ArticleGenetics2007
Comparative physical mapping between Oryza sativa (AA genome type) and O. punctata (BB genome type).
Article in Genetics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- A robust 1K-core marker set for wild germplasm management and targeted pre-breeding of rice: development and applications.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice.Nature communications · 2023Article
- Phylogenetic analysis of endogenous viral elements in the rice genome reveals local chromosomal evolution inFrontiers in plant science · 2023Article
- Article
- Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.Nature genetics · 2018Article
- Development of Oryza sativa L. by Oryza punctata Kotschy ex Steud. monosomic addition lines with high value traits by interspecific hybridization.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2016Article
- Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data.Scientific data · 2016Article
- A simple method for semi-random DNA amplicon fragmentation using the methylation-dependent restriction enzyme MspJI.BMC biotechnology · 2015Article
- Analysis of BAC-end sequences in common bean (Phaseolus vulgaris L.) towards the development and characterization of long motifs SSRs.Plant molecular biology · 2014Article
- Global genomic diversity of Oryza sativa varieties revealed by comparative physical mapping.Genetics · 2014Article
- A BAC based physical map and genome survey of the rice false smut fungus Villosiclava virens.BMC genomics · 2013Article
- Genomic resources for gene discovery, functional genome annotation, and evolutionary studies of maize and its close relatives.Genetics · 2013Article
- Role of transposon-derived small RNAs in the interplay between genomes and parasitic DNA in rice.PLoS genetics · 2012Article
- Integration of the Draft Sequence and Physical Map as a Framework for Genomic Research in Soybean (Glycine max (L.) Merr.) and Wild Soybean (Glycine soja Sieb. and Zucc.).G3 (Bethesda, Md.) · 2012Article
- Comparative sequence analysis of the Ghd7 orthologous regions revealed movement of Ghd7 in the grass genomes.PloS one · 2012Article
- A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure.Genome biology · 2011Article
- An integrated physical, genetic and cytogenetic map of Brachypodium distachyon, a model system for grass research.PloS one · 2010Article
- Integration of physical and genetic maps of common bean through BAC-derived microsatellite markers.BMC genomics · 2010Article
- A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat.BMC genomics · 2009Article
- Sequenced BAC anchored reference genetic map that reconciles the ten individual chromosomes of Brassica rapa.BMC genomics · 2009Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A comparative physical map of the AA genome (Oryza sativa) and the BB genome (O. punctata) was constructed by aligning a physical map of O. punctata, deduced from 63,942 BAC end sequences (BESs) and 34,224 fingerprints, onto the O. sativa genome sequence. The level of conservation of each chromosome between the two species was determined by calculating a ratio of BES alignments. The alignment result suggests more divergence of intergenic and repeat regions in comparison to gene-rich regions. Further, this characteristic enabled localization of heterochromatic and euchromatic regions for each chromosome of both species. The alignment identified 16 locations containing expansions, contractions, inversions, and transpositions. By aligning 40% of the punctata BES on the map, 87% of the punctata FPC map covered 98% of the O. sativa genome sequence. The genome size of O. punctata was estimated to be 8% larger than that of O. sativa with individual chromosome differences of 1.5-16.5%. The sum of expansions and contractions observed in regions >500 kb were similar, suggesting that most of the contractions/expansions contributing to the genome size difference between the two species are small, thus preserving the macro-collinearity between these species, which diverged approximately 2 million years ago.
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