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

• Published in: PLoS genetics Vol. 5; no. 11; p. e1000740
• Main Authors: Soderlund, Carol, 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
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.11.2009; Public Library of Science (PLoS)
• Subjects: Abiotic stress; Arabidopsis; Arabidopsis - genetics; Base Sequence; Chromosome Mapping - methods; Chromosomes, Plant - genetics; Cloning; Contig Mapping; Corn; DNA binding proteins; DNA Transposable Elements - genetics; DNA, Complementary - genetics; Expressed Sequence Tags; Gene expression; Genes, Plant - genetics; Genetic aspects; Genetics; Genetics and Genomics/Bioinformatics; Genetics and Genomics/Gene Discovery; Genetics and Genomics/Plant Genomes and Evolution; Genomes; Genomics; Internet; Minisatellite Repeats - genetics; Molecular Sequence Data; Oryza - genetics; Oryza sativa; Physiological aspects; Plant Proteins - metabolism; Poly A - genetics; Polymorphism, Single Nucleotide - genetics; Populus - genetics; Sequence Analysis, DNA - methods; Sequence Homology, Nucleic Acid; Sorghum; Sorghum - genetics; Transcription Factors - genetics; Transposons; Zea mays; Zea mays - genetics
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1000740

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).