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The Chromosome-Based Rubber Tree Genome Provides New Insights into Spurge Genome Evolution and Rubber Biosynthesis

Molecular Plant 2020年第2期13卷 336-350页

作者： Jin Liu Cong Shi Cheng-Cheng Shi Wei Li Qun-Jie Zhang Yun Zhang Kui Li Hui-Fang Lu Chao Shi Si-Tao Zhu Zai-Yun Xiao Hong Nan Yao Yue Xun-Ge Zhu Yu Wu Xiao-Ning Hong Guang-Yi Fan Yan Tong Dan Zhang Chang-Li Mao Yun-Long Liu Shi-Jie Hao Wei-Qing Liu Mei-Qi Lv Hai-Bin Zhang Yuan Liu Ge-Ran Hu-tang Jin-Peng Wang Jia-Hao Wang Ying-Huai Sun Shu-Bang Ni Wen-Bin Chen Xing-Cai Zhang Yuan-Nian Jiao Evan E.Eichler Guo-Hua Li Xin Liu Li-Zhi Gao Yunnan Institute of Tropical Crops Jinghong 666100China Plant germplasm and Genomics Center Germplasm Bank of Wild Species in Southwestern ChinaKunming Institute of BotanyChinese Academy of SciencesKunming 650204China University of Chinese Academy of Sciences Beijing 100049China BGI-Qingdao Qingdao 266555China lnstitution of Genomics and Bioinformatics South China Agricultural UniversityGuangzhou 510642China Asia-Pacific Tropical Forestry germplasm Institution Southwest China Forestry UniversityKunming 650224China School of Life Sciences Nanjing UniversityNanjing 210023China Novogene Bioinformatics Institute Beijing 100083China BGI-Shenzhen Shenzhen 518083China State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China John A.Paulson School of Engineering and Applied Sciences Harvard UniversityCambridgeMA 02138USA Howard Hughes Medical Institute University of WashingtonSeattleWA 98195USA

The rubber tree,Hevea brasiliensis,produces natural rubber that serves as an essential industrial raw ***,we present a high-quality reference genome for a rubber tree cultivar GT1 using single-molecule real-time sequencing(SMRT)and Hi-C technologies to anchor the～1.47-Gb genome assembly into 18 *** chromosome-based genome analysis enabled us to establish a model of spurge chromosome evolution,since the common paleopolyploid event occurred before the split of Hevea and *** show recent and rapid bursts of the three Hevea-specific LTR-retrotransposon families during the last 10 million years,leading to the massive expansion by～65.88%(～970 Mbp)of the whole rubber tree genome since the divergence from *** identify large-scale expansion of genes associated with whole rubber biosynthesis processes,such as basal metabolic processes,ethylene biosynthesis,and the activation of polysaccharide and glycoprotein lectin,which are important properties for latex production.A map of genomic variation between the cultivated and wild rubber trees was obtained,which contains～15.7 million high-quality single-nucleotide *** identified hundreds of candidate domestication genes with drastically lowered genomic diversity in the cultivated but not wild rubber trees despite a relatively short domestication history of rubber tree,some of which are involved in rubber *** genome assembly represents key resources for future rubber tree research and breeding,providing novel targets for improving plant biotic and abiotic tolerance and rubber production.

关键词： rubber tree rubber biosynthesis chromosome evolution whole-genome duplication domestication

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Temporal regulation of alternative splicing events in rice memory under drought stress

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Plant Diversity 2022年第1期44卷 116-125页

作者： Hong Yang Ping Li Guihua Jin Daping Gui Li Liu Chengjun Zhang germplasm bank of wild species Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan650201China State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-ResourcesHubei Key Laboratory of Industrial BiotechnologySchool of Life SciencesHubei UniversityWuhan430062China Haiyan Engineering&Technology Center Kunming Institute of BotanyChinese Academy of ScienceKunmingYunnan650201China University of Chinese Academy of Sciences Beijing100049China

