Acanthogobius ommaturus is one of the suitable species to study the genetic mechanism of adaptive evolution, but there are few reports on its genetics. In the present study, the genomic survey sequencing method was used to analyze the genome characters of A. ommaturus. A total of 50.50 G high-quality sequence data were obtained in the present study. From the 19-mer distribution frequency, the estimated genome size was 928.01 Mb. The calculated sequence repeat rate was about 38.31%, the heterozygosity was approximately 0.17%, and the GC% content was approximately 40.88%. Moreover, 475,724 simple sequence repeats (SSRs) were identified. Among them, dinucleotide repeats were the most (53.70% of the total SSRs), followed by tri- (35.36%), hexa- (4.59%), tetra- (4.57%) and penta- (1.77%) nucleotide repeats type. This is the first genome-wide feature of this species to be reported.

scholarly journals Genome features of common vetch ( Vicia sativa ) in natural habitats

Plant Direct ◽  
2021 ◽  
Vol 5 (10) ◽  
Author(s):  
Kenta Shirasawa ◽  
Shunichi Kosugi ◽  
Kazuhiro Sasaki ◽  
Andrea Ghelfi ◽  
Koei Okazaki ◽  
...  
Keyword(s):  
Vicia Sativa ◽  
Common Vetch ◽  
Natural Habitats ◽  
Genome Features

scholarly journals Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus

2020 ◽  
Vol 40 (2) ◽  
Author(s):  
Sheng-yong Xu ◽  
Na Song ◽  
Shi-jun Xiao ◽  
Tian-xiang Gao
Keyword(s):  
Microsatellite Markers ◽  
Gc Content ◽  
The Philippines ◽  
Whole Genome Sequence ◽  
Northwestern Pacific ◽  
Whole Genome ◽  
Survey Analysis ◽  
Genome Survey ◽  
Sebastiscus Marmoratus ◽  
Wide Range

Abstract The marbled rockfish Sebastiscus marmoratus is an ecologically and economically important marine fish species distributed along the northwestern Pacific coast from Japan to the Philippines. Here, next-generation sequencing was used to generate a whole genome survey dataset to provide fundamental information of its genome and develop genome-wide microsatellite markers for S. marmoratus. The genome size of S. marmoratus was estimated as approximate 800 Mb by using K-mer analyses, and its heterozygosity ratio and repeat sequence ratio were 0.17% and 39.65%, respectively. The preliminary assembled genome was nearly 609 Mb with GC content of 41.3%, and the data were used to develop microsatellite markers. A total of 191,592 microsatellite motifs were identified. The most frequent repeat motif was dinucleotide with a frequency of 76.10%, followed by 19.63% trinucleotide, 3.91% tetranucleotide, and 0.36% pentanucleotide motifs. The AC, GAG, and ATAG repeats were the most abundant motifs of dinucleotide, trinucleotide, and tetranucleotide motifs, respectively. In summary, a wide range of candidate microsatellite markers were identified and characterized in the present study using genome survey analysis. High-quality whole genome sequence based on the “Illumina+PacBio+Hi-C” strategy is warranted for further comparative genomics and evolutionary biology studies in this species.

scholarly journals Population genomics of East Asian ethnic groups

Hereditas ◽  
2020 ◽  
Vol 157 (1) ◽  
Author(s):  
Ziqing Pan ◽  
Shuhua Xu
Keyword(s):  
Genetic Diversity ◽  
East Asia ◽  
Ethnic Groups ◽  
Population Genomics ◽  
Sequence Data ◽  
East Asian ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Evolutionary Forces ◽  
Asian Populations

AbstractEast Asia constitutes one-fifth of the global population and exhibits substantial genetic diversity. However, genetic investigations on populations in this region have been largely under-represented compared with European populations. Nonetheless, the last decade has seen considerable efforts and progress in genome-wide genotyping and whole-genome sequencing of the East-Asian ethnic groups. Here, we review the recent studies in terms of ancestral origin, population relationship, genetic differentiation, and admixture of major East- Asian groups, such as the Chinese, Korean, and Japanese populations. We mainly focus on insights from the whole-genome sequence data and also include the recent progress based on mitochondrial DNA (mtDNA) and Y chromosome data. We further discuss the evolutionary forces driving genetic diversity in East-Asian populations, and provide our perspectives for future directions on population genetics studies, particularly on underrepresented indigenous groups in East Asia.

