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Comparative and Phylogenetic Analysis of the Complete Chloroplast Genomes of 19 Species in rosaceae Family

Phyton-International Journal of Experimental Botany 2024年第6期93卷 1203-1219页

作者： Riwa Mahai Rongpeng Liu Xiaolang Du Zejing Mu Xiaoyun Wang Jun Yuan Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine Jiangxi University of Chinese MedicineNanchang330004China College of Life Sciences Jiangxi University of Chinese MedicineNanchang330004China

rosaceae represents a vast and complex group of species,with its classiﬁcation being intricate and contentious.The taxonomic placement of many species within this family has been a subject of ongoing debate.The study utilized the Illumina platform to sequence 19 plant species from 10 genera in the rosaceae.The cp genomes,vary-ing in size from 153,366 to 159,895 bp,followed the typical quadripartite organization consisting of a large single-copy(LSC)region(84,545 to 87,883 bp),a small single-copy(SSC)region(18,174 to 19,259 bp),and a pair of inverted repeat(IR)regions(25,310 to 26,396 bp).These genomes contained 132–138 annotated genes,including 87 to 93 protein-coding genes(PCGs),37 tRNA genes,and 8 rRNA genes using MISA software,52 to 121 simple sequence repeat(SSR)loci were identiﬁed.D.arbuscular contained the least of SSRs and did not have hexanotides,A.lineata contained the richest SSRs.Long terminal repeats(LTRs)were primarily composed of palindromic and forward repeat sequences,meanwhile,The richest LTRs were found in Argentina lineata.Except for Argentina lineata,Fragariastrum eriocarpum,and Prunus trichostoma,which varied in gene type and position on both sides of the boundary,the remaining species were found to be mostly conserved according to IR boundary analysis.The examination of the Ka/Ks ratio revealed that only the infA gene had a value greater than 1,indicating that this gene was primarily subjected to positive selection during evolution.Additionally,9 hotspots of variation were identiﬁed in the LSC and SSC regions.Phylogenetic analysis conﬁrmed the scientiﬁc validity of the genus Prunus L.sensu lato(s.l.)within the rosaceae family.The separation of the three genera Argentina Hill,Fragariastrum Heist.ex Fabr.and Dasiphora Raf.from Potentilla L.may be a more scientiﬁc classiﬁcation.These results offer fresh perspectives on the taxonomy of the rosaceae.

关键词： rosaceae chloroplast genomes comparative genomes phylogeny

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A comprehensive review on pharmacognosy, phytochemistry and pharmacological activities of 8 potent Prunus species of southeast Asia

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Journal of Traditional Chinese Medicine 2024年第3期44卷 620-628页

作者： Shikha Agrawal Adarsh Kumar Ankit Kumar Singh Harshwardhan Singh Suresh Thareja Pradeep Kumar Department of Pharmaceutical Sciences and Natural Products Central University of Punjab

Genus Prunus comprising around 430 species is a vast important genus of family rosaceae, subfamily amygdalaoidae. Among all 430 species, around 19 important species are commonly found in Indian subcontinent due to their broad nutritional and economic importance. Some most common species of genus Prunus are Prunus amygdalus, Prunus persica, Prunus armeniaca, Prunus avium, Prunus cerasus, Prunus cerasoides, Prunus domestica, Prunus mahaleb, etc. A newly introduced species of Prunus i.e Prunus sunhangii is recently discovered which is morphologically very similar to Prunus cerasoides. Plants of Prunus species are short to medium-sized deciduous trees mainly found in the northern hemisphere. In India and its subcontinent,it extends from the Himalayas to Sikkim, Meghalaya,Bhutan, Myanmar etc. Different Prunus species have been extensively studied for their morphological,microscopic, pharmacological and phytoconstituents characteristics. Total phenolic content of Prunus species explains the presence of phenols in high quantity and pharmacological activity due to phenols. Phytochemical screening of species of genus Prunus shows the presence of wide phytoconstituents which contributes in their pharmacological significance and reveals the therapeutic potential and traditional medicinal significance of this genus. Genus Prunus showed a potent antioxidant activity analyzed by 1,1-diphenyl-2-picryl-hydrazyl radical assay. Plant species belonging to the genus Prunus is widely used traditionally for the treatment of various disorders. Some specific Prunus species possess potent anticancer, anti-inflammatory,hypoglycemic etc. activity which makes the genus more interesting for further research and findings. This review is an attempt to summarize the comprehensive study of Prunus species from its distribution, morphological characters to phytoconstituents, and pharmacological activity.

