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The Reference Genome of Tea Plant and Resequencing of 81 Diverse Accessions Provide Insights into Its Genome Evolution and Adaptation

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Molecular Plant 2020年第7期13卷 1013-1026页

作者： Enhua Xia Wei Tong Yan Hou Yanlin An Linbo Chen Qiong Wu Yunlong Liu Jie Yu Fangdong Li Ruopei Li Penghui Li Huijuan Zhao Ruoheng Ge Jin Huang Ali Inayat Mallano Yanrui Zhang Shengrui Liu Weiwei Deng Chuankui Song Zhaoliang Zhang Jian Zhao Shu Wei Zhengzhu Zhang Tao Xia Chaoling Wei Xiaochun Wan State Key Laboratory of Tea Plant Biology and Utilization Anhui Agricultural UniversityHefei 230036China Tea Research Institute Yunnan Academy of Agricultural SciencesMenghai 666201China germplasm bank of wild species in southwestern china Kunming Institute of BotanyChinese Academy of SciencesKunming 650204China

Tea plant is an important economic crop,which is used to produce the world's oldest and most widely consumed tea ***,we present a high-quality reference genome assembly of the tea plant(Camellia sinensis ***)consisting of 15 *** retrotransposons(LTR-RTs)account for 70.38%of the genome,and we present evidence that LTR-RTS play critical roles in genome size expansion and the transcriptional diversification of tea plant genes through preferential insertion in promoter regions and ***,particularly those coding for terpene biosynthesis pro-teins,associated with tea aroma and stress resistance were significantly amplified through recent tandem duplications and exist as gene clusters in tea plant *** analysis of the sequences of 81 tea plant accessions with diverse origins revealed three well-differentiated tea plant populations,support-ing the proposition for the southwest origin of the Chinese cultivated tea plant and its later spread to western Asia through *** and modern breeding left significant signatures on hundreds of genes in the tea plant genome,particularly those associated with tea quality and stress *** genomic sequences of the reported reference and resequenced tea plant accessions provide valuable resources for future functional genomics study and molecular breeding of improved cul-tivars of tea plants.

关键词： tea plant comparative genomics genome evolution adaptive evolution tea quality

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Building a better plant world through mutual learning: An introduction to a special issue on plant diversity and conservation in the Belt & Road Countries

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Plant Diversity 2019年第3期41卷 133-134页

作者： Xuefei Yang Yongping Yang Key Laboratory of Economic Plants and Biotechnology Kunming Institute of Botany Chinese Academy of Sciences China South Asian Biodiversity Research Institute Chinese Academy of Sciences China The germplasm bank of wild species Kunming Institute of Botany Chinese Academy of Sciences China

Plants play important roles in international trade and cultural exchange. Mention of the Silk Road instantly conjures images of plants and plant products, from the tea of china (Lagarde, 2017), to pepper, flax, spices, grapes, and pomegranates of South and Central Asia (Xi, 2017). In 2015, when china officially launched the Belt and Road Initiative (BRI), biodiversity conservation was repeatedly emphasized in joint communiques of the Leaders' Roundtable of the Belt and Road Forum for International Cooperation. However, our knowledge of both plant diversity and conservation in the Belt and Road Countries is limited, which hampers our planning and implementation on the eco-friendly infrastructural projects as promoted by the BRI. To promote regional cooperation and knowledge sharing on plant diversity and conservation, in September 2018, the Kunming Institute of Botany (KIB), under the sponsorship of Chinese Academy of Sciences (CAS), organized an international workshop entitled “International Workshop on Plant Diversity and Conservation of the One Belt and One Road Countries.” This special issue of Plant Diversity presents some of the outcomes of the workshop.

关键词： play international tea

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The first complete plastid genome of Burmannia disticha L. from the mycoheterotrophic monocot family Burmanniaceae

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Plant Diversity 2018年第5期40卷 232-237页

作者： Liuqing Ma Pengfei Ma Dezhu Li germplasm bank of wild species Kunming Institute of Botany Chinese Academy of Sciences Kunming Yunnan 650201 China Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Kunming Yunnan 650201China University of Chinese Academy of Sciences Beijing 100049 China

Burmanniaceae is one major group within the monocot order Dioscoreales that has not had its plastome *** of Burmanniaceae are mostly achlorophyllous,although the genus Burmannia also includes ***,we report sequencing and analysis of the first Burmanniaceae plastid genome from Burmannia disticha L..This plastome is 157,480 bp and was assembled as a circular sequence with the typical quadripartite structure of plant plastid *** plastome has a regular number of potentially functional genes with a total of 111,including 78 protein coding genes,4 ribosomal RNA(rRNA) genes,and 29 tRNA *** ratio of the total length of genic:intergenic DNA is 1.58:1,and the mean length of intergenic regions is 398 bp,the longest being 1918 *** overall GC content of the *** plastome is 34.90%,and the IR regions in *** are more GC rich(39.50%) than the LSC(32.30%) and SSC(28.80%) *** analysis of protein-coding sequences from plastomes of related species in the order Dioscoreales support a clade comprising Burmanniaceae and *** phylogenetic placement is congruent with previous findings based on nuclear and mitochondrial evidence.

