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Mitochondrial DNA B Resour
2018 Nov 14;32:1225-1227. doi: 10.1080/23802359.2018.1532335.
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The complete mitochondrial genome of the sea urchin, Echinometra sp. EZ.
Ketchum RN
,
DeBiasse MB
,
Ryan JF
,
Burt JA
,
Reitzel AM
.
Abstract
The complete mitogenome of Echinometra sp. EZ has been described and fully annotated in this study. Phylogenetic analysis of cytochrome c oxidase subunit I (COI) from 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.
Figure 1:. The maximum likelihood (ML) tree generated using Geneious v11.1.4 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). The ML tree was generated with an alignment of the whole mitogenome sequences of all species, using the GTRâ+âG model. The numbers above the branches specify bootstrap percentages (1000 replicates).
Bolger,
Trimmomatic: a flexible trimmer for Illumina sequence data.
2014, Pubmed
Bolger,
Trimmomatic: a flexible trimmer for Illumina sequence data.
2014,
Pubmed
Bronstein,
The taxonomy and phylogeny of Echinometra (Camarodonta: Echinometridae) from the red sea and western Indian Ocean.
2013,
Pubmed
,
Echinobase
Guindon,
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.
2010,
Pubmed
Kajitani,
Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads.
2014,
Pubmed
Kearse,
Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.
2012,
Pubmed
Kumar,
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
2016,
Pubmed
McCartney,
Dispersal barriers in tropical oceans and speciation in Atlantic and eastern Pacific sea urchins of the genus Echinometra.
2000,
Pubmed
,
Echinobase
Moulin,
Long-term mesocosms study of the effects of ocean acidification on growth and physiology of the sea urchin Echinometra mathaei.
2015,
Pubmed
,
Echinobase
Palumbi,
SPECIATION AND POPULATION GENETIC STRUCTURE IN TROPICAL PACIFIC SEA URCHINS.
1997,
Pubmed
,
Echinobase
Smith,
Testing the molecular clock: molecular and paleontological estimates of divergence times in the Echinoidea (Echinodermata).
2006,
Pubmed
,
Echinobase