关键词： Prunus rosaceae antineoplastic agents distribution hypoglycemic agents phytochemistry review

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Genome-wide identification and characterization of the IPT family members in nine rosaceae species and a functional analysis of MdIPT5b in cold resistance

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Horticultural Plant Journal 2023年第4期9卷 616-630页

作者： Yi Feng Jiahong Lv Mengqun Peng Jie Li Yue Wu Min Gao Xinyi Wu Yi Wang Ting Wu Xinzhong Zhang Xuefeng Xu Zhenhai Han College of Horticulture China Agricultural UniversityBeijing100193China State Key Laboratory of Plant Physiology and Biochemistry College of Biological SciencesChina Agricultural UniversityBeijing100193China

Cytokinins are members of a group of phytohormones involved in various growth and developmental processes in plants.Isopentenyl transferase(IPT)is the rate-limiting enzyme in catalyzing the biosynthesis of cytokinins.In this study,to understand the role of IPT family in cold resistance,78 IPT candidates were identified and characterized in nine rosaceae genomes.The expansion of IPT families in the rosaceae primarily occurred through segmental duplication rather than tandem duplication.In general,purifying selection controlled the evolution of IPT families in the rosaceae,with IPT3 and IPT5 homologs as the primary drivers of evolution.Cis-elements,which are involved in the responses to many environmental stresses or phytohormone signals,were identified in the promoters of MdIPT members.This was consistent with the trends of expression of the MdIPT genes in apple(Malus domestica)calli.MdIPT5b was also found to exhibit multiple responses to phytohormones and stress signals.The ectopic expression of MdIPT5b resulted in an increase in cold resistance in transformed apple calli and tomato(Solanum lycopersicum)plantlets.The redox balance was partially stabilized through the accumulation of proline under cold stress.However,the ascorbate–glutathione cycle cannot be stabilized in the cold.All physiological and biochemical assays are preformed in spectrophotometer.These results showed that regulating the expression of IPT genes for moderate cytokinin improvement could enhance the accumulation of proline to stabilize the osmotic and redox balances to improve resistance to cold stress.

关键词： rosaceae Apple Isopentenyl transferase Cytokinin Cold stress Bioinformatics

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Comparative genomic analysis of N6-methyladenosine regulators in nine rosaceae species and functional characterization in response to drought stress in pear

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Horticultural Plant Journal 2023年第4期9卷 693-704页

作者： Chenyang Han Huizhen Dong Qinghai Qiao Yuqin Dai Xiaosan Huang Shaoling Zhang College of Horticulture State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingJiangsu 210095China

N 6-methylated adenine(m6 A)is an emerging epigenetic marker in eukaryotic organisms that plays an important role in biological functions and in enriching genetic information.m6 A exerts these functions via the dynamic interplay among m6 A writers,erasers,and readers.However,little is known about the underlying mechanisms of m6 A in plant growth and stress responses.Here,we identified 276 masked m6 A regulators from nine rosaceae species(Pyrus bretschneideri,Pyrus betulifolia,Pyrus communis,Malus domestica,Fragaria vesca,Prunus avium,Prunus mume,Prunus persica,and Rubus occidentalis).We classified and named these genes in more detail based on phylogenetic and synteny analysis.The expansion of m6 A regulators in Maloideae was dated back to the recent whole-genome duplication(WGD)in rosaceae.Based on the expression pattern analysis and gene structure analysis of m6 A regulators,m6 A was shown to be a significant factor in regulating plant development and resistance.In addition,PbrMTA1-silenced pear plants displayed significantly reduced drought tolerance and chlorophyll content,as well as increased electrolyte leakage and concentrations of malondialdehyde and H2 O2.

关键词： Pyrus bretschneideri RNA methylation m6A regulators rosaceae Evolution Transcriptome Drought stress VIGS

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Molecular phylogeny and inflorescence evolution of Prunus(rosaceae)based on RAD-seq and genome skimming analyses

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Plant Diversity 2023年第4期45卷 397-408页

作者： Na Su Richard G.J.Hodel Xi Wang Jun-Ru Wang Si-Yu Xie Chao-Xia Gui Ling Zhang Zhao-Yang Chang Liang Zhao Daniel Potter Jun Wen College of Life Sciences Northwest A&F UniversityYangling 712100China Herbarium of Northwest A&F University Yangling 712100China Department of Botany National Museum of Natural HistoryMRC 166Smithsonian InstitutionWashingtonDC 20013-7012USA College of Life Sciences Tarim UniversityAlaer 843300China Department of Plant Sciences MS2University of CaliforniaDavisCA 95616USA

