PRJNA264055
Miscanthus sinensis Genome sequencing
Miscanthus is a perennial grass and candidate bioenergy crop that creates a challenge for variant discovery and genotyping because of its abundant repeats and the presence of a genome scale duplication with little subsequent divergence. In addition, the 2.4 GB Miscanthus genome contains high heterozygosity due to its self-incompatible breeding system. This complexity necessitates the discovery of sequence variants that distinguish paralogs from alleles, which are most frequent in the low-copy non-coding fraction of the genespace. To enrich for such sequences from Miscanthus genomes, we developed a sequence capture assay using Nimblegen's solution-based hybridization method. The probe set was designed to capture exons and flanking intronic sequences and some single copy genomic segments predicted from alignment of Miscanthus transcriptome, fosmid, and genomic reads to the largely syntenic Sorghum genome. To facilitate haplotype discovery and the sequencing of non-coding regions adjacent to exonic probes, we selected 250 to 500 bp randomly sheared fragments that were subsequently sequenced as paired-end reads using Illumina technology. This sequence capture was implemented on a doubled haploid M. sinensis, its parent, four other Miscanthus genotypes, and a member of the closely related Saccharum genus, an energy cane. The efficiency of the capture was evaluated by comparing pre and post capture libraries from the double haploid M. sinensis and its parent. The sequence capture was able to distinguish homeologous variation from allelic variation at high depth. Additionally, sequence capture serves as a useful tool for comparative genomics and provides evidence that Miscanthus sequence capture probe set can serve as a satisfactory tool to discover of genomic variation in Miscanthus as well as the closely related, yet highly polyploid genomes of Saccharum spp.