Multi-tissue RNA-Seq Analysis and Long-read-based Genome Assembly Reveal Complex Sex-specific Gene Regulation and Molecular Evolution in the Manila Clam

Genome Biology and Evolution, Journal Year: 2022, Volume and Issue: 14(12)

Published: Dec. 1, 2022

The molecular factors and gene regulation involved in sex determination gonad differentiation bivalve molluscs are unknown. It has been suggested that doubly uniparental inheritance (DUI) of mitochondria may be these processes species such as the ubiquitous commercially relevant Manila clam, Ruditapes philippinarum. We present first long-read-based de novo genome assembly a RNA-Seq multi-tissue analysis 15 females males. highly contiguous was used reference to investigate expression, alternative splicing, sequence evolution, tissue-specific co-expression networks, sexual contrasting SNPs. Differential expression (DE) differential splicing (DS) analyses revealed sex-specific transcriptional gonads, but not somatic tissues. Co-expression networks complex genes gonad-associated modules showed high tissue specificity. However, male patterns evolution One set related structural organization gametes presented slow pleiotropy, whereas another enriched reproduction-related characterized by fast Sexual SNPs were found overrepresented mitochondrial-related functions, providing new candidates for investigating relationship between DUI species. Together, results increase our understanding role DE, DS, an understudied taxon. also provide resourceful genomic data studies regarding diagnosis breeding bivalves.

Language: Английский

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Bivalves as Emerging Model Systems to Study the Mechanisms and Evolution of Sex Determination: A Genomic Point of View

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(10)

Published: Oct. 1, 2023

Bivalves are a diverse group of molluscs that have recently attained central role in plenty biological research fields, thanks to their peculiar life history traits. Here, we propose bivalves should be considered as emerging model systems also sex-determination (SD) studies, since they would allow investigate: 1) the transition between environmental and genetic SD, with respect different reproductive backgrounds sexual (from species strict gonochorism various forms hermaphroditism); 2) genomic evolution sex chromosomes (SCs), considering no heteromorphic SCs currently known homomorphic been identified only few scallops; 3) putative mitochondria at some level SD signaling pathway, mechanism may resemble cytoplasmatic male sterility plants; 4) evolutionary SD-related gene (SRG) families other animal groups. In particular, think this last topic lay foundations for expanding our understanding bivalve current knowledge is quite fragmented limited species. As matter fact, tracing phylogenetic diversity SRG (such Dmrt, Sox, Fox genes) not perform more targeted functional experiments analyses, but foster possibility establishing solid comparative framework.

Language: Английский

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High heteroplasmy is associated with low mitochondrial copy number and selection against non-synonymous mutations in the snail Cepaea nemoralis

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: June 13, 2024

Molluscan mitochondrial genomes are unusual because they show wide variation in size, radical genome rearrangements and frequently high (> 10%) within species. As progress understanding this has been limited, we used whole sequencing of a six-generation matriline the terrestrial snail Cepaea nemoralis, as well sequences from wild-collected C. sister species hortensis, multiple other to explore origins DNA (mtDNA) variation. The main finding is that rate SNP heteroplasmy somatic tissue was negatively correlated with mtDNA copy number both In individuals under ten copies per nuclear genome, more than 10% all positions were heteroplasmic, evidence for transmission through germline. Further analyses showed purifying selection acting on non-synonymous mutations, even at low frequency rare allele, especially cytochrome oxidase subunit 1 b. some nemoralis contained length heteroplasmy, including up 12 direct repeat tRNA-Val, 24 another snail, Candidula rugosiuscula, repeats tRNA-Thr hortensis. These likely arise due error prone replication but not nemoralis. Overall, findings provide key insights into mechanisms replication, mutation evolution molluscan mtDNA, so will inform wider studies biology across animal phyla.

Language: Английский

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Mitonuclear compatibility is maintained despite relaxed selection on male mitochondrial DNA in bivalves with doubly uniparental inheritance

Evolution, Journal Year: 2024, Volume and Issue: 78(11), P. 1790 - 1803

Published: July 11, 2024

Abstract Mitonuclear coevolution is common in eukaryotes, but bivalve lineages that have doubly uniparental inheritance (DUI) of mitochondria may be an interesting example. In this system, females transmit mtDNA (F mtDNA) to all offspring, while males a different (M solely their sons. Molecular evolution and functional data suggest oxidative phosphorylation (OXPHOS) genes encoded M evolve under relaxed selection due function being limited sperm only (vs. other tissues for F mtDNA). This has led the hypothesis mitonuclear less important mtDNA. Here, we use comparative phylogenetics, transcriptomics, proteomics understand interactions DUI bivalves. We found nuclear OXPHOS proteins coevolve maintain compatibility similarly with both proteins. Mitochondrial recombination did not influence nuclear-encoded were upregulated offset dysfunction. Our results support maintains despite on Strict transmission, lower effective population size, higher mutation rates explain study highlights broad features eukaryotes.

Language: Английский

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