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EST analysis of the heading leaf of Chinese cabbage (Brassica rapa L. ssp. pekinensis) in the early phase of the heading stage

Published online by Cambridge University Press:  12 February 2007

Gao Rui-Juan
Affiliation:
Beijing Agro-Biotechnology Research Center Beijing 100089, China Biology Department, Capital Normal University, Beijing 100037, China
Dai Da-Peng
Affiliation:
Beijing Agro-Biotechnology Research Center Beijing 100089, China Biology Department, Capital Normal University, Beijing 100037, China
Ma Rong-Cai*
Affiliation:
Beijing Agro-Biotechnology Research Center Beijing 100089, China Biology Department, Capital Normal University, Beijing 100037, China
Cao Ming-Qing
Affiliation:
Beijing Agro-Biotechnology Research Center Beijing 100089, China Biology Department, Capital Normal University, Beijing 100037, China
Yan Yue-Ming
Affiliation:
Biology Department, Capital Normal University, Beijing 100037, China
Wang Ya-Dong
Affiliation:
College of Computational Sciences, Haerbin University of Science and Technology, Haerbin 150000, China
Ren Shi-Jun
Affiliation:
College of Computational Sciences, Haerbin University of Science and Technology, Haerbin 150000, China
Guo Xin-Yu
Affiliation:
Beijing Agricultural Information Research Center Beijing 100089, China
*
*Corresponding author: Email: rcma1@yahoo.com

Abstract

A cDNA library was constructed from the heading leaf in the early phase of the heading stage of Chinese cabbage (Brassica rapa L. ssp. pekinensis). By sequencing the randomly selected clones, 1363 sequences longer than 200 bp were found, with better trace data. After removing the poly(A) and contamination sequences, 1162 ESTs longer than 150 bp were obtained, of which 1102 shared significant similarity with known sequences in protein and nucleotide databases of the National Center for Biotechnology Information (NCBI) as revealed by searches using the BLASTX and BLASTN engines. Functional assignment of the ESTs was based on the method used in the Arabidopsis thaliana genome-sequencing project. About 77% of the putative protein sequences with known biological functions best matched with those of A. thaliana deposited in the non-redundant database of NCBI. These data suggest that Chinese cabbage is closely related to A. thaliana. This result is different from that reported in other Brassica species. At nucleotide level, however, 51% of the ESTs were homologous to those deposited for A. thaliana when all ESTs were searched against the est-others database. In addition, 60 ESTs had no homology with any of the plant gene sequences deposited in GenBank. These ESTs are very important for understanding the unique developmental process of Chinesecabbage and elaborating its genetic mapping. Among the genes with assigned functions, the most abundant representatives were those involved in protein synthesis and energy metabolism. With the 1162 ESTs, 895 non-redundant contigs were generated after being aligned using the Seqman II module of DNAStar software at the threshold of more than 80% homology over a minimum of 40 base pairs. Of these, 723 were singletons containing only one EST sequence, indicating that many kinds of such genes are expressed in the heading leaf of Chinese cabbage. An expression profile of Chinese cabbage heading leaf with the 1162 ESTs was therefore acquired in this work. This could be very useful for uncovering the mechanism of the heading process, which is the most obvious characteristic of Chinese cabbage and perhaps other related species, such as Brassica oleracea. This work could accelerate the finding and characterization of genes specifically expressed in the heading stage of Chinese cabbage.

Type
Research Article
Copyright
Copyright © China Agricultural University and Cambridge University Press 2004

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EST analysis of the heading leaf of Chinese cabbage (Brassica rapa L. ssp. pekinensis) in the early phase of the heading stage
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