Construction and analysis of the miscanthus genespace

Miscanthus and energy cane are closely related perennial grasses and candidate bioenergy crops. Both genomes create a challenge for variant discovery and genotyping because of their abundant repeats and the presence of a genome scale duplication with little subsequent divergence. In addition, the Miscanthus genome has 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 array using a solution-based hybridization method. The probe set was designed to capture exons and flanking intronic sequences predicted from alignment of Miscanthus transcriptome, fosmid, and genomic reads to the largely syntenic Sorghum genome. To facilitate haplotype discovery, we selected for large insert sizes that were subsequently sequenced at high depth as 100x75 bp paired-end reads. Chapter 1 reports the sequence capture of a doubled haploid Miscanthus sinensis plant and its parent, and chapter 2 reports the sequence capture of energy cane and two other Miscanthus species. This sequence capture design was able to distinguish variation at high depth and it was found that amplification is imperative to achieve this depth. Further analysis of the reads verified that Miscanthus has undergone recent whole genome duplication. Additionally, sequence capture serves as a useful tool for comparative genomics and provides strong evidence that Miscanthus can serve as a satisfactory reference to the closely related, yet highly complex genomes of Saccharum spp.

Name thesis:degree_name

M.S.

Level thesis:degree_level

Thesis

Discipline thesis:degree_discipline

Bioinformatics

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2014

Author dc:creator

• Kirkpatrick, Jessica

Contributors dc:contributor

• Moose, Stephen P.

• Miscanthus
• sequence capture
• Saccharum
• variation
• comparative genomics
• genomics

Statement dc:rights

• Copyright 2013 Jessica Kirkpatrick

Language dc:language

en

Handle dc:identifier

http://hdl.handle.net/2142/46925

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/46925