Deciphering the Link between Doubly Uniparental Inheritance of mtDNA and Sex Determination in Bivalves: Clues from Comparative Transcriptomics

Abstract

Bivalves exhibit an astonishing diversity of sexual systems and sex-determining mechanisms. They can be gonochoric, hermaphroditic or androgenetic, with both genetic and environmental factors known to determine or influence sex. One unique sex-determining system involving the mitochondrial genome has also been hypothesized to exist in bivalves with doubly uniparental inheritance (DUI) of mtDNA. However, the link between DUI and sex determination remains obscure. In this study, we performed a comparative gonad transcriptomics analysis for two DUI-possessing freshwater mussel species to better understand the mechanisms underlying sex determination and DUI in these bivalves. We used a BLAST reciprocal analysis to identify orthologs between Venustaconcha ellipsiformis and Utterbackia peninsularis and compared our results with previously published sex-specific bivalve transcriptomes to identify conserved sex-determining genes. We also compared our data with other DUI species to identify candidate genes possibly involved in the regulation of DUI. A total of ∼12,000 orthologous relationships were found, with 2,583 genes differentially expressed in both species. Among these genes, key sex-determining factors previously reported in vertebrates and in bivalves (e.g., Sry, Dmrt1, Foxl2) were identified, suggesting that some steps of the sex-determination pathway may be deeply conserved in metazoans. Our results also support the hypothesis that a modified ubiquitination mechanism could be responsible for the retention of the paternal mtDNA in male bivalves, and revealed that DNA methylation could also be involved in the regulation of DUI. Globally, our results suggest that sets of genes associated with sex determination and DUI are similar in distantly-related DUI species.

Genome survey of the freshwater mussel Venustaconcha ellipsiformis (Bivalvia: Unionida) using a hybrid de novo assembly approach

“…Following this, mate-pairs are mapped onto the assembly to create scaffolds, and finally long reads (Pacific Biosciences long reads) and the V. ellipsiformis reference transcriptome from Capt et al (2018) were also mapped onto the assembly to create long-scaffolds. This reference transcriptome was assembled from a pool of sequences coming from four different male and female individuals and further details are provided in Capt et al (2018). Although ideally sequencing information would all come from a single individual, the current study design did not allow for this.…”

“…Mussels are filter feeders and tissues as gills can potentially harbor microbial fauna. In addition, freshwater mussels are prone to infection by trematodes (Müller et al 2015, Capt et al 2018. As suggested by Takeuchi et al (2012), we first checked for the presence of double peaks in the distribution of the GC content of the raw reads, which would indicate contamination in the genome.…”

“…Given the challenges in assembling a reference genome for saltwater mussels (Sun et al 2017;Murgarella et al 2016), we used a combination of different sequencing strategies (Illumina paired-end and mate pair libraries, Pacific Biosciences long reads, and a recently assembled reference transcriptome, Capt et al 2018) to assemble the first genome draft in the family Unionidae. Hybrid sequencing technologies using long read−low coverage and short read−high coverage offer an affordable strategy with the advantage of assembling repeated regions of the genome (for which short reads are ineffective) and circumventing the relatively higher error 100 rate of long reads (Koren et al 2012;Miller et al 2017).…”

Gonad transcriptome of golden musselLimnoperna fortuneireveals potential sex differentiation genes

“…Assembled contigs completeness assessment by the representation of 978 core metazoan genes using BUSCO found 99.3% complete recovered genes for the final L. fortunei transcriptome, which is the highest percentage found for completeness of a transcriptome assembly in bivalves (47)(48)(49)(50)(51)(52)(53). Additionally, 87.94% of the clean RNA-seq reads were successfully mapped back to the assembled transcriptome, showing most of the reads being represented in the final assembly.…”

“…To identify genes potentially involved with sex differentiation in L. fortunei, we used the BLASTx and Diamond results to search for genes previously associated to these processes in bivalves and model organisms (11,(14)(15)(16)18,22,51,58) and investigated their expression profile in male and female gonads. Similar to Zhang and collaborators (2014), we assumed that if a gene is involved with sex-determining mechanisms in other organisms, especially bivalves, and it shows sex-biased expression according to its known function, then it may be related to these processes in L. fortunei.…”