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Eco-evolutionary evidence for the global diversity pattern of Cycas(Cycadaceae)

Journal of Integrative plant Biology 2024年第6期66卷 1170-1191页

作者： Jian Liu Anders J.Lindstrom Yiqing Gong Shanshan Dong Yusheng(Chris) Liu Shouzhou Zhang Xun Gong CAS Key Laboratory for plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Department of Economic plants and Biotechnology Yunnan Key Laboratory for Wild Plant Resources Kunming Institute of BotanyChinese Academy of Sciences University of Chinese Academy of sciences Global Biodiversity Conservancy Key Laboratory of Southern Subtropical plant Diversity Fairy Lake Botanical Garden Shenzhen & Chinese Academy of Sciences Department of Earth and Environmental sciences Indiana University-Indianapolis

The evolution of the latitudinal diversity gradient(LDG), characterized by a peak in diversity toward the tropics, has captured significant attention in evolutionary biology and ecology.However, the inverse LDG(i-LDG) mechanism,wherein species richness increases toward the poles, remains inadequately explored. Cycads are among one of the oldest lineages of extant seed plants and have undergone extensive diversification in the tropics. Intriguingly, the extant cycad abundance exhibits an i-LDG pattern, and the underlying causes for this phenomenon remain largely elusive. Here,using 1,843 nuclear genes from a nearly complete sampling, we conducted comprehensive phylogenomic analyses to establish a robust species-level phylogeny for Cycas, the largest genus within cycads. We then reconstructed the spatial-temporal dynamics and integrated global environmental data to evaluate the roles of species ages, diversification rates,contemporary environment, and conservatism to ancestral niches in shaping the i-LDG pattern. We found Cycas experienced decreased diversification rates, coupled with the cooling temperature since its origin in the Eocene from continental Asia. Different regions have distinctively contributed to the formation of i-LDG for Cycas, with the northern hemisphere acting as evolutionary museums and the southern hemisphere serving as cradles. Moreover, water-related climate variables,specifically precipitation seasonality and potential evapotranspiration, were identified as paramount factors constraining Cycas species richness in the rainforest biome near the equator. Notably, the adherence to ancestral monsoonal climates emerges as a critical factor in sustaining the diversity pattern. This study underscores the imperative of integrating both evolutionary and ecological approaches to comprehensively unravel the mechanisms underpinning global biodiversity patterns.

关键词： cycads latitudinal diversity gradient niche conservatism spatiotemporal diversification species richness

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Comparative analyses of mitogenomes in the social bees with insights into evolution of long inverted repeats in the Meliponini

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Zoological Research 2024年第1期45卷 160-175页

作者： Yu-Ran Li Zheng-Wei Wang Richard T.Corlett Wen-Bin Yu Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants&Center for Integrative Conservation Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglaYunnan 666303China CAS Key Laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglaYunnan 666303China Southeast Asia Biodiversity Research institute Chinese Academy of SciencesMenglaYunnan 666303China University of Chinese Academy of sciences Shijingshan DistrictBeijing 100049China

The insect mitogenome is typically a compact circular molecule with highly conserved gene contents.Nonetheless,mitogenome structural variations have been reported in specific taxa,and gene rearrangements,usually the tRNAs,occur in different lineages.Because synapomorphies of mitogenome organizations can provide information for phylogenetic inferences,comparative analyses of mitogenomes have been given increasing attention.However,most studies use a very few species to represent the whole genus,tribe,family,or even order,overlooking potential variations at lower taxonomic levels,which might lead to some incorrect inferences.To provide new insights into mitogenome organizations and their implications for phylogenetic inference,this study conducted comparative analyses for mitogenomes of three social bee tribes(Meliponini,Bombini,and Apini)based on the phylogenetic framework with denser taxonomic sampling at the species and population levels.Comparative analyses revealed that mitogenomes of Apini and Bombini are the typical type,while those of Meliponini show diverse variations in mitogenome sizes and organizations.Large inverted repeats(IRs)cause significant gene rearrangements of protein coding genes(PCGs)and rRNAs in Indo-Malay/Australian stingless bee species.Molecular evolution analyses showed that the lineage with IRs have lower dN/dS ratios for PCGs than lineages without IRs,indicating potential effects of IRs on the evolution of mitochondrial genes.The finding of IRs and different patterns of gene rearrangements suggested that Meliponini is a hotspot in mitogenome evolution.Unlike conserved PCGs and rRNAs whose rearrangements were found only in the mentioned lineages within Meliponini,tRNA rearrangements are common across all three tribes of social bees,and are significant even at the species level,indicating that comprehensive sampling is needed to fully understand the patterns of tRNA rearrangements,and their implications for phylogenetic inference.

