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Haplotype-based phylogenetic analysis and population genomics uncover the origin and domestication of sweetpotato

Molecular plant 2024年第2期17卷 277-296页

作者： Mengxiao Yan Ming Li Yunze Wang Xinyi Wang M-Hossein Moeinzadeh Dora G.Quispe-Huamanquispe Weijuan Fan Yijie Fang Yuqin Wang Haozhen Nie Zhangying Wang Aiko Tanaka Bettina Heider Jan F.Kreuze Godelieve Gheysen Hongxia Wang Martin Vingron Ralph Bock Jun Yang Shanghai Key Laboratory of plant Functional Genomics and Resources Shanghai Chenshan Botanical GardenShanghai 201602China College of Life Sciences Chongqing Normal UniversityChongqing 401331China biotechnology and Nuclear Technology Research institute Sichuan Academy of Agricultural SciencesChengdu 610061China College of Life Sciences Shanghai Normal UniversityShanghai 200234China Department of Computational Molecular Biology Max Planck Institute for Molecular GeneticsIhnestraBe 63-7314195 BerlinGermany Department of biotechnology Ghent University9000 GhentBelgium Guangdong Provincial Key Laboratory of Crops Genetics and Improvement Crop Research InstituteGuangdong Academy of Agricultural SciencesGuangzhou 510640China Graduate School of Bioagricultural Sciences Nagoya UniversityChikusaNagoya 464-8601Japan international Potato Center(CIP) LimaPeru CAS Center for Excellence of Molecular plant Sciences Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200233China Max-Planck-Institut fur Molekulare Pflanzenphysiologie Am Muhlenberg 114476 Potsdam-GolmGermany

The hexaploid sweetpotato(lpomoea batatas)is one of the most important root crops ***,its genetic origin remains controversial,and its domestication history remains *** this study,we used a range of genetic evidence and a newly developed haplotype-based phylogenetic analysis to identify two probable progenitors of *** diploid progenitor was likely closely related to lpomoea ae-quatoriensis and contributed the B,subgenome,IbT-DNA2,and the lineage 1 type of chloroplast genome to *** tetraploid progenitor of sweetpotato was most likely *** 4x,which donated the B2 subgenome,IbT-DNA1,and the lineage 2 type of chloroplast *** most likely originated from reciprocal crosses between the diploid and tetraploid progenitors,followed by a subsequent whole-genome *** addition,we detected biased gene exchanges between the subgenomes;the rate of B,to B2 subgenome conversions was nearly three times higher than that of B2 to B subgenome *** analyses revealed that genes involved in storage root formation,maintenance of genome stabil-ity,biotic resistance,sugar transport,and potassium uptake were selected during the speciation and domestication of *** study sheds light on the evolution of sweetpotato and paves the way forimprovementofthiscrop.

关键词： sweetpotato origin gene conversion domestication IbT-DNA HPA

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Both host and diet shape bacterial communities of predatory mites

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Insect Science 2024年第2期31卷 551-561页

作者： Hong Yan Endong Wang Guo-Shu Wei Bo Zhang Xuenong Xu institute of plant Protection Chinese Academy of Agricultural SciencesBejingChina College of plant Protection Hebei Agricultural UniversityBaodingHebei ProvinceChina Key Laboratory of Natural Enemies Insects Ministry of Agriculture and Rural AffairsBeijingChina

Microbial communities,derived from food,ambient,and inner,can affect host ecological adaption and *** with most phytophagous arthropods,predators may have more opportunities to develop specific microbiota depending on the level of prey *** explore how diet sources affect host microbial communities and vary across predator species,we considered 3 types of predators from Phytoseiidae(Acari:Mesostigmata):polyphagous(Amblyseius orientalis Ehara,Neoseiulus barkeri Hughes,and Amblyseius swirski Athias-Henrio),oligophagous(Neoseiulus californicus McGregor),and monophagous(Phytoseiulus persimilis Athias-Henriot)predatory *** polyphagous species were fed on 2 types of diets,natural prey and alternative *** using 16S rRNA sequencing,we found that diet was the main source of microbiota in predatory mites,while there was no clear pattern affected by prey *** 3 polyphagous predators,host species had a larger impact than prey on microbial *** *** or *** which showed consistency in their microbiota,prey switching significantly affectedβ-diversity of bacterial composition in ***,with 56%of the microbial *** short,our results confirmed the substantial influence of diet on host microbial construction in predatory species,and highlighted species differences in shaping the microbiota which are not necessarily related to prey specialization.

