A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions.
A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions.
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DOI：
10.1186/s12864-017-3723-5
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发表时间：
2017-05-02
期刊：
影响因子：
4.4
通讯作者：
Kocher TD
中科院分区：
文献类型：
--
作者：
Conte MA;Gammerdinger WJ;Bartie KL;Penman DJ;Kocher TD
罗非鱼是世界上第二大养殖鱼类，也是一种可持续的食物来源。像许多其他鱼类一样，罗非鱼是两性异形的，性别是这些鱼类的重要商业特征。在这项研究中，我们使用最新的基因组测序方法开发了一种显着改进的罗非鱼基因组组装，并展示了它如何改善两个罗非鱼物种中两个性别决定区域的特征。使用Pacific Biosciences（PacBio）SMRT测序将纯合克隆XX雌性尼罗罗非鱼（尼罗罗非鱼）测序至44 X覆盖度。产生数十个候选从头组装体，并使用从几个配对末端测序文库计算的似然分数的主成分分析选择最佳组装体（3.3Mbp的重叠群NG 50）。新程序集与以前的O.尼罗基因组装配揭示了最近复制的基因组部分现在被很好地表示。新组合中的基因总数增加了27.3%，包括67%的假基因增加。新的罗非鱼基因组组装正确地代表了两个最近的vasa基因重复事件，已被BAC测序验证。现在总共组装了146 Mbp的额外转座因子序列，其中大部分是最近插入的。大着丝粒卫星重复序列的组装和注释在慈鲷鱼的第一次。最后，新的组装鉴定了O. niloticus的LG 3上存在一个约50 Mbp的WZ性别决定区。金黄色。 这项研究强调了使用长读段测序来正确组装最近的重复序列并表征基因组的重复填充区域。这项研究作为一个例子，需要高质量的基因组组装，并提供了一个框架，确定性别决定基因在罗非鱼和相关鱼类物种。本文的在线版本（doi：10.1186/s12864-017-3723-5）包含补充材料，可供授权用户使用。
Tilapias are the second most farmed fishes in the world and a sustainable source of food. Like many other fish, tilapias are sexually dimorphic and sex is a commercially important trait in these fish. In this study, we developed a significantly improved assembly of the tilapia genome using the latest genome sequencing methods and show how it improves the characterization of two sex determination regions in two tilapia species. A homozygous clonal XX female Nile tilapia (Oreochromis niloticus) was sequenced to 44X coverage using Pacific Biosciences (PacBio) SMRT sequencing. Dozens of candidate de novo assemblies were generated and an optimal assembly (contig NG50 of 3.3Mbp) was selected using principal component analysis of likelihood scores calculated from several paired-end sequencing libraries. Comparison of the new assembly to the previous O. niloticus genome assembly reveals that recently duplicated portions of the genome are now well represented. The overall number of genes in the new assembly increased by 27.3%, including a 67% increase in pseudogenes. The new tilapia genome assembly correctly represents two recent vasa gene duplication events that have been verified with BAC sequencing. At total of 146Mbp of additional transposable element sequence are now assembled, a large proportion of which are recent insertions. Large centromeric satellite repeats are assembled and annotated in cichlid fish for the first time. Finally, the new assembly identifies the long-range structure of both a ~9Mbp XY sex determination region on LG1 in O. niloticus, and a ~50Mbp WZ sex determination region on LG3 in the related species O. aureus. This study highlights the use of long read sequencing to correctly assemble recent duplications and to characterize repeat-filled regions of the genome. The study serves as an example of the need for high quality genome assemblies and provides a framework for identifying sex determining genes in tilapia and related fish species. The online version of this article (doi:10.1186/s12864-017-3723-5) contains supplementary material, which is available to authorized users.