ArticleGenome biology and evolution2012
The complete chloroplast genome of Ginkgo biloba reveals the mechanism of inverted repeat contraction.
Article in Genome biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 61 papers.
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61 citing papers in PubMed, 104 citations in OpenAlex.
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- Characterization of the complete chloroplast genome of Wolffia arrhiza and comparative genomic analysis with relative Wolffia species.Scientific reports · 2024Article
- The Development of Plant Genome Sequencing Technology and Its Conservation and Application in Endangered Gymnosperms.Plants (Basel, Switzerland) · 2023Review
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- Sequencing and Phylogenetic Analysis of the Chloroplast Genome of Three Apricot Species.Genes · 2023Article
- Molecular Characterization and Genetic Diversity of Ginkgo (Plants (Basel, Switzerland) · 2023Article
- Insights into phylogenetic relationships in Pinus inferred from a comparative analysis of complete chloroplast genomes.BMC genomics · 2023Article
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- Fifteen complete chloroplast genomes of Trapa species (Trapaceae): insight into genome structure, comparative analysis and phylogenetic relationships.BMC plant biology · 2022Article
- Comparative Analyses of 3,654 Plastid Genomes Unravel Insights Into Evolutionary Dynamics and Phylogenetic Discordance of Green Plants.Frontiers in plant science · 2022Article
- Comparative and phylogenetic analysis of complete chloroplast genomes from fiveFrontiers in plant science · 2022Article
- Does IR-loss promote plastome structural variation and sequence evolution?Frontiers in plant science · 2022Article
- Loss of the IR region in conifer plastomes: Changes in the selection pressure and substitution rate of protein-coding genes.Ecology and evolution · 2022Article
- The complete plastid genome sequence of the enigmatic moss, Takakia lepidozioides (Takakiopsida, Bryophyta): evolutionary perspectives on the largest collection of genes in mosses and the intensive RNA editing.Plant molecular biology · 2021Article
- The dynamic history of gymnosperm plastomes: Insights from structural characterization, comparative analysis, phylogenomics, and time divergence.The plant genome · 2021Article
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- Comparative plastomic analysis and insights into the phylogeny ofPlant diversity · 2021Article
1 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We determined the complete chloroplast genome (cpDNA) of Ginkgo biloba (common name: ginkgo), the only relict of ginkgophytes from the Triassic Period. The cpDNA molecule of ginkgo is quadripartite and circular, with a length of 156,945 bp, which is 6,458 bp shorter than that of Cycas taitungensis. In ginkgo cpDNA, rpl23 becomes pseudo, only one copy of ycf2 is retained, and there are at least five editing sites. We propose that the retained ycf2 is a duplicate of the ancestral ycf2, and the ancestral one has been lost from the inverted repeat A (IR(A)). This loss event should have occurred and led to the contraction of IRs after ginkgos diverged from other gymnosperms. A novel cluster of three transfer RNA (tRNA) genes, trnY-AUA, trnC-ACA, and trnSeC-UCA, was predicted to be located between trnC-GCA and rpoB of the large single-copy region. Our phylogenetic analysis strongly suggests that the three predicted tRNA genes are duplicates of trnC-GCA. Interestingly, in ginkgo cpDNA, the loss of one ycf2 copy does not significantly elevate the synonymous rate (Ks) of the retained copy, which disagrees with the view of Perry and Wolfe (2002) that one of the two-copy genes is subjected to elevated Ks when its counterpart has been lost. We hypothesize that the loss of one ycf2 is likely recent, and therefore, the acquired Ks of the retained copy is low. Our data reveal that ginkgo possesses several unique features that contribute to our understanding of the cpDNA evolution in seed plants.
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