关键词： Social bees Phylogeny Mitogenome structure Gene rearrangement Inverted repeats

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Photosynthetic response dynamics in the invasive species Tithonia diversifolia and two co-occurring native shrub species under fluctuating light conditions

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plant Diversity 2024年第2期46卷 265-273页

作者： Ju Li Shu-Bin Zhang Yang-Ping Li CAS Key Laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglunMengla 666303YunnanChina University of Chinese Academy of sciences Beijing 100049China

To determine the invasiveness of invasive plants,many studies have compared photosynthetic traits or strategies between invasive and native species.However,few studies have compared the photosynthetic dynamics between invasive and native species during light fluctuations.We compared photosynthetic induction,relaxation dynamics and leaf traits between the invasive species,Tithonia diversifolia and two native species,Clerodendrum bungei and Blumea balsamifera,in full-sun and shady habitats.The photosynthetic dynamics and leaf traits differed among species.T.diversifolia showed a slower induction speed and stomatal opening response but had higher average intrinsic water-use efficiency than the two native species in full-sun habitats.Thus,the slow induction response may be attributed to the longer stomatal length in T.diversifolia.Habitat had a significant effect on photosynthetic dynamics in T.diversifolia and B.balsamifera but not in C.bungei.In shady habitat,T.diversifolia had a faster photosynthetic induction response than in full-sun habitat,leading to a higher average stomatal conductance during photosynthetic induction in T.diversifolia than in the two native species.In contrast,B.balsamifera had a larger stomatal length and slower photosynthetic induction and relaxation response in shady habitat than in full-sun habitat,resulting in higher carbon gain during photosynthetic relaxation.Nevertheless,in both habitats,T.diversifolia had an overall higher carbon gain during light fluctuations than the two native species.Our results indicated that T.diversifolia can adopt more effective response strategies under fluctuating light environments to maximize carbon gain,which may contribute to its successful invasion.

关键词： Invasive plant Photosynthetic induction Photosynthetic relaxation Carbon gain Stomatal traits Tithonia diversifolia

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Direct somatic embryogenesis and related gene expression networks in leaf explants of Hippeastrum ‘Bangkok Rose’

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Horticultural plant Journal 2024年第2期10卷 556-572页

作者： Jingjue Zeng Yi Deng Shahid Iqbal Jiarui Zhang Kunlin Wu Guohua Ma Lin Li Guangyi Dai Rufang Deng Lin Fang Songjun Zeng Guangdong Provincial Key Laboratory of Applied Botany South China Botanical GardenChinese Academy of SciencesGuangzhouGuangdong 510650China University of the Chinese Academy of sciences Beijing 100049China South China National botanical garden GuangzhouGuangdong 510650China Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology ZhaoqingGuangdong 526000China Horticultural Science Department North Florida Research and Education CenterUniversity of Florida/IFASQuincyFL 32351USA Public Laboratory of South China botanical garden Chinese Academy of SciencesGuangzhouGuangdong 510650China Key Laboratory of South China Agricultural plant Molecular Analysis and Gene Improvement South China Botanical GardenChinese Academy of SciencesGuangzhouGuangdong 510650China

