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Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
The experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation. Expand
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data
A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Expand
The TIGR Rice Genome Annotation Resource: improvements and new features
  • S. Ouyang, Wei Zhu, +11 authors C. Buell
  • Medicine, Computer Science
  • Nucleic Acids Res.
  • 1 December 2006
Through incorporation of multiple transcript and proteomic expression data sets, the Institute for Genomic Research has been able to annotate 24 799 genes (31 739 gene models), representing ∼50% of the total gene models, as expressed in the rice genome. Expand
Genome-wide atlas of transcription during maize development.
A comprehensive atlas of global transcription profiles across developmental stages and plant organs is presented, and it is found that expansion of distinct gene families was accompanied by divergent, tissue-specific transcription patterns of the paralogs. Expand
The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000
The complete genome sequence of the model bacterial pathogen Pseudomonas syringae pathovar tomato DC3000 (DC3000), which is pathogenic on tomato and Arabidopsis thaliana, is reported and 1,159 genes unique to DC3000 are revealed, of which 811 lack a known function. Expand
Genome sequence and analysis of the tuber crop potato
The potato genome sequence provides a platform for genetic improvement of this vital crop and predicts 39,031 protein-coding genes and presents evidence for at least two genome duplication events indicative of a palaeopolyploid origin. Expand
The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants
Four databases of repetitive sequences have been combined into four databases to represent the Brassicaceae, Fabaceae, Gramineae and Solanaceae families to provide a resource for the identification, classification and analysis of repetitive sequence in plants. Expand
Sequencing of a rice centromere uncovers active genes
The results suggest that Cen8 may represent an intermediate stage in the evolution of centromres from genic regions, as in human neocentromeres, to fully mature centromeres that accumulate megabases of homogeneous satellite arrays. Expand
Gene RB cloned from Solanum bulbocastanum confers broad spectrum resistance to potato late blight
The cloning of the major resistance gene RB in S. bulbocastanum is reported by using a map-based approach in combination with a long-range (LR)-PCR strategy, demonstrating that LR-PCR is a valuable approach to isolate genes that cannot be maintained in the bacterial artificial chromosome system. Expand
Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis
Alternative splicing is widespread in both rice and Arabidopsis and these species share many common features, indicating that many isoforms will presumably have negative consequences for protein structure and function, suggesting that their biological role involves post-transcriptional regulation of gene expression. Expand