Microsatellite characterization and marker development from public EST and WGS databases in the reef-building coral Acropora millepora (Cnidaria, Anthozoa, Scleractinia).
Mining for microsatellites (also called simple sequence repeats [SSRs]) in public sequence databases of a common Indo-Pacific coral Acropora millepora identified 191 SSRs from 10 258 expressed sequence tag (EST) and 618 SSRs from 14 625 whole-genome shotgun (WGS) sequences. In contrast to other animals, trinucleotide repeats, rather than dinucleotide repeats, are dominant in the WGS-SSRs, and AAT is the most frequent trinucleotide motif in EST-SSRs. We successfully developed 40 polymorphic markers from EST-SSRs and WGS-SSRs. Both EST- and WGS-SSRs show high levels of polymorphism within corals from the same reef patch. Interestingly, markers WGS079 and WGS227 revealed SSR duplications in a few individuals, suggesting recent duplication events. Genotypic linkage disequilibrium was identified in 5 pairs of SSR markers, which will be invaluable for high-resolution studies of genetic admixture in natural populations of A. millepora. Transferability analysis showed that 25 of these markers can be successfully amplified in one of the most ubiquitous Indo-Pacific corals Acropora hyacinthus. The marker collection reported here is the largest ever developed for any reef-building coral. It holds great potential for addressing coral reef connectivity across the Indo-Pacific with an unprecedented precision, especially taking into account the cross-species transferability of a substantial number of markers.
Wang
Shi
S
University of Texas at Austin, 78712, USA. swang@mail.utexas.edu
Zhang
Lingling
L
Matz
Mikhail
M
D000818:Animals; D037421:Anthozoa / Q000235:genetics*; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D005819:Genetic Markers; D005838:Genotype; D015810:Linkage Disequilibrium; D018895:Microsatellite Repeats / Q000235:genetics*; D016133:Polymerase Chain Reaction
D005819:Genetic Markers