Sex and tissue specific gene expression patterns identified following de novo transcriptomic analysis of the Norway lobster, Nephrops norvegicus.
Sex and tissue specific gene expression patterns identified following de novo transcriptomic analysis of the Norway lobster, Nephrops norvegicus.
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DOI：
10.1186/s12864-017-3981-2
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发表时间：
2017-08-16
期刊：
影响因子：
4.4
通讯作者：
Mather PB
中科院分区：
文献类型：
--
作者：
Rotllant G;Nguyen TV;Sbragaglia V;Rahi L;Dudley KJ;Hurwood D;Ventura T;Company JB;Chand V;Aguzzi J;Mather PB
挪威龙虾（Nephropsnorvegicus）在欧洲渔业中具有重要的经济地位，也是当地海洋生态系统的重要生物。尽管人们对这个物种有多方面的科学兴趣，但我们目前对该物种遗传资源的了解仍然非常有限。在这里，我们从两性的多个组织中生成了褐藻的参考从头转录组。进行生物信息学分析以检测仅在男性或女性中表达的转录本。通过 RT-PCR 验证模式。对来自未成熟和成熟卵巢、睾丸和输精管（包括雄性化雄腺）的 16 个褐藻文库进行了测序。此外，还对雄性以及未成熟和成熟雌性的眼柄、大脑、胸神经节和肝胰腺组织进行了筛查。 RNA 测序产生了超过 6 亿次读数。从头组装将当前数据集与之前发布的两个来自眼柄组织的文库相结合，产生了包含 333,225 个转录本的参考转录组，平均大小为 708 个碱基对 (bp)，N50 为 1272 bp。性别特异性转录本主要在性腺中检测到，其次是肝胰腺、大脑、胸神经节和眼柄。突出显示了仅在男性或女性中表达的候选转录本，并通过 RT-PCR 验证了 10 个最丰富的转录本。表达最高的基因是睾丸中的丝氨酸苏氨酸蛋白激酶和女性肝胰腺中的卵黄蛋白原。这些结果与基因注释结果密切相关。此外，差异表达热图显示，大多数差异表达转录本是在性腺和眼柄组织中发现的。结果表明，挪威龙虾的性别特异性基因表达模式是由雄性和雌性体细胞组织中基因调控模式的差异控制的。目前的研究提出了挪威龙虾的第一个多组织参考转录组，可应用于未来的生物学、野生放养和渔业研究。性别特异性标记主要在男性中表达，这意味着男性可能比女性经历更强的选择。显然，差异表达是由于存在于体细胞组织中的性别特异性基因调控途径，而不是由于位于异配性染色体上的基因的影响。褐藻数据为未来基于基因的生殖研究奠定了基础。本文的在线版本 (doi:10.1186/s12864-017-3981-2) 包含补充材料，可供授权用户使用。
The Norway lobster, Nephrops norvegicus, is economically important in European fisheries and is a key organism in local marine ecosystems. Despite multi-faceted scientific interest in this species, our current knowledge of genetic resources in this species remains very limited. Here, we generated a reference de novo transcriptome for N. norvegicus from multiple tissues in both sexes. Bioinformatic analyses were conducted to detect transcripts that were expressed exclusively in either males or females. Patterns were validated via RT-PCR. Sixteen N. norvegicus libraries were sequenced from immature and mature ovary, testis and vas deferens (including the masculinizing androgenic gland). In addition, eyestalk, brain, thoracic ganglia and hepatopancreas tissues were screened in males and both immature and mature females. RNA-Sequencing resulted in >600 million reads. De novo assembly that combined the current dataset with two previously published libraries from eyestalk tissue, yielded a reference transcriptome of 333,225 transcripts with an average size of 708 base pairs (bp), with an N50 of 1272 bp. Sex-specific transcripts were detected primarily in gonads followed by hepatopancreas, brain, thoracic ganglia, and eyestalk, respectively. Candidate transcripts that were expressed exclusively either in males or females were highlighted and the 10 most abundant ones were validated via RT-PCR. Among the most highly expressed genes were Serine threonine protein kinase in testis and Vitellogenin in female hepatopancreas. These results align closely with gene annotation results. Moreover, a differential expression heatmap showed that the majority of differentially expressed transcripts were identified in gonad and eyestalk tissues. Results indicate that sex-specific gene expression patterns in Norway lobster are controlled by differences in gene regulation pattern between males and females in somatic tissues. The current study presents the first multi-tissue reference transcriptome for the Norway lobster that can be applied to future biological, wild restocking and fisheries studies. Sex-specific markers were mainly expressed in males implying that males may experience stronger selection than females. It is apparent that differential expression is due to sex-specific gene regulatory pathways that are present in somatic tissues and not from effects of genes located on heterogametic sex chromosomes. The N. norvegicus data provide a foundation for future gene-based reproductive studies. The online version of this article (doi:10.1186/s12864-017-3981-2) contains supplementary material, which is available to authorized users.
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DOI：
10.1668/0003-1569(2001)041
发表时间：
2001-04-01
期刊：
AMERICAN ZOOLOGIST
影响因子：
--
作者：
Kramer, DL;McLaughlin, RL
通讯作者：
McLaughlin, RL
DOI：
10.1073/pnas.96.5.1965
发表时间：
1999-03-02
影响因子：
11.1
作者：
Hall, M;Wang, RG;Söderhäll, K
通讯作者：
Söderhäll, K
影响因子：
11.4
作者：
Kopp, Artyom
通讯作者：
Kopp, Artyom
影响因子：
2.9
作者：
Clark, K. Fraser;Acorn, Adam R.;Greenwood, Spencer J.
通讯作者：
Greenwood, Spencer J.
影响因子：
4
作者：
De Loof, Arnold
通讯作者：
De Loof, Arnold