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Plastid phylogenomic insights into the evolution of subfamily Dialioideae (Leguminosae)

Plant Diversity 2021年第1期43卷 27-34页

作者： Han-Rui Bai Oyetola Oyebanji Rong Zhang ting-shuang yi Germplasm Bank of Wild Species Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan650201China College of Life Science Yunnan UniversityKunmingYunnan650201China Kunming College of Life Science University of Chinese Academy of SciencesKunmingYunnan650201China

The subfamily Dialioideae(Leguminosae)consists of 17 genera and about 85 *** studies have detected significant plastid genome(plastome)structure variations in legumes,particularly in subfamilies Papilionoideae and *** it is important to investigate plastomes from the newly recognized Dialioideae to better understand the plastome variation across the whole ***,we used nine plastomes representing nine genera of Dialioideae to explore plastome structural variation and intergeneric relationships in this *** plastomes of Dialioideae exhibited a typical quadripartite structure,and had relatively conserved structure compared with other legume ***,the genome size ranged from 154,124 bp to 165,973 bp and gene numbers ranged from 129 to132,mainly due to the expansion and contraction of the inverted repeat(IR)*** IR of Distemonanthus benthamianus has experienced two separate expansions into the large single copy(LSC)region and the small single copy(SSC)region,and one contraction from *** procera has experienced two separate IR expansions into LSC,while Dicorynia paraensis has experienced an IR contraction from *** divergent regions or genes(ndhC-trnV^(UAC),psbK-trnQ^(UUG),rps19-rps3,rpl33-rps18,accD-psaI,trnG^(UCC)-trnS^(GCU),psbI-trnS^(GCU),5'rps16-trnQ^(UUG)and ycf1)were identified as potential molecular markers for further species delimitation and population genetics analysis in *** analysis based on 77 protein-coding sequences fully resolved the intergeneric relationships among nine genera except a moderately supported sister relationship between Petalostylis labicheoides and Labichea *** study reveals new insights into the structural variations of plastomes in subfamily Dialioideae and advances our understanding of the evolutionary trajectories of legume plastomes.

关键词： Dialioideae Plastome IR expansion/contraction Fabaceae Variation

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Phylogenomics and the flowering plant tree of life

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Journal of Integrative Plant Biology 2023年第2期65卷 299-323页

作者： Cen Guo Yang Luo Lian-Ming Gao ting-shuang yi Hong-Tao Li Jun-Bo Yang De-Zhu Li Germplasm Bank of Wild Species Kunming Institute of Botanythe Chinese Academy of SciencesKunming 650201China CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botanythe Chinese Academy of SciencesKunming 650201China Lijiang Forest Diversity National Observation and Research Station Kunming Institute of BotanyChinese Academy of SciencesLijiang 674100China Kunming College of Life Science University of Chinese Academy of SciencesKunming 650201China

The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic *** the past decade,a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new *** the meantime,a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is *** review focuses on the utility of genomic data(from organelle genomes,to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations,describes the baseline methodology of experimental and analytical procedures,and summarizes recent progress in flowering plant phylogenomics at the ordinal,familial,tribal,and lower *** also discuss the challenges,such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors,and underlying biological factors,such as whole-genome duplication,hybridization/introgression,and incomplete lineage sorting,together suggesting that a bifurcating tree may not be the best model for the tree of ***,we discuss promising avenues for future plant phylogenomic studies.

关键词： angiosperms hybridization incomplete lineage sorting orthology inference phylogenetic conflicts reduced representation sequencing whole-genome sequencing whole-genome duplication

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Nuclear phylotranscriptomics and phylogenomics support numerous polyploidization events and hypotheses for the evolution of rhizobial nitrogenfixing symbiosis in Fabaceae

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Molecular Plant 2021年第5期14卷 748-773页

