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Background   Pseudostellaria heterophylla  produces both closed (cleistogamous, CL) and open (chasmogamous, CH) flowers on the same individual but in different seasons. The production of CH and CL flowers might be in response to environmental changes. To better understand the molecular mechanisms of CH and CL flowering, we compared the transcriptome of the two types of flowers to examine differential gene expression patterns, and to identify gene regulatory networks that control CH and CL flowering.    Results  Using RNA sequencing, we identified homologues of 428  Arabidopsis  genes involved in regulating flowering processes and estimated the differential gene expression patterns between CH and CL flowers. Some of these genes involved in gene regulatory networks of flowering processes showed significantly differential expression patterns between CH and CL flowers. In addition, we identified another 396 differentially expressed transcripts between CH and CL flowers. Some are involved in environmental stress responses and flavonoid biosynthesis.    Conclusions  We propose how the differential expression of key members of three gene regulatory modules may explain CH and CL flowering. Future research is needed to investigate how the environment impinges on these flowering pathways to regulate CH and CL flowering in  P. heterophylla .    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2732-0) contains supplementary material, which is available to authorized users.

bmc genomics

Genome-wide analysis of gene expression reveals gene regulatory networks that regulate chasmogamous and cleistogamous flowering in Pseudostellaria heterophylla (Caryophyllaceae)