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Diversity of metabolite accumulation patterns in inner and outer seed coats of pomegranate:exploring their relationship with genetic mechanisms of seed coat development

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Horticulture Research 2020年第1期7卷 2634-2647页

作者： Gaihua Qin Chunyan Liu Jiyu Li Yongjie Qi Zhenghui Gao Xiaoling Zhang Xingkai Yi Haifa Pan Ray Ming Yiliu Xu Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops Anhui ProvinceHorticultural Research InstituteAnhui Academy of Agricultural SciencesHefei 230001China Key Laboratory of Fruit Quality and Development Biology Anhui Academy of Agricultural SciencesHefei 230001China fafu and uiuc-sib joint center for genomics and biotechnology Fujian Agriculture and Forestry UniversityFuzhou 350002China Department of Plant Biology University of Illinois at Urbana-ChampaignUrbanaIL 61822USA

The expanded outer seed coat and the rigid inner seed coat of pomegranate seeds,both affect the sensory qualities of the fruit and its acceptability to *** seeds are also an appealing model for the study of seed coat differentiation and *** conducted nontarget metabolic profiling to detect metabolites that contribute to the morphological differentiation of the seed coats along with transcriptomic profiling to unravel the genetic mechanisms underlying this *** of metabolites in the lignin biosynthetic pathway accumulating in seed coat layers at different developmental stages revealed that monolignols,including coniferyl alcohol and sinapyl alcohol,greatly accumulated in inner seed coats and monolignol glucosides greatly accumulated in outer seed *** expression of genes involved in monolignol biosynthesis and transport might explain the spatial patterns of biosynthesis and accumulation of these *** constituents and flavonoids in particular accumulated in the inner seed coat,and candidate genes that might be involved in their accumulation were also *** encoding transcription factors regulating monolignol,cellulose,and hemicellulose metabolism were chosen by coexpression *** results provide insights into metabolic factors influencing seed coat differentiation and a reference for studying seed coat developmental biology and pomegranate genetic improvement.

关键词： outer mechanisms alcohol

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

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Horticulture Research 2020年第1期7卷 2698-2705页

作者： Li-Yu Chen Yinghui Xin Ching Man Wai Juan Liu Ray Ming fafu and uiuc joint center for genomics and biotechnology Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of GeneticsBreeding and Multiple Utilization of CropsMinistry of EducationFujian Agriculture and Forestry University350002 FuzhouFujianChina Department of Plant Biology University of Illinois at Urbana-ChampaignUrbanaIL 61801USA

Crassulacean acid metabolism(CAM)photosynthesis is an innovation of carbon concentrating mechanism that is characterized by nocturnal CO2 *** progresses in genomics,transcriptomics,proteomics,and metabolomics of CAM species yielded new knowledge and abundant genomic *** 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 *** 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 *** 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.

关键词： metabolism elements evolution

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

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Horticulture Research 2020年第1期7卷 1584-1598页

作者： Ping Zhou Xiaodan Zhang Mahpara Fatima Xinyi Ma Hongkun Fang Hansong Yan Ray Ming College of Life Sciences FAFU and UIUC Joint Center for Genomics and BiotechnologyFujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry University350002 FuzhouFujianChina Fruit Research Institute Fujian Academy of Agricultural Sciences350013 FuzhouFujianChina Department of Plant Biology University of Illinois at Urbana-ChampaignUrbanaIL 61801USA College of Agriculture Fujian Agriculture and Forestry University350002 FuzhouFujianChina

Separate sexes in dioecious plants display different morphology and physiological *** differences between the two sexes lie in their highly differentiated floral characteristics and in sex-related phenotype,which is genetically determined and epigenetically *** dioecious papaya(Carica papaya L.),global comparisons of epigenetic DNA methylation and gene expressions were still *** 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 *** variances between female and male papaya were conserved among three different ***,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 *** analyses showed diverse stress-responsive methylation alteration in male and female *** flower methylation was more responsive to stress whereas female flower methylation varied less under *** flowering of male papaya in spring might be associated with the variation in the transcription of CpSVP and CpAP1 coinciding with their gene-specific *** 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.

关键词： papaya flowers landscape

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A high-quality genome provides insights into the new taxonomic status and genomic characteristics of Cladopus chinensis(Podostemaceae)

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Horticulture Research 2020年第1期7卷 2246-2261页

作者： Ting Xue Xuehai Zheng Duo Chen Limin Liang Nan Chen Zhen Huang Wenfang Fan Jiannan Chen Wan Cen Shuai Chen Jinmao Zhu Binghua Chen Xingtan Zhang Youqiang Chen Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration Fujian Key Laboratory of Special Marine Bioresource Sustainable UtilizationKey Laboratory of Developmental and Neural BiologyCollege of Life SciencesFujian Normal UniversityFuzhouChina center of Engineering Technology Research for Microalga Germplasm Improvement of Fujian Southern Institute of OceanographyFujian Normal UniversityFuzhouChina College of Fine Arts Fujian Normal UniversityFuzhouChina fafu and uiuc-sib joint center for genomics and biotechnology Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of GeneticsBreeding and Multiple Utilization of CropsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina

