Complete mitochondrial genome of Holothuria leucospilata (Holothuroidea, Holothuriidae) and phylogenetic analysis

The mitogenome data of Holothuria (Mertensiothuria) leucospilota (Brandt,1835) from Malaysia

White threads fish Holothuria (Mertensiothuria) leucospilota (Brandt, 1835) or locally known as bat puntil is a neritic marine organism, and it is widely distributed in Indo Pacific. They serve many important roles in ecosystem services and were discovered to contain many bioactive compounds that are useful for medicinal value. However, despite its abundance in Malaysian seawater, there is still a lack of records on H. leucospilota mitochondrial genome (mitogenome) from Malaysia. The mitogenome of H. leucospilota originating from Sedili Kechil, Kota Tinggi, Johor, Malaysia, is presented here. Whole genome sequencing was successfully sequenced using Illumina NovaSEQ6000 sequencing system and the mitochondrial-derived contigs were assembled using de novo approach. The size of the mitogenome is 15,982 bp which consists of 13 protein-coding genes (PCGs), 21 transfer RNAs, and 2 ribosomal RNAs. The overall composition of nucleotide bases was estimated to be 25.8% for T, 25.9% for C, 31.8% for A and 16.5% for G (with A + T content of 57.6%). Maximum likelihood phylogenetic tree analysis revealed that the mitochondrial Protein-Coding Genes (PCGs) sequence data from our H. leucospilota is closely related to H. leucospilota from accession number MK940237 and H. leucospilota from accession number MN594790, followed by H. leucospilota from accession number MN276190, forming sister group with H. hilla (MN163001), known as Tiger tail sea cucumber. The mitogenome of H. leucospilota will be valuable for genetic research, mitogenome reference and future conservation management of sea cucumber in Malaysia. The mitogenome data of H. leucospilota from Sedili Kechil, Kota Tinggi, Johor, Malaysia is available in the GenBank database repository with accession number ON584426.

Complete mitochondrial genome of a sea cucumber, Euapta godeffroyi (Echinodermata, Holothuroidea, Apodida, Synaptidae)

We determined the complete mitochondrial genome sequence of a holothurian Euapta godeffroyi belonging to the order Apodida. The complete mitogenome of E. godeffroyi was 16,410 bp in length and consisted of 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. The orders of PCGs and rRNAs did not match those of any recorded holothurian mitogenomes. The maximum likelihood (ML) phylogenetic tree placed E. godeffroyi as the sister group to chiridotid species and supported the monophyly of the order Apodida.

The Complete Mitochondrial Genome of Stichopus naso (Aspidochirotida: Stichopodidae: Stichopus) and Its Phylogenetic Position

The mitochondrial genome is widely used to study the molecular evolution of and perform phylogenetic analyses on animals. In this study, the complete mitochondrial genome (mitogenome) of Stichopus naso was sequenced. The mitogenome was 16,239 bp in length and contained 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). The genome composition showed positive AT-skew (0.023) and negative GC-skew (−0.158). The order of the mitochondrial genes was consistent with those from the Stichopus and Isostichopus species, whereas it was different from those of other species of Aspidochirotida. The phylogenetic analysis, based on the nucleotide sequences of 13 PCGs through the methods of Bayesian inference (BI) and maximum likelihood (ML), indicated that S. naso has close relationships with S. horrens and S. monotuberculatus, and belongs to a member of Stichopodidae. Our study provides a reference mitogenome for further molecular evolution studies and phylogenetic research on sea cucumbers.

Draft Genome of the Sea Cucumber Holothuria glaberrima, a Model for the Study of Regeneration

Regeneration is one of the most fascinating and yet least understood biological processes. Echinoderms, one of the closest related invertebrate groups to humans, can contribute to our understanding of the genetic basis of regenerative processes. Among echinoderms, sea cucumbers have the ability to grow back most of their body parts following injury, including the intestine and nervous tissue. The cellular and molecular events underlying these abilities in sea cucumbers have been most extensively studied in the species Holothuria glaberrima. However, research into the regenerative abilities of this species has been impeded due to the lack of adequate genomic resources. Here, we report the first draft genome assembly of H. glaberrima and demonstrate its value for future genetic studies. Using only short sequencing reads, we assembled the genome into 89,105 scaffolds totaling 1.1 gigabases with an N50 of 25 kilobases. Our BUSCO assessment of the genome resulted in 894 (91.4%) complete and partial genes from 978 genes queried. We incorporated transcriptomic data from several different life history stages to annotate 51,415 genes in our final assembly. To demonstrate the usefulness of the genome, we fully annotated the melanotransferrin (Mtf) gene family, which have a potential role in the regeneration of the sea cucumber intestine. Using these same data, we extracted the mitochondrial genome, which showed high conservation to that of other holothuroids. Thus, these data will be a critical resource for ongoing studies of regeneration and other studies in sea cucumbers.

The complete mitochondrial genome sequence of Stichopus variegatus (Echinodermata: Holothuroidea) and phylogenetic studies of Echinodermata

At present, there exist some confusing issues on the species classification and phylogeny in Echinodermata. In this study, we first determined and described the complete mitochondrial genome of Stichopus variegatus. The complete mitogenome sequence had a circular mapping molecular with the total length of 16,315 bp and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a putative control region. To further validate the newly determined sequences, phylogenetic trees involving all the Holothuroidea and other Echinodermata species available in GenBank Database were constructed. These results would be used for the species identification and further phylogenetic studies of Echinodermata.