Mitochondrial phylogenomics of the Bivalvia (Mollusca): searching for the origin and mitogenomic correlates of doubly uniparental inheritance of mtDNA

Abstract

Background: Doubly uniparental inheritance (DUI) is an atypical system of animal mtDNA inheritance found only in some bivalves. Under DUI, maternally (F genome) and paternally (M genome) transmitted mtDNAs yield two distinct gender-associated mtDNA lineages. The oldest distinct M and F genomes are found in freshwater mussels (order Unionoida). Comparative analyses of unionoid mitochondrial genomes and a robust phylogenetic framework are necessary to elucidate the origin, function and molecular evolutionary consequences of DUI. Herein, F and M genomes from three unionoid species, Venustaconcha ellipsiformis, Pyganodon grandis and Quadrula quadrula have been sequenced. Comparative genomic analyses were carried out on these six genomes along with two F and one M unionoid genomes from GenBank (F and M genomes of Inversidens japanensis and F genome of Lampsilis ornata).

Results: Compared to their unionoid F counterparts, the M genomes contain some unique features including a novel localization of the trnH gene, an inversion of the atp8-trnD genes and a unique 3'coding extension of the cytochrome c oxidase subunit II gene. One or more of these unique M genome features could be causally associated with paternal transmission. Unionoid bivalves are characterized by extreme intraspecific sequence divergences between gender-associated mtDNAs with an average of 50% for V. ellipsiformis, 50% for I. japanensis, 51% for P. grandis and 52% for Q. quadrula (uncorrected amino acid p-distances). Phylogenetic analyses of 12 protein-coding genes from 29 bivalve and five outgroup mt genomes robustly indicate bivalve monophyly and the following branching order within the autolamellibranch bivalves: ((Pteriomorphia, Veneroida) Unionoida).

Conclusion: The basal nature of the Unionoida within the autolamellibranch bivalves and the previously hypothesized single origin of DUI suggest that (1) DUI arose in the ancestral autolamellibranch bivalve lineage and was subsequently lost in multiple descendant lineages and (2) the mitochondrial genome characteristics observed in unionoid bivalves could more closely resemble the DUI ancestral condition. Descriptions and comparisons presented in this paper are fundamental to a more complete understanding regarding the origins and consequences of DUI.

Figure 1

Bayesian inference majority-rule tree of bivalve mt genome relationships based on an analysis using the M3 codon substitution model and a nucleotide alignment of 12 mitochondrial protein-coding genes (atp8 excluded). Numbers above an internal branch, from top to bottom, indicate nodal support values from BI, ML and MP nucleotide-based analyses, respectively. Numbers below an internal branch, from top to bottom, indicate nodal support values from BI, ML and MP amino acid-based analyses, respectively. Only nodal support values > 50% are presented. An asterisk above an internal branch indicates that all three nucleotide-based nodal support values are 100; an asterisk below an internal branch indicates that all three amino acid-based nodal support values are 100. Branch lengths reflect substitutions per site and the taxonomic and gender-specific transmission affiliations of the individual sequences are indicated at the right. All phylogenetic analyses strongly indicate that the unionoids represent the basal lineage for the bivalve taxa represented in this analysis.

Figure 2

ML-based (A) and Dollo parsimony-based (B) ancestral character state reconstructions of presence/absence of DUI on a species-level tree derived from the tree presented in Figure 1. The ML-based reconstruction indicates three separate origins of DUI while the Dollo parsimony-based reconstruction indicates a single origin of DUI followed by three reversals to SMI.

Figure 3

Gene maps of the M and F mitochondrial genomes of Venustaconcha ellipsiformis, Pyganodon grandis, Inversidens japanensis and Quadrula quadrula. Protein and rRNA genes are named as in the text while tRNA genes are abbreviated by the one-letter code of the corresponding amino acid (L1 = trnL (cua), L2 = trnL (uaa), S1 = trnS (aga), and S2 = trnS (uaa)). Genes positioned inside the plain line are encoded on the heavy strand and genes outside the line are encoded on the light strand. Atp8* (= genomes lacking full size atp8 gene). Black arrows on the V. ellipsiformis M genome indicate regions that differ between male- and female-transmitted genomes and the arrow on the I. japanensis F genome indicates the region with a gene order distinct from that of the other figured F genomes. The circular gene maps of the genomes were drawn by GenomeVx [113] followed by manual modification.

Figure 4

ML-based ancestral character state reconstructions of mt genomic characteristics on the tree presented in Figure 1: (A) genes on one strand vs. genes on two strands, (B) presence/absence of full size atp8 gene, (C)nd4/nd4l separated by genes vs. nd4/nd4l not separated by genes, (D) presence/absence of an extra trnM gene. For each of these four mt genomic characteristics, the indicated character state for the unionoid bivalve ancestor is identical to that indicated for the molluscan ancestor. "Stars" indicate nodes for which the character state designations were not statistically significant (all other nodes were statistically significant).