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Abstract Detail



Genomics / Proteomics

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

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. Rapid expansion and contraction of gene families in independent lineages can give rise to dramatic shifts in biochemical complexity, and ultimately contribute to the differences observed among lineages. 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 anti-herbivore defenses and plant pollinator attraction and pollination fidelity. 


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1 - Oregon State University, Department Of Plant Biology, 2082 Cordley Hall, Corvallis, OR, 97331, USA
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

Keywords:
Transcriptome
Asclepias
Apocynaceae
gene family evolution
Comparative genomics.

Presentation Type: Oral Paper:Papers for Topics
Session: 35
Location: Pines South/Boise Centre
Date: Wednesday, July 30th, 2014
Time: 9:00 AM
Number: 35005
Abstract ID:436
Candidate for Awards:None

Canceled

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