Differentially Expressed Genes Study In Ginkgo Genome By Transcriptome Sequencing

Sex evolution mechanisms have only been explored in several flowering plants including papaya,cucumber and Silene latifolia,thus sex evolution mechanisms as well as evolution of sex regions/chromosomes in plants remained largely unknown.Ginkgo is an old ‘living fossil' dioecy gymnosperm,which located in the key phylogenetic position,is considered as a study model for the evolution of sex chromosome in plant.Although there were several studies reported a few candidate sex-related molecular markers of ginkgo,the systematically study of sex-related genes are still lacking.Now,the ginkgo genome provides a good foundation for the development of molecular markers of sex evolution.In this study,we aim to identify the different expressed genes between female and male ginkgo based on the transcriptome sequencing of six female and six male ginkgo flowers.Firstly,we identified four co-expression modules of female and male flowers using these twelve RNA-seq data,among of them,several genes involved in the development of flower or sex.For instance,in the turquoise module,we identified a basic helix-loop-helix domain-containing protein?Gb₀7087?,a transcription activator,involved in the control of sporophyte of cell wall pattern and gametophyte of pollen development,as well as a flowering time control protein FY?Gb₀9523?regulated the flowering time in the autonomic flowering pathway by reducing the expression level of FLC gene.Besides,we totally identified 11,161 significant different expressed genes?DEGs?between female and male flowers including 351 specific expressed genes?SEGs?of female and 328 SEGs of male.Among these SEGs,we identified 44 SEGs involved into plant resistant genes of female and male,such as allergen V5/Tpx-1-related family protein,a basic pathogenesis-related protein.We also detected an interactive gene network containing 30 SEGs of female and 29 SEGs of male,such as LATERAL ORGAN BOUNDARIES,ectopic expression of which causes male and female sterility.Furthermore,we also sequenced the transcriptome of three female leaves and three male leaves of ginkgo.Comparing to the DEGs of flower tissues,we identified 75 DEGs shared with these two tissues.Finally,we randomly validated the expression of 8 DEGs using RT-PCR and the results were showed high consistence with the RNA-seq results.Our results provide the different expressed genes between female and male ginkgo,as well as an available approach to identify the different expressed genes between two gender plant.