scholarly journals Optimizing Sample Size to Assess the Genetic Diversity in Common Vetch (Vicia sativa L.) Populations Using Start Codon Targeted (SCoT) Markers

Molecules ◽  
2017 ◽  
Vol 22 (4) ◽  
pp. 567 ◽  
Author(s):  
Xutian Chai ◽  
Rui Dong ◽  
Wenxian Liu ◽  
Yanrong Wang ◽  
Zhipeng Liu
Keyword(s):  
Genetic Diversity ◽  
Sample Size ◽  
Start Codon ◽  
Vicia Sativa ◽  
Common Vetch

scholarly journals Genomic Uniqueness of Local Sheep Breeds From Morocco

2021 ◽  
Vol 12 ◽  
Author(s):  
Abdessamad Ouhrouch ◽  
Simon Boitard ◽  
Frédéric Boyer ◽  
Bertrand Servin ◽  
Anne Da Silva ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Demographic History ◽  
Large Set ◽  
Whole Genome ◽  
Selection Signatures ◽  
Effective Population ◽  
High Genetic Diversity ◽  
Sheep Breeds ◽  
Genome Data ◽  
Genomic Regions

Sheep farming is a major source of meat in Morocco and plays a key role in the country’s agriculture. This study aims at characterizing the whole-genome diversity and demographic history of the main Moroccan sheep breeds, as well as to identify selection signatures within and between breeds. Whole genome data from 87 individuals representing the five predominant local breeds were used to estimate their level of neutral genetic diversity and to infer the variation of their effective population size over time. In addition, we used two methods to detect selection signatures: either for detecting selective sweeps within each breed separately or by detecting differentially selected regions by contrasting different breeds. We identified hundreds of genomic regions putatively under selection, which related to several biological terms involved in local adaptation or the expression of zootechnical performances such as Growth, UV protection, Cell maturation or Feeding behavior. The results of this study revealed selection signatures in genes that have an important role in traits of interest and increased our understanding of how genetic diversity is distributed in these local breeds. Thus, Moroccan local sheep breeds exhibit both a high genetic diversity and a large set of adaptive variations, and therefore, represent a valuable genetic resource for the conservation of sheep in the context of climate change.

scholarly journals Homogeneity of Arabian Peninsula dromedary camel populations with signals of geographic distinction based on whole genome sequence data

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Hussain Bahbahani ◽  
Faisal Almathen
Keyword(s):  
Genetic Diversity ◽  
Genome Sequence ◽  
Arabian Peninsula ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Dromedary Camels ◽  
Genome Sequence Data ◽  
Similarity Indices ◽  
Bactrian Camels

AbstractDromedary camels in the Arabian Peninsula distribute along different geographical and ecological locations, e.g. desert, mountains and coasts. Here, we are aiming to explore the whole genome sequence data of ten dromedary populations from the Arabian Peninsula to assess their genetic structure, admixture levels, diversity and similarity indices. Upon including reference dromedary and Bactrian camel populations from Iran and Kazakhstan, we characterise inter-species and geographic genetic distinction between the dromedary and the Bactrian camels. Individual-based alpha genetic diversity profiles are found to be generally higher in Bactrian camels than dromedary populations, with the exception of five autosomes (NC_044525.1, NC_044534.1, NC_044540.1, NC_044542.1, NC_044544.1) at diversity orders (q ≥ 2). The Arabian Peninsula camels are generally homogenous, with a small degree of genetic distinction correlating with three geographic groups: North, Central and West; Southwest; and Southeast of the Arabian Peninsula. No significant variation in diversity or similarity indices are observed among the different Arabian Peninsula dromedary populations. This study contributes to our understanding of the genetic diversity of Arabian Peninsula dromedary camels. It will help conserve the genetic stock of this species and support the design of breeding programmes for genetic improvement of favorable traits.

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