关键词： Burrnannia disticha Burmanniaceae Plastome Phylogenetic analysis

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Comparative analysis of 12 water lily plastid genomes reveals genomic divergence and evolutionary relationships in early flowering plants

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Marine Life Science & Technology 2024年第3期6卷 425-441页

作者： Weicai Song Wenbo Shi Huan Wang Zirui Zhang Ruiqing Tao Jin Liu Shuo Wang Michael S.Engel Chao Shi College of Marine Science and Biological Engineering Qingdao University of Science and TechnologyQingdao 266042China Plant germplasm and Genomics Center Germplasm Bank of Wild Species in Southwest ChinaKunming Institute of BotanyThe Chinese Academy of SciencesKunming 650204China Yunnan Institute of Tropical Crops Xishuangbanna 666100China American Museum of Natural History New YorkNY 10024-5192USA Natural History Museum and Department of Ecology&Evolutionary BiologyUniversity of KansasLawrenceKS 66045USA

The aquatic plant Nymphaea,a model genus of the early flowering plant lineage Nymphaeales and family Nymphaeaceae,has been extensively ***,the availability of chloroplast genome data for this genus is incomplete,and phylogenetic relationships within the order Nymphaeales remain *** this study,12 chloroplast genomes of Nymphaea were assembled and analyzed for the first *** genomes were 158,290-160,042 bp in size and contained 113 non-repeat genes,including 79 protein-coding genes,30 tRNA genes,and four rRNA *** also report on codon usage,RNA editing sites,microsatellite structures,and new repetitive sequences in this *** genomics revealed that expansion and contraction of IR regions can lead to changes in the gene ***,it was observed that the highly variable regions of the chloroplast genome were mainly located in intergenic ***,the phylogenetic tree showed the order Nymphaeales was divided into three families,and the genus Nymphaea can be divided into five(or three)subgenera,with the subgenus Nymphaea being the *** divergence times of nymphaealean taxa were analyzed,with origins of the order Nymphaeales and family Nymphaeaceae being about 194 and 131 million years,*** results of the phylo-genetic analysis and estimated divergence times will be useful for future evolutionary studies of basal angiosperm lineages.

关键词： Aquatic plants Nymphaea Phylogenetic analysis Plastid genomics Structural variation

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Physiological and biochemical analysis of mechanisms underlying cadmium tolerance and accumulation in turnip

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Plant Diversity 2018年第1期40卷 19-27页

作者： Xiong Li Xiaoming Zhang YuanshengWu Boqun Li Yongping Yang Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunmingChina china germplasm bank of wild species Kunming Institute of BotanyChinese Academy of SciencesKunmingChina University of Chinese Academy of Sciences BeijingChina College of Plant Protection Yunnan Agricultural UniversityKunmingChina

The capacity of plants to accumulate cadmium(Cd) is significant for phytoremediation of Cd-polluted soils. Turnips cultivated in china include species featuring high Cd accumulation and some of these plants act as Cd hyperaccumulator landraces. These plants can accumulate over 100 mg Cd kg^(-1) dry weight in leaves without injury. Hence, studies that explore mechanisms underlying Cd detoxification and transport in turnip plants are essential. In the present study, we compared physiological and biochemical changes in turnip leaves treated with two Cd concentrations to controls. We discovered that Cd stress significantly increased the enzymatic activities or compound contents in the antioxidant system, including members of the glutathione-ascorbic acid cycle, whereas oxidation of reactive oxygen species(ROS) remained stable. Cd treatments also increased the contents of phytochelatins as well as a number of amino acids. Based on these results, we conclude that turnips initiate a series of response processes to manage Cd treatment. First, the antioxidant system maintaining ROS homeostasis and osmotic adjustment is excited to maintain stability of cell osmotic potential. Cd is chelated into its stable form to reduce its toxicity. Cd is possibly transported to vacuoles or non-protoplasts for isolation. Amino acid synthesis may directly and indirectly play an important role in these processes. This study partly revealed physiological and biochemical mechanisms underlying turnip response to Cd stress and provides information on artificially increasing or decreasing Cd accumulation in turnips and other plants.

