The genome of New Zealand trevally (Carangidae: Pseudocaranx georgianus) uncovers a XY sex determination locus

Abstract Background The genetic control of sex determination in teleost species is poorly understood. This is partly because of the diversity of mechanisms that determine sex in this large group of vertebrates, including constitutive genes linked to sex chromosomes, polygenic constitutive mechanisms...

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Autores principales:	Andrew Catanach, Mike Ruigrok, Deepa Bowatte, Marcus Davy, Roy Storey, Noémie Valenza-Troubat, Elena López-Girona, Elena Hilario, Matthew J. Wylie, David Chagné, Maren Wellenreuther
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Pseudocaranx georgianus Sex determination Teleost Aromatase cyp19a1a cyp19a1b Cytochrome P450 aromatase Biotechnology TP248.13-248.65 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/b0032c807b414382b7379717f71f8b3c
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spelling	oai:doaj.org-article:b0032c807b414382b7379717f71f8b3c2021-11-08T10:57:23ZThe genome of New Zealand trevally (Carangidae: Pseudocaranx georgianus) uncovers a XY sex determination locus10.1186/s12864-021-08102-21471-2164https://doaj.org/article/b0032c807b414382b7379717f71f8b3c2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-08102-2https://doaj.org/toc/1471-2164Abstract Background The genetic control of sex determination in teleost species is poorly understood. This is partly because of the diversity of mechanisms that determine sex in this large group of vertebrates, including constitutive genes linked to sex chromosomes, polygenic constitutive mechanisms, environmental factors, hermaphroditism, and unisexuality. Here we use a de novo genome assembly of New Zealand silver trevally (Pseudocaranx georgianus) together with sex-specific whole genome sequencing data to detect sexually divergent genomic regions, identify candidate genes and develop molecular makers. Results The de novo assembly of an unsexed trevally (Trevally_v1) resulted in a final assembly of 579.4 Mb in length, with a N50 of 25.2 Mb. Of the assembled scaffolds, 24 were of chromosome scale, ranging from 11 to 31 Mb in length. A total of 28,416 genes were annotated after 12.8 % of the assembly was masked with repetitive elements. Whole genome re-sequencing of 13 wild sexed trevally (seven males and six females) identified two sexually divergent regions located on two scaffolds, including a 6 kb region at the proximal end of chromosome 21. Blast analyses revealed similarity between one region and the aromatase genes cyp19 (a1a/b) (E-value < 1.00E-25, identity > 78.8 %). Males contained higher numbers of heterozygous variants in both regions, while females showed regions of very low read-depth, indicative of male-specificity of this genomic region. Molecular markers were developed and subsequently tested on 96 histologically-sexed fish (42 males and 54 females). Three markers amplified in absolute correspondence with sex (positive in males, negative in females). Conclusions The higher number of heterozygous variants in males combined with the absence of these regions in females support a XY sex-determination model, indicating that the trevally_v1 genome assembly was developed from a male specimen. This sex system contrasts with the ZW sex-determination model documented in closely related carangid species. Our results indicate a sex-determining function of a cyp19a1a-like gene, suggesting the molecular pathway of sex determination is somewhat conserved in this family. The genomic resources developed here will facilitate future comparative work, and enable improved insights into the varied sex determination pathways in teleosts. The sex marker developed in this study will be a valuable resource for aquaculture selective breeding programmes, and for determining sex ratios in wild populations.Andrew CatanachMike RuigrokDeepa BowatteMarcus DavyRoy StoreyNoémie Valenza-TroubatElena López-GironaElena HilarioMatthew J. WylieDavid ChagnéMaren WellenreutherBMCarticlePseudocaranx georgianusSex determinationTeleostAromatase cyp19a1acyp19a1bCytochrome P450 aromataseBiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss 1, Pp 1-16 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Pseudocaranx georgianus Sex determination Teleost Aromatase cyp19a1a cyp19a1b Cytochrome P450 aromatase Biotechnology TP248.13-248.65 Genetics QH426-470
