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The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees

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Molecular plant 2024年第5期17卷 725-746页

作者： Tingting Shi Xinxin Zhang Yukang Hou Changfu Jia Xuming Dan Yulin Zhang Yuanzhong Jiang Qiang Lai Jiajun Feng Jianju Feng Tao Ma Jiali Wu Shuyu Liu Lei Zhang Zhiqin Long Liyang Chen Nathaniel R.Street Par K.Ingvarsson Jianquan Liu Tongming Yin Jing Wang Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education College of Life SciencesSichuan UniversityChengduSichuanChina College of Horticulture and Forestry Tarim UniversityAlar 843300China Umea plant Science centre Department of Plant PhysiologyUmea UniversityUmeaVasterbottenSweden Linnean centre for plant Biology Department of Plant BiologyUppsala BioCenterSwedish University of Agricultural SciencesUppsalaSweden The Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China Nanjing Forestry UniversityNanjingJiangsuChina

Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary ***,among the world’s most widely distributed and cultivated trees,exhibit extensive phenotypic diversity and environmental *** this study,we present a genus-level super-pangenome comprising 19 Populus genomes,revealing the likely pivotal role of private genes in facilitating local environmental and climate *** the integration of pangenomes with transcriptomes,methylomes,and chromatin accessibility mapping,we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures,notably CG methylation in gene-body *** comparative genomic analyses have enabled the identification of 142202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive *** have experimentally validated a∼180-bp presence/absence variant affecting the expression of the CUC2 gene,crucial for leaf serration ***,we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome(http://***).Together,the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.

关键词： Populus pangenomes whole-genome duplication structural variation genome evolution

Classical taxonomy,molecular phylogeny and genetic analysis of the genus Exitianus Ball,1929(Hemiptera:Cicadellidae:Deltocephalinae)from Egypt

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Zoological systematics 2024年第2期49卷 143-157页

作者： Rabab M.El-Hady Ahmed F.El-Sayed Survey&Taxonomy Department Plant Protection Research InstituteAgriculture Research CentreGizaEgypt Microbial Genetics Department Biotechnology Research InstituteNational Research CentreGizaEgypt Egypt Center for Research and Regenerative Medicine(ECRRM) CairoEgypt

Egyptian species of the leafhopper genus Exitianus Ball,1929,***(St?l,1855),***(Distant,1908),and *** Ross,1968 are ***,morphological descriptions,and a key for their identification are *** this study,we used molecular techniques to confirm morphological identification and detect phylogeny among the three Exitianus *** partial nucleotide sequences of the amplified products obtained were determined by Macrogen *** nucleotide sequences of 28S rDNA and COX genes of the EGY-ARC-9,EGY-ARC-4,and EGY-ARC-5 were determined by Macrogen Korea,blasted into BLAST at the National Center for Biotechnology Information website(NCBI)and compared with those deposited in the GenBank DNA *** results represented the homology percentage between the partial sequences of the 28S rRNA and COX genes from each species and related species obtained from GenBank DNA *** morphological identifications of the three Exitianus species were confirmed by molecular characterization and sequencing of 28S rDNA and COX genes and identified as ***,***,and ***,their sequences of 28srDNA and COX genes were deposited in GenBank with an accession number(LC670610,LC670607,and OQ196105)for 28srDNA gene and(LC775357,LC775358,and LC775359)for the COX gene.

关键词： Auchenorrhyncha Chaismini taxonomic 28S rDNA phylogenetic

Two diversities meet in the rhizosphere:root specialized metabolites and microbiome

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Journal of Genetics and Genomics 2024年第5期51卷 467-478页

作者： Xiaochen Wang Jingying Zhang Xinjun Lu Yang Bai Guodong Wang State Key Laboratory of plant Genomics Institute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijing 100101China CAS-JIC centre of Excellence for plant and Microbial Science Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Hainan Yazhou Bay Seed Laboratory SanyaHainan 572025China College of Advanced Agricultural Sciences Chinese Academy of SciencesBeijing 100049China

plants serve as rich repositories of diverse chemical compounds collectively referred to as specialized *** compounds are of importance for adaptive processes,including interactions with various microbes both beneficial and *** microbes as bioreactors,the chemical diversity undergoes dynamic changes when root-derived specialized metabolites(RSMs)and microbes encounter each other in the *** advancements in sequencing techniques and molecular biology tools have not only accelerated the elucidation of biosynthetic pathways of RSMs but also unveiled the significance of RSMs in plant-microbe *** this review,we provide a comprehensive description of the effects of RSMs on microbe assembly in the rhizosphere and the influence of corresponding microbial changes on plant health,incorporating the most up-to-date information ***,we highlight open questions that remain for a deeper understanding of and harnessing the potential of RSM-microbe interactions to enhance plant adaptation to the ***,we propose a pipeline for investigating the intricate associations between root exometabolites and the rhizomicrobiome.

