Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana

Lin, Xiaoying; Kaul, Samir; Rounsley, Steve; Shea, Terrance; Benito, Maria-Inés; Town, Christopher D.; Fujii, Claire; Mason, Tanya; Bowman, Cheryl L.; Barnstead, Mary; Feldblyum, Tamara; Buell, C. Robin; Ketchum, Karen A.; Lee, John; Ronning, Catherine M.; Koo, Hean; Moffat, Kelly; Cronin, Lisa A.; Shen, Mian; Pai, Grace; Aken, Susan Van; Umayam, Lowell; Tallon, Luke J.; Gill, John; Adams, Mark D.; Carrera, Ana J.; Creasy, Todd; Goodman, Howard M.; Somerville, Chris; Copenhaver, Gregory P.; Preuss, Daphne; Nierman, William C.; White, Owen; Eisen, Jonathan A.; Salzberg, Steven L.; Fraser, Claire M.; Venter, J. Craig

doi:10.1038/45471

Cited by 672 publications

(416 citation statements)

References 47 publications

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“…the sequences of Neisseria meningitidis [57], D. radiodurans [58], Drosophila melanogaster [59], chromosomes 2 and 4 from Arabidopsis thaliana [60,61], chromosomes 2 and 3 from Plasmodium falciparum [62,63], and chromosomes 21 and 22 from Homo sapiens [64,65] that were recently reported. For the few cases of homologies to these organisms, refer to [37^49].…”

Section: F Tekaia Et Al/febs Letters 487 (2000) 17^30mentioning

confidence: 93%

Genomic Exploration of the Hemiascomycetous Yeasts: 3. Methods and strategies used for sequence analysis and annotation

et al. 2000

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The primary analysis of the sequences for our Hemiascomycete random sequence tag (RST) project was performed using a combination of classical methods for sequence comparison and contig assembly, and of specifically written scripts and computer visualization routines. Comparisons were performed first against DNA and protein sequences from Saccharomyces cerevisiae, then against protein sequences from other completely sequenced organisms and, finally, against protein sequences from all other organisms. Blast alignments were individually inspected to help recognize genes within our random genomic sequences despite the fact that only parts of them were available. For each yeast species, validated alignments were used to infer the proper genetic code, to determine codon usage preferences and to calculate their degree of sequence divergence with S. cerevisiae. The quality of each genomic library was monitored from contig analysis of the DNA sequences. Annotated sequences were submitted to the EMBL database, and the general annotation tables produced served as a basis for our comparative description of the evolution, redundancy and function of the Hemiascomycete genomes described in other articles of this issue. ß

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Section: F Tekaia Et Al/febs Letters 487 (2000) 17^30mentioning

confidence: 93%

Genomic Exploration of the Hemiascomycetous Yeasts: 3. Methods and strategies used for sequence analysis and annotation

et al. 2000

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“…In Arabidopsis thaliana, an insertion of 270-kb mtDNA was found in the pericentromeric region on the short arm of chromosome 2 (Lin et al 1999). DNA fiber-based FISH analyses revealed that the mtDNA insert is 620 kb, 2.3 times greater than that determined by contig assembly and sequencing analysis (Stupar et al 2001).…”

Section: Satellite Dnas Are a Major Component Of Cucumis Centromeresmentioning

confidence: 99%

Molecular cytogenetic mapping of Cucumis sativus and C. melo using highly repetitive DNA sequences

et al. 2010

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Chromosomes often serve as one of the most important molecular aspects of studying the evolution of species. Indeed, most of the crucial mutations that led to differentiation of species during the evolution have occurred at the chromosomal level. Furthermore, the analysis of pachytene chromosomes appears to be an invaluable tool for the study of evolution due to its effectiveness in chromosome identification and precise physical gene mapping. By applying fluorescence in situ hybridization of 45S rDNA and CsCent1 probes to cucumber pachytene chromosomes, here, we demonstrate that cucumber chromosomes 1 and 2 may have evolved from fusions of ancestral karyotype with chromosome number n= 12. This conclusion is further supported by the centromeric sequence similarity between cucumber and melon, which suggests that these sequences evolved from a common ancestor. It may be after or during speciation that these sequences were specifically amplified, after which they diverged and specific sequence variants were homogenized. Additionally, a structural change on the centromeric region of

