Your browser doesn't support javascript.
loading
Multi-tissue RNA-Seq Analysis and Long-read-based Genome Assembly Reveal Complex Sex-specific Gene Regulation and Molecular Evolution in the Manila Clam.
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.
Afiliación
  • Xu R; Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy.
  • Martelossi J; Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy.
  • Smits M; Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy.
  • Iannello M; Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy.
  • Peruzza L; Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy.
  • Babbucci M; Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy.
  • Milan M; Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy.
  • Dunham JP; Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA.
  • Breton S; SeqOnce Biosciences Inc., Pasadena, CA, USA.
  • Milani L; Department of Biological Sciences, University of Montreal, Montreal, Canada.
  • Nuzhdin SV; Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy.
  • Bargelloni L; Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA.
  • Passamonti M; Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy.
  • Ghiselli F; Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy.
Genome Biol Evol ; 14(12)2022 12 07.
Article en En | MEDLINE | ID: mdl-36508337
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.
Asunto(s)
Palabras clave
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: ADN Mitocondrial / Bivalvos Límite: Animals Idioma: En Revista: Genome Biol Evol Asunto de la revista: BIOLOGIA / BIOLOGIA MOLECULAR Año: 2022 Tipo del documento: Article País de afiliación: Italia Pais de publicación: Reino Unido
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: ADN Mitocondrial / Bivalvos Límite: Animals Idioma: En Revista: Genome Biol Evol Asunto de la revista: BIOLOGIA / BIOLOGIA MOLECULAR Año: 2022 Tipo del documento: Article País de afiliación: Italia Pais de publicación: Reino Unido