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

Abstract

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

Related Concepts

Biological Markers
Amphibians
Exons
Genome
Exon-exon Junction Complex Location
Evaluation
Genomics
Oligonucleotides
Gene Duplication Abnormality
Species

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