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Abstract Detail


Genomics / Proteomics

Wickett, Norman [1], Leebens-Mack, Jim [2], Carpenter, Eric [3], Mirarab, Siavash [4], Ayyampalayam, Saravanaraj [5], Barker, Mike [6], Burleigh, J. Gordon [7], Gitzendanner, Matthew [8], Gonzales, Michael [3], Matasci, Naim [9], dePamphilis, Claude [10], Ruhfel, Brad [11], Wafula, Eric [12], Warnow, Tandy [13], Chen, Tao [3], Deyholos, Michael [14], Graham, Sean [15], Mathews, Sarah [16], Melkonian, Michael [17], Soltis, Douglas [18], Soltis, Pamela [19], Shaw, Jonathan [20], Stevenson, Dennis [21], Surek, Barbara [17], Villarreal, Juan [22], Zhang, Yong [3], Tian, Zhijian [3], Wong, Gane Ka-Shu [23].

Scaling phylogenomics to over one thousand species: Relationships of Viridiplantae inferred from the 1KP (One Thousand Plants) project pilot data set.

The origin of terrestrial plants (embryophytes) over 450 million years ago is undoubtedly one of the most consequential events in Earth's history. Arising from a streptophytic green algal ancestor, land plants transformed the terrestrial environment and set the stage for the diversification of all life on land. Reconstructing the origin and evolution of embryophytes and their ancestors is essential for understanding how critical adaptations arose, for example the embryo, vascular tissue, seeds, and flowers. Well-resolved relationships for the backbone phylogeny of Viridiplantae (green plants), and within its major lineages, will significantly contribute to reconstructions of the origins of these traits. Inferring phylogenies from molecular data at this scale can be problematic. However, the use of data sampled at the genome level(phylogenomics) should significantly increase the number of characters appropriate for analyses at this breadth of taxon sampling. Recent phylogenomic reconstructions focused on the major divergences of Viridiplantae have resulted in promising, but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of generating genome-scale data. The objective of the 1KP (One Thousand Plants) Initiative is to sequence transcriptomes of 1000 plants, thus providing a vastly denser data set, in terms of taxa and characters, for phylogenetic reconstruction. As of April 2012, 977 transcriptomes have been generated for this project. An additional 200 samples are in the sequencing queue, meaning that the goal of 1000 species will be exceeded. The physical and computational processing of this volume of data is challenging; here, we describe the analytical pipelines that have been put in place for this project, with an emphasis on a pilot data set of 86 species. For each transcriptome of the pilot set, a de novo assembly was performed, followed by robust translation step to generate reliable reading frames and amino acid sequences for downstream analysis. Each assembly was sorted into an a priori scaffold of gene families and the populated gene families were aligned for phylogenetic analysis. After filtering out poorly populated gene families, we arrived at a set of 9610 gene families to infer the relationships of Viridiplantae. All major lineages of green plants are represented in the pilot set, allowing us to not only reconstruct the phylogeny with an unprecedented amount of data, but to also assess the scalability of these analyses as we begin to process over 1000 transcriptomes.

Broader Impacts:


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Related Links:
The 1KP Project


1 - Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
2 - University Of Georgia, 4503 Miller Plant Sciences, Athens, GA, 30602, USA
3 -
4 - University of Texas, Computer Science
5 - University of Georgia, Plant Biology, Miller Plant Sciences, Athens, GA, 30602, USA
6 - University of Arizona, Ecology and Evolutionary Biology, BioSciences West 321E, Tucson, AZ, 85721, USA
7 - University Of Florida, Biology, Gainesville, FL, 32611, USA
8 - University Of Florida, Florida Museum Of Natural History, PO BOX 117800, GAINSVILLE, FL, 32611-7800, USA
9 - University Of Arizona, IPlant Collaborative, 1657 East Helen St, Tucson, AZ, 85721, USA
10 - Pennsylvania State University, Department Of Biology, 101 LIFE SCIENCES BUILDING, UNIVERSITY PARK, PA, 16802, USA
11 - University Of Florida, Department Of Biology, P.O. Box 118525, Carr Hall, Room 217, Gainesville, FL, 32611, USA
12 - Pennsylvania State University, Biology, 101 Life Sciences Building, University Park, PA, 16802, USA
13 - University of Texas, Computer Sciences
14 - University of Alberta, Biological Sciences
15 - University of British Columbia, Botany
16 - Harvard University, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA, 02138, USA
17 - UNIVERSITY OF COLOGNE, INSTITUTE OF BOTANY, GYRHOFSTR. 15, COLOGNE, 50931, Germany
18 - University Of Florida, Department Of Botany, 220 BARTRAM HALL, Gainesville, FL, 32611, USA
19 - University Of Florida, Florida Museum Of Natural History, PO BOX 117800, Gainesville, FL, 32611-7800, USA, 352/273-1964
20 - 130 Science Drive, Box 90338, Durham, NC, 27708, USA
21 - THE NY BOTANICAL GARDEN, 2900 SOUTHERN BLVD, BRONX, NY, 10458-5126, USA, 718/817-8632
22 - University Of Connecticut, Department Of Ecology & Evolutionary Biology, 75 N. Eagleville Road, Unit 43, Storrs, CT, 06269-3043, USA
23 - University of Alberta, Biology

Keywords:
Genomics
transcriptomes
phylogenomics
green plants
Viridiplantae
land plants
Embryophytes
single/low copy nuclear genes
species tree reconciliation
supertrees.

Presentation Type: Oral Paper:Papers for Topics
Session: 44
Location: Union B/Hyatt
Date: Wednesday, July 11th, 2012
Time: 9:15 AM
Number: 44006
Abstract ID:974


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