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

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.

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

Animals ◽

10.3390/ani9100756 ◽

2019 ◽

Vol 9 (10) ◽

pp. 756 ◽

Cited By ~ 2

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).

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

Bioscience Reports ◽

10.1042/bsr20201295 ◽

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.

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Genome survey sequencing of Dioscorea zingiberensis

Genome ◽

10.1139/gen-2018-0011 ◽

2018 ◽

Vol 61 (8) ◽

pp. 567-574 ◽

Cited By ~ 10

Author(s):

Wen Zhou ◽

Bin Li ◽

Lin Li ◽

Wen Ma ◽

Yuanchu Liu ◽

...

Keyword(s):

Flow Cytometry ◽

Genome Size ◽

Sequence Data ◽

Salvia Miltiorrhiza ◽

Economic Value ◽

Mononucleotide Repeat ◽

Next Generation Sequencing Technology ◽

Dioscorea Zingiberensis ◽

Genome Survey ◽

A Genome

Dioscorea zingiberensis (Dioscoreceae) is the main plant source of diosgenin (steroidal sapogenins), the precursor for the production of steroid hormones in the pharmaceutical industry. Despite its large economic value, genomic information of the genus Dioscorea is currently unavailable. Here, we present an initial survey of the D. zingiberensis genome performed by next-generation sequencing technology together with a genome size investigation inferred by flow cytometry. The whole genome survey of D. zingiberensis generated 31.48 Gb of sequence data with approximately 78.70× coverage. The estimated genome size is 800 Mb, with a high level of heterozygosity based on K-mer analysis. These reads were assembled into 334 288 contigs with a N50 length of 1079 bp, which were further assembled into 92 163 scaffolds with a total length of 173.46 Mb. A total of 4935 genes, 81 tRNAs, 69 rRNAs, and 661 miRNAs were predicted by the genome analysis, and 263 484 repeated sequences were obtained with 419 372 simple sequence repeats (SSRs). Among these SSRs, the mononucleotide repeat type was the most abundant (up to 54.60% of the total SSRs), followed by the dinucleotide (29.60%), trinucleotide (11.37%), tetranucleotide (3.53%), pentanucleotide (0.65%), and hexanucleotide (0.25%) repeat types. The 1C-value of D. zingiberensis was calibrated against Salvia miltiorrhiza and calculated as 0.87 pg (851 Mb) by flow cytometry, which was very close to the result of the genome survey. This is the first report of genome-wide characterization within this taxon.

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

Molecular Biology Reports ◽

10.1007/s11033-021-06875-z ◽

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.

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

10.21203/rs.3.rs-832190/v1 ◽

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.

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Genome survey of Zanthoxylum bungeanum and development of genomic-SSR markers in congeneric species

Bioscience Reports ◽

10.1042/bsr20201101 ◽

2020 ◽

Vol 40 (6) ◽

Author(s):

Jingmiao Li ◽

Siqiao Li ◽

Lijuan Kong ◽

Lihua Wang ◽

Anzhi Wei ◽

...

Keyword(s):

