PCA plot.

<p>Principal Component Analysis (PCA) based on both Jin-Nei and Kimura distances reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0153631#pone.0153631.t004" target="_blank">Table 4</a>. Colors refer to different families: blue, Unionidae with the exception of <i>Hyriopsis</i> spp. (brown; see text for details); Indian red, Mytilidae; green, Veneridae. AnAn, <i>Anodonta anatina</i>; HyCu, <i>Hyriopsis cumingii</i>; HySc, <i>Hyriopsis schlegelii</i>; MeLa, <i>Meretrix lamarckii</i>; MuSe, <i>Musculista senhousia</i>; MyCa, <i>Mytilus californianus</i>; MyEd, <i>Mytilus edulis</i>; MyGa, <i>Mytilus galloprovincialis</i>; MyTr, <i>Mytilus trossulus</i>; PyGr, <i>Pyganodon grandis</i>; QuQu; <i>Quadrula quadrula</i>; RuPh, <i>Ruditapes philippinarum</i>; SoCa, <i>Solenaia carinatus</i>; UtPe; <i>Utterbackia peninsularis</i>; VeEl, <i>Venustaconcha ellipsiformis</i>.</p

Nucleotide composition (%) of <i>Meretrix lamarckii</i> F and M genomes.

<p>Nucleotide composition (%) of <i>Meretrix lamarckii</i> F and M genomes.</p

Annotation of F and M mitochondrial genomes of <i>Meretrix lamarckii</i>.

<p>Annotation of F and M mitochondrial genomes of <i>Meretrix lamarckii</i>.</p

Phylogenetic analysis.

<p>Maximum Likelihood phylogenetic analysis of the family Veneridae using complete mitochondrial genomes and <i>Acanthocardia tuberculata</i> (Cardiidae), <i>Hiatella arctica</i> (Hiatellidae), and <i>Coelomactra antiquata</i> (Mactridae) as outgroups. Shown is the consensus of ML trees obtained from 1,000 bootstrap replicates; number at the nodes are bootstrap proportions. Purple bars mark known DUI species.</p

<i>Meretrix lamarckii cox2</i> gene alignment.

<p>Aminoacid alignment between female-type (F) and male-type (M) <i>Meretrix lamarckii</i> sequences of the <i>cox2</i> gene. Identical aminoacids are shaded following their hydropathy (see the legend below the figure for the meanings of the different colors); purple bars show aminoacid similarity. The 100-aminoacid insertion found in M-mtDNA is boxed in red. Sites are numbered above the sequences, conventionally starting at 1.</p

The Complete Female- and Male-Transmitted Mitochondrial Genome of <i>Meretrix lamarckii</i>

<div><p>Bivalve mitochondrial genomes show many uncommon features, like additional genes, high rates of gene rearrangement, high A-T content. Moreover, Doubly Uniparental Inheritance (DUI) is a distinctive inheritance mechanism allowing some bivalves to maintain and transmit two separate sex-linked mitochondrial genomes. Many bivalve mitochondrial features, such as gene extensions or additional ORFs, have been proposed to be related to DUI but, up to now, this topic is far from being understood. Several species are known to show this unusual organelle inheritance but, being widespread only among Unionidae and Mytilidae, DUI distribution is unclear. We sequenced and characterized the complete female- (F) and male-transmitted (M) mitochondrial genomes of <i>Meretrix lamarckii</i>, which, in fact, is the second species of the family Veneridae where DUI has been demonstrated so far. The two mitochondrial genomes are comparable in length and show roughly the same gene content and order, except for three additional tRNAs found in the M one. The two sex-linked genomes show an average nucleotide divergence of 16%. A 100-aminoacid insertion in <i>M</i>. <i>lamarckii</i> M-<i>cox2</i> gene was found; moreover, additional ORFs have been found in both F and M Long Unassigned Regions of <i>M</i>. <i>lamarckii</i>. Even if no direct involvement in DUI process has been demonstrated so far, the finding of <i>cox2</i> insertions and supernumerary ORFs in <i>M</i>. <i>lamarckii</i> both strengthens this hypothesis and widens the taxonomical distribution of such unusual features. Finally, the analysis of inter-sex genetic variability shows that DUI species form two separate clusters, namely Unionidae and Mytilidae+Veneridae; this dichotomy is probably due to different DUI regimes acting on separate taxa.</p></div

<i>Meretrix lamarckii</i> sex-linked mitochondrial genomes.

<p>Genomic map of F- (above) and M- (below) mtDNA of <i>Meretrix lamarckii</i> starting from <i>cox1</i>. Genes are all on "+" strand; genome lengths are shown in the middle of each map. Unassigned Regions (URs) are reported in black in the internal circle.</p

Origins of Replication.

<p>A, nucleotide composition at four-fold degenerate sites, using a sliding window of 700 bp with a step of 300 bp. The starting point is the first PCG after the LUR, i.e. <i>cox3</i>. Equations are as follows, for F/M, respectively. A (green): <i>y = 0</i>.<i>0004x+14</i>.<i>84</i>; <i>R</i>^<i>2</i> <i>= 0</i>.<i>0681; p = 0</i>.<i>0616</i> / <i>y = 0</i>.<i>0002x+14</i>.<i>62</i>; <i>R</i>^<i>2</i> <i>= 0</i>.<i>0409; p = 0</i>.<i>1546</i>. C (blue): <i>y = 0</i>.<i>0003x+2</i>.<i>15</i>; <i>R</i>^<i>2</i> <i>= 0</i>.<i>2263; p = 0</i>.<i>0004***</i> / <i>y = 0</i>.<i>0002x+3</i>.<i>17</i>; <i>R</i>^<i>2</i> <i>= 0</i>.<i>1087; p = 0</i>.<i>0181*</i>. G (black): <i>y = −0</i>.<i>0004x+20</i>.<i>39</i>; <i>R</i>^<i>2</i> <i>= 0</i>.<i>0796; p = 0</i>.<i>0428*</i> / <i>y = 0</i>.<i>0004x+17</i>.<i>33</i>; <i>R</i>^<i>2</i> <i>= 0</i>.<i>1448; p = 0</i>.<i>0059**</i>. T (red): <i>y = −0</i>.<i>0004x+62</i>.<i>61</i>; <i>R</i>^<i>2</i> <i>= 0</i>.<i>0595; p = 0</i>.<i>0815</i> / <i>y = −0</i>.<i>0008x+64</i>.<i>88</i>; <i>R</i>^<i>2</i> <i>= 0</i>.<i>2123; p = 0</i>.<i>0007***</i>. B, A-T skew at four-fold degenerate sites, using a sliding window as for (A); the starting point is again <i>cox3</i>.</p

Bivalves nucleotide and aminoacid (boldface) distances.

<p>Bivalves nucleotide and aminoacid (boldface) distances.</p

SmithRNAs Ruditapes philippinarum

Sequences of the 14 putative smithRNAs in Ruditapes philippinarum mitochondrial genome.<br