title: De Novo Sequencing and Analysis of the Safflower Transcriptome to Discover Putative Genes Associated with Safflor Yellow in Carthamus tinctorius L.
abstract: Safflower (Carthamus tinctorius L.), an important traditional Chinese medicine, is cultured widely for its pharmacological effects, but little is known regarding the genes related to the metabolic regulation of the safflower's yellow pigment. To investigate genes related to safflor yellow biosynthesis, 454 pyrosequencing of flower RNA at different developmental stages was performed, generating large databases.In this study, we analyzed 454 sequencing data from different flowering stages in safflower. In total, 1,151,324 raw reads and 1,140,594 clean reads were produced, which were assembled into 51,591 unigenes with an average length of 679 bp and a maximum length of 5109 bp. Among the unigenes, 40,139 were in the early group, 39,768 were obtained from the full group and 28,316 were detected in both samples. With the threshold of "log2 ratio ≥ 1", there were 34,464 differentially expressed genes, of which 18,043 were up-regulated and 16,421 were down-regulated in the early flower library. Based on the annotations of the unigenes, 281 pathways were predicted. We selected 12 putative genes and analyzed their expression levels using quantitative real time-PCR. The results were consistent with the 454 sequencing results. In addition, the expression of chalcone synthase, chalcone isomerase and anthocyanidin synthase, which are involved in safflor yellow biosynthesis and safflower yellow pigment (SYP) content, were analyzed in different flowering periods, indicating that their expression levels were related to SYP synthesis. Moreover, to further confirm the results of the 454 pyrosequencing, full-length cDNA of chalcone isomerase (CHI) and anthocyanidin synthase (ANS) were cloned from safflower petal by RACE (Rapid-amplification of cDNA ends) method according to fragment of the transcriptome.
authors.affiliation: Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, Jilin, China. xiuming1211@163.com.|College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China. xiuming1211@163.com.
authors.forename: Xiuming
authors.initials: X
authors.lastname: Liu
authors.affiliation: Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, Jilin, China. yydong@aliyun.com.
authors.forename: Yuanyuan
authors.initials: Y
authors.lastname: Dong
authors.affiliation: Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, Jilin, China. nayao@163.com.
authors.forename: Na
authors.initials: N
authors.lastname: Yao
authors.affiliation: College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China. jauzhangyu@163.com.
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, Jilin, China. wangnanlunwen@126.com.
authors.forename: Nan
authors.initials: N
authors.lastname: Wang
authors.affiliation: College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China. cuixiyan2005@163.com.
authors.forename: Xiyan
authors.initials: X
authors.lastname: Cui
authors.affiliation: Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, Jilin, China. xiuming1211@163.com.
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Li
authors.affiliation: Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, Jilin, China. nifengcao_2000@163.com.
authors.forename: Yanfang
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, Jilin, China. fw-1980@163.com.
authors.forename: Fawei
authors.initials: F
authors.lastname: Wang
authors.affiliation: Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, Jilin, China. yangjing5122010@163.com.
authors.forename: Jing
authors.initials: J
authors.lastname: Yang
authors.affiliation: Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, Jilin, China. guanll2004@163.com.
authors.forename: Lili
authors.initials: L
authors.lastname: Guan
authors.affiliation: Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, Jilin, China. dulinna0918@163.com.
authors.forename: Linna
authors.initials: L
authors.lastname: Du
authors.affiliation: Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, Jilin, China.|College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China.
authors.forename: Haiyan
authors.initials: H
authors.lastname: Li
authors.affiliation: Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, Jilin, China. xiaokunli@163.net.
authors.forename: Xiaokun
authors.initials: X
authors.lastname: Li
mesh_terms: D001483:Base Sequence; D031187:Carthamus tinctorius / Q000235:genetics*; D005419:Flavonoids / Q000096:biosynthesis; D035264:Flowers / Q000235:genetics; D018507:Gene Expression Regulation, Developmental; D017343:Genes, Plant; D008969:Molecular Sequence Data; D059467:Transcriptome
chemical_list: D005419:Flavonoids
keywords: 454 sequencing; Carthamus tinctorius L.; flavonoid biosynthesis; safflor yellow; transcriptome