Comparative analysis of a transposon-rich Brassica oleracea BAC clone with its corresponding sequence in A-thaliana

Gao, M. Q., Li, G. Y., McCombie, W. R., Quiros, C. F. (2005) Comparative analysis of a transposon-rich Brassica oleracea BAC clone with its corresponding sequence in A-thaliana. Theoretical and Applied Genetics, 111 (5). pp. 949-955. ISSN 0040-5752

URL: http://www.ncbi.nlm.nih.gov/pubmed/16044267
DOI: 10.1007/s00122-005-0029-9

Abstract

We compared the sequence of a 96.7 Kb-long BAC clone (B19N3) from Brassica oleracea (broccoli) with its corresponding regions in Arabidopsis thaliana. B19N3 contains eight genes and 5 transposable elements (TEs). The first two genes in this clone, Bo1 and Bo2, have its corresponding region at the end of chromosome V of Arabidopsis (24 Mb). The third gene, Bo3, corresponds to an ortholog at the opposite end (2.6 Mb) of the same chromosome. The other five genes, Bo4 to Bo8 also have a corresponding region on the same chromosome but at 7.7 Mb. These five genes are colinear with those found in the corresponding region of Arabidopsis, which contains, however, 15 genes. Therefore, a cluster of 10 genes is missing in B. oleracea clone (B19M). All five genes in common have the same order and orientation in the genomes of both species. Their 36 exons constituting the eight homologous genes have high conservation in size and sequence identity in both species. Among these, there is a major gene involved in aliphatic glucosinolate biosynthesis, BoGSL-ELONG (Bo4). Similar to A. thaliana, this gene, has a tandem duplicate, Bo5. A contig for this region was constructed by primer walking and BAC-end-sequencing, revealing general gene colinearity between both species. During the 20 million years separating A. thaliana from B. oleracea from a common ancestor both genomes have diverged by chromosomal rearrangements and differential TE activity. These events, in addition to changes in chromosome number are responsible for the evolution of the genomes of both species. In spite of these changes, both species conserve general colinearity for their corresponding genes.

Item Type: Paper
Uncontrolled Keywords: arabidopsis thaliana comparative map maize genome REGIONS retrotransposons ORGANIZATION prediction EVOLUTION pathway segment broccoli TE
Subjects: bioinformatics > genomics and proteomics > annotation > map annotation
bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > analysis and processing > Sequence Data Processing
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transposons
CSHL Authors:
Communities: CSHL labs > McCombie lab
Depositing User: CSHL Librarian
Date Deposited: 12 Jan 2012 21:59
Last Modified: 11 Apr 2013 19:52
Related URLs:
URI: http://repository.cshl.edu/id/eprint/22575

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