Hippeastrum, a highly diverse genus in the Amaryllidaceae family, is a valuable ornamental bulbous flowering plant. Somatic embryogenesis(SE) is an efficient method for mass production of Hippeastrum plantlets. Previous studies have been devoted to the in vitro propagation of Hippeastrum, but the SE and its regulatory networks are rarely reported. In this study, we established a direct SE method of Hippeastrum Bangkok Rose' using leaf bases as explants. MS supplemented with 1.00 mg·L^(-1)NAA +1.00 mg·L^(-1)KT + 0.25 mg·L^(-1)TDZ was the optimal medium for SE. Histological observations showed that the bipolar somatic embryo originated from the epidermal cell layer and underwent initiation,globular, scutellar and coleoptile stages. During SE, endogenous hormones of IAA, CTK, ABA, and SA were highly accumulated. Transcriptomic analysis revealed the genes encoding auxin biosynthesis/metabolic enzymes and efflux carriers were induced, while the auxin receptor of TIR1 and ARF transcriptional repressor of Aux/IAA were down-regulated and up-regulated, respectively, leading to suppression of auxin signaling. In contrast, cytokine signaling was promoted at the early stage of SE, as biosynthesis, transport, and signaling components were up-regulated.Various stress-related genes were up-regulated at the early or late stages of SE. Chromatin remodeling could also be dynamically regulated via distinct expression enzymes that control histone methylation and acetylation during SE. Moreover, key SE regulators, including WOXs and SERKs were highly expressed along with SE. Overall, the present study provides insights into the SE regulatory mechanisms of the Hippeastrum.

关键词： Hippeastrum Tissue culture Somatic embryogenesis Gene regulation

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Hydraulic properties and drought response of a tropical bamboo (Cephalostachyum pergracile)

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plant Diversity 2024年第3期46卷 406-415页

作者： Wanwalee Kongjarat Lu Han Amy Ny Aina Aritsara Shu-Bin Zhang Gao-Juan Zhao Yong-Jiang Zhang Phisamai Maenpuen Ying-Mei Li Yi-Ke Zou Ming-Yi Li Xue-Nan Li Lian-Bin Tao Ya-Jun Chen CAS Key Laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesYunnan 666303China University of the Chinese Academy of sciences Beijing 100049China T-STAR Core Team Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesYunnan 666303China School of Biology and Ecology University of MaineOronoMEUSA Climate Change institute University of MaineOronoME 04469USA School of Biological and Chemical Science Pu’er UniversityXueyuan RoadYunnan 665000China institute of Ecology and Geobotany School of Ecology and Environmental SciencesYunnan UniversityKunmingYunnan 650091China School of Ecology and Environment Southwest Forestry UniversityKunmingYunnan 650224China Yuanjiang Savanna Ecosystem Research Station Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesYuanjiangYunnan 653300China

Bamboo plants are an essential component of tropical ecosystems,yet their vulnerability to climate extremes,such as drought,is poorly understood due to limited knowledge of their hydraulic properties.Cephalostachyum pergracile,a commonly used tropical bamboo species,exhibited a substantially higher mortality rate than other co-occurring bamboos during a severe drought event in 2019,but the underlying mechanisms remain unclear.This study investigated the leaf and stem hydraulic traits related to drought responses,including leaf-stem embolism resistance(P50leaf;P50stem) estimated using optical and X-ray microtomography methods,leaf pressure-volume and water-releasing curves.Additionally,we investigated the seasonal water potentials,native embolism level(PLC) and xylem water source using stable isotope.We found that C.pergracile exhibited strong resistance to embolism,showing low P50leaf,P50stem,and turgor loss point,despite its rapid leaf water loss.Interestingly,its leaves displayed greater resistance to embolism than its stem,suggesting a lack of effective hydraulic vulnerability segmentation(HVS) to protect the stem from excessive xylem tension.During the dry season,approximately 49% of the water was absorbed from the upper 20-cm-deep soil layer.Consequently,significant diurnal variation in leaf water potentials and an increase in midday PLC from 5.87±2.33% in the wet season to 12.87±4.09%in the dry season were observed.In summary,this study demonstrated that the rapid leaf water loss,high reliance on surface water,and a lack of effective HVS in C.pergracile accelerated water depletion and increased xylem embolism even in the typical dry season,which may explain its high mortality rate during extreme drought events in 2019.

