De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity

Abstract

BackgroundAmong 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.ResultsA de novo assembly of transcriptome sequence from four genetic backgrounds produced 58,751 contigs and singletons. Over 50% of these assembled sequences were annotated allowing detection of transposable elements and new carrot anthocyanin genes. Presence of multiple genetic backgrounds in our assembly allowed the identification of 114 computationally polymorphic SSRs, and 20,058 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. Out of verified SSR and SNP markers 84% and 82% were polymorphic. About 25% of SNPs genotyped were polymorphic in two diverse mapping populations.ConclusionsThis 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.

Identification of novel and useful EST-SSR markers from de novo transcriptome sequence of wheat (Triticum aestivum L.)

“…Owing to the steady decrease in cost per sequenced nucleotide and increase in throughput data, NGS technologies have become a powerful approach for the high-throughput discovery of genes; they generate a large amount of sequence data for molecular marker identification (Iorizzo et al, 2011;Silva et al, 2013). Recently, de novo transcriptome assembly using Illumina sequences has been successfully developed and widely applied in various important plant species including rice, wheat, and maize (Lu and Lu.…”

Comparative transcriptome of rhizome and leaf in Ligusticum Chuanxiong

“…Ono et al 2011;Tang et al 2011). To our knowledge, only a few transcriptome databases have been obtained from celery (Fu et al 2013), carrot (Iorizzo et al 2011) and parsley (Li et al 2014a, b) in the Apiaceae family, which were belonged to Apium, Daucus and Petroselinum genus, respectively. The limited resources cannot provide more help to study the L. chuanxiong, which is belonged to Ligusticum genus.…”

An RNA-Seq Transcriptome Analysis of Orthophosphate-Deficient White Lupin Reveals Novel Insights into Phosphorus Acclimation in Plants

“…For many species, nextgeneration sequencing technology has allowed the development of a transcriptome sequence prior to the sequencing of the genome, as in alfalfa (Medicago sativa; Yang et al, 2011), lentil (Lens culinaris; Kaur et al, 2011), pea (Pisum sativum; Franssen et al, 2011), pigeon pea (Cajanus cajan; Dubey et al, 2011), sweet potato (Ipomoea batatas; Wang et al, 2010b), eucalyptus (Eucalyptus spp. ; Mizrachi et al, 2010), carrot (Daucus carota; Iorizzo et al, 2011), watermelon (Citrullis vulgaris; Guo et al, 2011), rubber tree (Hevea brasiliensis; Xia et al, 2011), pitcher plant (Sarracenia spp. ; Srivastava et al, 2011), and cucurbits (Cucurbitaceae spp.…”