Li Z et al. (2022), The Complete Mitochondrial Genome of Stichopus ...

ECB-ART-50307

Genes (Basel) 2022 May 05;135:. doi: 10.3390/genes13050825.

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

Li Z , Ma B , Li X , Lv Y , Jiang X , Ren C , Hu C , Luo P .

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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.

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References [+] :

Arndt, Mitochondrial gene rearrangement in the sea cucumber genus Cucumaria. 1998, Pubmed, Echinobase

	Figure 1. Gene maps of the Stichopus naso mitogenome. Blue arrows represent CDS, brown arrows represent tRNA, and lavender arrows represent rRNA, black, GC content, green, GC skew +, and dark purple, GC skew −.
	Figure 2. Relative synonymous codon usage in the Stichopus naso mitogenome. Codon families are indicated below the X-axis.
	Figure 3. Putative secondary structures of tRNAs from the Stichopus naso mitogenome. The tRNAs are labeled with the abbreviations of their corresponding amino acids.
	Figure 4. Linear representation of gene rearrangements of Stichopus naso, S. horrens, S. chloronotus, S. monotuberculatus, Isostichopus badionotus, Holothuria, Actinopyga, Parastichopus, and Apostichopus. All the genes are transcribed from left to right. The tRNA genes are represented by the corresponding single-letter amino acid code. S1 (AGN), S2 (UCN), L1 (CUN), and L2 (UUR). The rrnL and rrnS are the large and small ribosomal RNA subunits, respectively. The red arrow represents the transposition event, which shifts trnM from the position between trnG and trnL2 to the position between trnV and trnD.
	Figure 5. Phylogenetic trees constructed using the nucleotide sequences of the 13 PCGs in the Stichopus naso mitogenome. (a) BI method. (b) ML method. The numbers beside the nodes are posterior probabilities (BI) and bootstrap (ML), respectively.