Genome‐wide structural and functional features of single nucleotide polymorphisms revealed from the whole genome resequencing of 179 accessions of Arachis

AbstractsHongyingzi is a special waxy sorghum (Sorghum bicolor L. Moench) cultivar for brewing Moutai liquor. For an overall understanding of the whole genome of Hongyingzi, we performed whole-genome resequencing technology with 56.10 X depth to reveal its comprehensive variations. Compared with the BTx623 reference genome, 2.48% of genome sequences were altered in the Hongyingzi genome. Among these alterations, there were 1885774 single nucleotide polymorphisms (SNPs), 309381 small fragments insertions and deletions (Indels), 31966 structural variations (SVs), and 217273 copy number variations (CNVs). These alterations conferred 29614 genes variations. It was also predicted that 35 genes variations were related to the multidrug and toxic efflux (MATE) transporter, chalcone synthase (CHS), ATPase isoform 10 (AHA10) transporter, dihydroflavonol-4-reductase (DFR), the laccase 15 (LAC15), flavonol 3′-hydroxylase (F3′H), flavanone 3-hydroxylase (F3H), O-methyltransferase (OMT), flavonoid 3′5′ hydroxylase (F3′5′H), UDP-glucose:sterol-glucosyltransferase (SGT), flavonol synthase (FLS), and chalcone isomerase (CHI) involved in the tannin synthesis. These results would provide theoretical supports for the molecular markers developments and gene function studies related to the liquor-making traits, and the genetic improvement of waxy sorghum based on the genome editing technology.

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A survey of genome-wide single nucleotide polymorphisms through genome resequencing in the Périgord black truffle (Tuber melanosporum Vittad.)

Molecular Ecology Resources ◽

10.1111/1755-0998.12391 ◽

2015 ◽

Vol 15 (5) ◽

pp. 1243-1255 ◽

Cited By ~ 12

Author(s):

Thibaut Payen ◽

Claude Murat ◽

Anaïs Gigant ◽

Emmanuelle Morin ◽

Stéphane De Mita ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Tuber Melanosporum ◽

Nucleotide Polymorphisms ◽

Genome Resequencing ◽

Black Truffle ◽

Single Nucleotide ◽

Genome Wide

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Whole genome sequence and genome-wide distributed single nucleotide polymorphisms (SNPs) of the Black Bengal goat

F1000Research ◽

10.12688/f1000research.18316.1 ◽

2019 ◽

Vol 8 ◽

pp. 318

Author(s):

Md. Bazlur Rahman Mollah ◽

Md. Shamsul Alam Bhuiyan ◽

M.A.M. Yahia Khandoker ◽

Md. Abdul Jalil ◽

Gautam Kumar Deb ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Whole Genome Sequence ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

High Quality ◽

Single Nucleotide ◽

Genome Wide ◽

High Quality Snps ◽

Black Goat ◽

Black Bengal Goat

The Black Bengal goat (BBG) is a dwarf sized heritage goat (Capra hircus) breed from Bangladesh, and is well known for its high fertility, excellent meat and skin quality. Here we present the first whole genome sequence and genome-wide distributed single nucleotide polymorphisms (SNPs) of the BBG. A total of 833,469,900 raw reads consisting of 125,020,485,000 bases were obtained by sequencing one male BBG sample. The reads were aligned to the San Clemente and the Yunnan black goat genome which resulted in 98.65% (properly paired, 94.81%) and 98.50% (properly paired, 97.10%) of the reads aligning, respectively. Notably, the estimated sequencing coverages were 48.22X and 44.28X compared to published San Clemente and the Yunnan black goat genomes respectively. On the other hand, a total of 9,497,875 high quality SNPs (Q ≥ 20) along with 1,023,359 indels, and 8,746,849 high quality SNPs along with 842,706 indels were identified in BBG against the San Clemente and Yunnan black goat genomes respectively. The dataset is publicly available from NCBI BioSample (SAMN10391846), Sequence Read Archive (SRR8182317, SRR8549413 and SRR8549904), with BioProject ID PRJNA504436. These data might be useful genomic resources in conducting genome wide association studies, identification of quantitative trait loci (QTLs) and functional genomic analysis of the Black Bengal goat.

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Development a Set of 46 SNP Markers for the Yellow Catfish (Tachysurus Fulvidraco)

10.21203/rs.3.rs-501513/v1 ◽

2021 ◽

Author(s):

Huaxing Zhou ◽

Tingshuang Pan ◽

Huan Wang ◽

He Jiang ◽

Jun Ling ◽

...

Keyword(s):

Snp Markers ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Yellow Catfish ◽

Genome Resequencing ◽

Single Nucleotide ◽

Expected Heterozygosity ◽

Hardy Weinberg Equilibrium ◽

Whole Genome Resequencing ◽

Tachysurus Fulvidraco

Abstract The whole genome resequencing was used to develop single nucleotide polymorphisms (SNP) markers for the yellow catfish (Tachysurus fulvidraco). A total of 46 SNP markers were selected from 5550676 genotyping markers which distributed on 26 chromosomes. Of the 46 SNPs analyzed, 35 SNPs conformed to Hardy-Weinberg equilibrium. The observed and expected heterozygosity of these markers ranged from 0.2519 to 0.771 and from 0.265 to 0.5018, respectively. This set of markers will be of great useful for population genetics of the yellow catfish.

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Genome-wide identifying of G-quadruplex structures directly by whole-genome resequencing

10.21203/rs.3.rs-149290/v1 ◽

2021 ◽

Author(s):

Jing Tu ◽

Mengqin Duan ◽

Wenli Liu ◽

Na Lu ◽

Xiao Sun ◽

...

Keyword(s):

Individual Differences ◽

Whole Genome ◽

Genome Resequencing ◽

Single Nucleotide ◽

Genome Wide ◽

G Quadruplex ◽

Sequencing Quality ◽

Single Nucleotide Variations ◽

Whole Genome Resequencing ◽

The Given

Abstract We present a convenient genome-wide DNA G-quadruplex (G4) profiling method that identifies G4 structures from ordinary whole-genome resequencing data by seizing the slight fluctuation of sequencing quality. We identified 736,689 G4 structures within human genome, in which 44.9% of all predicted canonical G4-froming sequences were contained. We observed that some of the single nucleotide variations (SNVs) influenced the formation of G4 structures, including homozygous SNVs and heterozygous SNVs. Due to SNVs contain individual differences, the given approach is available to identify and characterize G4s genome-wide for specific individuals.

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