Comparing low coverage random shotgun sequence data fromBrassica oleraceaandOryza sativagenome sequence for their ability to add to the annotation ofArabidopsis thaliana

Katari, Manpreet S.; Balija, Vivekanand S.; Wilson, Richard K.; Martienssen, Robert A.; McCombie, W. Richard

doi:10.1101/gr.3239105

Cited by 28 publications

(28 citation statements)

References 59 publications

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“…We estimated that for these segments, approximately 16% of B. oleracea sequence and 10% of B. rapa sequence consist of TEs, which is not far from a global TE estimate of 20% for B. oleracea by Zhang and Wessler (2004) and Katari et al (2005). Of these, approximately 14% correspond to retroelements and 6% to DNA transposons.…”

Section: Discussionmentioning

confidence: 99%

Comparative sequence analysis for Brassica oleracea with similar sequences in B. rapa and Arabidopsis thaliana

Qiu

Gao

et al. 2008

Plant Cell Rep

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We sequenced five BAC clones of Brassica oleracea doubled haploid 'Early Big' broccoli containing major genes in the aliphatic glucosinolate pathway, and comparatively analyzed them with similar sequences in A. thaliana and B. rapa. Additionally, we included in the analysis published sequences from three other B. oleracea BAC clones and a contig of this species corresponding to segments in A. thaliana chromosomes IV and V. A total of 2,946 kb of B. oleracea, 1,069 kb of B. rapa sequence and 2,607 kb of A. thaliana sequence were compared and analyzed. We found conserved collinearity for gene order and content restricted to specific chromosomal segments, but breaks in collinearity were frequent resulting in gene absence likely not due to gene loss but rearrangements. B. oleracea has the lowest gene density of the three species, followed by B. rapa. The genome expansion of the Brassica species, B. oleracea in particular, is due to larger introns and gene spacers resulting from frequent insertion of DNA transposons and retrotransposons. These findings are discussed in relation to the possible origin and evolution of the Brassica genomes.

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Section: Discussionmentioning

confidence: 99%

Comparative sequence analysis for Brassica oleracea with similar sequences in B. rapa and Arabidopsis thaliana

Qiu

Gao

et al. 2008

Plant Cell Rep

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“…gene-finding program, BLAST search etc.) and help to provide a more accurate annotation (Katari et al 2005). Comparative genomics aids discovery and annotation of gene structures and other functionally important sequences in both genomes.…”

Section: Comparative Genomics Improve Genome Annotationmentioning

confidence: 99%

“…Comparative genomics aids discovery and annotation of gene structures and other functionally important sequences in both genomes. About 17% of predicted genes in both Arabidopsis (Katari et al 2005) and rice (http:// www.tigr.org/tdb/e2k1/osa1/riceInfo/info.shtml) were annotated hypothetical genes. Some of these hypothetical genes are artifacts of the annotation algorithms (Das et al 1997).…”

Section: Comparative Genomics Improve Genome Annotationmentioning

confidence: 99%

Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat

et al. 2009

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Brachypodium distachyon (Brachypodium) has been recently recognized as an emerging model system for both comparative and functional genomics in grass species. In this study, 55,221 repeat masked Brachypodium BAC end sequences (BES) were used for comparative analysis against the 12 rice pseudomolecules. The analysis revealed that *26.4% of BES have significant matches with the rice genome and 82.4% of the matches were homologous to known genes. Further analysis of paired-end BES and *1.0 Mb sequences from nine selected BACs proved to be useful in revealing conserved regions and regions that have undergone considerable genomic changes. Differential gene amplification, insertions/deletions and inversions appeared to be the common evolutionary events that caused variations of microcolinearity at different orthologous genomic regions. It was found that *17% of genes in the two genomes are not colinear in the orthologous regions. Analysis of BAC sequences also revealed higher gene density (*9 kb/gene) and lower repeat DNA content (*13.1%) in Brachypodium when compared to the orthologous rice regions, consistent with the smaller size of the Brachypodium genome. The 119 annotated Brachypodium genes were BLASTN compared against the wheat EST database and deletion bin mapped wheat ESTs. About 77% of the genes retrieved significant matches in the EST database, while 9.2% matched to the bin mapped ESTs. In some cases, genes in single Brachypodium BACs matched to multiple ESTs that were mapped to the same deletion bins, suggesting that the Brachypodium genome will be useful for ordering wheat ESTs within the deletion bins and developing specific markers at targeted regions in the wheat genome.

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“…The full-length amino acid sequence of TK59A01 is deduced from the genomic sequence around the EST, TK59A01 (accession no. CO048598; Katari et al, 2005), which is located on chromosome IV between At4g01030 and At4g01040. RPD1 and RPD1-like proteins share similarities throughout their sequences, except for the amino-and carboxyterminal extensions (Fig.…”

Section: Cloning Of the Rpd1 Genementioning

confidence: 99%

A Novel Plant-Specific Family Gene, ROOT PRIMORDIUM DEFECTIVE 1, Is Required for the Maintenance of Active Cell Proliferation

Konishi

Sugiyama

2006

Plant Physiology

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Hypocotyl segments of Arabidopsis (Arabidopsis thaliana) produce adventitious roots in response to exogenously supplied auxin. root primordium defective 1 (rpd1) is a temperature-sensitive mutant isolated on the basis of impairment in this phenomenon. This study describes further phenotypic analysis of the rpd1 mutant and isolation of the RPD1 gene. When adventitious root formation was induced from the rpd1 explants at the restrictive temperature, cell proliferation leading to root promordia formation was initiated at the same time as in wild-type explants. However, development of the root primordia was arrested thereafter in the mutant. Temperature-shift experiments indicated that RPD1 exerts its function before any visible sign of root primordium formation. The expression patterns of the auxin-responsive gene DR5:b-glucuronidase and the cytodifferentiation marker gene SCARECROW suggest that the rpd1 mutation interferes with neither axis formation nor cellular patterning at the initial stage of root primordium development. Taken together with the effect of the rpd1 mutation on callus cell proliferation, these data imply a role for RPD1 in prearranging the maintenance of the active cell proliferation during root primordium development. Positional cloning of the RPD1 gene revealed that it encodes a member of a novel protein family specific to the plant kingdom. Disruption of the RPD1 gene by a T-DNA insertion caused embryogenesis arrest at the globular to transition stages. This phenotype is consistent with the hypothesized function of RPD1 in the maintenance of active cell proliferation.The formation of adventitious and lateral roots is a typical example of de novo postembryonic organogenesis that is achieved through the elaborate regulation of cell proliferation. The process of morphogenesis common to adventitious and lateral roots can be summarized as follows. First, cell proliferation is initiated from quiescent cells in response to endogenous or external stimuli, including auxin (Boerjan et al

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Comparing low coverage random shotgun sequence data fromBrassica oleraceaandOryza sativagenome sequence for their ability to add to the annotation ofArabidopsis thaliana

Cited by 28 publications

References 59 publications

Comparative sequence analysis for Brassica oleracea with similar sequences in B. rapa and Arabidopsis thaliana

Comparative sequence analysis for Brassica oleracea with similar sequences in B. rapa and Arabidopsis thaliana

Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat

A Novel Plant-Specific Family Gene, ROOT PRIMORDIUM DEFECTIVE 1, Is Required for the Maintenance of Active Cell Proliferation

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