Multi-tissue RNA-Seq Analysis and Long-read-based Genome Assembly Reveal Complex Sex-specific Gene Regulation and Molecular Evolution in the Manila Clam.
Multi-tissue RNA-Seq Analysis and Long-read-based Genome Assembly Reveal Complex Sex-specific Gene Regulation and Molecular Evolution in the Manila Clam.
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DOI：
10.1093/gbe/evac171
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发表时间：
2022-12-07
影响因子：
3.3
通讯作者：
Ghiselli, Fabrizio
中科院分区：
文献类型：
--
作者：
Xu, Ran;Martelossi, Jacopo;Smits, Morgan;Iannello, Mariangela;Peruzza, Luca;Babbucci, Massimiliano;Milan, Massimo;Dunham, Joseph P.;Breton, Sophie;Milani, Liliana;Nuzhdin, Sergey, V;Bargelloni, Luca;Passamonti, Marco;Ghiselli, Fabrizio
关键词：
双壳类软体动物性别决定和性腺分化所涉及的分子因素和基因调控尚不清楚。有人认为线粒体的双重单亲遗传(DUI)可能参与了这些过程，例如普遍存在的商业相关的马尼拉文蛤，菲律宾蛤仔。我们介绍了第一个基于长阅读的马尼拉文蛤的从头基因组组装，并对15个雌性和15个雄性进行了RNA-Seq多组织分析。高度连续的基因组组装被用作研究基因表达、选择性剪接、序列进化、组织特异性共表达网络和性别对比SNPs的参考。差异表达(DE)和差异剪接(DS)分析揭示了性腺中的性别特异性转录调控，但在躯体组织中不存在。共表达网络揭示了性腺中复杂的基因调控，性腺相关模块中的基因显示出高度的组织特异性。然而，男性性腺相关模块在序列进化和组织特异性方面表现出截然不同的模式。一组基因与雄配子的结构组织有关，序列进化缓慢，但具有高度的多效性；另一组基因富含生殖相关过程，具有快速序列进化和组织特异性的特点。在线粒体相关功能过度表达的基因中发现了性别对比SNPs，为研究DUI物种线粒体与性别之间的关系提供了新的候选基因。总之，这些结果增加了我们对DE、DS的作用以及性别特异基因在一个未被研究的分类群中的序列进化的理解。我们还为双壳类的性别诊断和繁殖研究提供了丰富的基因组数据。
The molecular factors and gene regulation involved in sex determination and gonad differentiation in bivalve molluscs are unknown. It has been suggested that doubly uniparental inheritance (DUI) of mitochondria may be involved in these processes in species such as the ubiquitous and commercially relevant Manila clam, Ruditapes philippinarum. We present the first long-read-based de novo genome assembly of a Manila clam, and a RNA-Seq multi-tissue analysis of 15 females and 15 males. The highly contiguous genome assembly was used as reference to investigate gene expression, alternative splicing, sequence evolution, tissue-specific co-expression networks, and sexual contrasting SNPs. Differential expression (DE) and differential splicing (DS) analyses revealed sex-specific transcriptional regulation in gonads, but not in somatic tissues. Co-expression networks revealed complex gene regulation in gonads, and genes in gonad-associated modules showed high tissue specificity. However, male gonad-associated modules showed contrasting patterns of sequence evolution and tissue specificity. One gene set was related to the structural organization of male gametes and presented slow sequence evolution but high pleiotropy, whereas another gene set was enriched in reproduction-related processes and characterized by fast sequence evolution and tissue specificity. Sexual contrasting SNPs were found in genes overrepresented in mitochondrial-related functions, providing new candidates for investigating the relationship between mitochondria and sex in DUI species. Together, these results increase our understanding of the role of DE, DS, and sequence evolution of sex-specific genes in an understudied taxon. We also provide resourceful genomic data for studies regarding sex diagnosis and breeding in bivalves.
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影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
3.3
作者：
Dalpe, Andreanne;Lalonde-Larue, Ariane;Breton, Sophie
通讯作者：
Breton, Sophie
影响因子：
3
作者：
Crescente JM;Zavallo D;Helguera M;Vanzetti LS
通讯作者：
Vanzetti LS
使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
30.8
作者：
通讯作者：
--
影响因子：
2.9
作者：
Dean, Rebecca;Mank, Judith E.
通讯作者：
Mank, Judith E.