scholarly journals Genomic data shed light on sex-determination in Australian freshwater Percichthyid fish species: Many ways to be a male

2021 ◽  
Author(s):  
Alexandra Pavlova ◽  
Katherine Harrisson ◽  
Rustam Turakulov ◽  
Yin Peng Lee ◽  
Brett Ingram ◽  
...  
Keyword(s):  
Sex Differences ◽  
Sex Determination ◽  
Fish Species ◽  
Amplicon Sequencing ◽  
Molecular Sexing ◽  
Whole Genome ◽  
Genome Wide ◽  
Freshwater Biota ◽  
Whole Genome Resequencing ◽  
Australian Freshwater

Understanding sex-specific biology can aid conservation management. But understanding genomic sex differences of monomorphic fish species and developing molecular sexing assays is challenged by their diverse sex-determination systems. To facilitate research on Percichthyid fish, predominant in the Australian freshwater biota, we report whole genome sequences and annotations of the endangered Macquarie perch Macquaria australasica and its sister species, the golden perch M. ambigua. To identify sex-linked loci, we conducted whole genome resequencing on 100 known-sex Macquarie perch. In-silico pool-seq comparisons revealed few sex differences, but a 275-Kb SOX-containing scaffold was enriched for gametologous loci- homozygous in females, heterozygous in males. Within this scaffold we reconstructed X- and Y-linked 146-bp haplotypes containing 5 sex-linked SNPs, ~38 Kb upstream of SOX, and developed a PCR-RFLP sexing assay targeting the Y-linked allele of one SNP. We tested this assay in a panel of known-sex Macquarie perch, and smaller panels of three other confamilial species. Amplicon sequencing of 400 bp encompassing the 146-bp region revealed that the few sex-linked positions differ interspecifically, and within Macquarie perch such that its sexing test approached 100% reliability only for the populations used in assay development. Similarly, Macquarie- and golden perch genome-wide DArTseq SNPs revealed different sex-linked loci across non-homologous scaffolds. Overall, we identified 22 sex-linked SNPs in Macquarie perch in a predominantly XX/XY system in which females are homozygous at all 22, and males are heterozygous at 2 or more. The resources here will facilitate multi-locus sexing assays for both species and research on Percichthyid biology.

scholarly journals Identification of RAN1 orthologue associated with sex determination through whole genome sequencing analysis in fig (Ficus carica L.)

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Kazuki Mori ◽  
Kenta Shirasawa ◽  
Hitoshi Nogata ◽  
Chiharu Hirata ◽  
Kosuke Tashiro ◽  
...  
Keyword(s):  
Sex Determination ◽  
Genome Wide Association Study ◽  
Draft Genome ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Missense Mutations ◽  
Genome Wide ◽  
Determination System ◽  
Whole Genome Resequencing ◽  
Sex Determination System

Abstract With the aim of identifying sex determinants of fig, we generated the first draft genome sequence of fig and conducted the subsequent analyses. Linkage analysis with a high-density genetic map established by a restriction-site associated sequencing technique, and genome-wide association study followed by whole-genome resequencing analysis identified two missense mutations in RESPONSIVE-TO-ANTAGONIST1 (RAN1) orthologue encoding copper-transporting ATPase completely associated with sex phenotypes of investigated figs. This result suggests that RAN1 is a possible sex determinant candidate in the fig genome. The genomic resources and genetic findings obtained in this study can contribute to general understanding of Ficus species and provide an insight into fig’s and plant’s sex determination system.

scholarly journals Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus)

2014 ◽  
Author(s):  
Armando Geraldes ◽  
Charles A Hefer ◽  
Arnaud Capron ◽  
Natalia Kolosova ◽  
Felix Martinez-Nuñez ◽  
...  
Keyword(s):  
Sex Determination ◽  
Association Studies ◽  
Populus Trichocarpa ◽  
Significant Snps ◽  
Strong Linkage Disequilibrium ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Black Cottonwood ◽  
Genome Wide ◽  
Whole Genome Resequencing

All species of the genus Populus (poplar, aspen) are dioecious, suggesting an ancient origin of this trait. Theory suggests that non-recombining sex-linked regions should quickly spread, eventually becoming heteromorphic chromosomes. In contrast, we show using whole genome scans that the sex-associated region in P. trichocarpa is small and much younger than the age of the genus. This indicates that sex-determination is highly labile in poplar, consistent with recent evidence of “turnover” of sex determination regions in animals. We performed whole genome resequencing of 52 Populus trichocarpa (black cottonwood) and 34 P. balsamifera (balsam poplar) individuals of known sex. Genome-wide association studies (GWAS) in these unstructured populations identified 650 SNPs significantly associated with sex. We estimate the size of the sex-linked region to be ∼100 Kbp. All significant SNPs were in strong linkage disequilibrium despite the fact that they were mapped to six different chromosomes (plus 3 unmapped scaffolds) in version 2.2 of the reference genome. We show that this is likely due to genome misassembly. The segregation pattern of sex associated SNPs revealed this to be an XY sex determining system. Estimated divergence times of X and Y haplotype sequences (6-7 MYA) are much more recent than the divergence of P. trichocarpa (poplar) and P. tremuloides (aspen). Consistent with this, in P. tremuloides we found no XY haplotype divergence within the P. trichocarpa sex-determining region. These two species therefore have a different genomic architecture of sex, suggestive of at least one turnover event in the recent past.

