The First Illumina-Based De Novo Transcriptome Sequencing and Analysis of Safflower Flowers

Abstract

BackgroundThe safflower, Carthamus tinctorius L., is a worldwide oil crop, and its flowers, which have a high flavonoid content, are an important medicinal resource against cardiovascular disease in traditional medicine. Because the safflower has a large and complex genome, the development of its genomic resources has been delayed. Second-generation Illumina sequencing is now an efficient route for generating an enormous volume of sequences that can represent a large number of genes and their expression levels.Methodology/Principal FindingsTo investigate the genes and pathways that might control flavonoids and other secondary metabolites in the safflower, we used Illumina sequencing to perform a de novo assembly of the safflower tubular flower tissue transcriptome. We obtained a total of 4.69 Gb in clean nucleotides comprising 52,119,104 clean sequencing reads, 195,320 contigs, and 120,778 unigenes. Based on similarity searches with known proteins, we annotated 70,342 of the unigenes (about 58% of the identified unigenes) with cut-off E-values of 10−5. In total, 21,943 of the safflower unigenes were found to have COG classifications, and BLAST2GO assigned 26,332 of the unigenes to 1,754 GO term annotations. In addition, we assigned 30,203 of the unigenes to 121 KEGG pathways. When we focused on genes identified as contributing to flavonoid biosynthesis and the biosynthesis of unsaturated fatty acids, which are important pathways that control flower and seed quality, respectively, we found that these genes were fairly well conserved in the safflower genome compared to those of other plants.Conclusions/SignificanceOur study provides abundant genomic data for Carthamus tinctorius L. and offers comprehensive sequence resources for studying the safflower. We believe that these transcriptome datasets will serve as an important public information platform to accelerate studies of the safflower genome, and may help us define the mechanisms of flower tissue-specific and secondary metabolism in this non-model plant.

Whole-transcriptome sequencing of Pinellia ternata using the Illumina platform

“…The number of unigenes obtained from P. ternata was lower than that obtained from Carthamus tinctorius (120,778) (Lulin et al, 2012), Polygonum cuspidatum (86,418) (Hao et al, 2012), and Salvia miltiorrhiza (64,139) , However, the number of unigenes obtained from P. ternata was higher than that from Codonopsis pilosula (45,511) (Gao et al, 2015), and Isatis indigotica (36,367) (Chen et al, 2013). The average unigene length (611 bp) was slightly greater than that of other medicinal plants, including C. tinctorius (446 bp) (Lulin et al, 2012), S. miltiorrhiza (413 bp) , and P. cuspidatum (365 bp) (Hao et al, 2012). The unigene annotation rate observed in the present study (79.72%) was relatively higher.…”

Discovery of clubroot-resistant genes in Brassica napus by transcriptome sequencing

“…The rate of reads with Q20-value reached 98.68%. Based on these reads, 96,149 unigenes were assembled with an average length of 973 bp, which was larger than the mean unigene lengths found in butterfly (197 bp;Vera et al, 2008), sweet potato (581 bp; Guo et al, 2011), Salvia miltiorrhiza (331 bp; Zhang et al, 2012), safflower (446 bp; Lulin et al, 2012), and wax gourd (709 bp; Jiang et al, 2013). We aligned the unigene sequences to the Nr, Swiss-Prot, GO, COG, and KEGG protein databases and found that most unigene sequences could be matched to unique protein sequences in the various databases.…”

Salt and drought stresses in safflower: a review

“…Insight into the function of these genes and demonstration of their novelty may pilot to a better perception of the drought tolerance mechanisms in safflower and potentially other oilseed crops (Thippeswamy et al 2013). Lulin et al (2012) also conducted large-scale genomics, in order to investigate genes and pathways that may regulate flavonoids, the biosynthesis of unsaturated fatty acids (that can be beneficial to oxidative stress caused by abiotic stresses like drought), and other secondary metabolites in the safflower. Furthermore, these genes were moderately conserved in the safflower genome when compared to those of other plants.…”