DOI: 10.5061/dryad.20k3fj0
title: Data from: The complete mitochondrial genome of the sea urchin, Echinometra sp. EZ

description: 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.
description: 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.SuppFigure1_SeqAlign.fasMaximum likelihood tree Echinometra species COIEight 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.SuppFig1.pdfSNP tableTable 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.SNP Table.xlsxFigure 1: Complete mitogenome sequence alignmentThe 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.Fig1_Align_complemtdna.fas