雌雄同体的亚马逊食蚊鱼（Poecilia formosa）与有性繁殖祖先，墨西哥胎鱂（Poecilia mexicana）和宽鳍鱂（Poecilia latipinna）的性腺转录组比较。
The gonadal transcriptome of the unisexual Amazon molly Poecilia formosa in comparison to its sexual ancestors, Poecilia mexicana and Poecilia latipinna.
机构信息
Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 26, 14476, Potsdam, Germany.
Department of Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 14, 14476, Potsdam, Germany.
出版信息
BMC Genomics. 2018 Jan 3;19(1):12. doi: 10.1186/s12864-017-4382-2.
BACKGROUND
The unisexual Amazon molly (Poecilia formosa) originated from a hybridization between two sexual species, the sailfin molly (Poecilia latipinna) and the Atlantic molly (Poecilia mexicana). The Amazon molly reproduces clonally via sperm-dependent parthenogenesis (gynogenesis), in which the sperm of closely related species triggers embryogenesis of the apomictic oocytes, but typically does not contribute genetic material to the next generation. We compare for the first time the gonadal transcriptome of the Amazon molly to those of both ancestral species, P. mexicana and P. latipinna.
RESULTS
We sequenced the gonadal transcriptomes of the P. formosa and its parental species P. mexicana and P. latipinna using Illumina RNA-sequencing techniques (paired-end, 100 bp). De novo assembly of about 50 million raw read pairs for each species was performed using Trinity, yielding 106,922 transcripts for P. formosa, 115,175 for P. latipinna, and 133,025 for P. mexicana after eliminating contaminations. On the basis of sequence similarity comparisons to other teleost species and the UniProt databases, functional annotation, and differential expression analysis, we demonstrate the similarity of the transcriptomes among the three species. More than 40% of the transcripts for each species were functionally annotated and about 70% were assigned to orthologous genes of a closely related species. Differential expression analysis between the sexual and unisexual species uncovered 2035 up-regulated and 564 down-regulated genes in P. formosa. This was exemplary validated for six genes by qRT-PCR.
CONCLUSIONS
We identified more than 130 genes related to meiosis and reproduction within the apomictically reproducing P. formosa. Overall expression of these genes seems to be down-regulated in the P. formosa transcriptome compared to both ancestral species (i.e., 106 genes down-regulated, 29 up-regulated). A further 35 meiosis and reproduction related genes were not found in the P. formosa transcriptome, but were only expressed in the sexual species. Our data support the hypothesis of general down-regulation of meiosis-related genes in the apomictic Amazon molly. Furthermore, the obtained dataset and identified gene catalog will serve as a resource for future research on the molecular mechanisms behind the reproductive mode of this unisexual species.
背景
单性亚马逊丽鱼（Poecilia formosa）源自两个有性物种——帆鳍丽鱼（Poecilia latipinna）和大西洋丽鱼（Poecilia mexicana）——的杂交。亚马逊丽鱼通过依赖精子的孤雌生殖（雌核生殖）进行克隆繁殖，其中近亲物种的精子引发非融合卵的胚胎发生，但通常不会将遗传物质贡献给下一代。我们首次比较了亚马逊丽鱼的性腺转录组与两个祖先是 P. mexicana 和 P. latipinna 的转录组。
结果
我们使用 Illumina RNA-seq 技术（配对末端，100bp）对 P. formosa 及其亲种 P. mexicana 和 P. latipinna 的性腺转录组进行了测序。对每个物种约 5000 万个原始读对进行 de novo 组装，使用 Trinity 生成 106922 个转录本用于 P. formosa，115175 个转录本用于 P. latipinna，133025 个转录本用于 P. mexicana，消除污染后。基于与其他硬骨鱼类物种和 UniProt 数据库的序列相似性比较、功能注释和差异表达分析，我们证明了这三个物种的转录组相似性。每个物种的超过 40%的转录本进行了功能注释，约 70%的转录本被分配到了一个亲缘关系密切的物种的同源基因上。在有性和单性物种之间的差异表达分析中，在 P. formosa 中发现了 2035 个上调和 564 个下调基因。通过 qRT-PCR 对六个基因进行了示例验证。
结论
我们在单性生殖的 P. formosa 中鉴定了 130 多个与减数分裂和生殖相关的基因。与两个祖先是相比，这些基因在 P. formosa 转录组中的总体表达似乎下调（即 106 个下调，29 个上调）。在 P. formosa 转录组中未发现另外 35 个与减数分裂和生殖相关的基因，但仅在有性物种中表达。我们的数据支持减数分裂相关基因在单性亚马逊丽鱼中普遍下调的假说。此外，获得的数据集和鉴定的基因目录将作为未来研究这个单性物种生殖模式背后的分子机制的资源。
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