作者： yiyong Zhao Rong Zhang Kai-Wen Jiang Ji Qi yi Hu Jing Guo Renbin Zhu Taikui Zhang Ashley N.Egan ting-shuang yi Chien-Hsun Huang Hong Ma State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development Ministry of Education Key Laboratory of Biodiversity and Ecological EngineeringInstitute of Plant BiologyCenter of Evolutionary BiologySchool of Life SciencesFudan University2005 Songhu RoadShanghai 200433China Department of Biology The Huck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPA 16802USA Germplasm Bank of Wild Species Kunming Institute of BotanyChinese Academy of SciencesLanhei RoadKunming 650201China Key Laboratory of Biodiversity Conservation in Southwest China State Forestry AdministrationSouthwest Forestry UniversityKunming 650224PR China Ningbo Botanical Garden Herbarium Ningbo 315201PR China Xishuangbanna Tropical Botanical Garden Chinese Academy of SciencesMenglunYunnan 666303PR China Department of Biology Utah Valley UniversityOremUT 84058USA

Fabaceae are the third largest angiosperm family,with 765 genera and~19500 *** are important both economically and ecologically,and global Fabaceae crops are intensively studied in part for their nitrogen-fixing ***,resolution of the intrasubfamilial Fabaceae phylogeny and divergence times has remained elusive,precluding a reconstruction of the evolutionary history of symbiotic nitrogen fixation in ***,we report a highly resolved phylogeny using>1500 nuclear genes from newly sequenced transcriptomes and genomes of 391 species,along with other datasets,for a total of 463 legumes spanning all 6 subfamilies and 333 of 765 *** subfamilies are maximally supported as *** clade comprising subfamilies Cercidoideae and Detarioideae is sister to the remaining legumes,and Duparquetioideae and Dialioideae are successive sisters to the clade of Papilionoideae and *** clock estimation revealed an early radiation of subfamilies near the K/Pg boundary,marked by mass extinction,and subsequent divergence of most tribe-level clades within~15 million *** analyses of thousands of gene families support 28 proposed putative whole-genome duplication/whole-genome triplication events across Fabaceae,including those at the ancestors of Fabaceae and five of the subfamilies,and further analyses supported the Fabaceae ancestral *** evolution of rhizobial nitrogen-fixing nodulation in Fabaceae was probed by ancestral character reconstruction and phylogenetic analyses of related gene families and the results support the hypotheses of one or two switches)to rhizobial nodulation followed by multiple ***,these results provide a foundation for further morphological and functional evolutionary analyses across Fabaceae.

关键词： Fabaceae Leguminosae nuclear phylogeny divergence times whole-genome duplication rhizobial nodulation

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Honoring a legend: Celebrating the life and legacy of Professor Heng Li

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Plant Diversity 2023年第3期45卷 239-240页

作者： Hui-Jun Guo Jin-Ling Huang Yun-Heng Ji Rong Li Chun-Lin Long Qin-Er Yang Yong-Ping Yang ting-shuang yi National Plateau Wetlands Research Center Southwest Forestry UniversityKunming 650224YunnanChina Department of Biology East Carolina UniversityGreenville 27858NCUSA CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanChina Key Laboratory of Ecology and Environment in Minority Areas(Minzu University of China) National Ethnic Affairs CommissionBeijing 100081China College of Life and Environmental Sciences Minzu University of ChinaBeijing 100081China CAS Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical GardenChinese Academy of SciencesGuangzhou 510650GuangdongChina CAS Key Laboratory of Tropical Plant Resources and Sustainable Use Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesXishuangbanna 666303YunnanChina Germplasm Bank of Wild Species Kunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanChina

Professor Heng Li(李恒,March 9,1929-January 12,2023)was a legendary plant taxonomist and phytogeographer at the Kunming Institute of Botany,Chinese Academy of Sciences(Fig.1).She made important contributions to our understanding of China's flora,including the biodiversity and biogeography of Dulong Valley and the Gaoligong Mountains,as well as the vegetation of plateau lakes and wetlands in Southwest *** Heng Li received her Bachelor's degree in Russian from Beijing Foreign Studies University in 1956 and immediately joined the Institute of Geography(now Institute of Geographic Sciences and Natural Resources Research),Chinese Academy of Sciences,as a Russian *** 1961,Prof.

