ArticleGenome research2005
Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis.
Article in Genome research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed.
- Nitrogen Signaling Genes andInternational journal of molecular sciences · 2021Article
- Antioxidant defense gene analysis in Brassica oleracea and Trifolium repens exposed to Cd and/or Pb.Environmental science and pollution research international · 2016Article
- Recent progress in the use of 'omics technologies in brassicaceous vegetables.Frontiers in plant science · 2015Review
- Article
- High-density single nucleotide polymorphism (SNP) array mapping in Brassica oleracea: identification of QTL associated with carotenoid variation in broccoli florets.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2014Article
- Intergenomic single nucleotide polymorphisms as a tool for bacterial artificial chromosome contig building of homoeologous Brassica napus regions.BMC genomics · 2014Article
- High-throughput sequencing and de novo assembly of Brassica oleracea var. Capitata L. for transcriptome analysis.PloS one · 2014Article
- Bolbase: a comprehensive genomics database for Brassica oleracea.BMC genomics · 2013Article
- Screening of a Brassica napus bacterial artificial chromosome library using highly parallel single nucleotide polymorphism assays.BMC genomics · 2013Article
- Characterization of a new high copy Stowaway family MITE, BRAMI-1 in Brassica genome.BMC plant biology · 2013Article
- A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations.BMC genomics · 2011Article
- Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa.BMC genomics · 2010Article
- Sequence and structure of Brassica rapa chromosome A3.Genome biology · 2010Article
- Development of public immortal mapping populations, molecular markers and linkage maps for rapid cycling Brassica rapa and B. oleracea.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2009Article
- Genetic map construction and QTL mapping of resistance to blackleg (Leptosphaeria maculans) disease in Australian canola (Brassica napus L.) cultivars.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2009Article
- Development and genetic mapping of microsatellite markers from genome survey sequences in Brassica napus.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2009Article
- Comparative sequence analysis for Brassica oleracea with similar sequences in B. rapa and Arabidopsis thaliana.Plant cell reports · 2009Article
- Development of a set of public SSR markers derived from genomic sequence of a rapid cycling Brassica oleracea L. genotype.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2008Article
- Does sequence polymorphism of FLC paralogues underlie flowering time QTL in Brassica oleracea?TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2008Article
- Progress in understanding and sequencing the genome of Brassica rapa.International journal of plant genomics · 2008Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Through comparative studies of the model organism Arabidopsis thaliana and its close relative Brassica oleracea, we have identified conserved regions that represent potentially functional sequences overlooked by previous Arabidopsis genome annotation methods. A total of 454,274 whole genome shotgun sequences covering 283 Mb (0.44 x) of the estimated 650 Mb Brassica genome were searched against the Arabidopsis genome, and conserved Arabidopsis genome sequences (CAGSs) were identified. Of these 229,735 conserved regions, 167,357 fell within or intersected existing gene models, while 60,378 were located in previously unannotated regions. After removal of sequences matching known proteins, CAGSs that were close to one another were chained together as potentially comprising portions of the same functional unit. This resulted in 27,347 chains of which 15,686 were sufficiently distant from existing gene annotations to be considered a novel conserved unit. Of 192 conserved regions examined, 58 were found to be expressed in our cDNA populations. Rapid amplification of cDNA ends (RACE) was used to obtain potentially full-length transcripts from these 58 regions. The resulting sequences led to the creation of 21 gene models at 17 new Arabidopsis loci and the addition of splice variants or updates to another 19 gene structures. In addition, CAGSs overlapping already annotated genes in Arabidopsis can provide guidance for manual improvement of existing gene models. Published genome-wide expression data based on whole genome tiling arrays and massively parallel signature sequencing were overlaid on the Brassica-Arabidopsis conserved sequences, and 1399 regions of intersection were identified. Collectively our results and these data sets suggest that several thousand new Arabidopsis genes remain to be identified and annotated.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.