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).