关键词： translator plateau Hen

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Phylogenetic inferences in Prunus （Rosaceae） using chloroplast ndhF and nuclear ribosomal ITS sequences

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植物分类学报 2008年第3期46卷 322-332页

作者： Jun WEN Scott T. BERGGREN Chung-Hee LEE Stefanie ICKERT-BOND ting-shuang yi Ki-Oug YOO Lei XIE Joey SHAW Dan POTTER Department of Botany National Museum of Natural History MRC 166 Smithsonian Institution Washington DC 20013-7012 USA Department of Biology Colorado State University Fort Collins CO 80523 USA Korean National Arboretum 51-7 Jikdongni Soheur-eup Pocheon-si Gyeonggi-do 487-821 Korea UA Museum of the North and Department of Biology and Wildlife University of Alaska Fairbanks Fairbanks AK 99775-6960 USA Key Laboratory of Plant Biodiversity and Biogeography Kunming Institute of Botany Chinese Academy of Sciences Kunming 650204 China Division of Life Sciences Kangwon National University Chuncheon 200-701 Korea State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences Beijing 100093 China Department of Biological and Environmental Sciences University of Tennessee Chattanooga TN 37403-2598 USA Department of Plant Sciences MS 2 University of California Davis CA 95616 USA

Sequences of the chloroplast ndhF gene and the nuclear ribosomal ITS regions are employed to recon-struct the phylogeny of Prunus (Rosaceae), and evaluate the classification schemes of this genus. The two data sets are congruent in that the genera Prunus s.l. and Maddenia form a monophyletic group, with Maddenia nested within Prunus. However, the ndhF data set is incongruent with the ITS data supporting two major groups within Prunus: one consisting of subgenera Laurocerasus (including Pygeum) and Padus as well as the genus Maddenia and another of subgenera Amygdalus, Cerasus, and Prunus. The ITS data, on the other hand, support a clade composed of subgenera Amygdalus and Prunus and Prunus sect. Microcerasus in addition to a paraphyletic grade of subgenera Laurocerasus and Padus (and the genus Maddenia) taxa. In general, the subgeneric classifications of Prunus s.l. are not supported. The ITS and ndhF phylogenies differ mainly in interspecific relationships and the relative position of the Padus/Laurocerasus group. Both ITS and ndhF data sets suggest that the formerly recog-nized genus Pygeum is polyphyletic and that the distinction of the subgenera Padus and Laurocerasus is not supported. The biogeographic interactions of the temperate and tropical members in the Padus/Laurocera- sus/Maddenia alliance including Pygeum are shown to be highly dynamic and complex.

关键词：系统发生学叶绿体核糖体层序核子

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Phylogenomics,reticulation,and biogeographical history of Elaeagnaceae

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Plant Diversity 2024年第6期46卷 683-697页

作者： Wei Gu ting Zhang Shui-yin Liu Qin Tian Chen-Xuan Yang Qing Lu Xiao-Gang Fu Heather R.Kates Gregory W.Stull Pamela S.Soltis Douglas E.Soltis Ryan A.Folk Robert P.Guralnick De-Zhu Li ting-shuang yi Germplasm Bank of Wild Species&Yunnan Key Laboratory of Crop Wild Relatives Omics Kunming Institute of BotanyChinese Academy of SciencesKunming 650201China Kunming College of Life Science University of Chinese Academy of SciencesKunming 650201China Key Laboratory of Plant Diversity and Specialty Crops Chinese Academy of SciencesBeijing 100093China Florida Museum of Natural History University of FloridaGainesvilleFL 32611United States Department of Biology University of FloridaGainesvilleFL 32611United States Department of Biological Sciences Mississippi State UniversityMississippiMS 39762United States School of Life Sciences Yunnan UniversityKunming 650504YunnanChina

