Multi-tissue RNA-Seq Analysis and Long-read-based Genome Assembly Reveal Complex Sex-specific Gene Regulation and Molecular Evolution in the Manila Clam.
alternative splicing
co-expression network
differential transcription
long-read genome assembly
sexual contrasting genetic markers
tissue specificity
Journal
Genome biology and evolution
ISSN: 1759-6653
Titre abrégé: Genome Biol Evol
Pays: England
ID NLM: 101509707
Informations de publication
Date de publication:
07 12 2022
07 12 2022
Historique:
accepted:
30
11
2022
pubmed:
13
12
2022
medline:
4
1
2023
entrez:
12
12
2022
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 36508337
pii: 6889380
doi: 10.1093/gbe/evac171
pmc: PMC9803972
pii:
doi:
Substances chimiques
DNA, Mitochondrial
0
Banques de données
figshare
['10.6084/m9.figshare.21069946.v5']
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NCRR NIH HHS
ID : S10 RR025496
Pays : United States
Organisme : NIH HHS
ID : S10 OD010794
Pays : United States
Informations de copyright
© The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.
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