Transcriptomic Analysis of Flower Development in Wintersweet (Chimonanthus praecox)

Abstract

Wintersweet (Chimonanthus praecox) is familiar as a garden plant and woody ornamental flower. On account of its unique flowering time and strong fragrance, it has a high ornamental and economic value. Despite a long history of human cultivation, our understanding of wintersweet genetics and molecular biology remains scant, reflecting a lack of basic genomic and transcriptomic data. In this study, we assembled three cDNA libraries, from three successive stages in flower development, designated as the flower bud with displayed petal, open flower and senescing flower stages. Using the Illumina RNA-Seq method, we obtained 21,412,928, 26,950,404, 24,912,954 qualified Illumina reads, respectively, for the three successive stages. The pooled reads from all three libraries were then assembled into 106,995 transcripts, 51,793 of which were annotated in the NCBI non-redundant protein database. Of these annotated sequences, 32,649 and 21,893 transcripts were assigned to gene ontology categories and clusters of orthologous groups, respectively. We could map 15,587 transcripts onto 312 pathways using the Kyoto Encyclopedia of Genes and Genomes pathway database. Based on these transcriptomic data, we obtained a large number of candidate genes that were differentially expressed at the open flower and senescing flower stages. An analysis of differentially expressed genes involved in plant hormone signal transduction pathways indicated that although flower opening and senescence may be independent of the ethylene signaling pathway in wintersweet, salicylic acid may be involved in the regulation of flower senescence. We also succeeded in isolating key genes of floral scent biosynthesis and proposed a biosynthetic pathway for monoterpenes and sesquiterpenes in wintersweet flowers, based on the annotated sequences. This comprehensive transcriptomic analysis presents fundamental information on the genes and pathways which are involved in flower development in wintersweet. And our data provided a useful database for further research of wintersweet and other Calycanthaceae family plants.

Mining Simple Sequence Repeat and Single Nucleotide Polymorphism Markers in a Transcriptomic Database of Wintersweet (Chimonanthus praecox)

“…For example, 31 expressed sequence tags (ESTs)-SSR markers have been developed from wintersweet EST sequences, and only eight polymorphic EST-SSR markers have been used to analyze the genetic diversity and structure of 10 natural populations (Yang et al, 2013). Although the whole genome of wintersweet has not been sequenced yet, a transcriptomic database of wintersweet has been established using the Illumina RNA-Seq method and a total of 10,699 transcripts assembled (Liu et al, 2014). This study aimed to mine SSRs and SNPs within the transcriptomic database of wintersweet and identify a substantial set of genetic markers for use in genetics, evaluation, or QTL identification.…”

Transcriptomic and proteomic approaches to explore the differences in monoterpene and benzenoid biosynthesis between scented and unscented genotypes of wintersweet

“…However, in most angiosperm families, the full set of TPS genes remains poorly investigated (Chen et al ). Although some wintersweet monoterpene synthases have been reported (Liu et al ), the entire spectrum of volatile terpenes in the two genotypes that we studied remains unclear. To better understand the molecular mechanisms underlying floral fragrance in wintersweet, we identified 16 CpTPS genes that encode TPSs that were differentially expressed in the genotypes (Appendix S8).…”

Development of SSR markers in Paeonia based on De Novo transcriptomic assemblies

“…Raw data, including polymorphic information content (PIC), observed number of alleles (Na), effective number of alleles (Ne), heterozygosities (Ho), expected heterozygosities (He), and Shannon's diversity index (I) were analyzed using POPgene v1.32 software [20]. The genetic similarity of these materials was analyzed using NTSYS-PC software [21]. Based on these data, the cluster dendrogram of these varieties was drawn, and then the relationship among these varieties was analyzed.…”