Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution.

Genome Biology and Evolution
Angelica Cibrian-JaramilloRob Desalle

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 overrep...Continue Reading

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Citations

Jan 15, 2013·Genome Biology and Evolution·Chung-Shien WuYa-Yi Huang
Dec 24, 2011·PLoS Genetics·Ernest K LeeRob Desalle
Nov 30, 2013·Systematic Biology·Pascal-Antoine ChristinErika J Edwards
Feb 24, 2016·Frontiers in Genetics·Angélica Cibrián-Jaramillo, Francisco Barona-Gómez
Feb 5, 2013·Molecular Phylogenetics and Evolution·Elizabeth A Zimmer, Jun Wen
Feb 26, 2014·Molecular Phylogenetics and Evolution·Xiao-Quan Wang, Jin-Hua Ran
Oct 31, 2014·Proceedings of the National Academy of Sciences of the United States of America·Norman J WickettJames Leebens-Mack
Jul 31, 2012·Molecular Phylogenetics and Evolution·Elizabeth A Zimmer, Jun Wen
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Sep 17, 2016·Frontiers in Plant Science·Daniel Rodríguez-LealJean-Philippe Vielle-Calzada
May 2, 2017·Genome Biology and Evolution·Zhen LiYves Van de Peer
Nov 22, 2019·Protein and Peptide Letters·Xuan XiaoWang-Ren Qiu
May 16, 2020·F1000Research·Christopher D Rock
Mar 24, 2017·Molecular Biology and Evolution·Amanda R De La TorrePär K Ingvarsson

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Software Mentioned

NEXUS
ASAP Perl script
ASAP
Sungear
PAUP
OrthologID
Biomaps
VirtualPlant

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