Plant adaptation to drought stress is essential for plant survival and crop ***,harnessing drought memory,which is induced by repeated stress and recovery cycles,was suggested as a means to improve drought resistance at the transcriptional ***,the genetic mechanism underlying drought memory is ***,we carried out a quantitative analysis of alternative splicing(AS)events in rice memory under drought stress,generating 12 transcriptome ***,we identified exon skipping(ES)as the predominant AS type(>80%)in differential alternative splicing(DAS)in response to drought *** our analysis pipeline to investigate DAS events following drought stress in six other plant species revealed variable ES frequencies ranging from 9.94%to 60.70%depending on the species,suggesting that the relative frequency of DAS types in plants is likely to be *** dinucleotide sequence at AS splice sites in rice following drought stress was preferentially GC-AG and *** U12-type splicing uses the AFAC site,this suggests that drought stress may increase U12-type splicing,and thus increase ES *** hypothesize that multiple isofbrms derived from exon skipping may be induced by drought stress in *** also identified 20 transcription factors and three highly connected hub genes with potential roles in drought memory that may be good targets for plant breeding.

关键词： Alternative splicing Drought memory Exon skipping

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Genetic diversity and population genetic structure of Python bivittatus in china

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Journal of Forestry Research 2017年第3期28卷 621-628页

作者： Yubao Duan Yingshu Wang Suying Bai Xiuhua Tian Ke Rong Jianzhang Ma College of wild Resources Northeast Forestry UniversityHarbin 150040China Key Laboratory of Forest Disaster Warning and Control of Yunnan Province College of ForestrySouthwest Forestry UniversityKunming 650224China Shanghai wild Animal Park Shanghai 201399China

The Burmese python （Python bivittatus） has recently suffered large population declines in the wild in china due to illegal capture, overexploitation, deforestation and the loss of its natural habitat. Greater knowledge of the genetic diversity and structure of wild P. bivittatus populations is needed to help ensure its effective management. In this study, we investigated the genetic diversity and population genetic structure of wild P. bivittatus in china in detail. 109 P. bivittatus individuals from five distribution areas in Guangdong （GD）, Guangxi （GX）, Hainan （HN）, Fujian （FJ） and Yunnan （YN） province of china were collected, and their genetic structure and diversity were analyzed. Eight highly polymorphic microsatellite loci were utilized to reveal high levels of genetic diversity in the P. bivittatus population. Genetic diversity was highest in GX, and lowest in GD. All geographic populations demonstrated a bottleneck effect indicating recent population decline. Fst and AMOVA analyses revealed that there was moderate genetic differentiation among the five populations, and that only 10.59 % of total genetic diversity occurred among populations. Fst values between pop- ulations were positively correlated with their geographical distances. Genetic structure analyses revealed that the HN, GX and GD populations, which were geographically closest, were assigned to a genetic cluster, while the YN and FJ populations constituted a single cluster, respectively.

关键词： Python bivittatus Microsatellite Geneticdiversity Population genetic

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CsXDH1 gene promotes caffeine catabolism induced by continuous strong light in tea plant

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Horticulture Research 2023年第6期10卷 263-275页

作者： Qianhui Tang Keyi Liu Chuan Yue Liyong Luo Liang Zeng Zhijun Wu College of Food Science Southwest UniversityChongqing 400715China Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing Southwest UniversityChongqing 400715China Integrative Science Center of germplasm Creation Southwest UniversityChongqing 401329China Tea Research Institute Southwest UniversityChongqing 400715China