The angiosperm family Elaeagnaceae comprises three genera and ca.100 species distributed mainly in Eurasia and North *** family-wide phylogenetic and biogeographic research on Elaeagnaceae has been conducted,limiting the application and preservation of natural genetic ***,we reconstructed a strongly supported phylogenetic framework of Elaeagnaceae to better understand interand intrageneric relationships,as well as the origin and biogeographical history of the *** this purpose,we used both nuclear and plastid sequences from Hyb-Seq and genome skimming approaches to reconstruct a well-supported phylogeny and,along with current distributional data,infer historical biogeographical *** phylogenetic analyses of both nuclear and plastid data strongly support the monophyly of Elaeagnaceae and each of the three *** was resolved as sister to the well-supported clade of Hippophae and *** intrageneric relationships of Elaeagnus and Hippophae were also well *** levels of nuclear gene tree conflict and cytonuclear discordance were detected within Elaeagnus,and our analyses suggest putative ancient and recent *** inferred that Elaeagnaceae originated at ca.90.48 Ma(95%CI?89.91e91.05 Ma),and long-distance dispersal likely played a major role in shaping its intercontinentally disjunct *** work presents the most comprehensive phylogenetic framework for Elaeagnaceae to date,offers new insights into previously unresolved relationships in Elaeagnus,and provides a foundation for further studies on classification,evolution,biogeography,and conservation of Elaeagnaceae.

关键词： Biogeography Cytonuclear discordance Hybridization Phylogeny Long-distance dispersal

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Plastid phylogenomics offers resolution of major tribal relationship of legumes

Plastid phylogenomics offers resolution of major tribal rela...

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中国植物学会第十六次全国会员代表大会暨85周年学术年会

作者： Rong Zhang yinhuan Wang Jianjun Jin Anne Bruneau Siyun Chen De-Zhu Li ting-shuang yi Germplasm Bank of Wild Species Kunming Institute of BotanyChinese Academy of Sciences University of Chinese Academy of Sciences Present address: School of Primary Education Chongqing Normal University Université de Montréal

Leguminosae,the thirdly largest family of the angiosperm,is diverse in morphology,ecology and *** phylogenetic reconstructions of the Leguminosae based on one or a few genes have not resolved many deep phylogenetic relationships or some nodes only obtained low *** applied 151 complete/nearly complete plastomes of 187 species representing all 36 tribes and most major clades of six subfamilies to infer phylogenetic *** reconstructions were conducted on both coding and noncoding regions with various pruning and partitioning *** of our analyses fully resolved the deep relationships of legume with strong statistical support at most nodes,which are generally congruent with the those in previous studies but with some interesting *** deep relationships and some short internodes of Leguminosae were strongly supported both in coding and noncoding data sets but conflict relationships were *** phylogenetic signal analyses for all matrices,we detected conflict phylogenetic signals between coding and noncoding regions,and also among some coding loci at these *** phylogenomics offers new and important insights into deep phylogenetic relationships of *** robust phylogenetic backbone reconstructed in this study establish a framework for future studies on classification,evolution and diversification of this important family.

关键词： phylogenomics plastome Leguminosae maximum likelihood phylogenetic signals conflicts

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From Barcodes to Genomes:Building Genomic Resources for Plant Identification and Phylogenomics

From Barcodes to Genomes:Building Genomic Resources for Plan...

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首届植物科学前沿学术大会

作者： De-Zhu Li Jun-Bo Yang Hong-Tao Li Zeng-Xia Zeng Lian-Ming Gao ting-shuang yi Peter M.Hollingsworth Germplasm Bank of Wild Species and CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of Sciences Royal Botanic Garden Edinburgh

Advances in high-throughput,next-generation sequencing have greatly accelerated plant DN A barcoding and phylogenetic *** the past decade,genome skimming or low coverage genome sequencing of plants has generated large amounts of genomic data,which enable assembly of more or less complete plastid genomes(plastomes),nuclear ribosomal DNA(nrDNA) arrays,as well as partial mitochondrial genomes(mitogenomes).These data are fully compatible with the existing plant core barcodes,i.e.,the plastid rbcL and matK,and nrDNA ITS *** expanded data that result from these genomic approaches(*** sequences),has improved resolution of phylogenetic relationships at the ordinal,familial and tribal or lower ***,plastome-scale barcodes can increase levels of species discrimination of recalcitrant taxa and improve resolution in community phylogenetic *** skimming has been successfully applied at large-scale to herbarium materials and opens the genomic treasure chest of historical *** the enormous importance of herbaria for the development of a comprehensive reference DNA barcoding database,such genomic data can be used for a wide range of ***,with increasing coverage(up to 10 X to 20 X),hundreds of single-or low-copy nuclear genes have been efficiently recovered to successfully further resolve lower-level phylogenetic *** assembled a large data set for 19,616 samples of 19,018 species towards building genomic resources for a next-generation Flora of China,which will foster nation-wide plant DNA barcoding and phylogenomic studies.