The Podostemaceae are ecologically and morphologically unusual aquatic angiosperms that survive only in rivers with pristine hydrology and high water quality and are at a relatively high risk of *** taxonomic status of Podostemaceae has always been ***,we report the first high-quality genome assembly for Cladopus chinensis of Podostemaceae,obtained by incorporating Hi-C,Illumina and PacBio *** generated an 827.92 Mb genome with a contig N50 of 1.42 Mb and 27,370 annotated protein-coding *** assembled genome size was close to the estimated size,and 659.42 Mb of the assembly was assigned to 29 superscaffolds(scaffold N5021.22 Mb).A total of 59.20%repetitive sequences were identified,among which long terminal repeats(LTRs)were the most abundant class(28.97%of the genome).Genome evolution analysis suggested that the divergence time of Cladopus chinensis(106 Mya)was earlier than that of Malpighiales(82 Mya)and that this taxon diverged into an independent branch of Podestemales.A recent whole-genome duplication(WGD)event occurred 4.43 million years *** genomic analysis revealed that the expansion and contraction of oxidative phosphorylation,photosynthesis and isoflavonoid metabolism genes in Cladopus chinensis are probably related to the genomic characteristics of this growing submerged *** analysis revealed that upregulated genes in the shoot group compared to the root group were enriched in the NAC gene family and transcription factors associated with shoot development and defense responses,including WUSCHEL(WUS),ASYMMETRIC LEAVES(ASL),SHOOT MERISTEMLESS(STM),NAC2,NAC8,NAC29,NAC47,NAC73,NAC83 and *** findings provide new insights into the genomic diversity of unusual aquatic angiosperms and serve as a valuable reference for the taxonomic status and unusual shoot apical meristem of Podostemaceae.

关键词： characteristics metabolism submerged

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Papaya CpbHLH1/2 regulate carotenoid biosynthesis-related genes during papaya fruit ripening

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Horticulture Research 2019年第1期6卷 751-763页

作者： Dong Zhou Yanhong Shen Ping Zhou Mahpara Fatima Jishan Lin Jingjing Yue Xingtan Zhang Li-Yu Chen Ray Ming College of Resources and Environment Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China fafu and uiuc-sib joint center for genomics and biotechnology Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of GeneticsBreeding and Multiple Utilization of CropsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China Department of Plant Biology University of Illinois at Urbana-ChampaignUrbanaIL 61801USA

The ripening of papaya is a physiological and metabolic process associated with accumulation of carotenoids,alternation of flesh color and flavor,which depending on genotype and external factors such as light and *** factors regulating carotenoid biosynthesis have not been analyzed during papaya fruit ***-Seq experiments were implemented using different ripening stages of papaya fruit from two papaya ***-elements in lycopeneβ-cyclase genes(CpCYC-B and CpLCY-B)were identified,and followed by genome-wide analysis to identify transcription factors binding to these cis-elements,resulting in the identification of CpbHLH1 and CpbHLH2,two bHLH *** expressions of CpbHLH1/2 were changed during fruit development,coupled with transcript increase of carotenoid biosynthesis-related genes including CpCYC-B,CpLCY-B,CpPDS2,CpZDS,CpLCY-E,and *** onehybrid(Y1H)and transient expression assay revealed that CpbHLH1/2 could bind to the promoters of CpCYC-B and CpLCY-B,and regulate their *** response to strong light,the results of elevated expression of carotenoid biosynthesis-related genes and the changed expression of CpbHLH1/2 indicated that CpbHLH1/2 were involved in light-mediated mechanisms of regulating critical genes in the carotenoid biosynthesis ***,our findings demonstrated several TF family members participating in the regulation of carotenoid genes and proved that CpbHLH1 and CpbHLH2 individually regulated the transcription of lycopeneβ-cyclase genes(CpCYC-B and CpLCY-B).This study yielded novel findings on regulatory mechanism of carotenoid biosynthesis during papaya fruit ripening.

关键词： papaya elevated finding

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Auxin regulation involved in gynoecium morphogenesis of papaya flowers

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Horticulture Research 2019年第1期6卷 237-247页

作者： Ping Zhou Mahpara Fatima Xinyi Ma Juan Liu Ray Ming College of Life Sciences FAFU and UIUC Joint Center for Genomics and BiotechnologyFujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhou 350002 FujianChina Fruit Research Institute Fujian Academy of Agricultural SciencesFuzhou 350013 FujianChina College of Agriculture Fujian Agriculture and Forestry UniversityFuzhou 350002 FujianChina Department of Plant Biology University of Illinois at Urbana-ChampaignUrbanaIL 61801USA

The morphogenesis of gynoecium is crucial for propagation and productivity of fruit *** 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 *** and dioecious papaya varieties were used for analysis of differentially expressed genes followed by experiments using auxin and an auxin transporter *** 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 signal transduction in rudimentary gynoecium was *** 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 *** of auxin transport by 10 mg/L NPA treatment resulted in female fertility restoration in male flowers,while female flowers did not show *** treatment with higher concentration(30 and 50 mg/L)caused deformed flowers in both male and female *** hypothesize that the occurrence of rudimentary gynoecium patterning might associate with auxin homeostasis *** auxin concentration and auxin homeostasis might be crucial for functional gynoecium morphogenesis in papaya *** results will lead to further investigation on the auxin homeostasis and gynoecium morphogenesis in papaya.