关键词： Root specialized metabolites Microbiome plant-microbe interactions Rhizosphere diversity

BambooBase:A comprehensive database of bamboo omics and systematics

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Molecular plant 2024年第5期17卷 682-685页

作者： Yun-Long Liu Shu-Yang Gao Guihua Jin Meng-Yuan Zhou Qijuan Gao Cen Guo Yi-Zhou Yang Liang-Zhong Niu Enhua Xia Zhen-Hua Guo Peng-Fei Ma De-Zhu Li Germplasm Bank of Wild Species&Yunnan Key Laboratory of Crop Wild Relatives Omics Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan 650201China Kunming College of Life Science University of Chinese Academy of SciencesKunmingYunnan 650201China State Key Laboratory of Tea plant Biology and Utilization Anhui Agricultural UniversityHefeiAnhui 230036China School of Computer and Artificial Intelligence Hefei Normal UniversityHefeiAnhui 230061China Key Laboratory for plant diversity and Biogeography in East Asia Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan 650201China

Dear Editor,Bamboos(Bambusoideae,Poaceae)are of significant economic and ecological importance,supporting billions of people and contributing to international trade(Wu et al.,2023).They play a crucial role in carbon fixation and support a multitude of other species including the giant panda(Clark et al.,2015).Since the release of the first draft genome of moso bamboo(Phyllostachys edulis)(Peng et al.,2013),there has been a notable increase in the sequencing,assembly,and annotation of diverse bamboo genomes(Guo et al.,2019;Zheng et al.,2022;Ma et al.,2024).An existing resource for bamboo genomics,BambooGDB(Zhao et al.,2014),provides information based on the individual draft reference genome of moso *** is needed,however,is a resource reinforcing multiple genome assemblies in Bambusoideae to enable researchers to unravel the evolutionary history of chromosomes and genes through cladespecific comparative genomic ***,we present BambooBase(https://***/),a newly developed web-based database designed to provide a seamless user experience for bamboo omics and systematics.

关键词： enable supporting Bamboo

Plastid phylogenomics provides new insights into the systematics,diversification,and biogeography of Cymbidium(Orchidaceae)

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plant diversity 2024年第4期46卷 448-461页

作者： Hai-Yao Chen Zhi-Rong Zhang Xin Yao Ji-Dong Ya Xiao-Hua Jin Lin Wang Lu Lu De-Zhu Li Jun-Bo Yang Wen-Bin Yu Center for Integrative Conservation&Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglaYunnan 666303China University of Chinese Academy of Sciences Huairou DistrictBeijing 101408China plant Germplasm and Genomics Center Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingYunnan 650201China State Key Laboratory of plant diversity and Specility Crops Institute of BotanyChinese Academy of SciencesHaidian DistrictBeijing 100093China School of Pharmaceutical Sciences Yunnan Key Laboratory of Pharmacology for Natural Productsand Yunnan College of Modern Biomedical IndustryKunming Medical UniversityKunmingYunnan 650500China Southeast Asia Biodiversity Research Institute Chinese Academy of SciencesYezinNay Pyi Taw 05282Myanmar

Cymbidium(Orchidaceae:Epidendroideae),with around 60 species,is widely-distributed across Southeast Asia,providing a nice system for studying the processes that underlie patterns of biodiversity in the ***,phylogenetic relationships of Cymbidium have not been well resolved,hampering investigations of species diversification and the biogeographical history of this *** this study,we construct a plastome phylogeny of 56 Cymbidium species,with four well-resolved major clades,which provides a framework for biogeographical and diversification rate *** dating and biogeographical analyses show that Cymbidium likely originated in the region spanning northern IndoBurma to the eastern Himalayas during the early Miocene(~21.10 Ma).It then rapidly diversified into four major clades in East Asia within approximately a million years during the middle *** *** to the adjacent regions(Borneo,Philippines,and Sulawesi)primarily occurred during the Pliocene-Pleistocene *** analyses indicate that the net diversification rate of Cymbidium has decreased since its origin,and is positively associated with changes in temperature and monsoon *** hydrothermal conditions brought by monsoon intensification in the early Miocene possibly contributed to the initial rapid diversification,after which the net diversification rate was reduced with the cooling climate after the middle *** transition from epiphytic to terrestrial habits may have enabled adaptation to cooler environments and colonization of northern niches,yet without a significant effect on diversification *** study provides new insights into how monsoon activity and temperature changes affected the diversification dynamics of plants in Southeast Asia.