spellingShingle	Pseudocaranx georgianus Sex determination Teleost Aromatase cyp19a1a cyp19a1b Cytochrome P450 aromatase Biotechnology TP248.13-248.65 Genetics QH426-470 Andrew Catanach Mike Ruigrok Deepa Bowatte Marcus Davy Roy Storey Noémie Valenza-Troubat Elena López-Girona Elena Hilario Matthew J. Wylie David Chagné Maren Wellenreuther The genome of New Zealand trevally (Carangidae: Pseudocaranx georgianus) uncovers a XY sex determination locus
description	Abstract Background The genetic control of sex determination in teleost species is poorly understood. This is partly because of the diversity of mechanisms that determine sex in this large group of vertebrates, including constitutive genes linked to sex chromosomes, polygenic constitutive mechanisms, environmental factors, hermaphroditism, and unisexuality. Here we use a de novo genome assembly of New Zealand silver trevally (Pseudocaranx georgianus) together with sex-specific whole genome sequencing data to detect sexually divergent genomic regions, identify candidate genes and develop molecular makers. Results The de novo assembly of an unsexed trevally (Trevally_v1) resulted in a final assembly of 579.4 Mb in length, with a N50 of 25.2 Mb. Of the assembled scaffolds, 24 were of chromosome scale, ranging from 11 to 31 Mb in length. A total of 28,416 genes were annotated after 12.8 % of the assembly was masked with repetitive elements. Whole genome re-sequencing of 13 wild sexed trevally (seven males and six females) identified two sexually divergent regions located on two scaffolds, including a 6 kb region at the proximal end of chromosome 21. Blast analyses revealed similarity between one region and the aromatase genes cyp19 (a1a/b) (E-value < 1.00E-25, identity > 78.8 %). Males contained higher numbers of heterozygous variants in both regions, while females showed regions of very low read-depth, indicative of male-specificity of this genomic region. Molecular markers were developed and subsequently tested on 96 histologically-sexed fish (42 males and 54 females). Three markers amplified in absolute correspondence with sex (positive in males, negative in females). Conclusions The higher number of heterozygous variants in males combined with the absence of these regions in females support a XY sex-determination model, indicating that the trevally_v1 genome assembly was developed from a male specimen. This sex system contrasts with the ZW sex-determination model documented in closely related carangid species. Our results indicate a sex-determining function of a cyp19a1a-like gene, suggesting the molecular pathway of sex determination is somewhat conserved in this family. The genomic resources developed here will facilitate future comparative work, and enable improved insights into the varied sex determination pathways in teleosts. The sex marker developed in this study will be a valuable resource for aquaculture selective breeding programmes, and for determining sex ratios in wild populations.
format	article
author	Andrew Catanach Mike Ruigrok Deepa Bowatte Marcus Davy Roy Storey Noémie Valenza-Troubat Elena López-Girona Elena Hilario Matthew J. Wylie David Chagné Maren Wellenreuther
author_facet	Andrew Catanach Mike Ruigrok Deepa Bowatte Marcus Davy Roy Storey Noémie Valenza-Troubat Elena López-Girona Elena Hilario Matthew J. Wylie David Chagné Maren Wellenreuther
author_sort	Andrew Catanach
title	The genome of New Zealand trevally (Carangidae: Pseudocaranx georgianus) uncovers a XY sex determination locus
title_short	The genome of New Zealand trevally (Carangidae: Pseudocaranx georgianus) uncovers a XY sex determination locus
title_full	The genome of New Zealand trevally (Carangidae: Pseudocaranx georgianus) uncovers a XY sex determination locus
title_fullStr	The genome of New Zealand trevally (Carangidae: Pseudocaranx georgianus) uncovers a XY sex determination locus
title_full_unstemmed	The genome of New Zealand trevally (Carangidae: Pseudocaranx georgianus) uncovers a XY sex determination locus
title_sort	genome of new zealand trevally (carangidae: pseudocaranx georgianus) uncovers a xy sex determination locus
publisher	BMC
publishDate	2021
url	https://doaj.org/article/b0032c807b414382b7379717f71f8b3c
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The genome of New Zealand trevally (Carangidae: Pseudocaranx georgianus) uncovers a XY sex determination locus

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