Journal Article

A first nuclear and mitochondrial genomic portrait of Robinson Crusoe’s (Juan Fernández Island) spiny lobster Jasus frontalis (Crustacea: Decapoda: Achelata)

Baker, Alyssa, Richards, Vincent P., Baeza, J. Antonio, Kamal, Sadia A.

2025

Overview

Background The Juan Fernández rock lobster Jasus frontalis (H. Milne-Edwards, 1837) is found along the Juan Fernández archipelago and Desventuradas Islands in the southeastern Pacific Ocean where it supports a profitable but likely unsustainable artisanal fishery. Only a few genomic resources are available for this species to support efficient managing practices. In this study, we took a first look at the genome of J. frontalis profiting from recently developed bioinformatics tools that mine for biological insight from low sequencing-depth datasets. Specifically, we have (i) estimated the nuclear genome size, (ii) assembled and described in detail the mitochondrial genome, (iii) discovered, quantified, and annotated nuclear transposable elements, and (iv) examined the phylogenetic position of the genus Jasus among spiny lobsters (family Palinuridae) using a maximum likelihood phylogenetic analysis based on translated mitochondrial protein coding genes (PCG’s). Results Using an in-silico k-mer approach, the haploid nuclear genome size (GS) calculated for J. frontalis ranged between 1.42 Gbp (estimated using k-mer = 54 bp) and 1.65 Gbp (with k-mer = 18). Our GS estimates are well below the GS (= 4.56 Gbp) determined for the same species using flow cytometry. In J. frontalis , the circular mitochondrial genome is 15,514 bp in length and contains 22 transfer (tRNA) genes, 13 PCGs, and two ribosomal RNA genes (12 S and 16 S ribosomal RNA). In the nuclear genome of J. frontalis , repetitive elements content varied between 41% (with k-mer = 54) and 64% (using k-mer = 18 bp). Nearly a third (64.94%) of the transposable elements were not annotated. Among annotated transposable elements, Long Interspersed Nuclear Elements (LINEs, 12.64%), DNA transposons (7.35%), and Long Terminal Repeats (LTRs, 5.44%) were the most common. Less abundant transposable elements included Rolling Circles (1.3%), Short Interspersed Nuclear Elements (SINEs, 0.64%), Satellite DNA (0.43%), and simple repeats (0.42%), among others. A phylomitogenomic analysis based on PCGs indicated supported the monophyletic status of the infraorder Achelata and the superfamilies Paniluridae and Syllaridae. The genus Jasus together with Sagmariasus verreauxi were recovered as a monophyletic clade that also provided support for the monophyletic status of lobsters that do not produce sound (“Silentes”). Conclusion The genomic resources developed in this study will support conservation strategies and efficient fisheries management in this spiny lobster that is likely overexploited.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Achelata / Animal Genetics and Genomics / Animals / Annotations / Archipelagoes / Bats / Bioinformatics / Biomedical and Life Sciences / Cell Nucleus - genetics / Crustaceans / Decapoda / Deoxyribonucleic acid / DNA / DNA Transposable Elements / Fisheries / Fisheries management / Flow cytometry / Genes / Genome Size / Genome skimming / Genome, Mitochondrial / Genomes / Genomics / Islands / Jasus / Jasus frontalis / Life Sciences / Lobster / Lobsters / Long interspersed nucleotide elements / Low-coverage genome sequencing / Microarrays / Microbial Genetics and Genomics / Mitochondria / Mitochondrial genome / Palinuridae / Palinuridae - classification / Palinuridae - genetics / Phylogenetics / Phylogeny / Plant Genetics and Genomics / Proteomics / Repetitive elements / Ribonucleic acid / RNA / rRNA / Satellite DNA / Second dive into marine genomics / Shellfish / Short interspersed nucleotide elements / Transposons / tRNA