关键词： Cymbidium East Asia Asian monsoons Climate change Biogeographical patterns

Genetic diversity of RNA viruses infecting invertebrate pests of rice

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Science China(Life Sciences) 2024年第1期67卷 175-187页

作者： Haoran Wang Shufen Chao Qing Yan Shu Zhang Guoqing Chen Chonghui Mao Yang Hu Fengquan Yu Shuo Wang Liang Lv Baojun Yang Jiachun He Songbai Zhang Liangsheng Zhang Peter Simmonds Guozhong Feng State Key Laboratory of Rice Biology and Breeding China National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhou 311400China State Key Laboratory of Agricultural Microbiology College of Life Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China Institute of plant Protection&Soil Fertilizer Hubei Academy of Agricultural SciencesWuhan 430064China Institute of plant Protection Guizhou Academy of Agricultural SciencesGuiyang 550000China Institute of plant Protection Liaoning Academy of Agricultural SciencesShenyang 110161China Sanya Agricultural Technology Extension and Service centre Sanya 572000China College of Agriculture Yangtze UniversityJingzhou 434000China Fujian Provincial Key Laboratory of Haixia Applied plant Systems Biology Fujian Agriculture and Forestry UniversityFuzhou 350002China Genomics and Genetic Engineering Laboratory of Ornamental plants College of Agriculture and BiotechnologyZhejiang UniversityHangzhou 310012China Nuffield Department of Medicine Peter Medawar Building for Pathogen ResearchUniversity of OxfordOxford OX13SYUnited Kingdom

Invertebrate species are a natural reservoir of viral genetic diversity,and invertebrate pests are widely distributed in crop ***,information on viruses infecting invertebrate pests of crops is *** this report,we describe the deep metatranscriptomic sequencing of 88 invertebrate samples covering all major invertebrate pests in rice *** identified 296 new RNA viruses and 13 known RNA *** viruses clustered within 31 families,with many highly divergent viruses constituting potentially new families and *** the identified viruses,13 RNA viruses clustered within the Fiersviridae family of bacteriophages,and 48 RNA viruses clustered within families and genera of *** detected known rice viruses in novel invertebrate hosts at high ***,some novel RNA viruses have genome structures closely matching to known plant viruses and clustered within genera of several plant virus *** potential insect pathogenic RNA viruses were detected in invertebrate *** analysis revealed that host taxonomy plays a major role and geographical location plays an important role in structuring viral ***-species transmission of RNA viruses was detected between invertebrate *** identified viral genomes showed extensive variation for invertebrate viral families or ***,the large-scale metatranscriptomic analysis greatly expands our understanding of RNA viruses in rice invertebrate species,the results provide valuable information for developing efficient strategies to manage insect pests and virus-mediated crop diseases.

关键词： invertebrate species metatranscriptome viral diversity viral transmission viral genomes

Vallisneria spiralis L. adaptive capacity improves pore water chemistry and increasespotential nitrification in organic polluted sediments

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Ecological Processes 2024年第2期 72-89页

作者： Leonardo Morini Claudio Ferrari Marco Bartoli Mindaugas Zilius Elias Broman Giovanna Visioli Department of Chemistry Life Science and Environmental Sustainability University of Parma Department of Environmental and Prevention Sciences University of Ferrara Department of Integrative Marine Ecology (EMI) Genoa Marine Centre Stazione Zoologica Anton Dohrn-National Institute of Marine BiologyEcology and Biotechnology Marine Research Institute Klaipeda University Department of Ecology Environment and Plant Sciences Stockholm University Baltic Sea centre Stockholm University

