ArticleGenome biology and evolution2011
Loss of different inverted repeat copies from the chloroplast genomes of Pinaceae and cupressophytes and influence of heterotachy on the evaluation of gymnosperm phylogeny.
Article in Genome biology and evolution, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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88 citing papers in PubMed, 155 citations in OpenAlex.
- Chloroplast Phylogenomics and Evolutionary History of the Alpine EndemicInternational journal of molecular sciences · 2026Article
- New generic classification for Korean Peucedanum L. (Apiaceae) species based on deep phylogenomic study.BMC plant biology · 2026Article
- Comparative chloroplast genomics of Hibiscus (Malvaceae) and its phylogenetic implications.BMC plant biology · 2026Article
- The complete chloroplast genome of an ornamental plantMitochondrial DNA. Part B, Resources · 2026Article
- Beyond conservation: the landscape of chloroplast genome rearrangements in angiosperms.The New phytologist · 2025Review
- Genetic characterization and phylogenetic analysis of the Nigella sativa (black seed) plastome.Scientific reports · 2024Article
- Extraction and analysis of high-quality chloroplast DNA with reduced nuclear DNA for medicinal plants.BMC biotechnology · 2024Article
- Extreme Reconfiguration of Plastid Genomes in Papaveraceae: Rearrangements, Gene Loss, Pseudogenization, IR Expansion, and Repeats.International journal of molecular sciences · 2024Article
- Polyphyly ofFrontiers in plant science · 2024Article
- Bioinformatics Analysis ofInternational journal of molecular sciences · 2023Article
- Mitochondrial RNA editing sites affect the phylogenetic reconstruction of gymnosperms.Plant diversity · 2023Article
- Insights into phylogenetic relationships in Pinus inferred from a comparative analysis of complete chloroplast genomes.BMC genomics · 2023Article
- Evolutionary differences in gene loss and pseudogenization among mycoheterotrophic orchids in the tribe Vanilleae (subfamily Vanilloideae).Frontiers in plant science · 2023Article
- A Large Intergenic Spacer Leads to the Increase in Genome Size and Sequential Gene Movement around IR/SC Boundaries in the Chloroplast Genome ofInternational journal of molecular sciences · 2022Article
- The Chloroplast Genome of the Lichen PhotobiontGenes · 2022Article
- Chloroplast Genome Annotation Tools: Prolegomena to the Identification of Inverted Repeats.International journal of molecular sciences · 2022Article
- Evolution of mitochondrial RNA editing in extant gymnosperms.The Plant journal : for cell and molecular biology · 2022Article
- Article
- Comparative genome sequence and phylogenetic analysis of chloroplast for evolutionary relationship amongSaudi journal of biological sciences · 2022Article
- Comparative Plastid Genomics of Green-Colored Dinoflagellates Unveils Parallel Genome Compaction and RNA Editing.Frontiers in plant science · 2022Article
28 more citing papers are in PubMed but not listed here.
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5 authors at 2 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
The relationships among the extant five gymnosperm groups--gnetophytes, Pinaceae, non-Pinaceae conifers (cupressophytes), Ginkgo, and cycads--remain equivocal. To clarify this issue, we sequenced the chloroplast genomes (cpDNAs) from two cupressophytes, Cephalotaxus wilsoniana and Taiwania cryptomerioides, and 53 common chloroplast protein-coding genes from another three cupressophytes, Agathis dammara, Nageia nagi, and Sciadopitys verticillata, and a non-Cycadaceae cycad, Bowenia serrulata. Comparative analyses of 11 conifer cpDNAs revealed that Pinaceae and cupressophytes each lost a different copy of inverted repeats (IRs), which contrasts with the view that the same IR has been lost in all conifers. Based on our structural finding, the character of an IR loss no longer conflicts with the "gnepines" hypothesis (gnetophytes sister to Pinaceae). Chloroplast phylogenomic analyses of amino acid sequences recovered incongruent topologies using different tree-building methods; however, we demonstrated that high heterotachous genes (genes that have highly different rates in different lineages) contributed to the long-branch attraction (LBA) artifact, resulting in incongruence of phylogenomic estimates. Additionally, amino acid compositions appear more heterogeneous in high than low heterotachous genes among the five gymnosperm groups. Removal of high heterotachous genes alleviated the LBA artifact and yielded congruent and robust tree topologies in which gnetophytes and Pinaceae formed a sister clade to cupressophytes (the gnepines hypothesis) and Ginkgo clustered with cycads. Adding more cupressophyte taxa could not improve the accuracy of chloroplast phylogenomics for the five gymnosperm groups. In contrast, removal of high heterotachous genes from data sets is simple and can increase confidence in evaluating the phylogeny of gymnosperms.
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