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. 2020 May;20(3):807-818.
doi: 10.1111/1755-0998.13150. Epub 2020 Mar 24.

Transcriptome-based target-enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia)

Randolph Z B Quek  1 , Sudhanshi S Jain  1 , Mei Lin Neo  1   2 , Greg W Rouse  3 , Danwei Huang  1   2
Affiliations

Transcriptome-based target-enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia)

Randolph Z B Quek et al. Mol Ecol Resour. 2020 May.

Abstract

Despite the ecological and economic significance of stony corals (Scleractinia), a robust understanding of their phylogeny remains elusive due to patchy taxonomic and genetic sampling, as well as the limited availability of informative markers. To increase the number of genetic loci available for phylogenomic analyses in Scleractinia, we designed 15,919 DNA enrichment baits targeting 605 orthogroups (mean 565 ± SD 366 bp) over 1,139 exon regions. A further 236 and 62 barcoding baits were designed for COI and histone H3 genes respectively for quality and contamination checks. Hybrid capture using these baits was performed on 18 coral species spanning the presently understood scleractinian phylogeny, with two corallimorpharians as outgroup. On average, 74% of all loci targeted were successfully captured for each species. Barcoding baits were matched unambiguously to their respective samples and revealed low levels of cross-contamination in accordance with expectation. We put the data through a series of stringent filtering steps to ensure only scleractinian and phylogenetically informative loci were retained, and the final probe set comprised 13,479 baits, targeting 452 loci (mean 531 ± SD 307 bp) across 865 exon regions. Maximum likelihood, Bayesian and species tree analyses recovered maximally supported, topologically congruent trees consistent with previous phylogenomic reconstructions. The phylogenomic method presented here allows for consistent capture of orthologous loci among divergent coral taxa, facilitating the pooling of data from different studies and increasing the phylogenetic sampling of scleractinians in the future.

Keywords: coral reef; exon; genome sampling; hybrid capture; multilocus data; phylogenomics.

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Figures

FIGURE 1
FIGURE 1
Coverage of loci captured by target‐enrichment baits as determined by hybpiper post‐filtering (blue = absent, red = present)
FIGURE 2
FIGURE 2
Maximum likelihood phylogeny of Scleractinia for exons‐only data set (minimum taxon occupancy of three scleractinian taxa per locus; 30.86% missing data; 452 loci over 865 exon regions; 201,137 bp) with Rhodactis as outgroup. All nodes have maximum bootstrap values and posterior probabilities
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