ArticlePlant molecular biology2007
A collection of 10,096 indica rice full-length cDNAs reveals highly expressed sequence divergence between Oryza sativa indica and japonica subspecies.
Article in Plant molecular biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Field-crop transcriptome models are enhanced by measurements in systematically controlled environments.Genome biology · 2025Article
- Large-Scale Rice Mutant Establishment and High-Throughput Mutant Manipulation Help Advance Rice Functional Genomics.Plants (Basel, Switzerland) · 2025Review
- Novel QTL Associated with Aerenchyma-Mediated Radial Oxygen Loss (ROL) in Rice (Plants (Basel, Switzerland) · 2022Article
- Early Domestication History of Asian Rice Revealed by Mutations and Genome-Wide Analysis of Gene Genealogies.Rice (New York, N.Y.) · 2022Article
- Non-coding RNA expression analysis revealed the molecular mechanism of flag leaf heterosis in inter-subspecific hybrid rice.Frontiers in plant science · 2022Article
- A New Way of Rice Breeding: Polyploid Rice Breeding.Plants (Basel, Switzerland) · 2021Review
- Rapid and pervasive development- and tissue-specific homeolog expression partitioning in newly formed inter-subspecific rice segmental allotetraploids.BMC genomics · 2018Article
- Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice.Nature genetics · 2018Article
- Identification and molecular characterization of tissue-preferred rice genes and their upstream regularly sequences on a genome-wide level.BMC plant biology · 2014Article
- Genome-wide disruption of gene expression in allopolyploids but not hybrids of rice subspecies.Molecular biology and evolution · 2014Article
- Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica.Genome biology · 2014Article
- Article
- Visual analysis of transcriptome data in the context of anatomical structures and biological networks.Frontiers in plant science · 2012Article
- Advances in omics and bioinformatics tools for systems analyses of plant functions.Plant & cell physiology · 2011Review
- NAD (+) -dependent Formate Dehydrogenase from Plants.Acta naturae · 2011Article
- Efficient plant gene identification based on interspecies mapping of full-length cDNAs.DNA research : an international journal for rapid publication of reports on genes and genomes · 2010Article
- Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq.Genome research · 2010Article
- Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA sequences.BMC plant biology · 2010Article
- Natural and artificial mutants as valuable resources for functional genomics and molecular breeding.International journal of biological sciences · 2010Review
- Genomics and bioinformatics resources for crop improvement.Plant & cell physiology · 2010Review
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21 authors.
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Abstract
Relatively few indica rice full-length cDNAs were available to aid in the annotation of rice genes. The data presented here described the sequencing and analysis of 10,096 full-length cDNAs from Oryza sativa subspecies indica Guangluai 4. Of them, 9,029 matched rice genomic sequences in publicly-available databases, and 1,200 were identified as new rice genes. Comparison with the knowledge-based Oryza Molecular Biological Encyclopedia japonica cDNA collection indicated that 3,316 (41.6%) of the 7,965 indica-japonica cDNA pairs showed no distinct variations at protein level (2,117 indica-japonica cDNA pairs showed fully identical and 1,199 indica-japonica cDNA pairs showed no frame shift). Moreover, 3,645 (45.8%) of the indica-japonica pairs showed substantial differences at the protein level due to single nucleotide polymorphisms (SNPs), insertions or deletions, and sequence-segment variations between indica and japonica subspecies. Further experimental verifications using PCR screening and quantitative reverse transcriptional PCR revealed unique transcripts for indica subspecies. Comparative analysis also showed that most of rice genes were evolved under purifying selection. These variations might distinguish the phenotypic changes of the two cultivated rice subspecies indica and japonica. Analysis of these cDNAs extends known rice genes and identifies new ones in rice.
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