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利用系统发育基因组学模型及基因本体鉴定植物进化相关蛋白  

2012-04-23 09:29:16|  分类: 文献管理 |  标签: |举报 |字号 订阅

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Using Phylogenomic Patterns and Gene Ontology to Identify Proteins of Importance in Plant Evolution

Abstract
We use measures of congruence on a combined expressed sequenced tag genome phylogeny to identify proteins that have potential significance in the evolution of seed plants. Relevant proteins are identified based on the direction of partitioned branch and hidden support on the hypothesis obtained on a 16-species tree, constructed from 2,557 concatenated orthologous genes. We provide a general method for detecting genes or groups of genes that may be under selection in directions that are in agreement with the phylogenetic pattern. Gene partitioning methods and estimates of the degree and direction of support of individual gene partitions to the overall data set are used. Using this approach, we correlate positive branch support of specific genes for key branches in the seed plant phylogeny. In addition to basic metabolic functions, such as photosynthesis or hormones, genes involved in posttranscriptional regulation by small RNAs were significantly overrepresented in key nodes of the phylogeny of seed plants. Two genes in our matrix are of critical importance as they are involved in RNA-dependent regulation, essential during embryo and leaf development. These are Argonaute and the RNA-dependent RNA polymerase 6 found to be overrepresented in the angiosperm clade. We use these genes as examples of our phylogenomics approach and show that identifying partitions or genes in this way provides a platform to explain some of the more interesting organismal differences among species, and in particular, in the evolution of plants.
Keywords: phylogenomics, orthologs, partition metrics, gene ontology, micro-RNAs, small interfering RNAs

Angélica Cibrián-Jaramillo,*?1,2 Jose E. De la Torre-Bárcena,?3 Ernest K. Lee,1 Manpreet S. Katari,3 Damon P. Little,2 Dennis W. Stevenson,2 Rob Martienssen,4 Gloria M. Coruzzi,3 and Rob DeSalle1
1Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York
2Molecular Systematics, The New York Botanical Garden, Bronx, New York
3Center for Genomics and Systems Biology, Department of Biology, New York University
4Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
*Corresponding author: E-mail: acibrian@amnh.org.
?These authors contributed equally to this work.
Associate editor: Michael Purugganan
Accepted March 14, 2010.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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