关键词： diet switching feeding habits host-microbial interactions invertebrate microbiota 16S rRNA

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Unveiling the distinctive traits of functional rye centromeres:minisatellites, retrotransposons, and R-loop formation

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Science China Life Sciences 2024年第9期67卷 1989-2002页

作者： Chang Liu Shulan Fu Congyang Yi Yang Liu Yuhong Huang Xianrui Guo Kaibiao Zhang Qian Liu James A.Birchler Fangpu Han State Key Laboratory of plant Cell and Chromosome Engineering Institute of Genetics and Developmental Biology Chinese Academy of Sciences University of Chinese Academy of Sciences Key Laboratory for plant Genetics and Breeding Sichuan Agricultural University Division of Biological Science University of Missouri

Centromeres play a vital role in cellular division by facilitating kinetochore assembly and spindle attachments. Despite their conserved functionality, centromeric DNA sequences exhibit rapid evolution, presenting diverse sizes and compositions across species. The functional significance of rye centromeric DNA sequences, particularly in centromere identity, remains unclear. In this study, we comprehensively characterized the sequence composition and organization of rye centromeres. Our findings revealed that these centromeres are primarily composed of long terminal repeat retrotransposons(LTR-RTs) and interspersed minisatellites. We systematically classified LTR-RTs into five categories, highlighting the prevalence of younger CRS1, CRS2, and CRS3 of CRSs(centromeric retrotransposons of Secale cereale) were primarily located in the core centromeres and exhibited a higher association with CENH3 nucleosomes. The minisatellites, mainly derived from retrotransposons, along with CRSs, played a pivotal role in establishing functional centromeres in rye. Additionally, we observed the formation of R-loops at specific regions of CRS1, CRS2, and CRS3, with both rye pericentromeres and centromeres exhibiting enrichment in R-loops. Notably, these R-loops selectively formed at binding regions of the CENH3 nucleosome in rye centromeres, suggesting a potential role in mediating the precise loading of CENH3 to centromeres and contributing to centromere specification. Our work provides insights into the DNA sequence composition, distribution, and potential function of R-loops in rye centromeres. This knowledge contributes valuable information to understanding the genetics and epigenetics of rye centromeres, offering implications for the development of synthetic centromeres in future plant modifications and beyond.

关键词： centromere LTR-RTs minisatellite rye R-loop

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Enzymatic C1 reduction using hydrogen in cofactor regeneration

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Frontiers of Chemical Science and Engineering 2024年第7期18卷 33-40页

作者： Ruishuang Sun Chenqi Cao Qingyun Wang Hui Cao Ulrich Schwaneberg Yu Ji Luo Liu Haijun Xu Beijing Bioprocess Key Laboratory Beijing University of Chemical TechnologyBeijing 100029China institute of biotechnology Rheinisch-Westfälische Technische Hochschale(RWTH)AachenAachen 52074Germany

Carbon dioxide fixation presents a potential solution for mitigating the greenhouse gas *** carbon dioxide fixation,C1 compound reduction requires a high energy *** calculations suggest that the energy source for cofactor regeneration plays a vital role in the effective enzymatic C1 *** utilizes renewable hydrogen to achieve the regeneration and supply cofactor nicotinamide adenine dinucleotide(NADH),providing a driving force for the reduction reaction to reduce the thermodynamic barrier of the reaction cascade,and making the forward reduction pathway thermodynamically *** on the regeneration of cofactor NADH by hydrogenase,and coupled with formaldehyde dehydrogenase and formolase,a favorable thermodynamic mode of the C1 reduction pathway for reducing formate to dihydroxyacetone(DHA)was designed and *** resulted in accumulation of 373.19μmol·L^(-1) DHA after 2 h,and conversion reaching 7.47%.These results indicate that enzymatic utilization of hydrogen as the electron donor to regenerate NADH is of great significance to the sustainable and green development of bio-manufacturing because of its high economic efficiency,no by-products,and environment-friendly ***,formolase efficiently and selectively fixed the intermediate formaldehyde(FALD)to DHA,thermodynamically pulled formate to efficiently reduce to DHA,and finally stored the low-grade renewable energy into chemical energy with high energy density.

