Abstract
We describe restriction site associated RNA sequencing (RARseq), an RNAseq-based genotype by sequencing (GBS) method. It includes the construction of RNAseq libraries from double stranded cDNA digested with selected restriction enzymes. To test this, we constructed six single- and six-dual-digested RARseq libraries from six F2 pitcher plant individuals and sequenced them on a half of a Miseq run. On average, the de novo approach of population genome analysis detected 544 and 570 RNA SNPs, whereas the reference transcriptome-based approach revealed an average of 1907 and 1876 RNA SNPs per individual, from single- and dual-digested RARseq data, respectively. The average numbers of RNA SNPs and alleles per loci are 1.89 and 2.17, respectively. Our results suggest that the RARseq protocol allows good depth of coverage per loci for detecting RNA SNPs and polymorphic loci for population genomics and mapping analyses. In non-model systems where complete genomes sequences are not always available, RARseq data can be analyzed in reference to the transcriptome. In addition to enriching for functional markers, this method may prove particularly useful in organisms where the genomes are not favorable for DNA GBS.
Highlights
Generation sequencing (NGS) technologies make it possible to perform genome-wide genotyping in hundreds of individuals simultaneously
Our results suggest that restriction site associated RNA sequencing (RARseq) is an efficient method for genotyping and population genomic analysis
We showed here that RARseq is suitable for population genomic analysis of non-model species using both de novo and reference approaches
Summary
Generation sequencing (NGS) technologies make it possible to perform genome-wide genotyping in hundreds of individuals simultaneously. Several genome-wide genotyping methods using NGS have been developed and proven efficient (reviewed in [1].) These methods can be classified into two types: restriction digestion- and target enrichment-based methods. The main concept of both methods is that a reduction of genome complexity by restriction digestion or target enrichment is necessary to assure sufficient overlap across individuals in the sequence coverage of genomes, especially for the large genomes. NGS methods that deploy restriction digestions include, restriction-site DNA associated sequencing (RADseq)[2] and genotyping by sequencing (GBS)[3]. Both RADseq and GBS methods are similar in the concept, but different in their barcoding and multiplexing modules.
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
