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Bivalve_genomics.html
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<a class="navbar-brand" href="index.html">Jacopo Martelossi</a>
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<a href="Phasmids.html">Wings Evolution and sistematics in Phasmids</a>
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<a href="Notostraca_CompGen.html">Tadole shrimps genomics</a>
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<a href="Rluc.html">Termites genomics</a>
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<a href="Bivalve_genomics.html">Bivalves genomics</a>
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<a href="AboutMe.html">About me</a>
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<div
id="multi-tissue-rna-seq-analysis-and-long-read-based-genome-assembly-reveal-complex-sex-specific-gene-regulation-and-molecular-evolution-in-the-manila-clam"
class="section level2">
<h2>Multi-tissue RNA-Seq analysis and long-read-based genome assembly
reveal complex sex-specific gene regulation and molecular evolution in
the Manila clam</h2>
<p>Ran Xu1<sup>1</sup>, Jacopo Martelossi<sup>1</sup>, Morgan
Smits<sup>1</sup>, Mariangela Iannello<sup>1</sup>, Luca Peruzza,
Massimiliano Babbucci, Massimo Milan, Joseph P. Dunham, Sophie Breton,
Liliana Milani, Sergey V. Nuzhdin, Luca Bargelloni, Marco Passamonti,
Fabrizio Ghiselli1</p>
<p><strong><sup>1</sup> These author contribute equally to this
work</strong></p>
<div id="abstract" class="section level4">
<h4>Abstract:</h4>
<p>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 and differential splicing
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, while 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 differential
expression, differential splicing, 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.</p>
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<a href="https://twitter.com/JacopoM4" class="fa fa-twitter"></a>
<a href="https://github.com/jacopoM28" class="fa fa-github"></a></p>
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