Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome

We have used a combination of three high-throughput RNA capture and sequencing methods to refine and augment the transcriptome map of a well-studied genetic model, Caenorhabditis elegans. The three methods include a standard (non-directional) library preparation protocol relying on cDNA priming and foldback that has been used in several previous studies for transcriptome characterization in this species, and two directional protocols, one involving direct capture of single-stranded RNA fragments and one involving circular-template PCR (CircLigase). We find that each RNA-seq approach shows specific limitations and biases, with the application of multiple methods providing a more complete map than was obtained from any single method. Of particular note in the analysis were substantial advantages of CircLigase-based and ssRNA-based capture for defining sequences and structures of the precise 59 ends (which were lost using the double-strand cDNA capture method). Of the three methods, ssRNA capture was most effective in defining sequences to the poly(A) junction. Using data sets from a spectrum of C. elegans strains and stages and the UCSC Genome Browser, we provide a series of tools, which facilitate rapid visualization and assignment of gene structures.We thank Sam Gu for flow cell preparation; Cheryl Smith, Ziming Weng, Phil Lacroute, Anton Valouev, and Arend Sidow for flow cell preparation and sequencing; Jason Merker and Julia Pak for comments; Gary Schroth and Shujun Luo from Illumina for helping with the dsDNALigSeq method; and the Caenorhabditis Genetics Center for strains. This work was supported by NIH (R01GM37706 [A.Z.F.], T32HG00044 [J.I.G.]), National Science Foundation Graduate Research Fellowship and Stanford Graduate Fellowship program (M.R.S.), A*STAR (Agency for Science, Technology and Research) Singapore (H.Z.), and Stanford Dean’s Fellowship and Machiah Foundation (A.T.L.)