ORFans in Mitochondrial Genomes of Marine Polychaete Polydora

A twin of Polydora hoplura (Annelida: Spionidae) from the Arabian (Persian) Gulf, with review of primers used for barcoding of Spionidae

The spionid polychaete Polydora hoplura Claparède, 1868 has been widely recorded boring in shells of abalone, oysters, clams, barnacle tests and sponges in temperate and subtropical waters. Molecular studies have suggested conspecificity of individuals collected worldwide but showed high genetic variability of the species with the highest diversity of haplotypes in the South African population. We have compared the morphology and genetic data of shell-boring worms from Kuwait, which were previously assigned to P. hoplura, with American, Asian and European individuals, including those from the type locality in Italy. The Kuwaiti individuals share key diagnostic morphological characters with P. hoplura but differ in ochre pigment on the anterior chaetigers in life, pattern of pigmentation after fixation in formalin, and pattern of methyl green staining of fixed specimens. They also differ in the dimensions of mature spermatozoa. The analysis of sequence data of five gene fragments (total 3483 bp) showed that the intraspecific diversity of P. hoplura and the variability of Polydora individuals from Kuwait are less than the divergences in all studied genes, except for 28S rDNA, between these two groups. These data, as well as the absence of common cytochrome c oxidase subunit I (COI) and 16S haplotypes, and morphological differences between individuals from Kuwait and P. hoplura, allowed us to conclude that the Kuwaiti population is not conspecific with P. hoplura. This conclusion was confirmed by the results of the species delimitation analysis. In the Bayesian inference analysis of the sequence data individuals from Kuwait formed a well-supported clade sister to P. hoplura. These individuals are described and illustrated here as a new species, Polydora mohammadi sp. nov. Primers used for successful amplification of the mitochondrial COI gene in various species of Spionidae are reviewed and we suggest future studies on Polydora use a combination of two primer pairs (2F-spionid-LCO/1R-spionid-HCO and Dorid_COI.3F/Dorid_COI.1R) to target sequences that include the barcode fragments covered with "Folmer" and "Dorid" primers.

Comparative mitogenomics of Brachiopods reveals conservatism in articulate species and unusualness in inarticulate species

BACKGROUND

Brachiopods are a phylum of marine invertebrates with over 10,000 fossil species. Today, there are fewer than 500 extant species assigned to the class Articulata or Inarticulata and for which knowledge of evolutionary genetics and genomics is still poor. Until now, complete mitogenome sequences of two inarticulate species and four articulate species were available.

METHODS AND RESULTS

The complete mitogenome of the inarticulate brachiopod species Lingula reevii (20,778 bp) was obtained by using next generation sequencing. It contains 12 protein-coding genes (the annotation of atp8 is unsure), two ribosomal RNA genes, 26 transfer RNA genes, and one supernumerary ORF that is also conserved in the inarticulate species Lingula anatina. It is hypothesized that this ORF could represent a Lingula-specific mtORFan gene (without obvious homology to other genes). Comparative mitogenomics indicate the mitochondrial gene order of L. reevii is unique among brachiopods, and that compared to articulate species, inarticulate species exhibit massive mitogenome rearrangements, deviant ATP8 protein sequences and supernumerary ORFs, possibly representing species- or lineage-specific mtORFan genes.

CONCLUSION

The results of this study enrich genetics knowledge of extant brachiopods, which may eventually help to test hypotheses about their decline.