Wickett, Norman J , Duarte, Jill , Wafula, Eric , Leebens-Mack, Jim , DE PAMPHILIS , CLAUDE W .
Reconstructing plant phylogenies using the cDNA sequences of over 900 low copy nuclear genes.
The recent advances in Next Generation Sequencing technologies have led to a dramatic increase in the availability of plant transcriptomes that, in addition to their utility in detecting patterns of gene expression, can be mined for phylogenetically informative markers. A scaffold of orthologous gene clusters was created using orthoMCL to cluster the inferred protein sequences of 10 sequenced plant genomes; from this scaffold we identified 970 genes that are single copy in each of seven angiosperm genomes. We sorted both publicly available and newly sequenced transcriptomes, and recently sequence plant genomes into this scaffold and identified putative homologs of these 970 genes. The resultant super matrix consisted of over two million aligned sites and over 800,000 parsimony informative characters. Here, we discuss the phylogenetic hypotheses that result from using the cDNA sequences of these low copy nuclear genes with multiple sets of both taxa and genes.
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1 - Penn State University, Biology, 403 Life Sciences Building, University Park, PA, 16802, USA
2 - Penn State University, 403 Life Sciences Building, University Park, PA, 16802, USA
3 - University Of Georgia, 4503 Miller Plant Sciences, Athens, GA, 30602, USA
4 - Pennsylvania State University, Department Of Biology, 101 LIFE SCIENCES BUILDING, UNIVERSITY PARK, PA, 16802, USA
Next Generation Sequencing
Presentation Type: Oral Paper:Papers for Sections
Location: Lindell B/Chase Park Plaza
Date: Wednesday, July 13th, 2011
Time: 8:30 AM