Variation in the whole mitogenome of reef-building Porites corals
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TECHNICAL NOTE
Variation in the whole mitogenome of reef-building Porites corals David A. Paz-Garcı´a1,2 • Carolina Galva´n-Tirado3 • Juan Jose´ Alvarado4 Jorge Corte´s4 • Francisco J. Garcı´a-De-Leo´n3 • Michael E. Hellberg2 • Eduardo F. Balart1
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Received: 12 October 2015 / Accepted: 21 March 2016 Springer Science+Business Media Dordrecht 2016
Abstract The study of complete mitochondrial genomes (mitogenomes) revealed different gene rearrangements, highly variable markers, and delineated clades that have aided the understanding of the evolutionary history in corals. In this study, we examined mitogenomic variation of reef-building Porites corals and designed 34 primer pairs to target high diversity regions and to amplify the complete mitogenome of a widely-distributed Indo-Pacific species of Porites (P. lobata) and two endemic species of the Eastern Pacific (P. sverdrupi and P. panamensis). All primer pairs amplified for each species and the mitogenomes assembled yielded the same gene order as obtained from next-generation sequencing. Mitogenomic variation in Porites corals was three to ten times higher than in Acropora or Pocillopora, two other major reef builders. In contrast to these corals, the nucleotide variation in Porites species was distributed evenly along the mitogenome. Primers designed here are useful to amplify regions with the highest variation possible as well as to assemble the & Eduardo F. Balart [email protected] 1
Laboratorio de Necton y Ecologı´a de Arrecifes, Centro de Investigaciones Biolo´gicas del Noroeste (CIBNOR), Calle IPN 195, Col. Playa Palo de Santa Rita Sur, 23096 La Paz, B.C.S., Mexico
2
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
3
Laboratorio de Gene´tica para la Conservacio´n, Centro de Investigaciones Biolo´gicas del Noroeste (CIBNOR), Calle IPN 195, Col. Playa Palo de Santa Rita Sur, 23096 La Paz, B.C.S., Mexico
4
Centro de Investigacio´n en Ciencias del Mar y Limnologı´a (CIMAR), Universidad de Costa Rica, San Pedro, San Jose´ 11501-2060, Costa Rica
whole mitogenomes of different Porites species. The resulting mitogenomes should improve our understanding of evolutionary relationships, delimitation of species, and conservation within the genus Porites. Keywords Mitochondrial genome Porites corals Eastern Pacific Scleractinian corals
The animal mitochondrial genome (mitogenome) generally exhibits several characteristics that make it suitable for phylogenetic analysis: high substitution rate, maternal inheritance, and lack of recombination. In contrast, most of the mitochondrial genes studied in Class Anthozoa (i.e. anemones, corals and sea pens) show slow rates of nucleotide substitution, sometimes yielding few or no differences between closely related species (Shearer et al. 2002; Hellberg 2006; Prada et al. 2014). However, the recent study of the complete mitochondrial genome in this group have revealed different mitochondrial gene rearrangements (Lin et al. 2014; Figueroa and Baco 2015), the discovery of s
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