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Abstract Detail

Genomics / Proteomics

Straub, Shannon C.K. [1], Bailey, C. Donovan [2], Cronn, Richard C. [3], Fishbein, Mark [4], Liston, Aaron [5].

Challenges of using transcriptomes for comparative gene family evolution: Examples from Apocynaceae.

The rate of plant transcriptome sequencing has been rapidly increasing over the last several years, resulting in a wealth of data that can be used for comparative analyses. The expansion and contraction of gene families in different lineages can contribute to the biological differences observed among them. Complete genome sequences are traditionally used to analyze these changes because they allow detection of gene family members regardless of their expression in a particular tissue or developmental stage. However, with appropriate controls for data quality and completeness, transcriptome comparisons can be effectively utilized. In order to identify gene families that have significantly expanded in milkweeds, leaf and bud transcriptomes of common milkweed, Asclepias syriaca (Apocynaceae), were sequenced and characterized. Publicly available transcriptomes of three other species of Apocynaceae (Catharanthus roseus, Rhazya stricta, Rauvolfia serpentina) were characterized using the same pipeline. Significant overlap of gene family representation indicated that all transcriptomes were relatively complete and comparable with more than 5,600 gene families present in each. When analyzed in the phylogenetic context provided by these other transcriptomes, the gene family member complement of over 800 gene families has significantly increased in the Asclepias lineage. Members of some of these gene families are involved in biochemical pathways for the production of secondary chemicals and pigments that are likely important in plant reproductive biology and in anti-herbivore defenses.

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1 - Hobart and William Smith Colleges, Department of Biology, 300 Pulteney St., Geneva, NY, 14456, United States
2 - New Mexico State University, PO Box 30001 MSC 3AF, Las Cruces, NM, 88003, USA
3 - USDA Forest Service, 3200 SW Jefferson Way, Corvallis, OR, 97330, USA
4 - Oklahoma State University, Dept Of Botany, 301 Physical Science, Stillwater, OK, 74078, USA
5 - Oregon State University, Department Of Botany & Plant Pathology, 2082 Cordley Hall, Corvallis, OR, 97331-2902, USA, 541/737-5301

gene family evolution
Comparative Genomics.

Presentation Type: Oral Paper:Papers for Topics
Session: 39
Location: Salon 19/20/The Shaw Conference Centre
Date: Tuesday, July 28th, 2015
Time: 9:00 AM
Number: 39001
Abstract ID:166
Candidate for Awards:None

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