ARS | Publication request: De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 2, 2011
Publication Date: August 2, 2011
Citation: Iorizzo, M., Senalik, D.A., Grzebelus, D., Bowman, M., Cavagnaro, P.F., Matvienko, M., Ashrafi, H., Van Deynze, A., Simon, P.W. 2011. De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity. Biomed Central (BMC) Genomics. 12:389.

Interpretive Summary: The genome of an organism is the sum of all of its DNA that leads to genetic variation we are familiar with such as gender, height, and skin color in humans; and flower color, productivity, and resistance to pests and diseases in plants. Not all of the DNA of genomes is involved in this type of genetic variation, but rather some has no known function. The transcriptome is the portion of the genome of an organism that does include functioning, or “expressed” genes. In this study we characterized the transcriptome of carrot for the first time. The number of genes in the carrot transcriptome and range of their biological functions was found to be similar in carrot to other plants. We were able to demonstrate that genes in the carrot transcriptome could be located on the carrot map. This is important in both understanding where genes of related function are relative to one another, and also to understand where genes with known function in the transcriptome are relative to other genes we have placed on the carrot genetic map in previous studies. This research is of interest to genomicists, geneticists, plant breeders, seed companies, and crop producers.

Technical Abstract: Among next generation sequence technologies, platforms such as Illumina and SOLiD produce short reads but with higher coverage and lower cost per sequenced nucleotide than 454 or Sanger. A challenge now is to develop efficient strategies to use short-read length platforms for de novo assembly and marker development. The scope of this study was to develop a de novo assembly of carrot ESTs from multiple genotypes using the Illumina platform, and to identify polymorphisms. A de novo assembly of transcriptome sequence from four genetic backgrounds (three diverse inbred cultivated carrots and a pool of cultivated x wild carrot RILs) produced about 60,404ontigs. More than 50% of these assembled contigs were annotated. Presence of multiple genetic backgrounds in our EST collection allowed the identification of 114 computationally polymorphic SSRs, and 20,148 SNPs at a depth of coverage of 20× or more. Polymorphisms were predominantly between inbred lines except for the cultivated x wild RIL pool which had high intra-sample polymorphism. About 90% and 88% of tested SSR and SNP primers amplified a product, of which 70% and 46%, respectively, were of the expected size and 84% and 60% were polymorphic. About 25% of SNPs genotyped were polymorphic in two diverse mapping populations. This study confirmed the potential of short read platforms for de novo EST assembly and identification of genetic polymorphisms in carrot. In addition we produced the first large-scale transcriptome of carrot, a species lacking genomic resources.