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“…The sequences of chromosome 2 and 4 were first released in 1999 (Lin et al, 1999;Mayer et al, 1999), and the remaining three chromosomes were sequenced by the end of 2000 (Salanoubat et al, 2000;Tabata et al, 2000;Theologis et al, 2000). This provides scientists a wealth of information and knowledge with which to understand plant biology from a genomic perspective.…”

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confidence: 99%

Cloning and Sequencing of cDNAs for Hypothetical Genes from Chromosome 2 of Arabidopsis,

Xiao¹,

Malik²,

Whitelaw³

et al. 2002

Plant Physiology

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About 25% of the genes in the fully sequenced and annotated Arabidopsis genome have structures that are predicted solely by computer algorithms with no support from either nucleic acid or protein homologs from other species or expressed sequence matches from Arabidopsis. These are referred to as "hypothetical genes." On chromosome 2, sequenced by The Institute for Genomic Research, there are approximately 800 hypothetical genes among a total of approximately 4,100 genes. To test their expression under various growth conditions and in specific tissues, we used six cDNA populations prepared from cold-treated, heat-treated, and pathogen (Xanthomonas campestris pv campestris)-infected plants, callus, roots, and young seedlings. To date, 169 hypothetical genes were tested, and 138 of them are found to be expressed in one or more of the six cDNA populations. By sequencing multiple clones from each 5Ј-and 3Ј-rapid amplification of cDNA ends (RACE) product and assembling the sequences, we generated full-length sequences for 16 of these genes. For 14 genes, there was one full-length assembly that precisely supported the intron-exon boundaries of their gene predictions, adding only 5Ј-and 3Ј-untranslated region sequences. However, for three of these genes, the other assemblies represent additional exons and alternatively spliced or unspliced introns. For the remaining two genes, the cDNA sequences reveal major differences with predicted gene structures. In addition, a total of six genes displayed more than one polyadenylation site. These data will be used to update gene models in The Institute for Genomic Research annotation database ATH1.With the combined efforts of scientists from Europe, Japan, and the United States, the first higher plant genome-sequencing project, whole-genome sequencing of Arabidopsis has been completed. The sequences of chromosome 2 and 4 were first released in 1999 (Lin et al., 1999;Mayer et al., 1999), and the remaining three chromosomes were sequenced by the end of 2000 (Salanoubat et al., 2000;Tabata et al., 2000;Theologis et al., 2000). This provides scientists a wealth of information and knowledge with which to understand plant biology from a genomic perspective. The whole Arabidopsis genome encodes approximately 25,000 genes (The Arabidopsis Genome Initiative, 2000) and the functional analysis of these genes is a major challenge in this post-sequencing era. One approach to this, taken by several groups (Ceres, Stanford Genome Center, Salk Institute, Plant Gene Expression Center [in collaboration with RIKEN Genomic Sciences Center], and Institut National de la Recherche Agronomique/Genoplante) is to produce full-length cDNAs for all of the 25,000ϩ genes in the Arabidopsis genome, because these complete sequences are essential to fully understand their structure and function (Seki et al., 2001a(Seki et al., , 2001b. Recent comparison of full-length cDNAs from Ceres and SSP with previous genomic annotation revealed that the structures of about one-third of the genes could be improved based on c...

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Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana

Cited by 672 publications

References 47 publications

Genomic Exploration of the Hemiascomycetous Yeasts: 3. Methods and strategies used for sequence analysis and annotation

Genomic Exploration of the Hemiascomycetous Yeasts: 3. Methods and strategies used for sequence analysis and annotation

Molecular cytogenetic mapping of Cucumis sativus and C. melo using highly repetitive DNA sequences

Cloning and Sequencing of cDNAs for Hypothetical Genes from Chromosome 2 of Arabidopsis,

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