Genomic Survey and Resources for the Boring Giant Clam Tridacna crocea

Abstract

The boring giant clam Tridacna crocea is an evolutionary, ecologically, economically, and culturally important reef-dwelling bivalve targeted by a profitable ornamental fishery in the Indo-Pacific Ocean. In this study, we developed genomic resources for T. crocea. Using low-pass (=low-coverage, ~6×) short read sequencing, this study, for the first time, estimated the genome size, unique genome content, and nuclear repetitive elements, including the 45S rRNA DNA operon, in T. crocea. Furthermore, we tested if the mitochondrial genome can be assembled from RNA sequencing data. The haploid genome size estimated using a k-mer strategy was 1.31–1.39 Gbp, which is well within the range reported before for other members of the family Cardiidae. Unique genome content estimates using different k-mers indicated that nearly a third and probably at least 50% of the genome of T. crocea was composed of repetitive elements. A large portion of repetitive sequences could not be assigned to known repeat element families. Taking into consideration only annotated repetitive elements, the most common were classified as Satellite DNA which were more common than Class I-LINE and Class I-LTR Ty3-gypsy retrotransposon elements. The nuclear ribosomal operon in T. crocea was partially assembled into two contigs, one encoding the complete ssrDNA and 5.8S rDNA unit and a second comprising a partial lsrDNA. A nearly complete mitochondrial genome (92%) was assembled from RNA-seq. These newly developed genomic resources are highly relevant for improving our understanding of the biology of T. crocea and for the development of conservation plans and the fisheries management of this iconic reef-dwelling invertebrate.

Assessing taxonomic, functional and phylogenetic diversity of giant clams across the Indo‐Pacific for conservation prioritization

“…Evolutionary distinctiveness (ED) was used to assess the contribution of each species to the phylogeny, specifically PD F , by distributing the phylogenetic branches among all species on the tree (Isaac et al, 2007). The phylogeny of all 12 giant clam species was reconstructed using published mitochondrial and ribosomal gene sequences from (Tan et al, 2022; see also Baeza et al, 2022), following the study's methods in producing a maximum likelihood tree with RAxML v8.2.11 (Stamatakis, 2014; GTRGAMMA model, 100 random starting trees, and 1000 bootstrap pseudoreplicates) (Appendix S3). The full set of phylogenetic results are available at Zenodo (10.5281/zenodo.3761899).…”

Genome Survey Sequencing of the Mole Cricket Gryllotalpa orientalis

“…As described in Baeza [22], the repetitive elements of G. orientalis were identified, annotated, and quantified using RepeatExplorer [23,24] to cluster similar reads on Galaxy platform, http://repeatexplorer.org/ (accessed on 22 November 2022). The RepeatExplorer program provided a rapid analysis of plant and animal genomes' repeat composition and abundances.…”