关键词： Climate change Drought Hydraulic safety Hydraulic vulnerability segmentation Stable isotope Tree mortality

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Structure,bioavailability and physicochemical properties of icariin-soymilk nanoparticle

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Food Science and Human Wellness 2024年第2期13卷 972-981页

作者： Jinping Wang Lingrong Wen Yueming Jiang Hong Zhu Weizheng Sun Guangyi Dai Bao Yang Guangdong Provincial Key Laboratory of Applied Botany Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic ImprovementSouth China Botanical GardenChinese Academy of SciencesGuangzhou 510650China South China National botanical garden Guangzhou 510650China College of Food Science and Engineering Jilin Agricultural UniversityChangchun 130118China University of Chinese Academy of sciences Beijing 100049China School of Food sciences and Engineering South China University of TechnologyGuangzhou 510640China

Soymilk is a natural nanocarrier.However,the performance of flavonoid-soymilk nano-complex remains unclear.In this work,icariin-soymilk nano-complexes(ISNCs)were successfully fabricated and characterized.The effects of high-pressure homogenization(HPH)treatment on structure and physicochemical properties of soymilk and nano-complexes were investigated.HPH treatment could significantly improve the surface hydrophobicity and interfacial activity of soymilk.The soymilk with HPH treatment could significantly improve the water solubility(20 folds),thermal stability and bioavailability of icariin.The highest encapsulation efficiency(93.28%),loading capacity(39.09μg/mg),ζ-potentia(absolute value,31.20 mV)and bioavailability(72.14%)were observed in HSI-200(200 bar of homogenization pressure).While HSI-500(500 bar of homogenization pressure)showed the smallest particle size(183.73 nm).ISNCs showed a rougher surface and an irregular lamellar structure with large amount of fine particles by using Cryo-SEM,suggesting that icariin was encapsulated in soymilk.These data supplied a novel strategy to improve the performance of icariin in functional foods.

关键词： Encapsulation efficiency Flavonoid High pressure homogenization Loading capacity Nano-complex

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HvMPK4 phosphorylates HvWRKY1 to enhance its suppression of barley immunity to powdery mildew fungus

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Journal of Genetics and Genomics 2024年第3期51卷 313-325页

作者： Pengya Xue Ling Zhang Renchun Fan Yanan Li Xinyun Han Ting Qi Lifang Zhao Deshui Yu Qian-Hua Shen State Key Laboratory of plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China CAS Center for Excellence in Biotic Interactions College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijing 100049China Department of Nutritional sciences&Toxicology University of CaliforniaBerkeleyCA 94720USA Lushan botanical garden Chinese Academy of ScienceJiujiangJiangxi 332900China

Mitogen-activated protein kinase(MAPK)cascades play important roles in disease resistance in model plant species.However,the functions of MAPK signaling pathways in crop disease resistance are largely unknown.Here we report the function of HvMKK1-HvMPK4-HvWRKY1 module in barley immune system.HvMPK4 is identified to play a negative role in barley immune response against Bgh,as virus-induced gene silencing of HvMPK4 results in enhanced disease resistance whilst stably overexpressing HvMPK4 leads to super-susceptibility to Bgh infection.Furthermore,the barley MAPK kinase HvMKK1 is found to specifically interact with HvMPK4,and the activated HvMKK1^(DD) variant specifically phosphorylates HvMPK4 in vitro.Moreover,the transcription factor HvWRKY1 is identified to be a downstream target of HvMPK4 and phosphorylated by HvMPK4 in vitro in the presence of HvMKK1^(DD).Phosphorylation assay coupled with mutagenesis analyses identifies S122,T284,and S347 in HvWRKY1 as the major residues phosphorylated by HvMPK4.HvWRKY1 is phosphorylated in barley at the early stages of Bgh infection,which enhances its suppression on barley immunity likely due to enhanced DNA-binding and transcriptional repression activity.Our data suggest that the HvMKK1-HvMPK4 kinase pair acts upstream of HvWRKY1 to negatively regulate barley immunity against powdery mildew.

