title: Gene transcript profiles in the desert plant Nitraria tangutorum during fruit development and ripening.
abstract: Nitraria tangutorum Bobr., a valuable wild shrub distributed in Northwest China, produces edible and medicinal berries. However, little is known about the molecular mechanisms of its fruit development and ripening. We performed de novo transcriptome sequencing of N. tangutorum fruit using the Illumina HiSeq™ 2000 sequencing platform. More than 62.94 million reads were obtained and assembled into 69,306 unigenes (average length, 587 bp). These unigenes were annotated by querying against five databases (Nr, Swiss-Prot, GO, COG, and KEGG); 42,929 and 26,809 unigenes were found in the Nr and Swiss-Prot databases, respectively. In ortholog analyses, 33,363 unigenes were assigned with one or more GO terms, 15,537 hits were aligned to 25 COG classes, and 24,592 unigenes were classified into 128 KEGG pathways. Digital gene expression analyses were conducted on N. tangutorum fruit at the green (S1), yellow (S2), and red (S3) developmental stages. In total, 8240, 5985, and 4994 differentially expressed genes (DEGs) were detected for S1 vs. S2, S1 vs. S3, and S2 vs. S3, respectively. Cluster analyses showed that a large proportion of DEGs related to plant hormones and transcription factors (TFs) showed high expression in S1, down-regulated expression in S2, and up-regulated expression in S3. We analyzed the expression patterns of 23 genes encoding 12 putative enzymes involved in flavonoid biosynthesis. The expression profiles of 10 DEGs involved in flavonoid biosynthesis were validated by Q-PCR analysis. The assembled and annotated transcriptome sequences and gene expression profile analyses provide valuable genetic resources for research on N. tangutorum.
authors.affiliation: College of Life Sciences, Inner Mongolia University, Hohhot, 010021, People's Republic of China.
authors.forename: Jia
authors.initials: J
authors.lastname: Wang
authors.affiliation: College of Life Sciences, Inner Mongolia University, Hohhot, 010021, People's Republic of China.
authors.forename: Zhenhua
authors.initials: Z
authors.lastname: Dang
authors.affiliation: College of Life Sciences, Inner Mongolia University, Hohhot, 010021, People's Republic of China.
authors.forename: Huirong
authors.initials: H
authors.lastname: Zhang
authors.affiliation: College of Life Sciences, Inner Mongolia University, Hohhot, 010021, People's Republic of China.
authors.forename: Linlin
authors.initials: L
authors.lastname: Zheng
authors.affiliation: College of Life Sciences, Inner Mongolia University, Hohhot, 010021, People's Republic of China.|College of Mongolian Medicine, Inner Mongolia Medical University, Hohhot, 010110, People's Republic of China.
authors.forename: Tebuqin
authors.initials: T
authors.lastname: Borjigin
authors.affiliation: College of Life Sciences, Inner Mongolia University, Hohhot, 010021, People's Republic of China. ycwang@imu.edu.cn.
authors.forename: Yingchun
authors.initials: Y
authors.lastname: Wang
mesh_terms: D002681:China; D016000:Cluster Analysis; D003889:Desert Climate; D005638:Fruit / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D019684:Magnoliopsida / Q000235:genetics*; D058977:Molecular Sequence Annotation / Q000379:methods; D010940:Plant Proteins / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods; D059467:Transcriptome / Q000235:genetics*
chemical_list: D010940:Plant Proteins
keywords: Digital gene expression profiling; Fruit development and ripening; Nitraria tangutorum; RNA-seq