Tissue differential expression of lycopene β-cyclase gene in papaya

Carotene pigments in flowers and fruits are distinct features related to fitness advantages such as attracting insects forpollination and birds for seed dispersal.In papaya,the flesh color of the fruit is considered a quality trait that correlateswith nutritional value and is linked to shelf-life of the fruit.To elucidate the carotenoid biosynthesis pathway in papaya,we took a candidate gene approach to clone the lycopene β-cyclase gene,LCY-B.A papaya LCY-B ortholog,cpLCY-B,was successfully identified from both cDNA and bacterial artificial chromosome(BAC)libraries and complete genomicsequence was obtained from the positive BAC including the promoter region.This cpLCY-B shared 80% amino acididentity with citrus LCY-B.However,full genomic sequences from both yellow- and red-fleshed papaya were identical.Quantitative real-time PCR(qPCR)revealed similar levels of expression at six different maturing stages of fruits forboth yellow-and red-fleshed genotypes.Further expression analyses of cpLCY-B showed that its expression levels wereseven- and three-fold higher in leaves and,respectively,flowers than in fruits,suggesting that cpLCY-B is down-regulatedduring the fruit ripening process.

Cloning and characterization of a FLORICAULA/LEAFY ortholog, PFL, in polygamous papaya

The homologous genes FLORICAULA (FLO) in Antirrhinum and LEAFY (LFY) in Arabidopsis are known to regu- late the initiation of flowering in these two distantly related plant species. These genes are necessary also for the expression of downstream genes that control floral organ identity. We used Arabidopsis LFY cDNA as a probe to clone and sequence a papaya ortholog of LFY, PFL. It encodes a protein that shares 61% identity with the Arabidopsis LFY gene and 71% identity with the LFY homologs of the two woody tree species: California sycamore (Platanus racemosa) and black cottonwood (Populus trichocarpa). Despite the high sequence similarity within two conserved regions, the N-terminal proline-rich motif in papaya PFL differs from other members in the family. This difference may not affect the gene function of papaya PFL, since an equally divergent but a functional LFY ortholog NEEDLY of Pinus radiata has been reported. Genomic and BAC Southern analyses indicated that there is only one copy of PFL in the papaya genome. In situ hybridization experiments demonstrated that PFL is expressed at a relatively low level in leaf primordia, but it is expressed at a high level in the floral meristem. Quantitative PCR analyses revealed that PFL was expressed in flower buds of all three sex types - male, female, and hermaphrodite with marginal difference between hermaphrodite and unisexual flowers. These data suggest that PFL may play a similar role as LFY in flower development and has limited effect on sex differentiation 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.

PGD: Pineapple Genomics Database

Pineapple occupies an important phylogenetic position as its reference genome is a model for studying the evolution the Bromeliaceae family and the crassulacean acid metabolism(CAM)photosynthesis.Here,we developed a pineapple genomics database(PGD,http://pineapple.angiosperms.org/pineapple/html/index.html)as a central online platform for storing and integrating genomic,transcriptomic,function annotation and genetic marker data for pineapple(Ananas comosus(L.)Merr.).The PGD currently hosts significant search tools and available datasets for researchers to study comparative genomics,gene expression,gene co-expression molecular marker,and gene annotation of A.comosus(L).PGD also performed a series of additional pages for a genomic browser that visualizes genomic data interactively,bulk data download,a detailed user manual,and data integration information.PGD was developed with the capacity to integrate future data resources,and will be used as a long-term and open access database to facilitate the study of the biology,distribution,and the evolution of pineapple and the relative plant species.An email-based helpdesk is also available to offer support with the website and requests of specific datasets from the research community.