ArticlePlant physiology2004
A comparison of rice chloroplast genomes.
Article in Plant physiology, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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Who cites it
75 citing papers in PubMed.
- Article
- Plastomic insights into the genetic variation and phylogenetic relationships of Macadamia.Scientific reports · 2025Article
- Chloroplast Genome Variation and Phylogenetic Relationships of Autochthonous Varieties ofInternational journal of molecular sciences · 2024Article
- Characterization, comparison, and phylogenetic analyses of chloroplast genomes of Euphorbia species.Scientific reports · 2024Article
- Phylogenomics and plastomics offer new evolutionary perspectives on Kalanchoideae (Crassulaceae).Annals of botany · 2024Article
- Article
- Comparative Analysis of Chloroplast Pan-Genomes and Transcriptomics Reveals Cold Adaptation inInternational journal of molecular sciences · 2024Article
- The complete chloroplast genome ofMitochondrial DNA. Part B, Resources · 2024Article
- Complete chloroplast genome structural characterization of two Phalaenopsis (Orchidaceae) species and comparative analysis with their alliance.BMC genomics · 2023Article
- The First Complete Chloroplast Genome ofGenes · 2023Article
- Poaceae Chloroplast Genome Sequencing: Great Leap Forward in Recent Ten Years.Current genomics · 2023Review
- Phylogenetic relationship and comparative analysis of the main Bupleuri Radix species in China.PeerJ · 2023Article
- Article
- Genetic Structure and Geographical Differentiation of Traditional Rice (Plants (Basel, Switzerland) · 2021Article
- Plastome genomics in South American maize landraces: chloroplast lineages parallel the geographical structuring of nuclear gene pools.Annals of botany · 2021Article
- The Chloroplast Phylogenomics and Systematics ofPlants (Basel, Switzerland) · 2021Article
- Reference-based QUantification Of gene Dispensability (QUOD).Plant methods · 2021Article
- Resequencing of 1,143 indica rice accessions reveals important genetic variations and different heterosis patterns.Nature communications · 2020Article
- The dynamic evolution of mobile open reading frames in plastomes of Hymenophyllum Sm. and new insight on Hymenophyllum coreanum Nakai.Scientific reports · 2020Article
- Current status of genomic resources on wild relatives of rice.Breeding science · 2020Article
15 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Using high quality sequence reads extracted from our whole genome shotgun repository, we assembled two chloroplast genome sequences from two rice (Oryza sativa) varieties, one from 93-11 (a typical indica variety) and the other from PA64S (an indica-like variety with maternal origin of japonica), which are both parental varieties of the super-hybrid rice, LYP9. Based on the patterns of high sequence coverage, we partitioned chloroplast sequence variations into two classes, intravarietal and intersubspecific polymorphisms. Intravarietal polymorphisms refer to variations within 93-11 or PA64S. Intersubspecific polymorphisms were identified by comparing the major genotypes of the two subspecies represented by 93-11 and PA64S, respectively. Some of the minor genotypes occurring as intravarietal polymorphisms in one variety existed as major genotypes in the other subspecific variety, thus giving rise to intersubspecific polymorphisms. In our study, we found that the intersubspecific variations of 93-11 (indica) and PA64S (japonica) chloroplast genomes consisted of 72 single nucleotide polymorphisms and 27 insertions or deletions. The intersubspecific polymorphism rates between 93-11 and PA64S were 0.05% for single nucleotide polymorphisms and 0.02% for insertions or deletions, nearly 8 and 10 times lower than their respective nuclear genomes. Based on the total number of nucleotide substitutions between the two chloroplast genomes, we dated the divergence of indica and japonica chloroplast genomes as occurring approximately 86,000 to 200,000 years ago.
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