关键词： Barley MPK4 WRKY1 Phosphorylation Disease resistance Powdery mildew

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Multiomics analyses of two Leonurus species illuminate leonurine biosynthesis and its evolution

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Molecular plant 2024年第1期17卷 158-177页

作者： Peng Li Meng-Xiao Yan Pan Liu Dan-Jie Yang Ze-Kun He Yun Gao Yan Jiang Yu Kong Xin Zhong Sheng Wu Jun Yang Hong-Xia Wang Yan-Bo Huang Le Wang Xiao-Ya Chen Yong-Hong Hu Qing Zhao Ping Xu shanghai Key Laboratory of plant Functional Genomics and Resources Shanghai Chenshan Botanical GardenShanghai Chenshan Plant Science Research CenterChineseAcademy of SciencesShanghaiChina College of Life sciences Shanghai Normal UniversityShanghai 200234China State Key Laboratory of plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina University of the Chinese Academy of sciences Beijing 100049China The Research Center of Chiral Drugs Innovation Research Institute of Traditional Chinese MedicineShanghai University of Traditional Chinese Medicine1200 Cailun RoadShanghai 201203China College of Chemistry and Chemical Engineering Shanghai University of Engineering ScienceShanghai 201620China

The Lamiaceae family is renowned for its terpenoid-based medicinal components,but Leonurus,which has traditional medicinal uses,stands out for its alkaloid-rich composition.Leonurine,the principal active compound found in Leonurus,has demonstrated promising effects in reducing blood lipids and treating strokes.However,the biosynthetic pathway of leonurine remains largely unexplored.Here,we present the chromosome-level genome sequence assemblies of Leonurus japonicus,known for its high leonurine production,and Leonurus sibiricus,characterized by very limited leonurine production.By integrating genomics,RNA sequencing,metabolomics,and enzyme activity assay data,we constructed the leonurine biosynthesis pathway and identified the arginine decarboxylase(ADC),uridine diphosphate glucosyltransferase(UGT),and serine carboxypeptidase-like(SCPL)acyltransferase enzymes that catalyze key reactions in this pathway.Further analyses revealed that the UGT–SCPL gene cluster evolved by gene duplication in the ancestor of Leonurus and neofunctionalization of SCPL in L.japonicus,which contributed to the accumulation of leonurine specifically in L.japonicus.Collectively,our comprehensive study illuminates leonurine biosynthesis and its evolution in Leonurus.

关键词： Lamiaceae Leonurus japonicus Leonurus sibiricus genome sequence alkaloids leonurine gene cluster biosynthetic pathway evolution

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Rosemary extract improves egg quality by altering gut barrier function,intestinal microbiota and oviductal gene expressions in late-phase laying hens

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Journal of Animal Science and Biotechnology 2024年第1期15卷 295-312页

作者： Lianhua Zhang Junwei Ge Fei Gao Min Yang Hui Li Fei Xia Hongtong Bai Xiangshu Piao Zhiying Sun Lei Shi Key Laboratory of plant Resources Institute of BotanyChinese Academy of SciencesBeijing 100093China China National botanical garden Beijing 100093China College of Pharmacy Shandong University of Traditional Chinese MedicineJinan 250355China University of Chinese Academy of sciences Beijing 100049China State Key Laboratory of Animal Nutrition College of Animal Science and TechnologyChina Agricultural UniversityBeijing 100193China