Tea plant(Camellia sinensis)is an important cash crop with extensive adaptability in the ***,complex environmental factors force a large variation of tea quality-related *** is essential for the formation of bitter and fresh flavors in tea,and is the main compound of tea that improves human *** strong light stimulation was observed to cause caffeine reduction in tea leaves,but the mechanism is not *** this study,the response of tea plant to light intensity was analysed mainly by multi-omics association,antisense oligodeoxynucleotide(asODN)silencing technique,and in vitro enzyme activity *** results revealed multiple strategies for light intensity adaptation in tea plant,among which the regulation of chloroplasts,photosynthesis,porphyrin metabolism,and resistance to oxidative stress were *** catabolism was enhanced in continuous strong light,which may be a light-adapted strategy due to strict regulation by xanthine dehydrogenase(XDH).asODN silencing and enzymatic activity assays confirmed that CsXDH1 is a protein induced by light intensity to catalyze the substrate ***1 asODN silencing resulted in significant up-regulation of both caffeine and theobromine in in vitro enzyme activity assay,but not in ***1 may act as a coordinator in light intensity adaptation,thus disrupting this balance of caffeine catabolism.

关键词： metabolism stimulation caffeine

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DNA barcoding of Gaultheria L. in china(Ericaceae:Vaccinioideae)

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Journal of Systematics and Evolution 2011年第5期49卷 411-424页

作者： 1~He REN 1,2~Lu LU 1,2~Hong WANG 1,2~De-Zhu LI 1(Laboratory of Biodiversity and Biogeography,Kunming Institute of Botany,Chinese Academy of Sciences,Kunming 650204,china) 2(Plant germplasm and Genomics Center,germplasm bank of wild species,Kunming Institute of Botany,Chinese Academy of Sciences,Kunming 650204,china) (Laboratory of Biodiversity and Biogeography Kunming Institute of Botany Chinese Academy of Sciences Kunming 650204 China) (Plant germplasm and Genomics Center Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming 650204 China) *Correspondence: Hong WANG *Correspondence: E-mail: wanghong@*** Tel./Fax: 86-871-5223534.

Four DNA barcoding loci,chloroplast loci rbcL,matK,trnH-psbA,and nuclear locus internal transcribed spacer(ITS),were tested for the accurate discrimination of the Chinese species of Gaultheria by using intraspecific and interspecific pairwise P-distance,Wilcoxon signed rank test,and tree-based *** study included 186 individuals from 89 populations representing 30 *** all individuals,single locus markers showed high levels of sequencing universality but were ineffective for species *** chain reaction amplification and sequencing were successful for all four *** ITS and matK showed significantly higher levels of interspecific species delimitation than rbcL and trnH-psbA.A combination of matK and ITS was the most efficient DNA barcode among all studied regions,however,they do not represent an appropriate candidate barcode for Chinese Gaultheria,by which only 11 out of 30 species can be *** rbcL,matK,and trnH-psbA,which were recently proposed as universal plant barcodes,have a very poor capacity for species separation for Chinese *** barcodes may be reliable tools to identify the evolutionary units of this group,so further studies are needed to develop more efficient DNA barcodes for Gaultheria and other genera with complicated evolutionary histories.

关键词： DNA barcoding Ericaceae Gaultheria species discrimination taxonomy Vaccinioideae.

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Chemical constituents from the aerial parts of Euphorbia sikkimensis and their bioactivities

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Natural Products and Bioprospecting 2013年第3期3卷 112-116页

作者： Da-Song YANG Wei-Bing PENG Zi-Lei LI Xue WANG Jian-Guo WEI Ke-Chun LIU Yong-Ping YANG Xiao-Li LI Key Laboratory of Economic Plants and Biotechnology Kunming Institute of BotanyChinese Academy of SciencesKunming 650201China Plant germplasm and Genomics Center the Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunming 650201China Institute of Tibetan Plateau Research at Kunming Kunming Institute of BotanyChinese Academy of SciencesKunming 650201China Biology Institute of Shandong Academy of Sciences Jinan 250014China

Phytochemical investigation of the aerial parts of Euphorbia sikkimensis led to the isolation of one new diterpenoids,named sikkimenoid E(1),together with thirteen other known compounds(2-14).Their structures were established by means of spectroscopic *** 2 was identified to be a trinortriterpenoid,and derived for the first time from a natural *** this paper we reveal for the first time its comprehensive spectral data and NMR spectral *** 4 showed anti-angiogenic activity with an IC_(50) value of 5.66μM in a zebrafish model,and compounds 5 and 6 exhibited cytotoxicity toward A549 cell line with IC_(50) values of 12.12 and 6.45μM,respectively.

