TY - JOUR
T1 - Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing
AU - Meyers, Blake C.
AU - Vu, Tam H.
AU - Tej, Shivakundan Singh
AU - Ghazal, Hassan
AU - Matvienko, Marta
AU - Agrawal, Vikas
AU - Ning, Jianchang
AU - Haudenschild, Christian D.
N1 - Funding Information:
We thank Larry Tindell, Steve Edberg and Tanya Berardini for excellent technical assistance, and Hajime Sakai and Pam Green for critical reading of the manuscript. This work was supported by the National Science Foundation Plant Genome Research award #0110528 (B.C.M.).
PY - 2004/8
Y1 - 2004/8
N2 - Large-scale sequencing of short mRNA-derived tags can establish the qualitative and quantitative characteristics of a complex transcriptome. We sequenced 12,304,362 tags from five diverse libraries of Arabidopsis thaliana using massively parallel signature sequencing (MPSS). A total of 48,572 distinct signatures, each representing a different transcript, were expressed at significant levels. These signatures were compared to the annotation of the A. thaliana genomic sequence; in the five libraries, this comparison yielded between 17,353 and 18,361 genes with sense expression, and between 5,487 and 8,729 genes with antisense expression. An additional 6,691 MPSS signatures mapped to unannotated regions of the genome. Expression was demonstrated for 1,168 genes for which expression data were previously unknown. Alternative polyadenylation was observed for more than 25% of A. thaliana genes transcribed in these libraries. The MPSS expression data suggest that the A. thaliana transcriptome is complex and contains many as-yet uncharacterized variants of normal coding transcripts.
AB - Large-scale sequencing of short mRNA-derived tags can establish the qualitative and quantitative characteristics of a complex transcriptome. We sequenced 12,304,362 tags from five diverse libraries of Arabidopsis thaliana using massively parallel signature sequencing (MPSS). A total of 48,572 distinct signatures, each representing a different transcript, were expressed at significant levels. These signatures were compared to the annotation of the A. thaliana genomic sequence; in the five libraries, this comparison yielded between 17,353 and 18,361 genes with sense expression, and between 5,487 and 8,729 genes with antisense expression. An additional 6,691 MPSS signatures mapped to unannotated regions of the genome. Expression was demonstrated for 1,168 genes for which expression data were previously unknown. Alternative polyadenylation was observed for more than 25% of A. thaliana genes transcribed in these libraries. The MPSS expression data suggest that the A. thaliana transcriptome is complex and contains many as-yet uncharacterized variants of normal coding transcripts.
UR - http://www.scopus.com/inward/record.url?scp=3543007130&partnerID=8YFLogxK
U2 - 10.1038/nbt992
DO - 10.1038/nbt992
M3 - Article
C2 - 15247925
AN - SCOPUS:3543007130
SN - 1087-0156
VL - 22
SP - 1006
EP - 1011
JO - Nature Biotechnology
JF - Nature Biotechnology
IS - 8
ER -