Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs.
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).
Soderlund
Carol
C
BIO5 Institute, University of Arizona, Tucson, Arizona, USA. cari@agcol.arizona.edu
Descour
Anne
A
Kudrna
Dave
D
Bomhoff
Matthew
M
Boyd
Lomax
L
Currie
Jennifer
J
Angelova
Angelina
A
Collura
Kristi
K
Wissotski
Marina
M
Ashley
Elizabeth
E
Morrow
Darren
D
Fernandes
John
J
Walbot
Virginia
V
Yu
Yeisoo
Y
D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D032461:Chromosomes, Plant / Q000235:genetics; D020451:Contig Mapping; D004251:DNA Transposable Elements / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics*; D020224:Expressed Sequence Tags; D017343:Genes, Plant / Q000235:genetics; D020407:Internet; D018598:Minisatellite Repeats / Q000235:genetics; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics; D010940:Plant Proteins / Q000378:metabolism; D011061:Poly A / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D032107:Populus / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D045868:Sorghum / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics; D003313:Zea mays / Q000235:genetics*
D004251:DNA Transposable Elements; D018076:DNA, Complementary; D010940:Plant Proteins; D014157:Transcription Factors; D011061:Poly A