Open AccessGlobal transcript analysis of rice leaf and seed using SAGE technology
Author(s) -
Gibbings J. George,
Cook Brian P.,
Dufault Michael R.,
Madden Stephen L.,
Khuri Sawsan,
Turnbull Chris J.,
Dunwell Jim M.
Publication year - 2003
Publication title -
plant biotechnology journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.525
H-Index - 115
eISSN - 1467-7652
pISSN - 1467-7644
DOI - 10.1046/j.1467-7652.2003.00026.x
Subject(s) - biology , oryza sativa , serial analysis of gene expression , gene , gene expression , expressed sequence tag , genetically modified rice , sage , genetics , transcriptome , transgene , database , genetically modified crops , physics , nuclear physics , computer science
Summary We have compiled two comprehensive gene expression profiles from mature leaf and immature seed tissue of rice ( Oryza sativa ssp. japonica cultivar Nipponbare) using Serial Analysis of Gene Expression (SAGE) technology. Analysis revealed a total of 50 519 SAGE tags, corresponding to 15 131 unique transcripts. Of these, the large majority (∼70%) occur only once in both libraries. Unexpectedly, the most abundant transcript (∼3% of the total) in the leaf library was derived from a type 3 metallothionein gene. The overall frequency profiles of the abundant tag species from both tissues differ greatly and reveal seed tissue as exhibiting a non‐typical pattern of gene expression characterized by an over abundance of a small number of transcripts coding for storage proteins. A high proportion (∼80%) of the abundant tags (≥ 9) matched entries in our reference rice EST database, with many fewer matches for low abundant tags. Singleton transcripts that are common to both tissues were collated to generate a summary of low abundant transcripts that are expressed constitutively in rice tissues. Finally and most surprisingly, a significant number of tags were found to code for antisense transcripts, a finding that suggests a novel mechanism of gene regulation, and may have implications for the use of antisense constructs in transgenic technology.