The complete mitogenome of Echinometra sp. EZ has been described and fully annotated in this study. Cytochrome subunit one phylogenetic analysis of six Echinometra species confirms that our sample is E. sp. EZ. The mitogenome is 15,698 bp in length and contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a non-coding region with an identical organization to other Echinoidea. The E. sp. EZ mitogenome shared ~99.1% identity to the published Echinometra mathaei mitogenome, differing by 147 SNPs. The E. sp. EZ mitogenome will serve as a resource that can be applied to disentangling the Echinometra species complex and to future population genetic studies of this ecologically important sea urchin species.
COI Alignment Echinometra sp.
Eight Echinometra COI sequences were included in this alignment; E. sp. C, E. oblonga, E. sp. A, E. mathaei, E. sp. EZ, our sample, the COI sequence extracted from the published E. mathaei mitogenome (denoted with an asterisk), and E. lucunter as an outgroup. We used a MAFFT alignment and an E-INS-i algorithm to align COI sequences (441 column nucleotide alignment) in Geneious v11.1.4. Accession numbers are to the right of the species name.
Maximum likelihood tree Echinometra species COI
Eight Echinometra COI sequences were included in our Maximum likelihood tree (ML); E. sp. C, E. oblonga, E. sp. A, E. mathaei, E. sp. EZ, our sample, the COI sequence extracted from the published E. mathaei mitogenome (denoted with an asterisk), and E. lucunter as an outgroup. The published E. mathaei mitogenome COI sequence is most closely grouped with the E. sp. EZ sequences. In order to generate the ML tree, we used a MAFFT alignment and an E-INS-i algorithm to align COI sequences (441 column nucleotide alignment) in Geneious v11.1.4. MEGA v7.0.21 was used to determine that the best fit model for the ML tree construction was K2+G. The ML tree was constructed in the PhyML v.3.0 plugin in Geneious v11.1.4. The numbers above the branches specify bootstrap percentages (1,000 replicates) and accession numbers are to the right of the species name. The sequence alignment used to generate this tree is also included in this data package submission.
Table includes SNPs that differentiate our Echinometra sp. EZ mitogenome from the published Echinometra mathaei mitogenome. Table includes polymorphism type, the base pair found in each respective mitogenome for that SNP position, the numerical position of the SNP in the mitogenome, and mitochondrial region the SNP is found in.
Figure 1: Complete mitogenome sequence alignment
The sequence alignment used to generate the maximum likelihood (ML) tree (figure 1) with six Echinoidea species: Strongylocentrotus purpuratus (accession number: X12631.1), Lytechinus variegatus (NC_037785.1), Heterocentrotus mammillatus (NC_034768.1), Hemicentrotus pulcherrimus (NC_023771.1), Echinometra mathaei (NC_034767.1), Arbacia lixula (NC_001770.1), and one Holothuroidea as an outgroup: Holothuria forskali (FN562582.1). We used a MAFFT alignment (16,520 column alignment) with the E-INS-i algorithm implemented in Geneious v11.1.4.