Prunus is an economically important genus widely distributed in the temperate Northern Hemisphere.Previous studies on the genus using a variety of loci yielded conflicting phylogenetic hypotheses.Here,we generated nuclear reduced representation sequencing data and plastid genomes for 36 Prunus individuals and two outgroups.Both nuclear and plastome data recovered a well-resolved phylogeny.The species were divided into three main clades corresponding to their inflorescence types,-the racemose group,the solitary-flower group and the corymbose group-with the latter two sister to one another.Prunus was inferred to have diversified initially in the Late Cretaceous around 67.32 million years ago.The diversification of the three major clades began between the Paleocene and Miocene,suggesting that paleoclimatic events were an important driving force for Prunus diversification.Ancestral state reconstructions revealed that the most recent common ancestor of Prunus had racemose inflorescences,and the solitary-flower and corymb inflorescence types were derived by reduction of flower number and suppression of the rachis,respectively.We also tested the hybrid origin hypothesis of the racemose group proposed in previous studies.Prunus has undergone extensive hybridization events,although it is difficult to identify conclusively specific instances of hybridization when using SNP data,especially deep in the phylogeny.Our study provides well-resolved nuclear and plastid phylogenies of Prunus,reveals substantial cytonuclear discord at shallow scales,and sheds new light on inflorescence evolution in this economically important lineage.

关键词： Prunus rosaceae RAD-Seq Chloroplast genome Hybridization Inflorescence evolution

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The Gillenia trifoliata genome reveals dynamics correlated with growth and reproduction in rosaceae

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Horticulture Research 2021年第1期8卷 3144-3157页

作者： Hilary S.Ireland Chen Wu Cecilia H.Deng Elena Hilario Ali Saei Sylvia Erasmuson Ross N.Crowhurst Karine M.David Robert J.Schaffer David Chagn The New Zealand Institute for Plant and Food Research Ltd Private Bag 92196Auckland Mail CentreAuckland 1142New Zealand School of Biological Sciences The University of AucklandPrivate Bag 92019Auckland Mail CentreAuckland 1142New Zealand Genomics Aotearoa %Department of BiochemistryUniversity of OtagoPO Box 56Dunedin 9054New Zealand The New Zealand Institute for Plant and Food Research Ltd Private Bag 11600Palmerston North 4442New Zealand The New Zealand Institute for Plant and Food Research Ltd Private Bag 4704Christchurch Mail CentreChristchurch 8140New Zealand The New Zealand Institute for Plant and Food Research Ltd 55 Old Mill RoadRD 3Motueka 7198New Zealand

The rosaceae family has striking phenotypic diversity and high syntenic conservation.Gillenia trifoliata is sister species to the Maleae tribe of apple and~1000 other species.Gillenia has many putative ancestral features,such as herb/sub-shrub habit,dry fruit-bearing and nine base chromosomes.This coalescence of ancestral characters in a phylogenetically important species,positions Gillenia as a‘rosetta stone'for translational science within rosaceae.We present genomic and phenological resources to facilitate the use of Gillenia for this purpose.The Gillenia genome is the fi rst fully annotated chromosome-level assembly with an ancestral genome complement(x=9),and with it we developed an improved model of the rosaceae ancestral genome.MADS and NAC gene family analyses revealed genome dynamics correlated with growth and reproduction and we demonstrate how Gillenia can be a negative control for studying fl eshy fruit development in rosaceae.

关键词： rosaceae dynamics striking

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Evolution of the R2R3-MYB gene family in six rosaceae species and expression in woodland strawberry

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Journal of Integrative Agriculture 2019年第12期18卷 2753-2770页

作者： LIU Hui XIONG Jin-song JIANG Yue-ting WANG Li CHENG Zong-ming(Max) College of Horticulture Nanjing Agricultural UniversityNanjing 210095P.R.China Department of Plant Sciences University of TennesseeKnoxville 37996USA

