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PMID: 19936069 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs.

PLoS genetics ·Vol. 5 ·No. 11 ·2009-11-00 ·Pages e1000740

Soderlund C, Descour A, Kudrna D, Bomhoff M, Boyd L, Currie J, Angelova A, Collura K, Wissotski M, Ashley E, Morrow D, Fernandes J, Walbot V, Yu Y

Abstract

Full-length cDNA (FLcDNA) sequencing establishes the precise primary structure of individual gene transcripts. From two libraries representing 27 B73 tissues and abiotic stress treatments, 27,455 high-quality FLcDNAs were sequenced. The average transcript length was 1.44 kb including 218 bases and 321 bases of 5' and 3' UTR, respectively, with 8.6% of the FLcDNAs encoding predicted proteins of fewer than 100 amino acids. Approximately 94% of the FLcDNAs were stringently mapped to the maize genome. Although nearly two-thirds of this genome is composed of transposable elements (TEs), only 5.6% of the FLcDNAs contained TE sequences in coding or UTR regions. Approximately 7.2% of the FLcDNAs are putative transcription factors, suggesting that rare transcripts are well-enriched in our FLcDNA set. Protein similarity searching identified 1,737 maize transcripts not present in rice, sorghum, Arabidopsis, or poplar annotated genes. A strict FLcDNA assembly generated 24,467 non-redundant sequences, of which 88% have non-maize protein matches. The FLcDNAs were also assembled with 41,759 FLcDNAs in GenBank from other projects, where semi-strict parameters were used to identify 13,368 potentially unique non-redundant sequences from this project. The libraries, ESTs, and FLcDNA sequences produced from this project are publicly available. The annotated EST and FLcDNA assemblies are available through the maize FLcDNA web resource (www.maizecdna.org).

MeSH Terms
Arabidopsis/genetics Base Sequence Chromosome Mapping/methods Chromosomes, Plant/genetics Contig Mapping DNA Transposable Elements/genetics DNA, Complementary/genetics Expressed Sequence Tags Genes, Plant/genetics Internet Minisatellite Repeats/genetics Molecular Sequence Data Oryza/genetics Plant Proteins/metabolism Poly A/genetics Polymorphism, Single Nucleotide/genetics Populus/genetics Sequence Analysis, DNA/methods Sequence Homology, Nucleic Acid Sorghum/genetics Transcription Factors/genetics Zea mays/genetics
Chemicals
DNA Transposable Elements DNA, Complementary Plant Proteins Transcription Factors Poly A
Authors & Affiliations
14 authors, click to expand affiliations / ORCID
Soderlund Carol
BIO5 Institute, University of Arizona, Tucson, Arizona, USA. [email protected]
Descour Anne
Kudrna Dave
Bomhoff Matthew
Boyd Lomax
Currie Jennifer
Angelova Angelina
Collura Kristi
Wissotski Marina
Ashley Elizabeth
Morrow Darren
Fernandes John
Walbot Virginia
Yu Yeisoo
Conflict of Interest

The authors have declared that no competing interests exist.

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Article Info
Journal
PLoS genetics
Abbr.
PLoS Genet
ISSN
1553-7404
DOI
10.1371/journal.pgen.1000740
Email
[email protected]
Published
2009-11-00
Epub
2009-00-20
Pages
e1000740
Language
English
Region
United States
NLM ID
101239074
PMCID
PMC2774520
Subset
IM
External Links
PubMed source DOI: 10.1371/journal.pgen.1000740 PMC Full Text View journal details
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