An evaluation of transcriptome-based exon capture for frog phylogenomics across multiple scales of divergence (Class: Amphibia, Order: Anura)

BioRxiv : the Preprint Server for Biology
Daniel M PortikKe Bi


Custom sequence capture experiments are becoming an efficient approach for gathering large sets of orthologous markers with targeted levels of informativeness in non-model organisms. Transcriptome-based exon capture utilizes transcript sequences to design capture probes, often with the aid of a reference genome to identify intron-exon boundaries and exclude shorter exons (< 200 bp). Here, we test an alternative approach that directly uses transcript sequences for probe design, which are often composed of multiple exons of varying lengths. Based on a selection of 1,260 orthologous transcripts, we conducted sequence captures across multiple phylogenetic scales for frogs, including species up to ~100 million years divergent from the focal group. After several conservative filtering steps, we recovered a large phylogenomic data set consisting of sequence alignments for 1,047 of the 1,260 transcriptome-based loci (~630,000 bp) and a large quantity of highly variable regions flanking the exons in transcripts (~70,000 bp). We recovered high numbers of both shorter (< 100 bp) and longer exons (> 200 bp), with no major reduction in coverage towards the ends of exons. We observed significant differences in the performance of blocking oli...Continue Reading

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