ArticlePLoS genetics2011
A functional phylogenomic view of the seed plants.
Article in PLoS genetics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed, 152 citations in OpenAlex.
- CAnDI: A New Tool to Investigate Conflict in Homologous Gene Trees and Explain Convergent Trait Evolution.Systematic biology · 2026Article
- Developmentally regulated genes drive phylogenomic splits in ovule evolution.Nature communications · 2025Article
- Phylogenomics of angiosperms based on mitochondrial genes: insights into deep node relationships.BMC biology · 2025Article
- The Systematics and Evolution of Gymnosperms with an Emphasis on a Few Problematic Taxa.Plants (Basel, Switzerland) · 2024Review
- Genome-wide identification and systematic analysis of the HD-Zip gene family and its roles in response to pH in Panax ginseng Meyer.BMC plant biology · 2023Article
- Model Species to Investigate the Origin of Flowers.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Localized Phylogenetic Discordance Among Nuclear Loci Due to Incomplete Lineage Sorting and Introgression in the Family of Cotton and Cacao (Malvaceae).Frontiers in plant science · 2022Article
- Plant ecological genomics at the limits of life in the Atacama Desert.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- The dynamic history of gymnosperm plastomes: Insights from structural characterization, comparative analysis, phylogenomics, and time divergence.The plant genome · 2021Article
- Taxus yunnanensis genome offers insights into gymnosperm phylogeny and taxol production.Communications biology · 2021Article
- Can functional genomic diversity provide novel insights into mechanisms of community assembly? A pilot study from an invaded alpine streambed.Ecology and evolution · 2021Article
- Phylogenomic conflict coincides with rapid morphological innovation.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Diversity Patterns of Bermuda Grass along Latitudinal Gradients at Different Temperatures in Southeastern China.Plants (Basel, Switzerland) · 2020Article
- Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation.American journal of botany · 2020Article
- A large-scale species level dated angiosperm phylogeny for evolutionary and ecological analyses.Biodiversity data journal · 2020Article
- A role forF1000Research · 2020Article
- Small RNA profiling in Pinus pinaster reveals the transcriptome of developing seeds and highlights differences between zygotic and somatic embryos.Scientific reports · 2019Article
- The Role of UV-B light on Small RNA Activity During Grapevine Berry Development.G3 (Bethesda, Md.) · 2019Article
- Maternal small RNAs mediate spatial-temporal regulation of gene expression, imprinting, and seed development inProceedings of the National Academy of Sciences of the United States of America · 2019Article
- A transcriptome-based resolution for a key taxonomic controversy in Cupressaceae.Annals of botany · 2019Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors at 7 institutions in 2 countries.
Funding
Abstract
A novel result of the current research is the development and implementation of a unique functional phylogenomic approach that explores the genomic origins of seed plant diversification. We first use 22,833 sets of orthologs from the nuclear genomes of 101 genera across land plants to reconstruct their phylogenetic relationships. One of the more salient results is the resolution of some enigmatic relationships in seed plant phylogeny, such as the placement of Gnetales as sister to the rest of the gymnosperms. In using this novel phylogenomic approach, we were also able to identify overrepresented functional gene ontology categories in genes that provide positive branch support for major nodes prompting new hypotheses for genes associated with the diversification of angiosperms. For example, RNA interference (RNAi) has played a significant role in the divergence of monocots from other angiosperms, which has experimental support in Arabidopsis and rice. This analysis also implied that the second largest subunit of RNA polymerase IV and V (NRPD2) played a prominent role in the divergence of gymnosperms. This hypothesis is supported by the lack of 24nt siRNA in conifers, the maternal control of small RNA in the seeds of flowering plants, and the emergence of double fertilization in angiosperms. Our approach takes advantage of genomic data to define orthologs, reconstruct relationships, and narrow down candidate genes involved in plant evolution within a phylogenomic view of species' diversification.
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