Analysis of Brassica rapa ESTs: gene discovery and expression patterns of AP2/ERF family genes.
Chinese cabbage (Brassica rapa subsp. pekinensis) is among the most important vegetables and is widely cultivated in world. Genes in the AP2/ERF family encode transcriptional regulators that serve a variety of functions in the plants. Expressed sequence tags (ESTs) are created by partially sequencing randomly isolated gene transcripts and have proved valuable in molecular biology. Starting from the database with 142 947 ESTs of B. rapa, 62 putative AP2/ERF family genes were identified by in silico cloning using the conserved AP2/ERF domain amino acid sequence of Arabidopsis thaliana as a probe. Based on the number of AP2/ERF domains and functions of the genes, the AP2/ERF transcription factors from B. rapa were classified into four subfamilies (DREB, ERF, AP2 and RAV). Using large-scale available EST information as a source of expression data for digital expression profiling, differentially detected genes were identified among diverse plant tissues. Roots contained the largest number of transcripts of the AP2/ERF family genes, followed by leaves and seeds. Only a few of the 62 AP2/ERF family genes were detected in all tissues: most were detected only in some tissues but not in others. The maximum detected was that of BraERF-B2-5, and it was recorded from seed tissue.
Zhuang
Jing
J
Shanghai Academy of Agricultural Sciences, 201106 Shanghai, China.
Xiong
Ai-Sheng
AS
Peng
Ri-He
RH
Gao
Feng
F
Zhu
Bo
B
Zhang
Jian
J
Fu
Xiao-Yan
XY
Jin
Xiao-Feng
XF
Chen
Jian-Min
JM
Zhang
Zhen
Z
Qiao
Yu-Shan
YS
Yao
Quan-Hong
QH
D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics; D029741:Brassica rapa / Q000235:genetics*; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics*; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics*; D009928:Organ Specificity / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism
D010940:Plant Proteins; D014157:Transcription Factors
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