关键词： [NiFe]-hydrogenase SH formolase NADH regeneration C1 compound reduction thermodynamic calculation

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Reorganization of 3D genome architecture provides insights into pathogenesis of early fatty liver disease in laying hens

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Journal of Animal Science and biotechnology 2024年第3期15卷 1086-1100页

作者： Yanli Liu Zhuqing Zheng Chaohui Wang Yumeng Wang Xi Sun Zhouzheng Ren Xin Yang Xiaojun Yang College of Animal Science and Technology Northwest A&F UniversityYangling 712100China institute of Agricultural biotechnology Jingchu University of TechnologyJingmen 448000China

Background Fatty liver disease causes huge economic losses in the poultry industry due to its high occurrence and lethality ***-dimensional(3D)chromatin architecture takes part in disease processing by regulating tran-scriptional *** study is carried out to investigate the alterations of hepatic 3D genome and H3K27ac profiling in early fatty liver(FLS)and reveal their effect on hepatic transcriptional reprogramming in laying *** Results show that FLS model is constructed with obvious phenotypes including hepatic visible lipid deposi-tion as well as higher total triglyceride and cholesterol in serum.A/B compartment switching,topologically associat-ing domain(TAD)and chromatin loop changes are identified by high-throughput/resolution chromosome conforma-tion capture(HiC)*** genes of these alternations in hepatic 3D genome organization significantly enrich pathways related to lipid metabolism and hepatic damage.H3K27ac differential peaks and differential expres-sion genes(DEGs)identified through RNA-seq analysis are also enriched in these ***,certain DEGs are found to correspond with changes in 3D chromatin structure and H3K27ac binding in their *** motif analysis reveals that candidate transcription factors are implicated in regulating transcriptional ***,disturbed folate metabolism is observed,as evidenced by lower folate levels and altered enzyme *** Our findings establish a link between transcriptional reprogramming changes and 3D chromatin struc-ture variations during early FLS formation,which provides candidate transcription factors and folate as targets for FLS prevention or treatment.

关键词： 3D chromatin architecture Fatty liver disease Folate H3K27ac profiling Transcription reprogramming

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Camellia sinensis CsMYB4a participates in regulation of stamen growth by interaction with auxin signaling transduction repressor CsAUX/IAA4

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The Crop Journal 2024年第1期12卷 188-201页

作者： Guoliang Ma Mingzhuo Li Yingling Wu Changjuan Jiang Yifan Chen Dawei Xing Yue Zhao Yajun Liu Xiaolan Jiang Tao Xia Liping Gao School of Life Science Anhui Agricultural UniversityHefei 230036AnhuiChina plant for Human Health institute Department of Plant and Microbial BiologyNorth Carolina State UniversityKannapolisNC 28081USA State Key Laboratory of Tea plant Biology and Utilization/Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture/Anhui Provincial Laboratory of Tea plant Biology and Utilization Anhui Agricultural UniversityHefei 230036AnhuiChina

Subgroup 4(Sg4)members of the R2R3-MYB are generally known as negative regulators of the phenylpropanoid pathway in *** previous research showed that a R2R3-MYB Sg4 member from Camellia sinensis(CsMYB4a)inhibits expression of some genes in the phenylpropanoid pathway,but its physiological function in the tea plant remained ***,CsMYB4a was found to be highly expressed in anther and filaments,and participated in regulating filament *** analysis and exogenous auxin treatment showed that the target of CsMYB4a might be the auxin signal ***/indole-3-acetic acid 4(AUX/IAA4),a repressor in auxin signal transduction,was detected from a yeast two-hybrid screen using CsMYB4a as *** silencing assays showed that both CsIAA4 and CsMYB4a regulate filament *** plants overexpressing CsIAA4 were insensitive to exogenous a-NAA,consistent with overexpression of ***-protein interaction experiments revealed that CsMYB4a interacts with N-terminal of CsIAA4 to prevent CsIAA4 *** out of the endogenous NtIAA4 gene,a CsIAA4 homolog,in tobacco alleviated filament growth inhibition and a-NAA insensitivity in plants overexpressing *** results strongly suggest that CsMYB4a works synergistically with CsIAA4 and participates in regulation of the auxin pathway in stamen.

