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Abstract Detail

Genomics / Proteomics

dePamphilis, Claude [1], Wickett, Norman [2], Duarte, JIll [3], Der, Joshua [4], McCain, Michael [5], Leebens-Mack, Jim [6], Edger, Patrick [7], Pires, Joseph [8], Wafula, Eric [9], Zhang, Yeting [10], Ayyampalayam, Saravanaraj [11], Barrett, Craig [12], Davis, Jerrold [13], Graham, Sean [14], McCombie, Richard [15], Zomlefer, Wendy [16], Stevenson, Dennis [17], Givnish, Thomas [18].

Large-scale transcriptome sequencing and phylogenetic hypotheses for monocots based on analyses 970 (and up to 1888) low copy nuclear genes.

With more than 20% of angiosperm species occupying a wide diversity of terrestrial and aquatic habitats, and diverse structure, physiology, and biochemistry, the monocots represent one of the major radiations of flowering plants. The Monocot Tree of Life Project (MonATOL) is using a wide range of data to generate phylogenetic hypotheses and work to understand monocot evolutionary history. Here, we focus on the analysis of large transcriptome datasets that we are generating from across the ordinal diversity of monocots. Using Illumina paired-end sequencing of cDNA libraries constructed from young leaf tissue RNAs, we are obtaining tens of millions of sequence reads that represent the large majority of leaf expressed genes in each species. Following de novo assembly of the transcriptome sequence data and sorting of genes into a preclassified scaffold of protein-coding genes based on sequenced plant genomes, a variety of analyses are being used to explore phylogenetic history, with a focus on 970 single or low copy nuclear genes across angiosperms or up to 1888 single or low copy nuclear genes in monocots. Analysis including 44 species representing 29 families and 10 orders confirm many aspects of phylogenetic history obtained from plastid genomes, including monophyly of extant monocots, and the relationships of a majority of well studied ordinal groups, with a number of interesting differences between plastome and nuclear gene hypotheses. The data are also providing a massive resource for exploring the history of ancient gene and genome duplications, the evolution of biochemical pathways, molecular evolutionary dynamics, and the history of developmental regulators throughout the monocots. Transcriptome sequencing is the most economical route to large-scale gene discovery and a vastly improved understanding of molecular evolutionary history in plants.

Broader Impacts:

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1 - Pennsylvania State University, Department Of Biology, 101 LIFE SCIENCES BUILDING, UNIVERSITY PARK, PA, 16802, USA
2 - Chicago Botanic Garden, Department Of Ecology & Evolutionary Biology, 5108 N Ashland Ave, Apt 2, Chicago, IL, 60640, USA
3 - 403 Life Sciences Bldg, University Park, PA, 16802, USA
4 - Penn State University, Department Of Biology, 201 Life Sciences Building, University Park, PA, 16802, USA
5 - University of Georgia, Plant Biology, Athens, GA, 30602
6 - University of Georgia, 2502 Miller Plant Sciences, Athens, GA, 30602, USA
7 - University of Missouri - Columbia, Biological Sciences, 311 Life Science Center, 1201 E Rollins Rd, Columbia, MO, 65211, USA
8 - University Of Missouri, 371 Bond Life Sciences Center, 1201 Rollins Street, Columbia, MO, 65211-7310, USA
9 - Penn State University, Biology, University Park, PA, 16802, USA
10 - Penn State University, Genetics, University Park, PA, 16802, USA
11 - University of Georgia, Plant Biology, Athens, GA, 30602, USA
12 - Cornell University, Department of Plant Biology, 412 Mann Library Building , Ithaca, NY, 14853, USA
14 - University of British Columbia, Botanical Garden and Centre for Plant Research, Vancouver, BC, V6T 1Z4, Canada
15 -
16 - University Of Georgia, Department Of Plant Biology, 2052 Miller Plant Sciences Building, 120 Carlton Street, Athens, GA, 30602, USA
17 - THE NY BOTANICAL GARDEN, 2900 SOUTHERN BLVD, BRONX, NY, 10458-5126, USA, 718/817-8632
18 - University Of Wisconsin, Department Of Botany, Birge Hall, 430 Lincoln Drive, Madison, WI, 53706, USA

Single/low copy nuclear genes.

Presentation Type: Oral Paper:Papers for Topics
Session: 44
Location: Union B/Hyatt
Date: Wednesday, July 11th, 2012
Time: 11:00 AM
Number: 44012
Abstract ID:968

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