关键词： DNA barcoding species discrimination reference database comparative genomics

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Enhancing postoperative pain control by surgically-initiated rectus sheath block in abdominal aortic aneurysm open repair: A case report

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World Journal of Clinical Cases 2025年第6期13卷 41-47页

作者： Kuan-Hua Chen Ming-Yuan Kang yi-ting Chang Sheng-Yang Huang Yung-Szu Wu Center for Cardiovascular Disease Taichung Veterans General HospitalTaichung 407219TaiwanChina Department of Anesthesiology Taichung Veterans General HospitalTaichung 407219TaiwanChina Division of Pediatric Surgery Department of SurgeryTaichung Veterans General HospitalTaichung 407219TaiwanChina School of Medicine National Yang Ming Chiao Tung UniversityTaipei 112304TaiwanChina Department of Post-Baccalaureate Medicine National Chung Hsing UniversityTaichung 402202TaiwanChina

BACKGROUND Abdominal aortic aneurysm(AAA)repair often involves significant postoperative pain,traditionally managed with systemic opioids,which can cause undesirable side *** case report explores the novel use of a surgically-initiated rectus sheath block with a catheter-over-needle assembly for pain management in AAA *** SUMMARY A 67-year-old female with hypertension and previous aortic dissection underwent elective open repair of an infrarenal AAA,which had grown from 3.4 cm to 4.3 cm over 14 months.A rectus sheath block was initiated surgically for postoperative pain *** patient reported low pain scores and did not require systemic intravenous opioids,enabling early ambulation and discharge on postoperative day seven without *** preventing complications of systemic opi-oids,the method indicating a promising direction for postoperative pain management in major vascular *** Surgically-initiated rectus sheath block as a valuable tool for managing postoperative pain in AAA repair.

关键词： Abdominal aortic aneurysm Postoperative pain management Rectus sheath block Surgical anesthesia Opioid-sparing techniques Case report

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Atmospheric chemistry of 2-nitrobenzaldehyde:Initiated by photo-excitation,OH-oxidation,and small TiO_(2) clusters adsorption catalysis

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Journal of Environmental Sciences 2024年第5期139卷 123-137页

作者： Feng-Yang Bai Xiang-Huan Liu ting-ting Meng Zhou Yu yi-Chen Wang shuang Ni Zhen Zhao Institute of Catalysis for Energy and Environment College of Chemistry and Chemical EngineeringShenyang Normal UniversityShenyang 110034China

The fate of 2-nitrobenzaldehyde(2-NBA)is of interest in atmospheric chemistry as it is a semi-volatile organic compound with high *** study presents a quantum chemical study of the gas-phase reactions of 2-NBA photo-excitation and OH-oxidation in the absence and presence of small TiO_(2) *** further understand the unknown photolysis mechanism,the photo-reaction pathways of ground singlet state and the lying excited triplet state of 2-NBA were investigated including the initial and subsequent reactions of proton transfer,direct CO,NO_(2),and HCO elimination routes in the presence of O_(2) and ***,the OH-mediated degradation of 2-NBA proceeded via five H-extraction and six OH-addition channels by indirect mechanism,which follows a succession of reaction steps initiated by the formation of weakly stable intermediate *** H-extraction from the-CHO group was the dominant pathway with a negative activation energy of-1.22 kcal/*** calculated rate coefficients at 200–600 K were close to the experimental data in literature within 308-352 K,and the kinetic negative temperature independence was found in both experimental literature and computational ***,2-NBA was favored to be captured onto small TiO_(2) clusters via six adsorption configurations formed via various combination of three types of bonds of Ti…O,Ti…C,and O…H between the molecularly adsorbed 2-NBA and TiO_(2) *** indicted that the chemisorptions of aldehyde oxygen have largest *** results suggested adsorption conformations have a respectable impact on the catalysis *** study is significant for understanding the atmospheric chemistry of 2-nitrobenzaldehyde.

关键词： 2-nitrobenzaldehyde OH radical oxidation Rate coefficient Photolysis mechanism Adsorption catalysis

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