ArticleGenome biology and evolution2016
Large-Scale Comparative Analysis Reveals the Mechanisms Driving Plastomic Compaction, Reduction, and Inversions in Conifers II (Cupressophytes).
Article in Genome biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed.
- Comparative Plastome Analysis ofEcology and evolution · 2026Article
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- Comparative Analysis of Chloroplast Genomes of 19International journal of molecular sciences · 2025Article
- Plastome structure, phylogeny and evolution of plastid genes in Reevesia (Helicteroideae, Malvaceae).Journal of plant research · 2024Article
- A comparative plastome approach enhances the assessment of genetic variation in the Melilotus genus.BMC genomics · 2024Article
- Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae).BMC genomics · 2023Article
- Structural Plastome Evolution in Holoparasitic Hydnoraceae with Special Focus on Inverted and Direct Repeats.Genome biology and evolution · 2022Article
- The dynamic history of gymnosperm plastomes: Insights from structural characterization, comparative analysis, phylogenomics, and time divergence.The plant genome · 2021Article
- Comparative analysis of plastomes in Oxalidaceae: Phylogenetic relationships and potential molecular markers.Plant diversity · 2021Article
- Molecular evolution and SSRs analysis based on the chloroplast genome ofEcology and evolution · 2021Article
- Tight association of genome rearrangements with gene expression in conifer plastomes.BMC plant biology · 2021Article
- Genome skimming and exploration of DNA barcodes for Taiwan endemic cypresses.Scientific reports · 2020Article
- Comparative chloroplast genomics of the genus Taxodium.BMC genomics · 2020Article
- Methods of analysis of chloroplast genomes of CPlant methods · 2020Article
- The Origin and Evolution of Plastid Genome Downsizing in Southern Hemispheric Cypresses (Cupressaceae).Frontiers in plant science · 2020Article
- Plastome Evolution inFrontiers in plant science · 2020Article
- New Insights Into the Plastome Evolution of the Millettioid/Phaseoloid Clade (Papilionoideae, Leguminosae).Frontiers in plant science · 2020Article
- Long-Reads Reveal That the Chloroplast Genome Exists in Two Distinct Versions in Most Plants.Genome biology and evolution · 2019Article
- Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide.Scientific reports · 2019Article
- Comparative Genomic Analysis Reveals the Mechanism Driving the Diversification of Plastomic Structure in Taxaceae Species.Frontiers in genetics · 2019Article
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2 authors.
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Abstract
Conifers II (cupressophytes), comprising about 400 tree species in five families, are the most diverse group of living gymnosperms. Their plastid genomes (plastomes) are highly variable in size and organization, but such variation has never been systematically studied. In this study, we assessed the potential mechanisms underlying the evolution of cupressophyte plastomes. We analyzed the plastomes of 24 representative genera in all of the five cupressophyte families, focusing on their variation in size, noncoding DNA content, and nucleotide substitution rates. Using a tree-based method, we further inferred the ancestral plastomic organizations of internal nodes and evaluated the inversions across the evolutionary history of cupressophytes. Our data showed that variation in plastome size is statistically associated with the dynamics of noncoding DNA content, which results in different degrees of plastomic compactness among the cupressophyte families. The degrees of plastomic inversions also vary among the families, with the number of inversions per genus ranging from 0 in Araucariaceae to 1.27 in Cupressaceae. In addition, we demonstrated that synonymous substitution rates are significantly correlated with plastome size as well as degree of inversions. These data suggest that in cupressophytes, mutation rates play a critical role in driving the evolution of plastomic size while plastomic inversions evolve in a neutral manner.
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