title: De novo assembly and annotation of Salvia splendens transcriptome using the Illumina platform.
abstract: BACKGROUND
  As an important perennial herbaceous flower, Salvia splendens possesses high ornamental value. Understanding its branching processes may help scientists select the best plant type. Although Salvia splendens is a frequently-used horticultural flower, only limited transcriptomic or genomic research is available in public databases. In the present study, we, for the first time, constructed a comprehensive dataset for Salvia splendens through de novo high-throughput transcriptome sequencing.
  
  
  RESULTS
  We performed de novo transcriptome sequencing on two different branching type plants (Strain 35 and Cailinghong) using the Illumina paired-end sequencing technology. For Strain 35, a total of 16,488,829 reads were generated and assembled into 38,498 unigenes, with a mean length of approximately 779 bp. For Cailinghong, 16,464,713 reads were generated and assembled into 34,302 unigenes, with a mean length of approximately 812 bp. Moreover, a total of 49,310 unigenes for Salvia splendens were identified, among them 33,925 (68.80%) were annotated in the non-redundant NCBI database, 25,371 (51.45%) were annotated in the Swiss-Prot database, while 24,888 (50.47%) and 9,896 (20.07%) unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. Using the Kyoto Encyclopedia of Genes and Genomes pathway database, we identified 134 differently expressed unigenes between Strain 35 and Cailinghong, and then these unigenes were mapped to 79 pathways. In addition, we detected 2,453 simple sequence repeats (SSRs).
  
  
  CONCLUSIONS
  We obtained a comprehensive transcriptomic information from this work and provided a valuable resource of transcript sequences of Salvia splendens in public databases. Moreover, some candidate genes potentially involved in branching were identified. Furthermore, numerous obtained SSRs might contribute to marker-assisted selection. These data could be further utilized in functional genomics studies on Salvia splendens.
authors.affiliation: College of Biological Science and Engineering, Beijing University of Agriculture, Beijing, P. R. China.
authors.forename: Xiuxiu
authors.initials: X
authors.lastname: Ge
authors.affiliation: College of Urban & Rural Development, Beijing University of Agriculture, Beijing, P. R. China.
authors.forename: Hongwei
authors.initials: H
authors.lastname: Chen
authors.affiliation: College of Horticulture, Beijing University of Agriculture, Beijing, P. R. China.
authors.forename: Hongli
authors.initials: H
authors.lastname: Wang
authors.affiliation: College of Horticulture, Beijing University of Agriculture, Beijing, P. R. China.
authors.forename: Aiping
authors.initials: A
authors.lastname: Shi
authors.affiliation: College of Urban & Rural Development, Beijing University of Agriculture, Beijing, P. R. China.
authors.forename: Kefeng
authors.initials: K
authors.lastname: Liu
mesh_terms: D020869:Gene Expression Profiling; D017343:Genes, Plant / Q000235:genetics; D058977:Molecular Sequence Annotation; D018520:Plant Shoots / Q000235:genetics / Q000254:growth & development; D027544:Salvia / Q000235:genetics* / Q000254:growth & development; D017421:Sequence Analysis