Liston, Aaron .
Simultaneous sequencing of hundreds of nuclear loci for phylogenetic analyses across Rosaceae: A next generation sequencing approach.
Phylogenetic reconstruction using organelles or small numbers of nuclear loci often fails to accurately reconstruct organismal relationships, especially in groups with high rates of speciation and/or reticulate evolution, such as Rosaceae. The apple, peach and strawberry genomes have been sequenced, and these genera represent 3 of the 4 lineages of the family. To simultaneously obtain sequence data from hundreds of nuclear loci, probes were designed for solution hybridization-based target enrichment followed by sequencing on the Illumina HiSeq platform (Hyb-Seq). Conserved orthologous exons (<15% sequence divergence in pairwise comparisons across the three genomes and >10% divergence among loci in a genome) were targeted from 257 single-copy nuclear loci in strawberry and peach. Due to a lineage-specific genome duplication and a highly heterozygous genotype, most loci are represented by two or more copies in apple; a single sequence from each paralogous locus was retained. The average locus is 1704 bp in length and includes 1-20 exons (mean = 5.3). The strawberry, peach and apple probe sets will be used individually, and in combination, to test the performance of Hyb-Seq in taxonomically diverse species representing the four lineages of Rosaceae. The approach described here can be applied in other plant families, utilizing genomes and transcriptomes that are rapidly becoming available.
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1 - Oregon State University, Department Of Botany & Plant Pathology, 2082 Cordley Hall, Corvallis, OR, 97331-2902, USA, 541/737-5301
Single/low copy nuclear genes
next generation sequencing
Presentation Type: Oral Paper:Papers for Sections
Location: Delaware D/Hyatt
Date: Wednesday, July 11th, 2012
Time: 8:15 AM