Ssr Markers ◽

Gc Content ◽

Repeat Sequence ◽

Pcr Analysis ◽

Minimum Length ◽

Dinucleotide Repeats ◽

Genome Survey ◽

Genomic Ssr ◽

Ssr Loci ◽

Zanthoxylum Bungeanum

Abstract Zanthoxylum bungeanum, a spice and medicinal plant, is cultivated in many parts of China and some countries in Southeast Asia; however, data on its genome are lacking. In the present study, we performed a whole-genome survey and developed novel genomic-SSR markers of Z. bungeanum. Clean data (∼197.16 Gb) were obtained and assembled into 11185221 scaffolds with an N50 of 183 bp. K-mer analysis revealed that Z. bungeanum has an estimated genome size of 3971.92 Mb, and the GC content, heterozygous rate, and repeat sequence rate are 37.21%, 1.73%, and 86.04%, respectively. These results indicate that the genome of Z. bungeanum is complex. Furthermore, 27153 simple sequence repeat (SSR) loci were identified from 57288 scaffolds with a minimum length > 1 kb. Mononucleotide repeats (19706) were the most abundant type, followed by dinucleotide repeats (5154). The most common motifs were A/T, followed by AT/AT; these SSRs accounted for 71.42% and 11.84% of all repeats, respectively. A total of 21243 non-repeating primer pairs were designed, and 100 were randomly selected and validated by PCR analysis using DNA from 10 Z. bungeanum individuals and 5 Zanthoxylum armatum individuals. Finally, 36 polymorphic SSR markers were developed with polymorphism information content (PIC) values ranging from 0.16 to 0.75. Cluster analysis revealed that Z. bungeanum and Z. armatum could be divided into two major clusters, suggesting that these newly developed SSR markers are useful for genetic diversity and germplasm resource identification in Z. bungeanum and Z. armatum.

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Genomic survey sequencing, development and characterization of single- and multi-locus genomic SSR markers of Elymus sibiricus L

BMC Plant Biology ◽

10.1186/s12870-020-02770-0 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yi Xiong ◽

Xiong Lei ◽

Shiqie Bai ◽

Yanli Xiong ◽

Wenhui Liu ◽

...

Keyword(s):

Ssr Markers ◽

Draft Genome ◽

Gc Content ◽

Single Locus ◽

Tibet Plateau ◽

Elymus Sibiricus ◽

Genome Survey ◽

A Genome ◽

Ssr Loci ◽

Next Generation Sequencing Ngs

Abstract Background Siberian wildrye (Elymus sibiricus L.) attracts considerable interest for grassland establishment and pasture recovery in the Qinghai-Tibet Plateau (QTP) due to its excellence in strong stress tolerance, high nutritional value and ease to cultivate. However, the lack of genomic information of E. sibiricus hampers its genetics study and breeding process. Results In this study, we performed a genome survey and developed a set of SSR markers for E. sibiricus based on Next-generation sequencing (NGS). We generated 469.17 Gb clean sequence which is 58.64× of the 6.86 Gb estimated genome size. We assembled a draft genome of 4.34 Gb which has 73.23% repetitive elements, a heterozygosity ratio of 0.01% and GC content of 45.68%. Based on the gnomic sequences we identified 67,833 SSR loci and from which four hundred were randomly selected to develop markers. Finally, 30 markers exhibited polymorphism between accessions and ten were identified as single-locus SSR. These newly developed markers along with previously reported 30 ones were applied to analyze genetic polymorphism among 27 wild E. sibiricus accessions. We found that single-locus SSRs are superior to multi-loci SSRs in effectiveness. Conclusions This study provided insights into further whole genome sequencing of E. sibiricus in strategy selection. The novel developed SSR markers will facilitate genetics study and breeding for Elymus species.

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Genomic Survey Sequencing, Development and Characterization of Single- and Multi-Locus Genomic SSR Markers of Elymus Sibiricus L.

10.21203/rs.3.rs-47577/v1 ◽

2020 ◽

Author(s):

Yi Xiong ◽

Xiong Lei ◽

Shiqie Bai ◽

Yanli Xiong ◽

Wenhui Liu ◽

...

Keyword(s):

