scholarly journals Direct genome-wide identification of G-quadruplex structures by whole-genome resequencing

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jing Tu ◽  
Mengqin Duan ◽  
Wenli Liu ◽  
Na Lu ◽  
Yue Zhou ◽  
...  
Keyword(s):  
Whole Genome ◽  
Genome Resequencing ◽  
Detection Rates ◽  
Genome Wide ◽  
G Quadruplex ◽  
Sequencing Quality ◽  
Whole Genome Resequencing ◽  
Public Datasets ◽  
User Friendly ◽  
The Given

AbstractWe present a user-friendly and transferable 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. In the human genome, 736,689 G4 structures were identified, of which 45.9% of all predicted canonical G4-forming sequences were characterized. Over 89% of the detected canonical G4s were also identified by combining polymerase stop assays with next-generation sequencing. Testing using public datasets of 6 species demonstrated that the present method is widely applicable. The detection rates of predicted canonical quadruplexes ranged from 32% to 58%. Because single nucleotide variations (SNVs) influence the formation of G4 structures and have individual differences, the given method is available to identify and characterize G4s genome-wide for specific individuals.

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

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.

scholarly journals Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes

2021 ◽  
Author(s):  
Adam Ciezarek ◽  
Antonia Ford ◽  
Graham Etherington ◽  
Kasozi Nasser ◽  
Milan Malinsky ◽  
...  
Keyword(s):  
Native Species ◽  
Cichlid Fish ◽  
Snp Markers ◽  
Whole Genome ◽  
The Novel ◽  
Genome Resequencing ◽  
Genome Wide ◽  
In The Wild ◽  
Snp Panel ◽  
Whole Genome Resequencing

Cichlid fish of the genus Oreochromis form the basis of the global tilapia aquaculture and fisheries industry. Non-native farmed tilapia populations are known to be widely distributed across Africa and to hybridize with native Oreochromis species. However, many species are difficult to distinguish morphologically, hampering attempts to maintain good quality farmed strains or to identify pure populations of native species. Here, we describe the development of a single nucleotide polymorphism (SNP) genotyping panel from whole-genome resequencing data that enables targeted species identification in Tanzania. We demonstrate that an optimized panel of 96 genome-wide SNPs based on FST outliers performs comparably to whole genome resequencing in distinguishing species and identifying hybrids. We also show this panel outperforms microsatellite-based and phenotype-based classification methods. Case studies indicate several locations where introduced aquaculture species have become established in the wild, threatening native Oreochromis species. The novel SNP markers identified here represent an important resource for assessing broodstock purity and helping to conserve unique endemic biodiversity, and in addition potentially for assessing broodstock purity in hatcheries.

scholarly journals Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection

2015 ◽  
Vol 38 (5) ◽  
pp. 466-473 ◽  
Author(s):  
Jung-Woo Choi ◽  
Bong-Hwan Choi ◽  
Seung-Hwan Lee ◽  
Seung-Soo Lee ◽  
Hyeong-Cheol Kim ◽  
...  
Keyword(s):  
Whole Genome ◽  
Genome Resequencing ◽  
Genome Wide ◽  
Signatures Of Selection ◽  
Whole Genome Resequencing

scholarly journals A Y-linked anti-Müllerian hormone type-II receptor is the sex-determining gene in ayu, Plecoglossus altivelis

PLoS Genetics ◽  
2021 ◽  
Vol 17 (8) ◽  
pp. e1009705
Author(s):  
Masatoshi Nakamoto ◽  
Tsubasa Uchino ◽  
Eriko Koshimizu ◽  
Yudai Kuchiishi ◽  
Ryota Sekiguchi ◽  
...  
Keyword(s):  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Whole Genome ◽  
Type Ii ◽  
Genome Resequencing ◽  
Plecoglossus Altivelis ◽  
Genome Wide ◽  
Males And Females ◽  
Whole Genome Resequencing ◽  
Male Specific

Whole-genome duplication and genome compaction are thought to have played important roles in teleost fish evolution. Ayu (or sweetfish), Plecoglossus altivelis, belongs to the superorder Stomiati, order Osmeriformes. Stomiati is phylogenetically classified as sister taxa of Neoteleostei. Thus, ayu holds an important position in the fish tree of life. Although ayu is economically important for the food industry and recreational fishing in Japan, few genomic resources are available for this species. To address this problem, we produced a draft genome sequence of ayu by whole-genome shotgun sequencing and constructed linkage maps using a genotyping-by-sequencing approach. Syntenic analyses of ayu and other teleost fish provided information about chromosomal rearrangements during the divergence of Stomiati, Protacanthopterygii and Neoteleostei. The size of the ayu genome indicates that genome compaction occurred after the divergence of the family Osmeridae. Ayu has an XX/XY sex-determination system for which we identified sex-associated loci by a genome-wide association study by genotyping-by-sequencing and whole-genome resequencing using wild populations. Genome-wide association mapping using wild ayu populations revealed three sex-linked scaffolds (total, 2.03 Mb). Comparison of whole-genome resequencing mapping coverage between males and females identified male-specific regions in sex-linked scaffolds. A duplicate copy of the anti-Müllerian hormone type-II receptor gene (amhr2bY) was found within these male-specific regions, distinct from the autosomal copy of amhr2. Expression of the Y-linked amhr2 gene was male-specific in sox9b-positive somatic cells surrounding germ cells in undifferentiated gonads, whereas autosomal amhr2 transcripts were detected in somatic cells in sexually undifferentiated gonads of both genetic males and females. Loss-of-function mutation for amhr2bY induced male to female sex reversal. Taken together with the known role of Amh and Amhr2 in sex differentiation, these results indicate that the paralog of amhr2 on the ayu Y chromosome determines genetic sex, and the male-specific amh-amhr2 pathway is critical for testicular differentiation in ayu.

