Phylogenomic Inference Suggests Differential Deep Time Phylogenetic Signals from Nuclear and Organellar Genomes in Gymnosperms
Abstract
1. Introduction
2. Results
2.1. Multiple-Copy Nuclear Gene Families Support the Ginkgo–Cycads Sister Relationship and the Gnepines Hypothesis
2.2. Discordant Mitochondrial and Plastid Phylogenomic Trees
2.3. Mitochondrial RNA Editing Sites Influence on Tree Topology
3. Discussion
4. Materials and Methods
4.1. Data Access
4.2. Classification of Nuclear Multiple-Copy Gene Families and Construction of Gene and Species Trees
4.3. Construction of Mitochondrial and Plastid Trees
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
NCBI | National Center for Biotechnology Information |
CNCB | China National Center for Bioinformation |
References
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Taxonomic Group | Species | BioProject Accession Number | Assembly Level | Size (Gb) |
---|---|---|---|---|
Conifers I | Larix kaempferi | PRJNA587041 N | Scaffold | 10.9 |
Picea abies | PRJEB1822 N | Scaffold | 12 | |
Picea sitchensis | PRJNA304257 N | Scaffold | 20.5 | |
Pinus albicaulis | PRJNA1034085 N | Scaffold | 27.6 | |
Pinus lambertiana | PRJNA174450 N | Scaffold | 27.6 | |
Pinus taeda | PRJNA174450 N | Scaffold | 20.5 | |
Pseudotsuga menziesii | PRJNA174450 N | Scaffold | 14.7 | |
Conifers II | Cryptomeria japonica | PRJDB13806 N | Chromosome | 9 |
Metasequoia glyptostroboides | PRJCA016596 C | Chromosome | 8.1 | |
Nageia nagi * | PRJNA1179671 N | Chromosome | 4.3 | |
Sequoia sempervirens | PRJNA542879 N | Scaffold | 26.5 | |
Sequoiadendron giganteum | PRJNA541481 N | Chromosome | 8.1 | |
Taxus chinensis | PRJNA730337 N | Chromosome | 10.2 | |
Torreya grandis | PRJNA938254 N | Scaffold | 19.1 | |
Cycads | Cycas panzhihuaensis | PRJNA734434 N | Chromosome | 10.5 |
Ginkgo | Ginkgo biloba | PRJCA001755 C | Chromosome | 9.8 |
Gnetophytes | Gnetum montanum | PRJNA339497 N | Scaffold | 2.1 |
Welwitschia mirabilis | PRJCA004995 C | Chromosome | 6.8 |
Genome Dataset | Ginkgo–Cycads | Gnepines | Gnecup |
---|---|---|---|
Nuclear | Yes | Yes | No |
Mito | No | Yes | No |
Plastid | Yes | No | Yes |
ME-genomic | No | No | Yes |
ME-protein | No | No | Yes |
ME-ES * corrected | No | No | Yes |
ME-ES * excluded | No | Yes | No |
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Lin, Y.-E.; Wu, C.-S.; Wu, Y.-W.; Chaw, S.-M. Phylogenomic Inference Suggests Differential Deep Time Phylogenetic Signals from Nuclear and Organellar Genomes in Gymnosperms. Plants 2025, 14, 1335. https://doi.org/10.3390/plants14091335
Lin Y-E, Wu C-S, Wu Y-W, Chaw S-M. Phylogenomic Inference Suggests Differential Deep Time Phylogenetic Signals from Nuclear and Organellar Genomes in Gymnosperms. Plants. 2025; 14(9):1335. https://doi.org/10.3390/plants14091335
Chicago/Turabian StyleLin, Yu-En, Chung-Shien Wu, Yu-Wei Wu, and Shu-Miaw Chaw. 2025. "Phylogenomic Inference Suggests Differential Deep Time Phylogenetic Signals from Nuclear and Organellar Genomes in Gymnosperms" Plants 14, no. 9: 1335. https://doi.org/10.3390/plants14091335
APA StyleLin, Y.-E., Wu, C.-S., Wu, Y.-W., & Chaw, S.-M. (2025). Phylogenomic Inference Suggests Differential Deep Time Phylogenetic Signals from Nuclear and Organellar Genomes in Gymnosperms. Plants, 14(9), 1335. https://doi.org/10.3390/plants14091335