Genomic survey sequencing and complete mitochondrial genome of the elkhorn coral crab Domecia acanthophora (Desbonne in Desbonne & Schramm, 1867) (Decapoda: Brachyura: Domeciidae)

Author:

Bravo Henrique1ORCID,Baeza J Antonio234,van der Meij Sancia E T15ORCID

Affiliation:

1. Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen , Groningen , The Netherlands

2. Department of Biological Sciences, Clemson University , Clemson, SC 29634 , USA

3. Smithsonian Marine Station at Fort Pierce , Florida , USA

4. Universidad Católica del Norte , Coquimbo , Chile

5. Marine Biodiversity Group, Naturalis Biodiversity Center , Leiden , The Netherlands

Abstract

Abstract The elkhorn coral crab Domecia acanthophora inhabits shallow-water coral reefs in the Western Atlantic. The species has a wide distribution and, although primarily associated with endangered Acropora corals, has been recorded from a myriad of hosts. Here we conducted the first genomic survey and complete mitochondrial assemblage and characterisation of any species of Domeciidae, as well as the first species within Trapezioidea. The estimated size of the nuclear genome ranged from 0.64 Gbp to 1.76 Gbp, revealing a small genome. Repetitive elements of the genome were estimated here at 66.4% and 74%, respectively, with the majority of the repetitive elements consisting of LINE, LTR, and satellite DNA. The assembled A-T rich mitochondrial genome consisted of 15,568 bp in length, with 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes and two ribosomal RNA (rRNA) genes. A 619 bp long non-coding region was identified as the supposed D-loop/control region, containing eight microsatellites. The 22 tRNA genes, ranging from 65 to 71 bp in length, displayed a typical “cloverleaf” secondary structure, with the exception of tRNA-Ser1 which lacked part of the DHU arm and tRNA-Asp displayed a deletion of the TΨC loop but not the arm. Two transposition events of two tRNA genes were also found when comparing the gene order of D. acanthophora to that of the brachyuran basic gene order, which had not been reported before. Despite belonging to a widely distributed, well-known superfamily of coral-associated crabs, the Trapezioidea, very little was known about this species from a genetics perspective, which is remedied here by providing a new genomic resource for D. acanthophora.

Funder

TREUB-maatschappij

Publisher

Oxford University Press (OUP)

Subject

Aquatic Science

Reference63 articles.

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