DNA methylome and transcriptome landscapes revealed differential characteristics of dioecious flowers in papaya

Separate sexes in dioecious plants display different morphology and physiological characteristics.The differences between the two sexes lie in their highly differentiated floral characteristics and in sex-related phenotype,which is genetically determined and epigenetically modified.In dioecious papaya(Carica papaya L.),global comparisons of epigenetic DNA methylation and gene expressions were still limited.We conducted bisulfite sequencing of early-stage flowers grown in three seasons(spring,summer and winter)and compared their methylome and transcriptome profiles to investigate the differential characteristics of male and female in papaya.Methylation variances between female and male papaya were conserved among three different seasons.However,combined genome-scale transcriptomic evidence revealed that most methylation variances did not have influence on the expression profiles of neighboring genes,and the differentially expressed genes were most overrepresented in phytohormone signal transduction pathways.Further analyses showed diverse stress-responsive methylation alteration in male and female flowers.Male flower methylation was more responsive to stress whereas female flower methylation varied less under stress.Early flowering of male papaya in spring might be associated with the variation in the transcription of CpSVP and CpAP1 coinciding with their gene-specific hypomethylation.These findings provide insights into the sex-specific DNA methylation and gene expression landscapes of dioecious papaya and a foundation to investigate the correlation between differentiated floral characteristics and their candidate genes.

Auxin regulation involved in gynoecium morphogenesis of papaya flowers

The morphogenesis of gynoecium is crucial for propagation and productivity of fruit crops.For trioecious papaya(Carica papaya),highly differentiated morphology of gynoecium in flowers of different sex types is controlled by gene networks and influenced by environmental factors,but the regulatory mechanism in gynoecium morphogenesis is unclear.Gynodioecious and dioecious papaya varieties were used for analysis of differentially expressed genes followed by experiments using auxin and an auxin transporter inhibitor.We first compared differential gene expression in functional and rudimentary gynoecium at early stage of their development and detected significant difference in phytohormone modulating and transduction processes,particularly auxin.Enhanced auxin signal transduction in rudimentary gynoecium was observed.To determine the role auxin plays in the papaya gynoecium,auxin transport inhibitor(N-1-Naphthylphthalamic acid,NPA)and synthetic auxin analogs with different concentrations gradient were sprayed to the trunk apex of male and female plants of dioecious papaya.Weakening of auxin transport by 10 mg/L NPA treatment resulted in female fertility restoration in male flowers,while female flowers did not show changes.NPA treatment with higher concentration(30 and 50 mg/L)caused deformed flowers in both male and female plants.We hypothesize that the occurrence of rudimentary gynoecium patterning might associate with auxin homeostasis alteration.Proper auxin concentration and auxin homeostasis might be crucial for functional gynoecium morphogenesis in papaya flowers.These results will lead to further investigation on the auxin homeostasis and gynoecium morphogenesis in papaya.

Sex biased expression of hormone related genes at early stage of sex differentiation in papaya flowers

Sex types of papaya are controlled by a pair of nascent sex chromosomes,but molecular genetic mechanisms of sex determination and sex differentiation in papaya are still unclear.We performed comparative analysis of transcriptomic profiles of male and female floral buds at the early development stage before the initiation of reproductive organ primordia at which there is no morphological difference between male and female flowers.A total of 1734 differentially expressed genes(DEGs)were identified,of which 923 showed female-biased expression and 811 showed male-biased expression.Functional annotation revealed that genes related to plant hormone biosynthesis and signaling pathways,especially in abscisic acid and auxin pathways,were overrepresented in the DEGs.Transcription factor binding motifs,such as MYB2,GAMYB,and AP2/EREBP,were enriched in the promoters of the hormone-related DEGs,and transcription factors with those motifs also exhibited differential expression between sex types.Among these DEGs,we also identified 11 genes in the non-recombining region of the papaya sex chromosomes and 9 genes involved in stamen and carpel development.Our results suggested that sex differentiation in papaya may be regulated by multiple layers of regulation and coordination and involved transcriptional,epigenetic,and phytohormone regulation.Hormones,especially ABA and auxin,transcription factors,and genes in the non-recombination region of the sex chromosome could be involved in this process.Our findings may facilitate the elucidation of signal transduction and gene interaction in sex differentiation of unisexual flowers in papaya.

The role of cis-elements in the evolution of crassulacean acid metabolism photosynthesis

Crassulacean acid metabolism(CAM)photosynthesis is an innovation of carbon concentrating mechanism that is characterized by nocturnal CO2 fixation.Recent progresses in genomics,transcriptomics,proteomics,and metabolomics of CAM species yielded new knowledge and abundant genomic resources.In this review,we will discuss the pattern of cis-elements in stomata movement-related genes and CAM CO2 fixation genes,and analyze the expression dynamic of CAM related genes in green leaf tissues.We propose that CAM photosynthesis evolved through the re-organization of existing enzymes and associated membrane transporters in central metabolism and stomatal movement-related genes,at least in part by selection of existing circadian clock cis-regulatory elements in their promoter regions.Better understanding of CAM evolution will help us to design crops that can thrive in arid or semiarid regions,which are likely to expand due to global climate change.