ArticleGenome biology and evolution2010
Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution.
Article in Genome biology and evolution, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 30 citations in OpenAlex.
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- Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses.Scientific reports · 2017Article
- Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants.Molecular biology and evolution · 2017Article
- Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants.Genome biology and evolution · 2017Article
- Bioinformatics Approach in Plant Genomic Research.Current genomics · 2016Article
- Increasing Metagenomic Resolution of Microbiome Interactions Through Functional Phylogenomics and Bacterial Sub-Communities.Frontiers in genetics · 2016Article
- A Primary Sequence Analysis of the ARGONAUTE Protein Family in Plants.Frontiers in plant science · 2016Article
- Phylotranscriptomic analysis of the origin and early diversification of land plants.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Article
- Chloroplast phylogenomics indicates that Ginkgo biloba is sister to cycads.Genome biology and evolution · 2013Article
- A functional phylogenomic view of the seed plants.PLoS genetics · 2011Article
- What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodon salamanders and 13 other vertebrate clades.BMC evolutionary biology · 2011Article
- Novel tools for an old lineage: Population genomics for cycads.Communicative & integrative biology · 2011Article
- Loss of different inverted repeat copies from the chloroplast genomes of Pinaceae and cupressophytes and influence of heterotachy on the evaluation of gymnosperm phylogeny.Genome biology and evolution · 2011Article
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 1 country.
Funding
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.
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