Mitochondrial genomes of the Baltic clam Macoma balthica(Bivalvia: Tellinidae): setting the stage for studying mito-nuclear incompatibilities

Abstract

BackgroundAllopatric divergence across lineages can lead to post-zygotic reproductive isolation upon secondary contact and disrupt coevolution between mitochondrial and nuclear genomes, promoting emergence of genetic incompatibilities. A previous FST scan on the transcriptome of the Baltic clam Macoma balthica highlighted several genes potentially involved in mito-nuclear incompatibilities (MNIs). As proteins involved in the mitochondrial oxidative phosphorylation (OXPHO) chain are prone to MNIs and can contribute to the maintenance of genetic barriers, the mitochondrial genomes of six Ma. balthica individuals spanning two secondary contact zones were sequenced using the Illumina MiSeq plateform.ResultsThe mitogenome has an approximate length of 16,806 bp and encodes 13 protein-coding genes, 2 rRNAs and 22 tRNAs, all located on the same strand. atp8, a gene long reported as rare in bivalves, was detected. It encodes 42 amino acids and is putatively expressed and functional. A large unassigned region was identified between rrnS and tRNAMet and could likely correspond to the Control Region. Replacement and synonymous mutations were mapped on the inferred secondary structure of all protein-coding genes of the OXPHO chain. The atp6 and atp8 genes were characterized by background levels of replacement mutations, relative to synonymous mutations. However, most nad genes (notably nad2 and nad5) were characterized by an elevated proportion of replacement mutations.ConclusionsSix nearly complete mitochondrial genomes were successfully assembled and annotated, providing the necessary roadmap to study MNIs at OXPHO loci. Few replacement mutations were mapped on mitochondrial-encoded ATP synthase subunits, which is in contrast with previous data on nuclear-encoded subunits. Conversely, the high population divergence and the prevalence of non-synonymous mutations at nad genes are congruent with previous observations from the nuclear transcriptome. This further suggest that MNIs between subunits of Complex I of the OXPHO chain, coding for NADH dehydrogenase, may play a role in maintaining barriers to gene flow in Ma. balthica.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-014-0259-z) contains supplementary material, which is available to authorized users.

First complete female mitochondrial genome in four bivalve species genus Donax and their phylogenetic relationships within the Veneroida order

“…The typical 13 PCGs were identified in the four new mitogenomes analyzed here, including the atp8 gene, which had been reported as missing in several bivalve species [ 51 , 53 , 54 , 55 , 56 , 57 , 58 ], but subsequent analysis found its presence in several of them [ 48 , 50 , 52 , 59 , 60 , 61 , 62 ]. It was suggested that the short and variable length of this protein, along with its high variation in amino acid composition, might hinder the finding of this gene due to annotation difficulties [ 22 ].…”

“…vittatus ). Although gene organization is known to vary extensively, even among species from the same genus [ 22 , 48 , 49 ], all four complete Donax mt genomes showed the same gene order and they are located on the “+” strand, likewise in Macoma balthica , other member of the Tellinoidea superfamily for which the whole mt genome is available [ 50 ]. The only difference was noted in the location of the longest NCR which, in M .…”

“…Likewise, these two genes also fail to be adjacent in the mitogenome of other heterodont bivalves, such as Hiatella arctica [ 59 ], M . balthica [ 50 ] and Meretrix lamarckii [ 64 ]. On the contrary, they are adjacent in the Unionidae [ 65 ] and Solemydae [ 66 ], as well as in basal molluscs like Chaetoderma nitidilum (EF211990) and Katharina tunicata [ 67 ].…”

“…These features are similar to those previously reported in M . balthica [ 50 ] and five other species of the Tellinoidea superfamily ( Moerella iridescens , Sanguilonaria diphos , Sanguinolaria olivacea , Semele scabra and Solecurtus divaricatus ) [ 51 ].…”

Unorthodox features in two venerid bivalves with doubly uniparental inheritance of mitochondria

“…The two F-type contigs (tig00000885 and tig00000888) were then merged. The quality of the mitogenome assembly was checked at each step of the pipeline (initial Canu assembly, Nanopolish polishing, Pilon polishing) by calculating the percent identity between our F-type unitigs and a published F-type mitogenome from the same sampling locality (KM373201) 43 using MUMmer 3.23 81 .…”