关键词： AUX/IAA4 Auxin signaling CsMYB4a Subgroup 4 R2R3-MYB

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Dynamics and functionalities of bacterial community during foxtail millet dough fermentation by metagenomic analysis

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Journal of Future Foods 2024年第4期4卷 343-352页

作者： Junli Liu Wei Zhao Aixia Zhang Pengliang Li Jingke Liu institute of biotechnology and Food Science Hebei Academy of Agriculture and Forestry SciencesShijiazhuang 050000China

Sourdough flavors were closely related to microbial *** microbial diversity of foxtail millet dough during fermentation has never been ***,the metabolic potential and diversity of the bactenial community were analyzed by metagenomic during dough *** was the dominant phylum in the dough,within heterofementative lactic acid bacteria(***,Limosilactobacillus,Pediococcus and Lactobacillus)as the most abundant *** was gradually inhibited after ***_crustorum was notably found abundant during dough ***_fermentum increased markedly during fermentation,while Companilactobacillus_cnustorum decreased *** futher exploration,genes associated with metabolism were annotated through ***,Companilactobacillus and Pediococcus were actively engaged in glycolysis(ko00010),starch and sucrose metabolism(ko00500),and pyruvate metabolism(ko00620),leading in part to 1actic and acetic acid acumulations and dough *** and Lactiplantibacillus were the main contributors to key aninopeptidases ox/and transaminases involved in amino acid metabolism,which was nesponsible for flavor metabolite *** study will provide an enhanced understanding of the predominance and diversity of dough bactenial communities,and contribute to future strain screening in the dough for better flavor.

关键词： Sourdough Foxtail millet Metagenomics Gilycolysis Amino acid biosynthesis

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Multi-omics analysis reveals the pivotal role of phytohormone homeostasis in regulating maize grain water content

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The Crop Journal 2024年第4期12卷 1081-1092页

作者： Yuanliang Liu Manman Li Jianju Liu Suining Deng Yan Zhang Yuanfeng Xia Baoshen Liu Mingliang Xu State Key Laboratory of plant Environmental Resilience/College of Agronomy and biotechnology/National Maize Improvement Center/Center for Crop Functional Genomics and Molecular Breeding China Agricultural UniversityBeijing 100193China College of Agronomy/State Key Laboratory of Crop Biology Shandong Agricultural UniversityTai’an 271018ShandongChina institute of Agricultural biotechnology Jilin Academy of Agricultural SciencesGongzhuling 136100JilinChina Maize Research institute Jilin Academy of Agricultural SciencesGongzhuling 136100JilinChina

Grain water content(GWC)is a key determinant for mechanical harvesting of maize(Zea mays).In our previous research,we identified a quantitative trait locus,qGWC1,associated with GWC in ***,we examined near-isogenic lines(NILs)NILL and NILH that differed at the qGWC1 *** GWC in NILL was primarily attributed to reduced grain water weight(GWW)and smaller fresh grain size,rather than the accumulation of dry *** difference in GWC between the NILs became more pronounced approximately 35 d after pollination(DAP),arising from a faster dehydration rate in *** an integrated analysis of the transcriptome,proteome,and metabolome,coupled with an examination of hormones and their derivatives,we detected a marked decrease in JA,along with an increase in cytokinin,storage forms of IAA(IAA-Glu,IAA-ASP),and IAA precursor IPA in immature NILL *** kernel development,genes associated with sucrose synthases,starch biosynthesis,and zein production in NILL,exhibited an initial up-regulation followed by a gradual down-regulation,compared to those in *** discovery highlights the crucial role of phytohormone homeostasis and genes related to kernel development in balancing GWC and dry matter accumulation in maize kernels.

