Novel Repetitive Structures, Deviant Protein-Encoding Sequences andUnidentified ORFs in the Mitochondrial Genome of the BrachiopodLingula anatina

Abstract

Complete sequence determination of the brachiopod Lingula anatina mtDNA (28,818 bp) revealed an organization that is remarkably atypical for an animal mt-genome. In addition to the usual set of 37 animal mitochondrial genes, which make up only 57% (16,555 bp) of the entire sequence, the genome contains lengthy unassigned sequences. All the genes are encoded in the same DNA strand, generally in a compact way, whereas the overall gene order is highly divergent in comparison with known animal mtDNA. Individual genes are generally longer and deviate considerably in sequence from their homologues in other animals. The genome contains two major repeat regions, in which 11 units of unassigned sequences and six genes (atp8, trnM, trnQ, trnV, and part of cox2 and nad2) are found in repetition, in the form of nested direct repeats of unparalleled complexity. One of the repeat regions contains unassigned repeat units dispersed among several unique sequences, novel repetitive structure for animal mtDNAs. Each of those unique sequences contains an open reading frame for a polypeptide between 80 and 357 amino acids long, potentially encoding a functional molecule, but none of them has been identified with known proteins. In both repeat regions, tRNA genes or tRNA gene-like sequences flank major repeated units, supporting the view that those structures play a role in the mitochondrial gene rearrangements. Although the intricate repeated organization of this genome can be explained by recurrent tandem duplications and subsequent deletions mediated by replication errors, other mechanisms, such as nonhomologous recombinations, appear to explain certain structures more easily.

Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species

“…On the contrary, Mollusca, enoplean Nematoda and Porifera exhibit a strong heterogeneity in genome size (high standard deviation in Figure 1). By way of contrast, the large standard deviation observed in Brachiopoda and Chelicerata is due to the presence of a single mtDNA with a very large size compared to the almost constant size of remaining mtDNAs (the L. anatina mtDNA is 28.8 kb long (Endo et al, 2005) against a mean value of 14.6±0.8 kb for three other brachiopods; the Metaseiulus occidentalis mtDNA is 24.9 kb long (Jeyaprakash and Hoy, 2007) against a mean of 14.8±0.8 kb for 27 other chelicerates).…”

The Evolution of Brachiopoda

“…Other studies have identified major conflicts between molecular and morphological phylogenetic analyses of extant brachiopod species (Saito et al 2001, Bitner & Cohen 2015. Genomic (Stechmann & Schlegel 1999, Helfenbein et al 2001, Endo et al 2005, Adachi et al 2013, Luo et al 2015 and, more recently, proteomic (Immel et al 2015, Jackson et al 2015) studies, as well as studies of gene expression in brachiopod species, are now being tackled, with exciting, compelling results (Altenburger et al 2011, Passamaneck et al 2015. Establishing relationships between genetic variation, gene expression, and morphology is the next frontier in linking geological and biological approaches to the study of brachiopod evolution.…”

Complete mitochondrial genome analysis of Lingula anatina from Korea (Brachiopoda, Lingulida, Lingulidae)

“…DNA barcoding researches due to on cytochrome c oxidase subunit I (COI) and elongation factor 1 alpha (EF-1a) genes from specimens collected from different localities in this species also showed variations on lengths of gene and amino acid sequences (Reyment et al 2007;Yang et al 2013). Previously, it has been declared that the complete mitochondrial genome structure of L anatina which collected from Japan has unusual characteristics on genome size, gene order and elongated genes (Endo et al 2005). In this study, complete mitochondrial genome of L. anatina from Korea sequenced, analysed and compared with previous record.…”