Background Rosemary extract(RE)has been reported to exert antioxidant property.However,the application of RE in late-phase laying hens on egg quality,intestinal barrier and microbiota,and oviductal function has not been systematically studied.This study was investigated to detect the potential effects of RE on performance,egg quality,serum parameters,intestinal heath,cecal microbiota and metabolism,and oviductal gene expressions in late-phase laying hens.A total of 21065-week-old“Jing Tint 6”laying hens were randomly allocated into five treatments with six replicates and seven birds per replicate and fed basal diet(CON)or basal diet supplemented with chlortetracycline at 50 mg/kg(CTC)or RE at 50 mg/kg(RE50),100 mg/kg(RE100),and 200 mg/kg(RE200).Results Our results showed that RE200 improved(P<0.05)Haugh unit and n-6/n-3 of egg yolk,serum superoxide dismutase(SOD)compared with CON.No significant differences were observed for Haugh unit and n-6/n-3 of egg yolk among CTC,RE50,RE100 and RE200 groups.Compared with CTC and RE50 groups,RE200 increased serum SOD activity on d 28 and 56.Compared with CON,RE supplementation decreased(P<0.05)total cholesterol(TC)level.CTC,RE100 and RE200 decreased(P<0.05)serum interleukin-6(IL-6)content compared with CON.CTC and RE200 increased jejunal m RNA expression of ZO-1 and Occludin compared with CON.The biomarkers of cecal microbiota and metabolite induced by RE 200,including Firmicutes,Eisenbergiella,Paraprevotella,Papillibacter,and butyrate,were closely associated with Haugh unit,n-6/n-3,SOD,IL-6,and TC.PICRUSt2 analysis indicated that RE altered carbohydrate and amino acid metabolism of cecal microbiota and increased butyrate synthesizing enzymes,including 3-oxoacid Co A-transferase and butyrate-acetoacetate Co A-transferase.Moreover,transcriptomic analysis revealed that RE200 improved gene expressions and functional pathways related to immunity and albumen formation in the oviductal magnum.Conclusions Dietary supplementation with 200 mg/kg RE could increase egg quality of late-p

关键词： Intestinal health Laying hens Microbiota Oviductal function Phytochemicals Production

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Genomic data and ecological niche modeling reveal an unusually slow rate of molecular evolution in the Cretaceous Eupteleaceae

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Science China(Life sciences) 2024年第4期67卷 803-816页

作者： Kun-Li Xiang Sheng-Dan Wu Lian Lian Wen-Chuang He Dan Peng Huan-Wen Peng Xiao-Ni Zhang Hong-Lei Li Jia-Yu Xue Hong-Yan Shan Gui-Xia Xu Yang Liu Zhi-Qiang Wu Wei Wang State Key Laboratory of plant Diversity and Specialty Crops Institute of BotanyChinese Academy of SciencesBeijing 100093China Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Synthetic BiologyLaboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China China National botanical garden Beijing 100093China State Key Laboratory of Grassland Agro-Ecosystems and College of Ecology Lanzhou UniversityLanzhou 730000China University of Chinese Academy of sciences Beijing 100049China College of Landscape Architecture and Life Science/institute of Special plants Chongqing University of Arts and SciencesChongqing 402160China College of Horticulture Academy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjing 210095China Fairylake botanical garden Shenzhen&Chinese Academy of SciencesShenzhen 518004China

Living fossils are evidence of long-term sustained ecological success.However,whether living fossils have little molecular changes remains poorly known,particularly in plants.Here,we have introduced a novel method that integrates phylogenomic,comparative genomic,and ecological niche modeling analyses to investigate the rate of molecular evolution of Eupteleaceae,a Cretaceous relict angiosperm family endemic to East Asia.We assembled a high-quality chromosome-level nuclear genome,and the chloroplast and mitochondrial genomes of a member of Eupteleaceae(Euptelea pleiosperma).Our results show that Eupteleaceae is most basal in Ranunculales,the earliest-diverging order in eudicots,and shares an ancient whole-genome duplication event with the other Ranunculales.We document that Eupteleaceae has the slowest rate of molecular changes in the observed angiosperms.The unusually low rate of molecular evolution of Eupteleaceae across all three independent inherited genomes and genes within each of the three genomes is in association with its conserved genome architecture,ancestral woody habit,and conserved niche requirements.Our findings reveal the evolution and adaptation of living fossil plants through large-scale environmental change and also provide new insights into early eudicot diversification.

关键词： conservation genomics eudicots evolutionary rates niche conservatism phylogenomics

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