Simultaneously Collecting Coding and Noncoding Phylogenomic Data Using Homemade Full-length cDNA Probes, Tested by Resolving the High-level Relationships of Colubridae

 We used the FLc-Capture method for data collection. In short, this method used full-length cDNAs as capture probes to simultaneously collect coding and noncoding sequences from genomes. For ORF (coding) sequence extraction, FLc-Capture assembled reads into contigs, and identified exons from contigs using EXONERATE based on the reference ORF sets. The identified exons are then mapped onto the reference ORF sequences to make the orthologous ORF sequences, based on the position information resulted from the EXONERATE searches. For UTR (noncoding) sequence extraction, based on the reference UTRs, FLc-Capture uses a mutual best-hit (MBH) strategy to identify orthologous UTR sequences and truncate sequences according to its optimal aligning region.