R2R3-MYB gene family play important roles in plants development, metabolism, and responses to various biotic and abiotic stresses. In this study, 838 R2 R3-MYB genes were identified from six rosaceae species, including 105 in woodland strawberry(Fragaria vesca), 173 in European pear(Pyrus communis), 219 in apple(Malus domestica), 121 in peach(Prunus persica), 121 in Chinese rose(Rosa chinensis), and 99 in black raspberry(Rubus occidentalis). All R2 R3-MYB genes in the six rosaceae species were clustered into 51 species-specific duplicated clades with 109 genes and 50 lineage-specific duplicated clades with 242 genes according to phylogenetic analysis. R2 R3-MYB genes were distributed on all chromosomes in each of the six species, with a small amount of tandem duplication events. The proportion of tandem repeat genes ranged from 0 to 25.1%. The R2 R3-MYB protein was conserved in a clade and likely to share similar functions. The distribution of Ks showed the duplication times of R2 R3-MYB genes in six rosaceae species. Furthermore, most of the R2 R3-MYB genes had Ka/Ks values less than 1, which indicated they were driven by purifying selection during the evolutionary processes. The GO term enrichment analysis revealed that R2 R3-MYB genes in strawberry and black raspberry were more divergent than in other rosaceae species. Analysis of transcriptomes of 42 different tissues and development stages of woodland strawberry showed that high expression levels of R2 R3-MYB suggested that the R2 R3-MYB genes in strawberry played a key role in growth and development of both vegetative tissues and fruits. The strawberry R2 R3-MYB genes in sub-group of S1, S2, S11, S20, and S22 had high expression levels both in young leaves(YL) and old leaves(OL) strawberry tissues under drought treatments.

关键词： R2R3-MYB gene rosaceae species duplicati on eve nts

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Fungal diversity notes 709–839: taxonomic and phylogenetic contributions to fungal taxa with an emphasis on fungi on rosaceae

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Fungal Diversity 2018年第2期89卷 1-236页

作者： Dhanushka N.Wanasinghe Chayanard Phukhamsakda Kevin D.Hyde Rajesh Jeewon Hyang Burm Lee E.B.Gareth Jones Saowaluck Tibpromma Danushka S.Tennakoon Asha J.Dissanayake Subashini C.Jayasiri Yusufjon Gafforov Erio Camporesi Timur SBulgakov Anusha HEkanayake Rekhani Hansika Perera Milan CSamarakoon Ishani DGoonasekara Ausana Mapook Wen-Jing Li Indunil CSenanayake Junfu Li Chada Norphanphoun Mingkwan Doilom Ali H Bahkali Jianchu Xu Peter EMortimer Leif Tibell Sanja Tibell Samantha C.Karunarathna Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of ScienceKunming 650201YunnanPeople’s Republic of China Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand World Agroforestry Centre East and Central AsiaKunming 650201YunnanPeople’s Republic of China Mushroom Research Foundation 128 M.3 Ban Pa Deng T.Pa PaeA.Mae TaengChiang Mai 50150Thailand Department of Health Sciences Faculty of ScienceUniversity of MauritiusReduitMauritius Environmental Microbiology Lab Division of Food TechnologyBiotechnology&AgrochemistryCollege of Agriculture and Life SciencesChonnam National UniversityYongbong-Dong 300Buk-GuGwangju 61186Korea Nantgaredig 33 B St.Edwards Road Southsea HantsHampshire PO53DHUK Institute of Plant and Environment Protection Beijing Academy of Agriculture and Forestry SciencesBeijing 100097People’s Republic of China Laboratory of Mycology Institute of BotanyAcademy of Sciences of the Republic of Uzbekistan32 Durmon Yuli StreetTashkentUzbekistan 100125 A.M.B.Gruppo Micologico Forlivese"Antonio Cicognani"Via Roma 18Forlı`Italy A.M.B Circolo Micologico"Giovanni Carini"C.P.314 BresciaItaly Societa`per gli Studi Naturalistici della Romagna C.P.144 BagnacavalloRAItaly Russian Research Institute of Floriculture and Subtropical Crops 2/28 Yana Fabritsiusa StreetSochiKrasnodar RegionRussia 354002 Department of Biology Faculty of ScienceChiang Mai UniversityChiang Mai 50200Thailand Engineering Research Center of Southwest BioPharmaceutical Resources Ministry of EducationGuizhou UniversityGuiyang 550025GuizhouPeople’s Republic of China Department of Botany and Microbiology College of ScienceKing Saud UniversityP.O.Box:2455Riyadh 1145Saudi Arabia Department of Plant Medicine National Chiayi University300 Syuefu RoadChiayi City 60004Taiwan Department of Ecology University of KasselHeinrich-PlettStrasse4034132 KasselGermany Department of Organismal Biology Uppsala Univer