关键词： Euphorbia sikkimensis ingenol trinortriterpenoid tocopherol derivatives bioactivities

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Incomplete reproductive isolation between Rhododendron taxa enables hybrid formation and persistence

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Journal of Integrative Plant Biology 2019年第4期61卷 433-448页

作者： Li-Jun Yan Kevin S.Burgess Wei Zheng Zhi-Bin Tao De-Zhu Li Lian-Ming Gao Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany the Chinese Academy of Sciences germplasm bank of wild species Kunming Institute of Botany the Chinese Academy of Sciences Kunming College of Life Science University of the Chinese Academy of Sciences College of Vocational and Technical Education Yunnan Normal University Department of Biology College of Letters & Sciences Columbus State University University System of Georgia

The evolutionary consequences of hybridization ultimately depend on the magnitude of reproductive isolation between hybrids and their parents. We evaluated the relative contributions of pre-and post-zygotic barriers to reproduction for hybrid formation, hybrid persistence and potential for reproductive isolation of hybrids formed between two Rhododendron species,R. spiciferum and R. spinuliferum. Our study established that incomplete reproductive isolation promotes hybrid formation and persistence and delays hybrid *** pre-zygotic barriers to reproduction leading to hybrid formation are incomplete: parental species have overlapping flowering; they share the same pollinators;reciprocal assessments of pollen tube germination and growth do not differ among parents. The absence of post-zygotic barriers between parental taxa indicates that the persistence of hybrids is likely. Reproductive isolation was incomplete between hybrids and parents in all cases studied, although asymmetric differences in reproductive fitness were prevalent and possibly explain the genetic structure of natural hybrid swarms where hybridization is known to be bidirectional but asymmetric. Introgression, rather than speciation, is a probable evolutionary outcome of hybridization between the two Rhododendron taxa. Our study provides insights into understanding the evolutionary implications of natural hybridization in woody plants.

关键词： Incomplete reproductive isolation Rhododendron taxa

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RAD-seq data reveals robust phylogeny and morphological evolutionary history of Rhododendron

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Horticultural Plant Journal 2024年第3期10卷 866-878页

作者： Yuanting Shen Gang Yao Yunfei Li Xiaoling Tian Shiming Li Nian Wang Chengjun Zhang Fei Wang Yongpeng Ma Yunnan Key Laboratory for Integrative Conservation of Plant species with Extremely Small Populations Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan 650201China Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan 650201China University of Chinese Academy of Sciences Beijing 100049China Beijing Genomics of Institute ShenzhenGuangdong 518120China Guiyang Institute of Humanities and Technology GuiyangGuizhou 550025China State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River College of ForestryShandong Agricultural UniversityTai'anShandong 271018China the southwest china of germplasm bank of wild species Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan 650201China West china Subalpine Botanical Garden Institute of BotanyChinese Academy of SciencesChengduSichuan 611834China

Rhododendron is famous for its high ornamental ***,the genus is taxonomically difficult and the relationships within Rhododendron remain *** addition,the origin of key morphological characters with high horticulture value need to be *** problems largely hinder utilization of germplasm *** studies attempted to disentangle the phylogeny of Rhododendron,but only used a few genomic markers and lacked large-scale sampling,resulting in low clade support and contradictory phylogenetic ***,we used restriction-site associated DNA sequencing(RAD-seq)data and morphological traits for 144 species of Rhododendron,representing all subgenera and most sections and subsections of this species-rich genus,to decipher its intricate evolutionary history and reconstruct ancestral *** results revealed high resolutions at subgenera and section levels of Rhododendron based on RAD-seq *** optimal phylogenetic tree and split tree recovered five lineages among ***(cladeⅠ)formed the basal *** and Azaleastrum formed cladeⅡand had sister ***Ⅲincluded all scaly rhododendron ***(cladeⅣ)formed a sister group to ***(cladeⅤ).The results of ancestral state reconstruction showed that Rhododendron ancestor was a deciduous woody plant with terminal inflorescence,ten stamens,leaf blade without scales and broadly funnelform corolla with pink or purple *** study shows significant distinguishability to resolve the evolutionary history of Rhododendron based on high clade support of phylogenetic tree constructed by RAD-seq *** also provides an example to resolve discordant signals in phylogenetic trees and demonstrates the application feasibility of RAD-seq with large amounts of missing data in deciphering intricate evolutionary ***,the reconstructed ancestral state of six important characters provides insights into the inn

