Screening and characterization of sex-linked DNA markers and marker-assisted selection in the Southern catfish (Silurus meridionalis)

Zheng, Shuqing; Wang, Xiaoshuang; Zhang, Shuai; Long, Juan; Tao, Wenjing; Li, Minghui; Wang, Deshou

doi:10.1016/j.aquaculture.2019.734783

Cited by 36 publications

(10 citation statements)

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“…This suggests that, all populations retain the ancestral state and that our makers are likely to have broad applicability across the entire species range. The identification of sex-specific sequence has important practical value in many contexts, including ecological studies [62][63][64], conservation of threatened or endangered species [65][66][67][68], captive breeding [69], aquaculture [70,71], elimination of mortality as a possible explanation for sex ratio bias [32,72] sex forensics [73] and identifying genotypic sex [32,74,75] or in studies of early developmental processes where sex of the developing embryo is important [76,77].…”

Section: Discussionmentioning

confidence: 99%

Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in-silico whole genome subtraction.

Dissanayake

Holleley

Hill

et al. 2020

Preprint

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Background: Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the heterozygous homolog. Divergence in the non-recombining regions leads to the accumulation of Y or W specific sequence useful for developing sex-linked markers. Here we use in-silico whole-genome subtraction to identify putative sex-linked sequences in the scincid lizard Bassiana duperreyi which has heteromorphic XY sex chromosomes. Results: We generated 96.7 x 109 150bp paired-end genomic sequence reads from a XY male and 81.4 x 109 paired-end reads from an XX female for in-silico whole genome subtraction to yield Y enriched contigs. We identified 7 reliable markers which were validated as XY male-specific by polymerase chain reaction (PCR) against a panel of 20 males and 20 females. Conclusions: The sex of B. duperreyi can be reversed by low temperatures (XX genotype reversed to a male phenotype). We have developed sex-specific markers to identify the underlying genotypic sex and its concordance or discordance with phenotypic sex in wild populations of B. duperreyi. Our pipeline can be applied to isolate Y or W chromosome-specific sequences of any organism and is not restricted to sequence residing within single-copy genes. This study greatly improves our knowledge of the Y chromosome in B. duperreyi and will enhance future studies of reptile sex determination and sex chromosome evolution.

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Section: Discussionmentioning

confidence: 99%

Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in-silico whole genome subtraction.

Dissanayake

Holleley

Hill

et al. 2020

Preprint

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“…Southern catfish has 2 n = 58 chromosomes and the sex chromosome pair is homomorphic [11]. Our previous study identified sex-linked DNA markers and demonstrated an XX/XY sex-determination system in this species [12]. We also generated a whole-genome assembly anchored on chromosomes for an XX female individual [13].…”

Section: Introductionmentioning

confidence: 99%

Identification of sex chromosome and sex-determining gene of southern catfish ( Silurus meridionalis ) based on XX, XY and YY genome sequencing

et al. 2022

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Teleosts are important models to study sex chromosomes and sex-determining (SD) genes because they present a variety of sex determination systems. Here, we used Nanopore and Hi-C technologies to generate a high-contiguity chromosome-level genome assembly of a YY southern catfish ( Silurus meridionalis ). The assembly is 750.0 Mb long, with contig N50 of 15.96 Mb and scaffold N50 of 27.22 Mb. We also sequenced and assembled an XY male genome with a size of 727.2 Mb and contig N50 of 13.69 Mb. We identified a candidate SD gene through comparisons to our previous assembly of an XX individual. By resequencing male and female pools, we characterized a 2.38 Mb sex-determining region (SDR) on Chr24. Analysis of read coverage and comparison of the X and Y chromosome sequences showed a Y specific insertion (approx. 500 kb) in the SDR which contained a male-specific duplicate of amhr2 (named amhr2y ). amhr2y and amhr2 shared high-nucleotide identity (81.0%) in the coding region but extremely low identity in the promotor and intron regions. The exclusive expression in the male gonadal primordium and loss-of-function inducing male to female sex reversal confirmed the role of amhr2y in male sex determination. Our study provides a new example of amhr2 as the SD gene in fish and sheds light on the convergent evolution of the duplication of AMH/AMHR2 pathway members underlying the evolution of sex determination in different fish lineages.

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“…That said, the amplified sex specific region revealed some divergence between the Anglesea population and the Piccadilly Circus populations, suggesting that mutations could occur in the primer sites of some populations/taxa, limiting the generality of the sex- linked markers. The identification of sex-specific sequence has important practical value in many contexts, including ecological studies [63][64][65], conservation of threatened or endangered species [66][67][68][69], captive breeding [70], aquaculture [71,72], elimination of mortality as a possible explanation for sex ratio bias [32,73] sex forensics [74] and identifying genotypic sex [32,75,76] or in studies of early developmental processes where sex of the developing embryo is important [77,78]. Two approaches for identifying sex linked markers using whole genome sequencing seem appropriate, both relying on the divergence of the X and Y homologues in the region of recombination suppression.…”

Section: Discussionmentioning

confidence: 99%

Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction

et al. 2020

View full text Add to dashboard Cite

Background Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the hemizygous homolog. Divergence in the non-recombining regions leads to the accumulation of Y or W specific sequence useful for developing sex-linked markers. Here we use in silico whole-genome subtraction to identify putative sex-linked sequences in the scincid lizard Bassiana duperreyi which has heteromorphic XY sex chromosomes. Results We generated 96.7 × 109 150 bp paired-end genomic sequence reads from a XY male and 81.4 × 109 paired-end reads from an XX female for in silico whole genome subtraction to yield Y enriched contigs. We identified 7 reliable markers which were validated as Y chromosome specific by polymerase chain reaction (PCR) against a panel of 20 males and 20 females. Conclusions The sex of B. duperreyi can be reversed by low temperatures (XX genotype reversed to a male phenotype). We have developed sex-specific markers to identify the underlying genotypic sex and its concordance or discordance with phenotypic sex in wild populations of B. duperreyi. Our pipeline can be applied to isolate Y or W chromosome-specific sequences of any organism and is not restricted to sequence residing within single-copy genes. This study greatly improves our knowledge of the Y chromosome in B. duperreyi and will enhance future studies of reptile sex determination and sex chromosome evolution.

show abstract

Screening and characterization of sex-linked DNA markers and marker-assisted selection in the Southern catfish (Silurus meridionalis)

Cited by 36 publications

References 100 publications

Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in-silico whole genome subtraction.

Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in-silico whole genome subtraction.

Identification of sex chromosome and sex-determining gene of southern catfish ( Silurus meridionalis ) based on XX, XY and YY genome sequencing

Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction

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