Catanach Andrew, Ruigrok Mike, Bowatte Deepa, Davy Marcus, Storey Roy, Valenza-Troubat Noémie, López-Girona Elena, Hilario Elena, Wylie Matthew J, Chagné David, Wellenreuther Maren
The New Zealand Institute for Plant & Food Research Ltd, Christchurch, New Zealand.
Department of Bioinformatics, University of Applied Sciences Leiden, Leiden, The Netherlands.
BMC Genomics. 2021 Nov 2;22(1):785. doi: 10.1186/s12864-021-08102-2.
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.
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).
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.
硬骨鱼类性别决定的遗传控制机制尚不清楚。部分原因在于，在这一大类脊椎动物中，决定其性别的机制具有多样性，包括与性染色体相关的组成基因、多基因组成机制、环境因素、雌雄同体现象及孤雌生殖现象。在此，我们利用新西兰真鲹（Pseudocaranx georgianus）的从头基因组组装以及性别特异性全基因组测序数据，来检测性别差异基因组区域，鉴定候选基因并开发分子标记。
对一条未鉴定性别的真鲹（Trevally_v1）进行从头组装，最终组装长度为579.4 Mb，N50为25.2 Mb。在组装的支架中，有24个达到染色体级别，长度从11 Mb到31 Mb不等。在对12.8%的组装序列用重复元件进行屏蔽后，共注释出28,416个基因。对13条野生性别已知的真鲹（7条雄性和6条雌性）进行全基因组重测序，确定了位于两个支架上的两个性别差异区域，其中一个位于21号染色体近端的6 kb区域。Blast分析显示，其中一个区域与芳香化酶基因cyp19（a1a/b）具有相似性（E值<1.00E - 25，一致性>78.8%）。在这两个区域中，雄性的杂合变异数量更多，而雌性则显示出极低的测序深度区域，表明该基因组区域具有雄性特异性。开发了分子标记，并随后在96条经组织学鉴定性别的鱼（42条雄性和54条雌性）上进行测试。三个标记的扩增与性别完全对应（雄性为阳性，雌性为阴性）。
雄性中较高的杂合变异数量以及雌性中不存在这些区域，支持了XY性别决定模型，这表明Trevally_v1基因组组装是基于一个雄性样本构建的。这种性别系统与在近缘鲹科物种中记录的ZW性别决定模型不同。我们的结果表明cyp19a1a样基因具有性别决定功能，这表明在这个科中性别决定的分子途径在一定程度上是保守的。在此开发的基因组资源将有助于未来的比较研究，并能更深入地了解硬骨鱼类中多样的性别决定途径。本研究中开发的性别标记将是水产养殖选择性育种计划以及确定野生种群性别比例的宝贵资源。