Background Macrophytes may modify benthic biodiversity and biogeochemistry via radial oxygen loss from roots. This condition contrasts sediments anoxia, allows roots respiration, and facilitates aerobic microbial communities and processes in the rhizosphere. Simultaneously, the rhizosphere can stimulate anaerobic microorganisms and processes via exudates or by favoring the build-up of electron acceptors as nitrate. As eutrophication often results in organic enrichment in sediments and large internal nutrients recycling, an interesting research question is to investigate whether plants maintain the capacity to stimulate aerobic or anaerobic microbial communities and processes also under elevated organic *** A manipulative experiment was carried out under laboratory-controlled conditions. Microcosms containing bare sediments and sediments transplanted with the macrophyte Vallisneria spiralis L. were created. The effect of the plant was investigated on sediments with moderate(8%) and elevated(21%) organic matter content, after an acclimatization period of 30 days. Chemical and physical parameters, microbial community composition and the potential rates of nitrification, denitrification and nitrate ammonification were measured at two different depths(0–1 and 1–5 cm) after the acclimatization period to evaluate the role of *** Vallisneria spiralis grew and assimilated pore water nutrients at the two organic matter levels and vegetated sediments had always nutrient-depleted porewaters as compared to bare sediments. Nitrifying microbes had a lower relative abundance and diversity compared to denitrifying bacteria. However, regardless of the organic content, in vegetated sediments nitrifiers were detected in deeper horizons as compared to bare sediments, where nitrification was confined near the surface. In contrast, potential denitrification rates were not affected by the presence of roots, but probably regulated by the presence of nitrate and by ro

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Pre-and post-pollination barriers between two exotic and five native Sagittaria species:Implications for species conservation

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plant diversity 2023年第4期45卷 456-468页

作者： Ting-Ting Zou Sen-Tao Lyu Qi-Lin Jiang Shu-He Shang Xiao-Fan Wang Laboratory of plant systematics and Evolutionary Biology College of Life SciencesWuhan UniversityWuhan 430072China

Anthropogenic introduction of species has resulted in a breakdown of geographical barriers and hybridization in previously allopatric ***,examining hybridization proneness of exotic species contributes to revealing its potential ***,reproductive barriers may be strengthened or weakened due to long-term geographical isolation for these newly sympatric ***,few studies have evaluated multiple barriers between alien and native *** this study,we quantified the importance of four pre-pollination barriers(phenological,floral traits,pollen production,and floral constancy)and four post-pollination barriers(pollen-pistil incompatibility,seed set,seed viability,and seedling survival)between two introduced and five native Sagittaria *** showed that introduced *** was cross-compatible with two native species,whereas introduced *** was incapable of hybridizing with any native *** barriers were asymmetric within species pairs and multiple barriers acted in concert to maintain species *** barriers contributed more to total reproductive isolation in native species,whereas prepollination barriers played a stronger role in total reproductive isolation for two introduced *** set was the only barrier that was positively correlated with genetic *** results provide a perspective to better understand reproductive barriers for secondary contact *** highlight the importance of monitoring hybridization events before human introduction and the possible conservation strategies to remove invasive species with hybridization proneness.

关键词： Alismataceae Introduced species Conservation Hybridization Reproductive isolation Sagittaria

Dietary diversity and Food Security Status among Cameroonian Adults Living in Semi-Urban Areas: A Cross-Sectional Study

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Food and Nutrition Sciences 2024年第7期15卷 548-564页

作者： Tonou Boris Ronald Tchuente Pauline Vervaine Hagbe Eliane Flore Eyenga Kemadjou Ruth Edwige Dibacto Ngassa Dany Joël Ngoumen Fotso Janvier Aime Youovop Nguemto Roussel Guy Takuissu Judith Laure Ngondi Julius Enyong Oben Department of Biochemistry Faculty of Science University of Yaound 1 Yaound Cameroon centre for Food Food Security and Nutrition Research Institute of Medical Research and Medicinal Plant Studies Yaound Cameroon Center of Nutrition and Functional Foods Yaound Cameroon

Introduction: Food security is one of the greatest challenges that most African countries face. It is a concept that considers not only food quantity but also food quality. The objective of this study was to describe dietary diversity and food security status at the individual level in Cameroonian populations. Methods: A total of 1180 men and women aged 20 and over and living in the West, North West, and Littoral regions of Cameroon were recruited. Data on dietary habits were collected through the frequency of consumption of various food groups. Dietary diversity was assessed using a 24-hour dietary recall. Food security status was determined by combining two indicators (food consumption score and individual food diversity score). Results: The mean dietary diversity score of the population was 3.53 ± 1.44, p Conclusion: The diet diversity of adults living in the West, North West, and Littoral regions of Cameroon is medium. Although half of the study population was food secure, there is a need to implement food security policies further to reduce food insecurity among the Cameroonian population.

关键词： Dietary diversity Individual Food Security Littoral West North West Cameroon