Genomic investigation of benthic invertebrates from the Clarion-Clipperton fields of polymetallic nodules

By

Gastineau, Romain
Mianowicz, Kamila
Dąbek, Przemysław
Otis, Christian
Stoyanova, Valcana
Krawcewicz, Artur
Abramowski, Tomasz

Type

Article

Date of Publication

2025

Original Publication

ZooKeys

Volume

1231

Pages

11--44

Subjects

Brachiopoda , Bryozoa , genome-skimming , Holothuroidea , Introns , mitochondrial genomes , Ophiuroidea , Polychaeta , Porifera , ribosomal RNA genes

Contributed by

Pensoft Publishers

Language

English

Published by

Sofia, Bulgaria Pensoft Publishers

Identifiers

DOI: https://doi.org/10.3897/zookeys.1231.135347

 

Abstract

The abyssal plains of the Clarion-Clipperton Zone (CCZ) are famous for their fields of polymetallic nodules, which are inhabited by benthic invertebrates. Ten specimens from the Interoceanmetal Joint Organisation (IOM) licence area in the CCZ were collected in 2014 and submitted to a short-read genome skimming sequencing. In total, mitochondrial genomes and nuclear ribosomal genes were retrieved for nine different organisms belonging to Ophiuroidea, Holothuroidea, Polychaeta, Bryozoa, Porifera, and Brachiopoda (assigned to these phyla immediately upon retrieval from the seafloor). As many of these samples were partial and physically deteriorated following their seven-year storage in IOM’s collections, their morphology-based taxonomic identification could rarely be performed at the lowest possible level (species or genus) prior to preparing the samples for molecular or genomic investigations. Therefore, it was not possible to apply the reverse identification scheme recommended for such investigations. However, several of these specimens represent poorly studied groups for which few molecular references are available as of now. In two cases, the presence of introns in the mitochondrial genome questions the practicability of using the cox1 gene for further routine molecular barcoding of these organisms. These results might be useful in future DNA primers design, molecular barcoding, and phylogeny or population genetic studies when more samples are obtained.