First mitochondrial genomes of Capitellidae and Opheliidae (Annelida) and their phylogenetic placement

A single coelomic cell type is involved in both immune and respiratory functions of the coastal bioindicator annelid: Capitella C-Channel1 from the English Channel

The polychaete Capitella is a typical member of the 'thiobiome', and is commonly used as an eutrophication indicator species in environmental assessment studies. To deal with a sulfide-rich and poisonous surrounding, cells in close contact with the environment, and thus able to play a major role in detoxication and survival, are circulating cells. This work aimed to morpho-functionally describe the circulating coelomic cells of Capitella from the English Channel inhabiting the sulfide-rich mud in Roscoff Harbor. In general, worms have three types of circulating cells, granulocytes involved in bacterial clearance and defense against microorganisms, eleocytes with an essentially trophic role and elimination of cellular waste, and erythrocytes which play a role in detoxification and respiration via their intracellular hemoglobin. By combining diverse microscopic and cellular approaches, we provide evidence that Capitella does not possess granulocytes and eleocytes, but rather a single abundant rounded cell type with the morphological characteristics of erythrocytes i.e. small size and production of intracellular hemoglobin. Surprisingly, our data show that in addition to their respiratory function, these red cells could exert phagocytic activities, and produce an antimicrobial peptide. This latter immune role is usually supported by granulocytes. Our data highlight that the erythrocytes of Capitella from the English Channel differ in morphology and bear more functions than the erythrocytes of other annelids. The simplicity of this multi-task (or polyvalent) single-cell type makes Capitella an interesting model for studies of the impact of the environment on the immunity of this bioindicator species.

Buried treasure in a public repository: Mining mitochondrial genes of 32 annelid species from sequence reads deposited in the Sequence Read Archive (SRA)

Background

The mitochondrial genomes (mitogenomes) of metazoans generally include the same set of protein-coding genes, which ensures the homology of mitochondrial genes between species. The mitochondrial genes are often used as reference data for species identification based on genetic data (DNA barcoding). The need for such reference data has been increasing due to the application of environmental DNA (eDNA) analysis for environmental assessments. Recently, the number of publicly available sequence reads obtained with next-generation sequencing (NGS) has been increasing in the public database (the NCBI Sequence Read Archive, SRA). Such freely available NGS reads would be promising sources for assembling mitochondrial protein-coding genes (mPCGs) of organisms whose mitochondrial genes are not available in GenBank. The present study aimed to assemble annelid mPCGs from raw data deposited in the SRA.

Methods

The recent progress in the classification of Annelida was briefly introduced. In the present study, the mPCGs of 32 annelid species of 19 families in clitellates and allies in Sedentaria (echiurans and polychaetes) were newly assembled from the reads deposited in the SRA. Assembly was performed with a recently published pipeline mitoRNA, which includes cycles of Bowtie2 mapping and Trinity assembly. Assembled mPCGs were deposited in GenBank as Third Party Data (TPA) data. A phylogenetic tree was reconstructed with maximum likelihood (ML) analysis, together with other mPCGs deposited in GenBank.

Results and Discussion

mPCG assembly was largely successful except for Travisia forbesii; only four genes were detected from the assembled contigs of the species probably due to the reads targeting its parasite. Most genes were largely successfully obtained, whereas atp8, nad2, and nad4l were only successful in 22-24 species. The high nucleotide substitution rates of these genes might be relevant to the failure in the assembly although nad6, which showed a similarly high substitution rate, was successfully assembled. Although the phylogenetic positions of several lineages were not resolved in the present study, the phylogenetic relationships of some polychaetes and leeches that were not inferred by transcriptomes were well resolved probably due to a more dense taxon sampling than previous phylogenetic analyses based on transcriptomes. Although NGS data are generally better sources for resolving phylogenetic relationships of both higher and lower classifications, there are ensuring needs for specific loci of the mitochondrial genes for analyses that do not require high resolutions, such as DNA barcoding, eDNA, and phylogenetic analysis among lower taxa. Assembly from publicly available NGS reads would help design specific primers for the mitochondrial gene sequences of species, whose mitochondrial genes are hard to amplify by Sanger sequencing using universal primers.

First report of the mitogenome of the invasive reef-building polychaete Ficopomatus enigmaticus (Annelida: Serpulidae) and a cryptic lineage from the Japanese Archipelago

BACKGROUND

The mitochondrial genomes (mitogenomes) of the family Serpulidae are characterized by a high nucleotide sequence divergence and a significant number of gene order rearrangements compared with other families within the phylum Annelida. However, only two of 50 genera of serpulids have mitogenomes already sequenced. In this study, we report the first sequencing and assembly of the complete mitogenome of Ficopomatus, thus providing further knowledge on mitochondrial gene sequences of Serpulidae.

METHODS AND RESULTS

A mitogenome of the invasive reef-building polychaete Ficopomatus enigmaticus was amplified by long PCR and sequenced using the Illumina MiSeq System. It comprised 15,853 bp and consisted of 12 protein-coding genes (atp8 was not found), 23 tRNA, and two rRNA genes. The AT and GC skew values were infrequent when compared to annelid mitogenomes but similar to other serpulids sequenced to date (i.e., Spirobranchus and Hydroides). The mitochondrial gene order of F. enigmaticus was highly rearranged compared to other serpulids. To amplify 16S rRNA gene sequences, we developed a 16S rRNA primer set by modifying the universal primer set 16SarL/16SbrH. We detected the 16S rRNA sequence of F. enigmaticus deposited in GenBank erroneously characterized as of serpulid origin. We reported for the first time the presence of two lineages of F. enigmaticus in Japan, which have already been identified in California, Australia, and the Mediterranean.

CONCLUSIONS

The first mitochondrial genome of F. enigmaticus showed a unique gene order rearrangement, corroborating the remarkable diversity in the previously reported mitogenomes of other serpulid species. The presence of the two lineages of F. enigmaticus identified for the first time in Japan represents another case of cryptic invasion. The first 16S rRNA gene sequences of F. enigmaticus obtained in the present study can be used as reference sequences in future DNA metabarcoding studies.

Mitochondrial genome of Leocrates chinensis Kinberg, 1866 (Annelida: Hesionidae)

We report the complete mitochondrial genome of Leocrates chinensis Kinberg, 1866 - the type species of the genus. It is 15061 bp long, and contains 13 protein-coding genes (PCGs), 22 tRNA genes (tRNAs), and 2 rRNA genes (rRNAs), and 1 putative control region. Phylogenetic analysis indicated that L. chinensis was placed as sister to Sirsoe methanicola (BS = 100) of the same family Hesionidae.