<i>De Novo</i> Assembly and Annotation of <i>Salvia splendens</i> Transcriptome Using the Illumina Platform

<div><p>Background</p><p>As an important perennial herbaceous flower, <i>Salvia splendens</i> possesses high ornamental value. Understanding its branching processes may help scientists select the best plant type. Although <i>Salvia splendens</i> 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 <i>Salvia splendens</i> through <i>de novo</i> high-throughput transcriptome sequencing.</p><p>Methodology/Principal Findings</p><p>We performed <i>de novo</i> 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 <i>Salvia splendens</i> 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).</p><p>Conclusions</p><p>We obtained a comprehensive transcriptomic information from this work and provided a valuable resource of transcript sequences of <i>Salvia splendens</i> 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 <i>Salvia splendens</i>.</p></div

COG annotation.

<p>COG annotation.</p

Similarity analysis based on the best hit.

<p>Similarity analysis based on the best hit.</p

Summary of transcriptome sequencing for Sal<i>via splendens</i>.

<p>Summary of transcriptome sequencing for Sal<i>via splendens</i>.</p

Repeats of di- and tri-nucleotides.

<p>Repeats of di- and tri-nucleotides.</p

Summary of transcripts for Sal<i>via splendens</i>.

<p>Summary of transcripts for Sal<i>via splendens</i>.</p

GO annotation.

<p>GO annotation.</p

Summary of unigenes for Sal<i>via splendens</i>.

<p>Summary of unigenes for Sal<i>via splendens</i>.</p

Cell proliferation rates in human ADH and their relationships with pSTAT5 and pSTAT3.

<p>A. Quantification of Ki67 staining in normal TDLU, ADH, and UDH. B-C. No association between percentage of pSTAT5+ (B) and Ki67+ cells or between pSTAT3+ (C) and Ki67+ cells in ADH. Each dot represents an individual ADH lesion.</p

Complementary expression patterns of pSTAT5 and pSTAT3 in human ADH.

<p>A. Representative IHC staining for pSTAT5 (top panel) and pSTAT3 (bottom panel) in consecutive ADH lesions. B-C. Inverse correlation between percentage of pSTAT5+ and pSTAT3+ cells in ADH (B) or normal TDLU (C). Each dot represents an individual ADH lesion (B) or TDLU (C).</p