Annotation of the Arabidopsis Genome

Wortman, Jennifer; Haas, Brian J.; Hannick, Linda I.; Smith, Roger K.; Maiti, Rama; Ronning, Catherine M.; Chan, Agnes P.; Yu, Chenglong; Ayele, Mulu; Whitelaw, Catherine A.; White, Owen; Town, Christopher D.

doi:10.1104/pp.103.022251

Cited by 129 publications

(91 citation statements)

References 25 publications

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“…Li et al (2006) make an excellent case for the need for large-scale plant protein localization studies given that, for Arabidopsis, only 48% of the genes have been assigned putative molecular functions, 30% have no predicted molecular functions, and 22% have not yet been annotated. For the majority of these genes that are assigned putative molecular functions, function was predicted from sequence similarity to other genes (Wortman et al, 2003). Worse yet, only 3.5% (917) of all predicted Arabidopsis proteins have had their molecular functions elucidated empirically, while only 5% (1,300) of all predicted Arabidopsis proteins have had their subcellular locations determined empirically.…”

Section: New Gateway-compatible Vectors For Expression Of Autofluoresmentioning

confidence: 99%

New Gateways to Discovery

et al. 2007

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Section: New Gateway-compatible Vectors For Expression Of Autofluoresmentioning

confidence: 99%

New Gateways to Discovery

et al. 2007

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“…The breakdown of TFs into families and the queries used for their identification are shown in Table I. AtTFDB provides hidden Markov models, ClustalW alignments, references, and protein and nucleotide sequences for each family listed and links to the databases Munich Information Center for Protein Sequences (MIPS) Arabidopsis thaliana Database (Schoof et al, 2004), SALK (Borevitz and Ecker, 2004), The Arabidopsis Information Resource (TAIR; Rhee et al, 2003), and The Institute for Genomic Research (TIGR; Wortman et al, 2003) for each gene in the family.…”

Section: Attfdbmentioning

confidence: 99%

AGRIS and AtRegNet. A Platform to Link cis-Regulatory Elements and Transcription Factors into Regulatory Networks

et al. 2006

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Gene regulatory pathways converge at the level of transcription, where interactions among regulatory genes and between regulators and target genes result in the establishment of spatiotemporal patterns of gene expression. The growing identification of direct target genes for key transcription factors (TFs) through traditional and high-throughput experimental approaches has facilitated the elucidation of regulatory networks at the genome level. To integrate this information into a Web-based knowledgebase, we have developed the Arabidopsis Gene Regulatory Information Server (AGRIS). AGRIS, which contains all Arabidopsis (Arabidopsis thaliana) promoter sequences, TFs, and their target genes and functions, provides the scientific community with a platform to establish regulatory networks. AGRIS currently houses three linked databases: AtcisDB (Arabidopsis thaliana cis-regulatory database), AtTFDB (Arabidopsis thaliana transcription factor database), and AtRegNet (Arabidopsis thaliana regulatory network). AtTFDB contains 1,690 Arabidopsis TFs and their sequences (protein and DNA) grouped into 50 (October 2005) families with information on available mutants in the corresponding genes. AtcisDB consists of 25,806 (September 2005) promoter sequences of annotated Arabidopsis genes with a description of putative cis-regulatory elements. AtRegNet links, in direct interactions, several hundred genes with the TFs that control their expression. The current release of AtRegNet contains a total of 187 (September 2005) direct targets for 66 TFs. AGRIS can be accessed at http://Arabidopsis.med.ohio-state.edu.

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“…Ab initio gene predictions were obtained for each BAC, using four different computational gene-finding programs-FGENESH (Solovyev et al 1994), GenemarkHMM (Borodovsky and McIninch 1993), Genscan1 (Burge and Karlin 1997), and GlimmerM (Salzberg et al 1998) (Arabidopsis training data set; Wortman et al 2003). Independently, each BAC was screened against a large Solanaceae EST database (239,593 tomato ESTs, 134,365 potato ESTs, 3181 eggplant ESTs, and 20,738 pepper ESTs; http:/ /www.sgn.cornell.edu/) and against the Arabidopsis proteome.…”

Section: Identification and Sequencing Of Bacsmentioning

confidence: 99%

Sequencing and Comparative Analysis of a Conserved Syntenic Segment in the Solanaceae

Wang

Diehl²,

Wu³

et al. 2008

Genetics

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Comparative genomics is a powerful tool for gaining insight into genomic function and evolution. However, in plants, sequence data that would enable detailed comparisons of both coding and noncoding regions have been limited in availability. Here we report the generation and analysis of sequences for an unduplicated conserved syntenic segment (CSS) in the genomes of five members of the agriculturally important plant family Solanaceae. This CSS includes a 105-kb region of tomato chromosome 2 and orthologous regions of the potato, eggplant, pepper, and petunia genomes. With a total neutral divergence of 0.73-0.78 substitutions/site, these sequences are similar enough that most noncoding regions can be aligned, yet divergent enough to be informative about evolutionary dynamics and selective pressures. The CSS contains 17 distinct genes with generally conserved order and orientation, but with numerous smallscale differences between species. Our analysis indicates that the last common ancestor of these species lived $27-36 million years ago, that more than one-third of short genomic segments (5-15 bp) are under selection, and that more than two-thirds of selected bases fall in noncoding regions. In addition, we identify genes under positive selection and analyze hundreds of conserved noncoding elements. This analysis provides a window into 30 million years of plant evolution in the absence of polyploidization. G ENOME sequences are now rarely studied in isolation, but instead are examined alongside their neighbors on the tree of life. Most animal species of primary research importance in genetics-including human, mouse, Drosophila melanogaster, and Caenorhabditis elegans-now belong to whole ''sequenced clades,'' consisting of at least half a dozen and in some cases more than two dozen sequenced species (e.g., LindbladToh et al. 2005; Rhesus Macaque Genome Sequencing and Analysis Consortium 2007;Clark et al. 2007;Miller et al. 2007;Stark et al. 2007) (http://www. genome.gov/Pages/Research/Sequencing/SeqProposals/ CaenorhabditisSEQ.pdf). The same is true of the model yeast Saccharomyces cerevisiae (Cliften et al. 2003;Kellis et al. 2003). The species within each of these clades are evolutionarily close enough that noncoding as well as coding sequences can be aligned, yet distant enough that genomic comparisons reveal clear signatures of natural selection. In addition, the generally similar physiology, behavior, and genetics of the organisms within each clade help to facilitate comparative analyses. Comparative genomic analyses of sequenced clades have, among other things, allowed for the identification of new genes, regulatory elements, noncoding RNAs, and conserved sequences of unknown function (e.g., Guigó et al. 2003;Kellis et al. 2003;Bejerano et al. 2004;Siepel et al. 2007;Stark et al. 2007 scrambled with respect to the others by millions of years of rearrangement, duplication, insertion, and deletion, further complicating comparative analyses. Consequently, with a few exceptions (Inada et al. 2003;Ma and...

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Annotation of the Arabidopsis Genome

Cited by 129 publications

References 25 publications

New Gateways to Discovery

New Gateways to Discovery

AGRIS and AtRegNet. A Platform to Link cis-Regulatory Elements and Transcription Factors into Regulatory Networks

Sequencing and Comparative Analysis of a Conserved Syntenic Segment in the Solanaceae

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