Ssr Markers ◽

Draft Genome ◽

Gc Content ◽

Single Locus ◽

Tibet Plateau ◽

Elymus Sibiricus ◽

Genome Survey ◽

A Genome ◽

Ssr Loci ◽

Next Generation Sequencing Ngs

Abstract Background: Siberian wildrye (Elymus sibiricus L.) attracts considerable interest for grassland establishment and pasture recovery in the Qinghai-Tibet Plateau (QTP) due to its excellence in strong stress tolerance, high nutritional value and ease to cultivate. However, the lack of genomic information of E. sibiricus hampers its genetics study and breeding process.Results: In this study, we performed a genome survey and developed a set of SSR markers for E. sibiricus based on Next-generation sequencing (NGS). We generated 469.17 Gb clean sequence which is 58.64× of the 6.86 Gb estimated genome size. We assembled a draft genome of 4.34 Gb which has 73.23% repetitive elements, a heterozygosity ratio of 0.01% and GC content of 45.68%. Based on the gnomic sequences we identified 67,833 SSR loci and from which four hundred were randomly selected to develop markers. Finally, 30 markers exhibited polymorphism between accessions and ten were identified as single-locus SSR. These newly developed markers along with previously reported 30 ones were applied to analyze genetic polymorphism among 27 wild E. sibiricus accessions. We found that single-locus SSRs are superior to multi-loci SSRs in effectiveness.Conclusions: This study provided insights into further whole genome sequencing of E. sibiricus in strategy selection. The novel developed SSR markers will facilitate genetics study and breeding for Elymus species.

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Genomic survey sequencing, development and characterization of single- and multi-locus genomic SSR markers of Elymus sibiricus L.

10.21203/rs.3.rs-47577/v3 ◽

2020 ◽

Author(s):

Yi Xiong ◽

Xiong Lei ◽

Shiqie Bai ◽

Yanli Xiong ◽

Wenhui Liu ◽

...

Keyword(s):

Ssr Markers ◽

Draft Genome ◽

Gc Content ◽

Single Locus ◽

Tibet Plateau ◽

Elymus Sibiricus ◽

Genome Survey ◽

A Genome ◽

Ssr Loci ◽

Next Generation Sequencing Ngs

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Genome Survey of Misgurnus Anguillicaudatus to Identify Genomic Information, Simple Sequence Repeat (SSR) Markers and Mitochondrial Genome

10.21203/rs.3.rs-767195/v1 ◽

2021 ◽

Author(s):

Guiyun Huang ◽

Jianmeng Cao ◽

Chen Chen ◽

Miao Wang ◽

Zhigang Liu ◽

...

Keyword(s):

Mitochondrial Genome ◽

Microsatellite Loci ◽

Complete Mitochondrial Genome ◽

Gc Content ◽

Repeat Sequence ◽

Misgurnus Anguillicaudatus ◽

Population Genetic Analysis ◽

Next Generation Sequencing Technology ◽

Genome Survey ◽

A Genome

Abstract The dojo loach Misgurnus anguillicaudatus is an important economic species in Asia because of its nutritional value and broad environmental adaptability. Despite its economic importance, genomic data from M. anguillicaudatus was unavailable. In the present study, we conducted a genome survey of M. anguillicaudatus using next-generation sequencing technology. Its genome size was estimated to be 1105.97 Mb by using K-mer analysis, and its heterozygosity ratio, repeat sequence content, GC content were 1.45%, 58.98%, and 38.03%, respectively. A total of 376,357 microsatellite motifs were identified and mononucleotides, with a frequency of 42.57%, were the most frequently repeated motifs, followed by 40.83% dinucleotide, 7.49% trinucleotide, 8.09% tetranucleotide, and 0.91% pentanucleotide motifs. The AC/GT, AAT/ATT, and ACAG/CTGT repeats were the most abundant motifs among dinucleotide, trinucleotide, and tetranucleotide motifs, respectively. Besides, a complete mitochondrial genome was sequenced. Based on the maximum likelihood and Bayesian inference analyses, M. anguillicaudatus in this study was the “introgressed” mitochondrial type. Furthermore, a total of 376,357 SSR motifs were detected from the genome survey assembly. Seventy microsatellite loci were randomly selected from these SSR loci to test polymorphic, of which, twenty microsatellite loci were assessed in 30 individuals from a wild population. The number of alleles (Na), observed heterozygosity (Ho), and expected heterozygosity (He) per locus ranged from 7 to 19, 0.400 to 0.933, and 0.752 to 0.938, respectively. All twenty loci were highly informative (PIC > 0.700). Eight loci deviated from Hardy–Weinberg equilibrium after Bonferroni correction (P < 0.05). This is the first report of a genome survey in M. anguillicaudatus, and genome information, mitochondrial genome, and microsatellite markers will be valuable for further studies on population genetic analysis, natural resource conservation, and molecular marker-assisted selective breeding.

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