RNA-Seq Based De Novo Transcriptome Assembly and Gene Discovery of Cistanche deserticola Fleshy Stem.
BACKGROUND
Cistanche deserticola is a completely non-photosynthetic parasitic plant with great medicinal value and mainly distributed in desert of Northwest China. Its dried fleshy stem is a crucial tonic in traditional Chinese medicine with roles of mainly improving male sexual function and strengthening immunity, but few mechanistic studies have been conducted partly due to the lack of genomic and transcriptomic resources.


RESULTS
In this study, we performed deep transcriptome sequencing in fleshy stem of C. deserticola, and about 80 million reads were generated using Illumina pair-end sequencing on HiSeq2000 platform. Using trinity assembler, we obtained 95,787 transcript sequences with transcript lengths ranging from 200 bp to 15,698 bp, having an average length of 950 bases and the N50 length of 1,519 bases. 63,957 transcripts were identified actively expressed with FPKM ≥ 0.5, in which 30,098 transcripts were annotated with gene descriptions or gene ontology terms by sequence similarity analyses against several public databases (Uniprot, NR and Nt at NCBI, and KEGG). Furthermore, we identified key enzyme genes involved in biosynthesis of lignin and phenylethanoid glycosides (PhGs) which are known to be the primary active ingredients. Four phenylalanine ammonia-lyase (PAL) genes, the first key enzyme in lignin and PhG biosynthesis, were identified based on sequences comparison and phylogenetic analysis. Two biosynthesis pathways of PhGs were also proposed for the first time.


CONCLUSIONS
In all, we completed a global analysis of the C. deserticola fleshy stem transcriptome using RNA-seq technology. A collection of enzyme genes related to biosynthesis of lignin and phenylethanoid glysides were identified from the assembled and annotated transcripts, and the gene family of PAL was also predicted. The sequence data from this study will provide a valuable resource for conducting future phenylethanoid glysides biosynthesis researches and functional genomic studies in this important medicinal plant.
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
Yuli
Y
Li
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
Xiliang
X
Wang
Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
Tingting
T
Chen
Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
Fuwen
F
Yao
Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
Cuiping
C
Li
HongKui CongRong Group, Alashan, Inner Mongolia, China.
Qingli
Q
Tang
Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
Min
M
Sun
Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
Gaoyuan
G
Sun
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
Songnian
S
Hu
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
Jun
J
Yu
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
Shuhui
S
Song
D031671:Cistanche / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D056726:Genetic Association Studies; D059014:High-Throughput Nucleotide Sequencing; D053858:Metabolic Networks and Pathways; D058977:Molecular Sequence Annotation; D010650:Phenylalanine Ammonia-Lyase / Q000235:genetics / Q000378:metabolism; D018547:Plant Stems / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
D010650:Phenylalanine Ammonia-Lyase