关键词： papaya morphogenesis flowers

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Allele-defined genome reveals biallelic differentiation during cassava evolution

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Molecular Plant 2021年第6期14卷 851-854页

作者： Wei Hu Changmian Ji Haitao shi Zhe Liang Zehong Ding Jianqiu Ye Wenjun Ou Gang Zhou Weiwei Tie Yan Yan Jinghao Yang Xiaoying Yang Yunxie Wei Zhiqiang Jin Jianghui Xie Ming Peng Wenquan Wang Anping Guo Biyu Xu Jianchun Guo Songbi Chen Liming Ma Mingcheng Wang Yang Zhou Xiaolong Li Ruoxi Li Siyi Guo Xinhui Xiao Zhongqing Wan Feifei An Jie Zhang Qingyun Leng Yin Li Ray Ming Kaimian Li Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences SanyaHainanChina Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions Key Laboratory of Biology and Genetic Resources of Tropical CropsInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouHainanChina Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources Hainan Institute for Tropical Agricultural ResourcesChinese Academy of Tropical Agricultural SciencesHaikouHainanChina Biomarker Technologies Corporation BeijingChina Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources College of Tropical CropsHainan UniversityHaikouHainanChina biotechnology Research Institute Chinese Academy of Agricultural SciencesBeijingChina Tropical Crops Genetic Resources Institute Chinese Academy of Tropical Agricultural SciencesHaikouHainanChina College of Food Science and Technology Qilu University of Technology(Shandong Academy of Sciences)JinanChina Fu Foundation School of Engineering and Applied Science Columbia UniversityNew YorkUSA State Key Laboratory of Crop Stress Adaptation and Improvement School of Life SciencesHenan UniversityKaifengChina The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology the Key Laboratory of Molecular Biophysics of Chinese Ministry of EducationCollege of Life Science and TechnologyHuazhong University of Science&TechnologyWuhanChina fafu and uiuc-sib joint center for genomics and biotechnology Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of GeneticsBreeding and Multiple Utilization of CropsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina Department of Plant Biology University of Illinois at Urbana-ChampaignUrbanaILUSA

Dear Editor,Generation of heterozygous genomes by hybridization between or within species can help maintain plant diversity and serve as a potential source of new species(Baek et al.,2018).Moreover,genomic heterozygosity is associated with genomic coadaptation,developmental stability,and *** definition of alleles in haplotypes is necessary to precisely characterize allelic variation controlling agriculturally important traits(Shi et al.,2019).Currently,most released genomes have mosaic assembly of haplotypes due to random selection or collapse of alleles during genome assembly(Shi et al.,2019),which masked allelic variation and functional differentiation of divergent alleles in heterozygous species.

关键词： maintain evolution assembly

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

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Horticulture Research 2021年第1期8卷 2082-2094页

作者： Juan Liu Li-Yu Chen Ping Zhou Zhenyang Liao Hai Lin Qingyi Yu Ray Ming fafu and uiuc joint center for genomics and biotechnology Key Laboratory of GeneticsBreeding and Multiple Utilization of CropsMinistry of EducationFujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyCollege of Life ScienceFujian Agriculture and Forestry UniversityFuzhou 350002 FujianChina Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Chinese Academy of SciencesWuhan Botanical GardenWuhan 430074China Texas A&M AgriLife Research center at Dallas Texas A&M University SystemDallasTX 75252USA Department of Plant Pathology&Microbiology Texas A&M UniversityCollege StationTX 77843USA Department of Plant Biology School of Integrative BiologyUniversity of Illinois at Urbana-ChampaignUrbanaIL 61801USA

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 *** 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 *** annotation revealed that genes related to plant hormone biosynthesis and signaling pathways,especially in abscisic acid and auxin pathways,were overrepresented in the *** 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 *** 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 *** results suggested that sex differentiation in papaya may be regulated by multiple layers of regulation and coordination and involved transcriptional,epigenetic,and phytohormone ***,especially ABA and auxin,transcription factors,and genes in the non-recombination region of the sex chromosome could be involved in this *** findings may facilitate the elucidation of signal transduction and gene interaction in sex differentiation of unisexual flowers in papaya.

关键词： expression flowers papaya

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