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Abstract
BackgroundThe Solanaceae family includes several economically important vegetable crops. The tomato (Solanum lycopersicum) is regarded as a model plant of the Solanaceae family. Recently, a number of tomato resources have been developed in parallel with the ongoing tomato genome sequencing project. In particular, a miniature cultivar, Micro-Tom, is regarded as a model system in tomato genomics, and a number of genomics resources in the Micro-Tom-background, such as ESTs and mutagenized lines, have been established by an international alliance.ResultsTo accelerate the progress in tomato genomics, we developed a collection of fully-sequenced 13,227 Micro-Tom full-length cDNAs. By checking redundant sequences, coding sequences, and chimeric sequences, a set of 11,502 non-redundant full-length cDNAs (nrFLcDNAs) was generated. Analysis of untranslated regions demonstrated that tomato has longer 5'- and 3'-untranslated regions than most other plants but rice. Classification of functions of proteins predicted from the coding sequences demonstrated that nrFLcDNAs covered a broad range of functions. A comparison of nrFLcDNAs with genes of sixteen plants facilitated the identification of tomato genes that are not found in other plants, most of which did not have known protein domains. Mapping of the nrFLcDNAs onto currently available tomato genome sequences facilitated prediction of exon-intron structure. Introns of tomato genes were longer than those of Arabidopsis and rice. According to a comparison of exon sequences between the nrFLcDNAs and the tomato genome sequences, the frequency of nucleotide mismatch in exons between Micro-Tom and the genome-sequencing cultivar (Heinz 1706) was estimated to be 0.061%.ConclusionThe collection of Micro-Tom nrFLcDNAs generated in this study will serve as a valuable genomic tool for plant biologists to bridge the gap between basic and applied studies. The nrFLcDNA sequences will help annotation of the tomato whole-genome sequence and aid in tomato functional genomics and molecular breeding. Full-length cDNA sequences and their annotations are provided in the database KaFTom http://www.pgb.kazusa.or.jp/kaftom/ via the website of the National Bioresource Project Tomato http://tomato.nbrp.jp.
Highlights
The Solanaceae family includes several economically important vegetable crops
For tomato expressed sequence tags (ESTs), several repositories are available worldwide, such as the Dana-Farber Cancer Institute (DFCI) Tomato Gene Index, The Solanaceae Project (SOL) Genomics Network (SGN) [5], MiBASE [10], PlantGDB [11], and TomatEST [12], and the number of tomato ESTs accumulated in the databases is 296,957 (January 8, 2010)
We developed a set of 13,227 full-length cDNAs from the model tomato cultivar Micro-Tom, and we generated a set of 11,502 nrFLcDNAs, each of which represents a non-redundant transcript coding a fulllength CDS
Summary
The Solanaceae family includes several economically important vegetable crops. The tomato (Solanum lycopersicum) is regarded as a model plant of the Solanaceae family. The Solanaceae family comprises 1000-2000 species that show wide morphological variability and ecological adaptability [1] This taxon includes a number of vegetable crops including fruit-bearing vegetables, tuber-bearing vegetables, and ornamental plants, many of which have economic importance. A more direct approach to collecting DNA information of individual genes is to analyze full-length cDNA sequences. Major advantages of sequencing full-length cDNA over the EST assembly include that the data is derived from a single clone rather than the assembly of multiple ESTs which can generate contigs containing sequences from multiple transcripts. Another major advantage of this approach is that full-length cDNA clones have complete sequences of transcripts including coding regions (CDSs) and untranslated regions (UTRs) This facilitates the subsequent annotation and prediction of genomic structures. Full-length cDNAs are a powerful genomic research tool
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