关键词： Rhododendron RAD-seq Missing data Quartet sampling(QS) Ancestral state reconstruction

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CRISPR-Cas13-mediated RNA editing in the silkworm Bombyx mori

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Zoological Research 2024年第6期45卷 1249-1260页

作者： Yao-Hao Tang Xing Zhang Zong-Cai Dai Hao Li Yan Yang Tu-Jing Zhao Dong-Qin Yuan Wen-Liang Qian Dao-Jun Cheng Integrative Science Center of germplasm Creation in Western china(CHONGQING)Science City Biological Science Research CenterSouthwest UniversityChongqing 400715China State Key Laboratory of Resource Insects Southwest UniversityChongqing 400715China

The CRISPR-Cas13 system,an RNA-guided editing tool,has emerged as a highly efficient and stable RNA editing *** the CRISPR-Cas13 system has been developed in several insect species,its application in lepidopterans has not yet been *** the present study,we evaluated the RNA cleavage activity of the CRISPR-Cas13 system in the silkworm(Bombyx mori),a model lepidopteran insect,both ex vivo and in *** established two stable silkworm BmE cell lines expressing PspCas13b and CasRx,*** analysis demonstrated that both PspCas13b and CasRx effectively down-regulated the transcription of exogenouslyintroduced target and endogenous genes in these cell *** addition,we generated two transgenic silkworm strains,one expressing CasRx and the other expressing RNA-guided CRISPR RNA targeting Sex combs reduced(Scr).Further crossing experiments showed that CasRx induced a down-regulation of Scr transcription in silkworms,which impaired systemic growth of ***,this study demonstrated that the CRISPR-Cas13RNA editing system works efficiently in the silkworm,providing a potential alternative approach for RNA manipulation in lepidopteran insects.

关键词： Silkworm CRISPR PspCas13b CasRx RNA editing

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Minor Prenylated Flavonoids from the Twigs of Macaranga adenantha and Their Cytotoxic Activity

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Natural Products and Bioprospecting 2015年第2期5卷 105-109页

作者： Da-Song Yang Shuang-Mei Wang Wei-Bing Peng Yong-Ping Yang Ke-Chun Liu Xiao-Li Li Wei-Lie Xiao Key Laboratory of Economic Plants and Biotechnology Germplasm Bank of Wild Species in Southwest ChinaInstitute of Tibetan Plateau Research at KunmingKunming Institute of BotanyChinese Academy of SciencesKunming 650201People’s Republic of China Biology Institute of Shandong Academy of Sciences Jinan 250014People’s Republic of China State Key Laboratory of Phytochemistry and Plant Resources in West china Kunming Institute of BotanyChinese Academy of SciencesKunming 650201People’s Republic of China

Three new minor prenylated flavonoids,named macadenanthins A–C(1–3),together with three known ones(4–6),were isolated from the twigs of Macaranga *** structures were elucidated on the basis of extensive spectroscopic analysis including NMR,UV and *** prenyl moieties in compounds 1–3 were further modified by cyclization and *** new compounds were tested for their cytotoxicity against four cancer cell lines(MCF-7,Hep G2,Hela and P388)and showed IC50 values in the range of 13.76–22.27 lM.

关键词： Macaranga adenantha Prenylated Flavonoids Macadenanthins A-C Cytotoxicity

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