关键词： Turnip Cadmium Detoxification Antioxidant system Phytochelatin

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A new subtribal classification of Arundinarieae(Poaceae,Bambusoideae)with the description of a new genus

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Plant Diversity 2020年第3期42卷 127-134页

作者： Yu-Xiao Zhang Cen Guo De-Zhu Li Yunnan Academy of Biodiversity Southwest Forestry UniversityKunmingYunnan650224China Gennplasm bank of wild species Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan650201China Kunming College of Life Science University of Chinese Academy of SciencesKunmingYunnan650201China

A new subtribal classification of the woody bamboo tribe Arundinarieae is proposed based on recent phylogenomic *** subtribes,corresponding to the five major lineages of the ddRAD-seq based phylogenomic trees,are recognised:Arundinariinae(the leptomorph lineage),Ampelocalaminae(the ADH lineage),Gaoligongshaniinae(represented by Gaoligongshania),Hsuehochloinae(represented by Hsuehochloa) and Thamnocalaminae(the pachymorph lineage,i.e.,alpine bamboos).Subtribes Ampelocalaminae,Gaoligongshaniinae and Hsuehochloinae are newly established,while the circumscriptions of subtribes Arundinariinae and Thamnocalaminae differ from the traditional *** Arundinariinae also includes those taxa that were previous members of the subtribe ***,among the five redefined subtribes,Arundinariinae is the most heterogenous in terms of *** Arundinarieae,rhizome type has greater implications for classification than other vegetative and reproductive characters at the subtribal *** addition,the new monotypic genus Ravenochloa is described on the basis of its mo rphological characteristics and geographical distribution to accommodate the unique phylogenetic entity of Indocalamus wilsonii.

关键词： Ampelocalaminae Gaoligongshaniinae Hsuehochloinae Ravenochloa Rhizome type Temperate woody bamboos

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Using MiddRAD-seq data to develop polymorphic microsatellite markers for an endangered yew species

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Plant Diversity 2017年第5期39卷 294-299页

作者： Hantao Qin Guoqian Yang Jim Provan Jie Liu Lianming Gao Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan650201 China University of Chinese Academy of Sciences Beijing100049China germplasm bank of wild species in southwest china Kunming Institute of BotanyChinese Academy of SciencesKunming650201China Institute of Biological Environmental and Rural Sciences (IBERS)Aberystwyth UniversityPengiaisAberystwythSY23 3DAUK

Microsatellites are highly polymorphic markers which have been used in a wide range of genetic *** recent years, various sources of next-generation sequencing data have been used to develop new microsatellite loci, but compared with the more common shotgun genomic sequencing or transcriptome data, the potential utility of RAD-seq data for microsatellite ascertainment is comparatively *** this study, we employed MiddRAD-seq data to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. Of 8,823,053 clean reads generated for ten individuals of a population, 94,851(~1%) contained microsatellite motifs. These corresponded to 2993 unique loci, of which 526(~18%) exhibited polymorphism. Of which, 237 were suitable for designing microsatellite primer pairs, and 128 loci were randomly selected for PCR validation and microsatellite screening. Out of the 128 primer pairs, 16 loci gave clear, reproducible patterns, and were then screened and characterized in 24 individuals from two populations. The total number of alleles per locus ranged from two to ten(mean=4.875), and within-population expected heterozygosity from zero to 0.789(mean = 0.530),indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.

关键词： MiddRAD-seq Endangered species Microsatellite Next-generation sequencing Taxus florinii

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Characterisation of manganese toxicity tolerance in Arabis paniculata

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Plant Diversity 2021年第2期43卷 163-172页

作者： Ting Tang Faqing Tao Weiqi Li School of Life Sciences Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated UtilizationKey Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted SoilsHunan University of Science and TechnologyXiangtan411201China Plant germplasm and Genomics Center Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunming650201China

