title: Transcriptomic comparison of the self-pollinated and cross-pollinated flowers of Erigeron breviscapus to analyze candidate self-incompatibility-associated genes.
abstract: BACKGROUND
  Self-incompatibility (SI) is a widespread and important mating system that promotes outcrossing in plants. Erigeron breviscapus, a medicinal herb used widely in traditional Chinese medicine, is a self-incompatible species of Asteraceae. However, the genetic characteristics of SI responses in E. breviscapus remain largely unknown. To understand the possible mechanisms of E. breviscapus in response to SI, we performed a comparative transcriptomic analysis with capitulum of E. breviscapus after self- and cross-pollination, which may provide valuable information for analyzing the candidate SI-associated genes of E. breviscapus.
  
  
  METHODS
  Using a high-throughput next-generation sequencing (Illumina) approach, the transcriptionexpression profiling of the different genes of E. breviscapus were obtained, some results were verified by quantitative real time PCR (qRT-PCR).
  
  
  RESULTS
  After assembly, 63,485 gene models were obtained (average gene size 882 bp; N50 = 1485 bp), among which 38,540 unigenes (60.70% of total gene models) were annotated by comparisons with four public databases (Nr, Swiss-Prot, KEGG and COG): 38,338 unigenes (60.38% of total gene models) showed high homology with sequences in the Nr database. Differentially expressed genes were identified among the three cDNA libraries (non-, self- and cross-pollinated capitulum of E. breviscapus), and approximately 230 genes might be associated with SI responses. Several these genes were upregulated in self-pollinated capitulum but downregulated in cross-pollinated capitulum, such as SRLK (SRK-like) and its downstream signal factor, MLPK. qRT-PCR confirmed that the expression patterns of EbSRLK1 and EbSRLK3 genes were not closely related to SI of E. breviscapus.
  
  
  CONCLUSIONS
  This work represents the first large-scale analysis of gene expression in the self-pollinated and cross-pollinated flowers of E. breviscapus. A larger number of notable genes potentially involved in SI responses showed differential expression, including genes playing crucial roles in cell-cell communication, signal transduction and the pollination process. We thus hypothesized that those genes showing differential expression and encoding critical regulators of SI responses, such as MLPK, ARC1, CaM, Exo70A1, MAP, SF21 and Nod, might affect SI responses in E. breviscapus. Taken together, our study provides a pool of SI-related genes in E. breviscapus and offers a valuable resource for elucidating the mechanisms of SI in Asteraceae.
authors.affiliation: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China. zw_biology2@126.com.|The Life Science and Technology College, Honghe University, Mengzi, 661100, Yunnan, People's Republic of China. zw_biology2@126.com.
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
authors.affiliation: The Life Science and Technology College, Honghe University, Mengzi, 661100, Yunnan, People's Republic of China. 302719308@qq.com.
authors.forename: Xiang
authors.initials: X
authors.lastname: Wei
authors.affiliation: The Life Science and Technology College, Honghe University, Mengzi, 661100, Yunnan, People's Republic of China. menghengl@163.com.
authors.forename: Heng-Lin
authors.initials: HL
authors.lastname: Meng
authors.affiliation: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China. pony0207@126.com.
authors.forename: Chun-Hua
authors.initials: CH
authors.lastname: Ma
authors.affiliation: Key Laboratory of Tropical Agro-environment, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642, People's Republic of China. jnhskip@hotmail.com.
authors.forename: Ni-Hao
authors.initials: NH
authors.lastname: Jiang
authors.affiliation: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China. zgh73107310@163.com.
authors.forename: Guang-Hui
authors.initials: GH
authors.lastname: Zhang
authors.affiliation: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China. shengchaoyang@163.com.
authors.forename: Sheng-Chao
authors.initials: SC
authors.lastname: Yang
mesh_terms: D049919:Erigeron / Q000235:genetics* / Q000502:physiology*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D063990:Gene Ontology; D017343:Genes, Plant; D056726:Genetic Association Studies; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D054817:Pollination / Q000235:genetics*; D057945:Self-Fertilization / Q000235:genetics*; D060436:Self-Incompatibility in Flowering Plants / Q000235:genetics*; D017423:Sequence Analysis, RNA; D015398:Signal Transduction / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*