Conclusion
In this study, we demonstrated that the FLc-Capture method could efficiently capture and enrich a large number of coding and noncoding loci for nonmodel organisms without any prior genome information. The direct use of homemade full-length cDNA probes in FLc-Capture can skip the expensive commercial probe design and synthesis, significantly reducing experimental cost. FLc-Capture can generate transcriptome-level data just based on DNA samples, which facilitates including more number of taxa in a phylogenomic study. In summary, FLc-Capture holds substantial promise in phylogenomic researches as a universally applicable and cost-effective sequence capture method of simultaneously collecting genome-level coding and noncoding orthologous loci for any organism.