Manganese(Mn)contamination limits the production and quality of crops,and affects human health by disrupting the food *** paniculata is a pioneer species of Brassicaceae found in mining areas,and has the ability to accumulate heavy ***,little is known about the genetic mechanisms of Mn tolerance in *** this study,we found that Mn tolerance and ability to accumulate Mn were higher in *** than in Arabidopsis *** mechanisms underlying the response and recovery of *** to Mn toxicity were further investigated using transcriptome analysis.A total of 69,862,281 base pair clean reads were assembled into 61,627 high-quality unigenes,of which 41,591(67.5%)and 39,297(63.8%)were aligned in the Kyoto Encyclopedia of Genes and Genomes(KEGG)and Gene Ontology(GO),*** response to Mn toxicity,genes were expressed in twelve distinct patterns,which can be divided into four general categories:initial,stable,dose-dependent,and *** that were differentially expressed during Mn response and recovery belong to several dominant KEGG *** early response to Mn toxicity in *** includes the upregulation of genes involved in glutathione ***-binding cassette(ABC)transporter proteins were up-regulated during the entire response phase,and genes involved in glycerophospholipid metabolism were upregulated during the late phase of the Mn *** in the phenylpropanoid pathway were differentially expressed in the repair process after Mn *** findings reveal ideal material and genetic resources for phytoremediation in Mn-contaminated areas and highlight new knowledge and theoretical perspectives on the mechanisms of Mn tolerance.

关键词： Arabis paniculata Manganese toxicity Transcriptome Gene expression

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Novel umami peptides from two Termitomyces mushrooms and molecular docking to the taste receptor T1R1/T1R3

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Food Science and Human Wellness 2024年第2期13卷 1055-1064页

作者： Lanyun Zhang Li Zhang Jesus Pérez-Moreno Lu Bin Fengming Zhang Fuqiang Yu The germplasm bank of wild species Yunnan Key Laboratory for Fungal Diversity and Green DevelopmentKunming Institute of BotanyChinese Academy of SciencesKunming 650201China College of Chemical Science and Technology Yunnan UniversityKunming 650091China College of Food Science and Technology Yunnan Agricultural UniversityKunming 650201China Colegio Postgraduados Campus MontecilloEdafologíaTexcoco 56230México Key Laboratory for Forest Resources Conservation and Use in the southwest Mountains of china Southwest Forestry UniversityKunming 650224China

wild edible Termitomyces mushrooms are popular in southwest china and umami is important flavor qualities of edible *** study aimed to understand the umami taste of Termitomyces intermedius and Termitomyces *** umami peptides from aqueous extracts were separated using a Sephadex G-15 gel filtration *** intense umami fraction was evaluated by both sensory evaluation and electronic *** were identified as KLNDAQAPK,DSTDEKFLR,VGKGAHLSGEH,MLKKKKLA,SLGFGGPPGY,TVATFSSSTKPDD,AMDDDEADLLLLAM,VEDEDEKPKEK,SPEEKKEEET and *** peptides,except VEDEDEKPKEK,SPEEKKEEET and PEGADKPNK were selectively synthesized to verify their taste *** these 10 peptides had umami or salt *** 10 peptides were conducted by molecular docking to study their interaction with identified peptides and the umami taste receptor T1R1/*** these 10 peptides perfectly docked the active residues in the T1R3 *** results provide theoretical basis for the umami taste and address the umami mechanism of two wild edible Termitomyces mushrooms.

关键词： Termitomyces Non-volatile flavor compounds Umami peptides Taste characteristics Molecular docking

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The coexistence of hermaphroditic and dioecious plants is associated with polyploidy and gender dimorphism in Dasiphora fruticosa

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Plant Diversity 2019年第5期41卷 323-329页

作者： Lin-Lin Wang Zhi-Qiang Zhang Yong-Ping Yang Yuan-Wen Duan Key Laboratory for Plant Diversity and Biogeography of East Asia Germplasm Bank of Wild SpeciesInstitute of Tibetan Plateau Research at KunmingKunming Institute of BotanyChinese Academy of SciencesKunmingYunnan650201China University of the Chinese Academy of Sciences Beijing100049China Laboratory of Ecology and Evolutionary Biology Yunnan UniversityKunmingYunnan650091China

Dasiphora fruticosa comprises male,female and hermaphrodite plants,which are distributed sympatrically in some populations on the Qinghai-Tibet *** explore what governs the coexistence of these three sexual phenotypes,we investigated the DNA contents,pollen and ovule production,pollen deposition,and performed hand-pollination in both hermaphroditic and dioecious individuals of *** cytometry confirmed that the DNA content of males and females were almost twice as much as that of the *** and female flowers produced more pollen grains and ovules than hermaphroditic ***-pollinated treatments showed that unisexual flowers were sterile in one sexual function and bisexual flowers were fertile for both functions,but no sterile seeds were produced between unisexual and bisexual *** findings imply that polyploidy is related to gender dimorphism,and both are likely to play a strong role in the coexistence of two cryptic biological species of ***(low ploidy hermaphroditic species and high ploidy dioecious species)in the Qinghai-Tibet Plateau.

关键词： Gender polymorphism Dioecy Dasiphora fruticosa Polyploidy Reproductive isolation

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