关键词： Grain water content Maize kernel Phytohormone homeostasis

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The transcriptional landscape of the developmental switch from regular pollen maturation towards microspore-derived plant regeneration in barley

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The Crop Journal 2024年第4期12卷 1064-1080页

作者： Anna Nowicka Martin Kovacik Anna Maksylewicz Przemysław Kopec Ewa Dubas Monika Krzewska Agnieszka Springer Robert E.Hoffie Diaaeldin S.Daghma Zbynek Milec Ales Pecinka Jochen Kumlehn Iwona Zur The Franciszek Górski institute of plant Physiology Polish Academy of Sciences Niezapominajek 2130-239 KrakówPoland institute of Experimental Botany of the Czech Academy of Sciences Centre of Plant Structural and Functional GenomicsŠlechtitelu3177900 OlomoucCzech Republic Department of Cell Biology and Genetics Faculty of SciencePalacky UniversityŠlechtitelu°2777900 OlomoucCzech Republic Malopolska Centre of biotechnology Jagiellonian University30-387 KrakówPoland Leibniz institute of plant Genetics and Crop plant Research(IPK)Gatersleben Corrensstraße 306466 Stadt SeelandGermany institute for Breeding Research on Horticultural Crops Julius Kühn Institute(JKI)-Federal Research Centre for Cultivated PlantsErwin-Baur Straße 2706484 QuedlinburgGermany Global Change Research institute Czech Academy of Sciences Beˇlidla 986/4a60300 BrnoCzech Republic

plant formation from in vitro-cultivated microspores involves a complex network of internal and environmental ***/doubled haploids(DHs)derived from in vitro-cultured microspores are widely used in plant breeding and genetic ***,the mechanism underlying the developmental switch from regular pollen maturation towards microspore-derived plant regeneration remains poorly ***,RNA-sequencing was employed to elucidate the transcriptional landscapes of four early stages of microspore embryogenesis(ME)in barley cultivars Golden Promise and Igri,which exhibit contrasting responsiveness to microspore-derived plant *** experiments revealed fundamental regulatory networks,specific groups of genes,and transcription factor(TF)families potentially regulating the developmental *** identified a set of candidate genes crucial for genotype-dependent responsiveness/recalcitrance to *** high-resolution temporal transcriptome atlas provides an important resource for future functional studies on the genetic control of microspore developmental transition.

关键词： Hordeum vulgare Marker gene Microspore embryogenesis Stress response Transcriptome analysis

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Global characterization of OsPIP aquaporins reveals that the H_(2)O_(2)transporter OsPIP2;6 increases resistance to rice blast

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The Crop Journal 2024年第1期12卷 102-109页

作者： Gousi Li Jingluan Han Chen Yi Hao Luo Yuzhu Wang Fengpin Wang Xiaoyu Wang Letian Chen Yaling Zhang State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources College of Life SciencesSouth China Agricultural UniversityGuangzhou 510642GuangdongChina Guangdong Laboratory for Lingnan Modern Agriculture Guangzhou 510642GuangdongChina National Key Laboratory of plant Molecular Genetics Shanghai Center for Plant Stress BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200032China

Plasma membrane intrinsic proteins(PIPs)are conserved plant aquaporins that transport small molecules across the plasma membrane to trigger instant stress responses and maintain cellular homeostasis under biotic and abiotic *** elucidate their roles in plant immunity to pathogen attack,we characterized the expression patterns,subcellular localizations,and H_(2)O_(2)-transport ability of 11 OsPIPs in rice(Oryza sativa),and identified OsPIP2;6 as necessary for rice disease ***2;6 resides on the plasma membrane and facilitates cytoplasmic import of the immune signaling molecule H_(2)O_(2).Knockout of OsPIP2;6 increases rice susceptibility to Magnaporthe oryzae,indicating a positive function in plant ***2;6 interacts with OsPIP2;2,which has been reported to increase rice resistance to pathogens via H_(2)O_(2)*** findings suggest that OsPIP2;6 cooperates with OsPIP2;2 as a defense signal transporter complex during plant–pathogen interaction.

关键词： Aquaporin plant immunity Rice blast H_(2)O_(2)transport

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