scholarly journals Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes

2021 ◽  
Author(s):  
Atal Saha ◽  
Anastasia Andersson ◽  
Sara Kurland ◽  
Naomi Keehnen ◽  
Verena Esther Kutschera ◽  
...  
Keyword(s):  
Reproductive Isolation ◽  
Brown Trout ◽  
Genetic Divergence ◽  
Salmo Trutta ◽  
Sequence Data ◽  
Whole Genome ◽  
Similar Data ◽  
Genome Resequencing ◽  
Genome Wide ◽  
Whole Genome Resequencing

The sympatric existence of genetically distinct populations of the same species remains a puzzle in ecology. Coexisting salmonid fish populations are known from over 100 freshwater lakes. Most studies of sympatric populations have used limited numbers of genetic markers making it unclear if genetic divergence involves only certain parts of the genome. We return to the first reported case of salmonid sympatry, initially detected through contrasting homozygosity at a single allozyme locus (lactate dehydrogenase, LDH-A1) in brown trout in the small Lakes Bunnersjöarna, central Sweden. We use DNA from samples collected in the 1970s and a 96 SNP fluidigm array to verify the existence of the coexisting demes. We then apply whole-genome resequencing of pooled DNA to explore genome-wide diversity within and between these demes; strong genetic divergence is observed with genome-wide FST=0.13. Nucleotide diversity is estimated to 0.0013 in Deme I but only 0.0005 in Deme II. Individual whole-genome resequencing of two individuals per deme suggests considerably higher inbreeding in Deme II vs. Deme I. Comparing with similar data from other lakes we find that the genome-wide divergence between the demes is similar to that between reproductively isolated populations. We located two genes for LDH-A and found divergence between the demes in a regulatory section of one of the genes, but we could not find a perfect fit between allozyme and sequence data. Our data demonstrate genome-wide divergence governed by genetic drift and diversifying selection, confirming reproductive isolation between the sympatric demes.

scholarly journals Whole Genome Resequencing of Heugu (Korean Black Cattle) for the Genome-Wide SNP Discovery

2013 ◽  
Vol 33 (6) ◽  
pp. 715-722 ◽  
Author(s):  
Jung-Woo Choi ◽  
Won-Hyong Chung ◽  
Kyung-Tai Lee ◽  
Jae-Won Choi ◽  
Kyoung-Sub Jung ◽  
...  
Keyword(s):  
Whole Genome ◽  
Snp Discovery ◽  
Genome Resequencing ◽  
Genome Wide ◽  
Whole Genome Resequencing

scholarly journals Whole-Genome Resequencing of Near-Isogenic Lines Reveals a Genomic Region Associated with High Trans-Lycopene Contents in Watermelon

Plants ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 8
Author(s):  
Siyoung Lee ◽  
Girim Park ◽  
Yunseo Choi ◽  
Seoyeon Park ◽  
Hoytaek Kim ◽  
...  
Keyword(s):  
Genomic Region ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Near Isogenic Lines ◽  
Genome Resequencing ◽  
Isogenic Lines ◽  
Genome Wide ◽  
Donor Parent ◽  
Caps Markers ◽  
Whole Genome Resequencing

Trans-lycopene is a functional phytochemical abundant in red-fleshed watermelons, and its contents vary among cultivars. In this study, the genetic basis of high trans-lycopene contents in scarlet red flesh was evaluated. Three near-isogenic lines (NILs) with high trans-lycopene contents were derived from the scarlet red-fleshed donor parent DRD and three coral red-fleshed (low trans-lycopene contents) recurrent parents. The lycopene contents of DRD (589.4 ± 71.8 µg/g) were two times higher than that of the recurrent parents, and values for NILs were intermediate between those of the parents. Coral red-fleshed lines and F1 cultivars showed low trans-lycopene contents (135.7 ± 18.0 µg/g to 213.7 ± 39.5 µg/g). Whole-genome resequencing of two NILs and their parents and an analysis of genome-wide single-nucleotide polymorphisms revealed three common introgressed regions (CIRs) on chromosomes 6, 9, and 10. Twenty-eight gene-based cleaved amplified polymorphic sequence (CAPS) markers were developed from the CIRs. The CAPS markers derived from CIR6 on chromosome 6, spanning approximately 1 Mb, were associated (R2 = 0.45–0.72) with the trans-lycopene contents, particularly CIR6-M1 and CIR6-M4. Our results imply that CIR6 is a major genomic region associated with variation in the trans-lycopene contents in red-fleshed watermelon, and CIR6-M1 and CIR6-M4 may be useful for marker-assisted selection.

scholarly journals Genome-wide variations analysis of special waxy sorghum cultivar Hongyingzi for brewing Moutai liquor

2019 ◽  
Author(s):  
Can Wang ◽  
Lingbo Zhou ◽  
Xu Gao ◽  
Yanqing Ding ◽  
Bin Cheng ◽  
...  
Keyword(s):  
Chalcone Synthase ◽  
Reference Genome ◽  
Copy Number Variations ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Structural Variations ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Whole Genome Resequencing

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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