Comparison with the EecSeq method
In general, our method has some similarity to the expressed exome capture sequencing (EecSeq) recently presented by Puritz and Lotterhos (2017), because our FLc-Capture method and EecSeq both prepare homemade cDNA probes from expressed mRNAs and use them to capture target sequences from genomic libraries. However, FLc-Capture also has two apparent differences to EecSeq. First, these two methods have a different focus on capturing genomic targets, so that the requirement of the cDNA probes are different. EecSeq only focuses on capturing coding sequences, so using fragmented cDNA probes is sufficient because fragmented cDNAs can essentially cover most coding regions. While FLc-Capture aims to capture both coding and noncoding sequences, so using the SMART technology to synthesize full-length cDNAs is critical because the full-length cDNA contains not only ORF (coding), but also UTR (noncoding) regions. Second, the application scenarios of these two methods are different. EecSeq generates genome-wide exome-derived SNP data, which is more suitable for identifying loci under selection at the population level to understand the genetic basis of adaptation. While FLc-Capture generates genome-scale sequence data, which is better suited to infer the evolutionary relationships for organisms across multiple phylogenetic scales. The unique feature of simultaneously collecting coding and noncoding sequences makes FLc-Capture advantageous in studying difficult phylogenetic questions (e.g., rapid radiation).