title: Transcriptome analysis of Houttuynia cordata Thunb. by Illumina paired-end RNA sequencing and SSR marker discovery.
abstract: BACKGROUND
  Houttuynia cordata Thunb. is an important traditional medical herb in China and other Asian countries, with high medicinal and economic value. However, a lack of available genomic information has become a limitation for research on this species. Thus, we carried out high-throughput transcriptomic sequencing of H. cordata to generate an enormous transcriptome sequence dataset for gene discovery and molecular marker development.
  
  
  RESULTS
  Illumina paired-end sequencing technology produced over 56 million sequencing reads from H. cordata mRNA. Subsequent de novo assembly yielded 63,954 unigenes, 39,982 (62.52%) and 26,122 (40.84%) of which had significant similarity to proteins in the NCBI nonredundant protein and Swiss-Prot databases (E-value <10(-5)), respectively. Of these annotated unigenes, 30,131 and 15,363 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. In addition, 24,434 (38.21%) unigenes were mapped onto 128 pathways using the KEGG pathway database and 17,964 (44.93%) unigenes showed homology to Vitis vinifera (Vitaceae) genes in BLASTx analysis. Furthermore, 4,800 cDNA SSRs were identified as potential molecular markers. Fifty primer pairs were randomly selected to detect polymorphism among 30 samples of H. cordata; 43 (86%) produced fragments of expected size, suggesting that the unigenes were suitable for specific primer design and of high quality, and the SSR marker could be widely used in marker-assisted selection and molecular breeding of H. cordata in the future.
  
  
  CONCLUSIONS
  This is the first application of Illumina paired-end sequencing technology to investigate the whole transcriptome of H. cordata and to assemble RNA-seq reads without a reference genome. These data should help researchers investigating the evolution and biological processes of this species. The SSR markers developed can be used for construction of high-resolution genetic linkage maps and for gene-based association analyses in H. cordata. This work will enable future functional genomic research and research into the distinctive active constituents of this genus.
authors.affiliation: The College of Life Science, Huaihua University, Huaihua, China ; Key Laboratory of Hunan Province for Study and Utilization of Ethnic Medicinal Plant Resources, Huaihua, China ; Key Laboratory of Hunan Higher Education for Hunan-Western Medicinal Plant and Ethnobotany, Huaihua, China.
authors.forename: Lin
authors.initials: L
authors.lastname: Wei
authors.affiliation: The College of Life Science, Huaihua University, Huaihua, China ; Key Laboratory of Hunan Province for Study and Utilization of Ethnic Medicinal Plant Resources, Huaihua, China ; Key Laboratory of Hunan Higher Education for Hunan-Western Medicinal Plant and Ethnobotany, Huaihua, China.
authors.forename: Shenghua
authors.initials: S
authors.lastname: Li
authors.affiliation: The College of Life Science, Huaihua University, Huaihua, China ; Key Laboratory of Hunan Province for Study and Utilization of Ethnic Medicinal Plant Resources, Huaihua, China ; Key Laboratory of Hunan Higher Education for Hunan-Western Medicinal Plant and Ethnobotany, Huaihua, China.
authors.forename: Shenggui
authors.initials: S
authors.lastname: Liu
authors.affiliation: The College of Life Science, Huaihua University, Huaihua, China ; Key Laboratory of Hunan Province for Study and Utilization of Ethnic Medicinal Plant Resources, Huaihua, China ; Key Laboratory of Hunan Higher Education for Hunan-Western Medicinal Plant and Ethnobotany, Huaihua, China.
authors.forename: Anna
authors.initials: A
authors.lastname: He
authors.affiliation: The College of Life Science, Huaihua University, Huaihua, China.
authors.forename: Dan
authors.initials: D
authors.lastname: Wang
authors.affiliation: The College of Life Science, Huaihua University, Huaihua, China ; The College of Life Science, Hunan University, Changsha, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Wang
authors.affiliation: The College of Life Science, Huaihua University, Huaihua, China ; Key Laboratory of Hunan Province for Study and Utilization of Ethnic Medicinal Plant Resources, Huaihua, China ; Key Laboratory of Hunan Higher Education for Hunan-Western Medicinal Plant and Ethnobotany, Huaihua, China.
authors.forename: Yulian
authors.initials: Y
authors.lastname: Tang
authors.affiliation: The College of Life Science, Huaihua University, Huaihua, China ; Key Laboratory of Hunan Province for Study and Utilization of Ethnic Medicinal Plant Resources, Huaihua, China ; Key Laboratory of Hunan Higher Education for Hunan-Western Medicinal Plant and Ethnobotany, Huaihua, China.
authors.forename: Xianjin
authors.initials: X
authors.lastname: Wu
mesh_terms: D019295:Computational Biology / Q000379:methods; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling; D005819:Genetic Markers; D059014:High-Throughput Nucleotide Sequencing; D052859:Houttuynia / Q000235:genetics* / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D011110:Polymorphism, Genetic; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D005819:Genetic Markers