Abstract Detail

Recent Topics Posters

Der, Joshua [1], Wafula, Eric [2], Wickett, Norman [3], Ayyampalayam, Saravanaraj [4], Matasci, Naim [5], Leebens-Mack, Jim [6], dePamphilis, Claude [7].

A plant gene family classification and analysis pipeline for comparative genomics.

To meet the needs of an expanding plant genomics community, we have developed an objective gene family classification using the complete predicted protein sequences from 22 sequenced land plant genomes and have developed a suite of modular analysis pipelines to enable the large-scale evolutionary analysis of gene families. Our primary classification circumscribes deeply conserved, but narrowly defined gene lineages (orthogroups). We have further extended this classification with a hierarchical higher-level classification using multiple stringencies (super-orthogroups) and a domain-based functional annotation. We have developed automated pipelines to process large scale user data sets (e.g. de novo transcriptome assemblies or genome annotations not currently included in the classification). These pipelines include modules for frame-shift corrected translation of transcript sequences, classifying sequences into orthogroups and super-orthogroups with homology-based functional annotations, multiple sequence alignment and gene tree inference, and extraction of single copy genes for species tree phylogenomics. To make this resource broadly available to the plant science community without the need for extensive computational resources and advanced bioinformatics expertise, we will be making these pipelines available in the iPlant Discovery Environment. I will provide an overview of our classification and the analytical modules incorporated into our comparative genomics workflow.

1 - Penn State University, Department Of Biology, 201 Life Sciences Building, University Park, PA, 16802, USA
2 - Penn State University, Department of Biology, 201 Life Science Bldg, University Park, Pennsylvania, 16802, United States
3 - Chicago Botanic Garden, 1000 Lake Cook Rd., Apt 2, Glencoe, IL, 60022, USA
4 - University of Georgia, Department of Plant Biology, Athens, GA, 30602, USA
5 - University Of Arizona, IPlant Collaborative, 1657 East Helen St, Tucson, AZ, 85721, USA
6 - University Of Georgia, Plant Biology, 2502 Miller Plant Sciences, Athens, GA, 30602, USA
7 - Pennsylvania State University, Department Of Biology, 101 LIFE SCIENCES BUILDING, UNIVERSITY PARK, PA, 16802, USA

Keywords:
Transcriptome
gene family
iPlant Discovery Environment
Comparative genomics.

Presentation Type: Recent Topics Poster
Session: P
Location: /
Date: Monday, July 28th, 2014
Time: 5:30 PM
Number: PRT026
Abstract ID:1263
Candidate for Awards:None