Comparative analysis of gender-associated complete mitochondrial genomes in marine mussels (Mytilus spp.)

Abstract

Marine mussels of the genus Mytilus have an unusual mode of mitochondrial DNA (mtDNA) transmission termed doubly uniparental inheritance (DUI). Female mussels are homoplasmic for the F mitotype, which is inherited maternally, while males are usually heteroplasmic, carrying a mixture of the maternal F mitotype and the paternally inherited M genome. Two classes of M genomes have been observed: "standard" M genomes and "recently masculinized" M genomes. The latter are more similar to F genomes at the sequence level but are transmitted paternally like standard M genomes. In this study we report the complete sequences of two standard male M. edulis and one recently masculinized male M. trossulus mitochondrial genome. A comparative analysis, including the previously sequenced M. edulis F and M. galloprovincialis F and M mtDNAs, reveals that these genomes are identical in gene order, but highly divergent in nucleotide and amino acid sequence. The large amount (>20%) of nucleotide substitutions that fall in coding regions implies that there are several amino acid replacements between the F and M genomes, which likely have an impact on the structural and functional properties of the mitochondrial proteome. Correlation of the divergence rate of different protein-coding genes indicates that mtDNA-encoded proteins of the M genome are still under selective constraints, although less highly than genes of the F genome. The mosaic F/M control region of the masculinized F genome provides evidence for lineage-specific sequences that may be responsible for the different mode of transmission genetics. This analysis shows the value of comparative genomics to better understand the mechanisms of maintenance and segregation of mtDNA sequence variants in mytilid mussels.

Figure 1.

Gene maps of a mitochondrial genome of Mytilus. All genes are transcribed clockwise. Names of the tRNA genes are indicated by the amino acid (one-letter code) that they specify. Solid areas indicate noncoding regions; UR1–UR5, unassigned regions 1–6. Noncoding sequences of <30 bp are not shown. 16S and 12S, large and small subunits of ribosomal RNA. The recombinant region in the recently masculinized mtDNA is shown by the dotted line. Control region ♂, corresponds to the 1265-bp male part; ΔtrnS-ΔtrnQ are full copies of the trnS, trnN, trnI, and trnQ; Δ16S corresponds to a portion sharing 89% nt identity with the normal 16S; control region ♀ corresponds to the 1340-bp female part; ΔtrnY is a full copy of trnY; Δcob corresponds to the 5′-end of the cytochrome b gene.

Figure 2.

Additional tRNA-like structures found only in M. trossulus recently masculinized mtDNA.

Figure 3.

Comparisons between the number of nonsynonymous substitutions per nonsynonymous site (K_a) and the number of synonymous substitutions per synonymous site (K_s) among mytilid mussel mtDNA-encoded protein genes.

Figure 4.

Unrooted neighbor-joining tree for the male and female D-loop portions of the recently masculinized M. trossulus mt genome (Mtr_RM in boldface type), the male and female control region portions (TFCR5′ and TFCR3′, respectively) of the M. trossulus F₂ and F₃ haplotypes (P. D. Rawson, personal communication), and the M- and F-type control regions for M. edulis, M. galloprovincialis, and M. trossulus (footnote a, Hoffmann et al. 1992; b, Cao et al. 2004b; c, Mizi et al. 2005; d, Rawson 2005; e, T. Barna and R. Showman, personal communication). Numbers indicate bootstrap support from 1000 replicates. Parsimony analysis yielded the same topology.

Figure 5.

Relationships between intraspecies divergence in amino acid substitutions for protein-coding genes relative to interspecies divergences. Each diamond denotes an individual gene.

Figure 6.

Variability of amino acids across the mitochondrial genome detected in sliding windows of 50 amino acids (aa) with an increment of 25 aa. Protein sequences have been concatenated as shown in the bar at the bottom. Sliding-window analyses comparing the variability among (A) male mitochondrial genomes (considering the masculinized molecule). (B) Female mitochondrial genomes (considering the masculinized molecule). (C) Male mitochondrial genomes.