title: Efficient plant gene identification based on interspecies mapping of full-length cDNAs.
abstract: We present an annotation pipeline that accurately predicts exon-intron structures and protein-coding sequences (CDSs) on the basis of full-length cDNAs (FLcDNAs). This annotation pipeline was used to identify genes in 10 plant genomes. In particular, we show that interspecies mapping of FLcDNAs to genomes is of great value in fully utilizing FLcDNA resources whose availability is limited to several species. Because low sequence conservation at 5'- and 3'-ends of FLcDNAs between different species tends to result in truncated CDSs, we developed an improved algorithm to identify complete CDSs by the extension of both ends of truncated CDSs. Interspecies mapping of 71 801 monocot FLcDNAs to the Oryza sativa genome led to the detection of 22 142 protein-coding regions. Moreover, in comparing two mapping programs and three ab initio prediction programs, we found that our pipeline was more capable of identifying complete CDSs. As demonstrated by monocot interspecies mapping, in which nucleotide identity between FLcDNAs and the genome was ∼80%, the resultant inferred CDSs were sufficiently accurate. Finally, we applied both inter- and intraspecies mapping to 10 monocot and dicot genomes and identified genes in 210 551 loci. Interspecies mapping of FLcDNAs is expected to effectively predict genes and CDSs in newly sequenced genomes.
authors.affiliation: Bioinformatics Research Unit, Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan.
authors.forename: Naoki
authors.initials: N
authors.lastname: Amano
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Tanaka
authors.forename: Hisataka
authors.initials: H
authors.lastname: Numa
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Sakai
authors.forename: Takeshi
authors.initials: T
authors.lastname: Itoh
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D019295:Computational Biology; D018548:Cotyledon / Q000033:anatomy & histology; D020732:Cytogenetic Analysis; D018076:DNA, Complementary; D018744:DNA, Plant / Q000235:genetics*; D030541:Databases, Genetic; D005091:Exons; D005544:Forecasting; D015723:Gene Library; D017343:Genes, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D007438:Introns; D008957:Models, Genetic; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D012275:Oryza / Q000235:genetics; D010944:Plants / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D018076:DNA, Complementary; D018744:DNA, Plant