This paper is the seventh in the Fungal Diversity Notes series,where 131 taxa accommodated in 28 families are mainly described from Rosa(rosaceae)and a few other hosts.Novel fungal taxa are described in the present study,including 17 new genera,93 new species,four combinations,a sexual record for a species and new host records for 16 species.Bhatiellae,Cycasicola,Dactylidina,Embarria,Hawksworthiana,Italica,Melanocucurbitaria,Melanodiplodia,Monoseptella,Uzbekistanica,Neoconiothyrium,Neopaucispora,Pararoussoella,Paraxylaria,Marjia,Sporormurispora and Xenomassariosphaeria are introduced as new ascomycete genera.We also introduce the new species Absidia jindoensis,Alternaria doliconidium,A.hampshirensis,Angustimassarina rosarum,Astragalicola vasilyevae,Backusella locustae,Bartalinia rosicola,Bhatiellae rosae,Broomella rosae,Castanediella camelliae,Coelodictyosporium rosarum,Comoclathris rosae,C.rosarum,Comoclathris rosigena,Coniochaeta baysunika,C.rosae,Cycasicola goaensis,Dactylidina shoemakeri,Dematiopleospora donetzica,D.rosicola,D.salsolae,Diaporthe rosae,D.rosicola,Endoconidioma rosaehissaricae,Epicoccum rosae,Hawksworthiana clematidicola,H.lonicerae,Italica achilleae,Keissleriella phragmiticola,K.rosacearum,K.rosae,K.rosarum,Lophiostoma rosae,Marjia tianschanica,M.uzbekistanica,Melanocucurbitaria uzbekistanica,Melanodiplodia tianschanica,Monoseptella rosae,Mucor fluvius,Muriformistrickeria rosae,Murilentithecium rosae,Neoascochyta rosicola,Neoconiothyrium rosae,Neopaucispora rosaecae,Neosetophoma rosarum,N.rosae,N.rosigena,Neostagonospora artemisiae,Ophiobolus artemisiicola,Paraconiothyrium rosae,Paraphaeosphaeria rosae,P.rosicola,Pararoussoella rosarum,Parathyridaria rosae,Paraxylaria rosacearum,Penicillium acidum,P.aquaticum,Phragmocamarosporium rosae,Pleospora rosae,P.rosae-caninae,Poaceicola agrostina,P.arundinicola,P.rosae,Populocrescentia ammophilae,P.rosae,Pseudocamarosporium pteleae,P.ulmi-minoris,Pseudocercospora rosae,Pseudopithomyces rosae,Pseudostrickeria rosae,Sclerostagonospora lathyri,S.rosa

关键词： Ascomycota Dothideomycetes Eurotiomycetes Italy Lecanoromycetes Mucoromycetes Phylogeny Rosa rosaceae Russia Sordariomycetes Taxonomy UK Uzbekistan

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Two new triterpenes from Duchesnea indica

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Chinese Chemical Letters 2009年第5期20卷 572-575页

作者： Wei Qiao Zhi Yao Wen Zhang Hong Quan Duan School of Pharmaceutica SciencesResearch Center of Basic Medical SciencesTianjin Medical University Tianjin 300070 China Department of Immunology Tianjin Medical University Tianjin 300070 China

Two new triterpenes, 2α,3β-dihydroxyurs- 12-en- 18,19-epoxy-28-oic acid （1） and 18,19-seco, 2α, 2α-dihydroxyl-19-oxo-urs- 11,13（18）-dien-28-oic acid （2） were isolated from the herbaceous part of Duchesnea indica. Their structures were elucidated by spectroscopic analysis, including 2D NMR technique. The isolated compounds exhibited moderate cytotoxic activities against HeLa and L929 cell lines.

关键词： Duchesnea indica rosaceae 2α,3-Dihydroxyurs-12-en-18,19-epoxy-28-oic acid 18,19-Seco,2α,3α-dihydroxyl-19-oxours-11,13 （18）-dien-28-oic acid

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Two New Glycosides from Rubus amabilis

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Chinese Chemical Letters 2000年第10期11卷 897-900页

作者： Chen, XC Jia, ZJ Lanzhou Univ Natl Lab Appl Organ Chem Dept Chem Lanzhou 730000 Peoples R China

A pregnane glycoside and a lignan glycoside were isolated from the aerial parts of Rubus amabilis. Their structures were elucidated as 3-O-beta-D-glucopyranosyl-3 beta.15 alpha-dihydroxypregn-5-en-20-one and (-)-secoi... 详细信息

关键词： Rubus amabilis rosaceae pregnane lignan glycoside

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