scholarly journals Fine Mapping Using Whole-Genome Sequencing Confirms Anti-Müllerian Hormone as a Major Gene for Sex Determination in Farmed Nile Tilapia (Oreochromis niloticus L.)

2019 ◽  
Vol 9 (10) ◽  
pp. 3213-3223 ◽  
Author(s):  
Giovanna Cáceres ◽  
María E. López ◽  
María I. Cádiz ◽  
Grazyella M. Yoshida ◽  
Ana Jedlicki ◽  
...  
Keyword(s):  
Sex Determination ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Major Gene ◽  
Whole Genome ◽  
Important Species ◽  
Genome Wide ◽  
A Genome

Nile tilapia (Oreochromis niloticus) is one of the most cultivated and economically important species in world aquaculture. Intensive production promotes the use of monosex animals, due to an important dimorphism that favors male growth. Currently, the main mechanism to obtain all-male populations is the use of hormones in feeding during larval and fry phases. Identifying genomic regions associated with sex determination in Nile tilapia is a research topic of great interest. The objective of this study was to identify genomic variants associated with sex determination in three commercial populations of Nile tilapia. Whole-genome sequencing of 326 individuals was performed, and a total of 2.4 million high-quality bi-allelic single nucleotide polymorphisms (SNPs) were identified after quality control. A genome-wide association study (GWAS) was conducted to identify markers associated with the binary sex trait (males = 1; females = 0). A mixed logistic regression GWAS model was fitted and a genome-wide significant signal comprising 36 SNPs, spanning a genomic region of 536 kb in chromosome 23 was identified. Ten out of these 36 genetic variants intercept the anti-Müllerian (Amh) hormone gene. Other significant SNPs were located in the neighboring Amh gene region. This gene has been strongly associated with sex determination in several vertebrate species, playing an essential role in the differentiation of male and female reproductive tissue in early stages of development. This finding provides useful information to better understand the genetic mechanisms underlying sex determination in Nile tilapia.

scholarly journals Labile sex chromosomes and a novel candidate sex-determination gene in the Australian freshwater fish family Percichthyidae

2021 ◽  
Author(s):  
Alexandra Pavlova ◽  
Katherine Harrisson ◽  
Rustam Turakulov ◽  
Yin Peng Lee ◽  
Brett Ingram ◽  
...  
Keyword(s):  
Sex Chromosome ◽  
Amplicon Sequencing ◽  
Genomic Research ◽  
Sequencing Data ◽  
Fish Family ◽  
Reduced Representation ◽  
Gonad Differentiation ◽  
Pcr Rflp ◽  
Whole Genome Resequencing ◽  
Australian Freshwater

Sex-specific ecology has management implications, but rapid sex-chromosome turnover in fishes hinders development of markers to sex monomorphic species. Here, we use annotated genomes and reduced-representation sequencing data for two Australian percichthyids, the Macquarie perch Macquaria australasica and the golden perch M. ambigua, and whole genome resequencing data for 50 Macquarie perch of each sex, to detect sex-linked loci, identify a candidate sex-determining gene and develop an affordable sexing assay. In-silico pool-seq tests of 1,492,004 Macquarie perch SNP loci revealed that a 275-Kb scaffold, containing the transcription factor SOX1b gene, was enriched for gametologous loci. Within this scaffold, 22 loci were sex-linked in a predominantly XY system, with females being homozygous at all 22, and males being heterozygous at two or more. Seven XY-gametologous loci were within a 146-bp region. Being ~38 Kb upstream of SOX1b, it might act as an enhancer controlling SOX1b transcription in the bipotential gonad that drives gonad differentiation. A PCR-RFLP sexing assay, targeting one of the Y-linked SNPs, tested in 66 known-sex Macquarie perch and two individuals of each sex of three confamilial species, and amplicon sequencing of 400 bp encompassing the 146-bp region, revealed that the few sex-linked positions differ between species and between Macquarie perch populations. This indicates sex-chromosome lability in Percichthyidae, also supported by non-homologous scaffolds containing sex-linked loci for Macquarie- and golden perches. The resources developed here will facilitate genomic research in Percichthyidae. Sex-linked markers will be useful for determining genetic sex in some populations and studying sex chromosome turnover.

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 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.

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