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Comprehensive DNA barcode reference library and optimization of genetic divergence threshold facilitate the exploration of species diversity of green lacewings (Neuroptera: Chrysopidae)

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Insect Science 2024年第2期31卷 613-632页

作者： Yan Lai Kaiyu Li Xingyue Liu Deparment of Entomology Cllege of Plant ProtectionChina Agricultural UniversityBejingChina College of Bioogical Sciencs China Agricultural UniversityBeijingChina

Chrysopidae are a family of Neuroptera of significant importance in biocontrol against agricultural pests because of their predatory ***,the taxonomy of Chrysopidae lacks a comprehensive revision,which impedes the exploration of species diversity as well as the selection and the conservation of green lacewings as biocontrol *** have established a DNA barcode reference library of the Chinese green lacewings based on an approximately complete sampling(95.63%)in 25 of the 34 provincial regions in China,comprising 1119 barcodes of 25 genera and 197 species(representing 85%genera and 43.62%species from China).Combining other 1049 high quality green lacewing DNA barcodes,we first inferred the optimal threshold of interspecific genetic divergence(1.87%)for successful species identification in multiple simulated scenarios based on present *** further inferred the threshold of genetic divergence(7.77%)among genera with biocontrol *** inference and performance of the threshold appears to be mainly associated with the completeness of sampling,the proportion of closely related species,and the analytical *** new combinations,Apertochrysa platypa(Yang&Yang,1991)***.,Apertochrysa shennongana(Yang&Wang,1990)***.,Apertochrysa pictifacialis(Yang,1988)***.,Apertochrysa helana(Yang,1993)***.,Plesiochrysa rosulata(Yang&Yang,2002)***.,and Signochrysa hainana(Yang&Yang,1991),are proposed according to integrative species *** library and optimal threshold will effectively facilitate the exploration of species diversity of green *** study also provides a methodological reference in molecular delimitation of other insects.

关键词： Chrysopidae DNA barcode genetic distance optimal threshold species delimitation

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Characterization of an extreme alkaline-stable keratinase from the draft genome of feather-degrading Bacillus ***7 from deep-sea

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Acta Oceanologica Sinica 2019年第2期38卷 87-95页

作者： Min Jin Chen Chen Xiongfei He Runying Zeng State Key Laboratory Breeding base of Marine genetic resource Third Institute of Oceanography Ministry of Natural Resources South China Sea Bio-resource Exploitation and Utilization Collaborative Innovation center Fujian Collaborative Innovation center for Exploitation and Utilization of Marine Biological resources

Bacillus sp. JM7, a strain isolated from the deep-sea of the South China Sea, was found to efficiently degrade 79.4% native chicken feather within 30 h. Scanning electron microscopy analysis showed that JM7 strain could gradually degrade feather by modifying the microstructure of feather keratin. A total of 25 protease genes were predicted from the draft genome of JM7 strain, among which a predicted subtilisin-like serine protease(designated as Ker02562) was further characterized for its keratinolytic activity. The recombinant Ker02562 functioned at a wide range of temperatures from 30℃ to 60℃, with an optimum at 40–50℃. Ker02562 was highly active at various pHs ranging from 5.0 to 13.0, with a maximum activity observed at pH 7.0–9.0. Remarkably, recombinant Ker02562 was stable in extreme alkaline environments(pH 10–13), which was much better than most other reported keratinases. Collectively, these favorable properties could make Bacillus sp. JM7 and Ker02562 attractive to be applied in the detergent formulation and feather bioconversion.

关键词： Bacillus deep-sea feather-degradation keratinases feather bioconversion alkaline-stable

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A chromosome-level genome assembly of anesthetic drug–producing Anisodus acutangulus provides insights into its evolution and the biosynthesis of tropane alkaloids

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plant Communications 2024年第1期5卷 231-244页

作者： Wei Zhou Can Wang Xiaolong Hao Fei Chen Qikai Huang Tingyao Liu Jiang Xu Shuai Guo Baosheng Liao Zhixiang Liu Yue Feng Yao Wang Pan Liao Jiayu Xue Min Shi Itay Maoz Guoyin Kai Zhejiang Provincial International S&T Cooperation base for Active Ingredients of Medicinal and Edible plants and Health Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and TransformationSchool of Pharmaceutical SciencesJinhua AcademyZhejiang Chinese Medical UniversityHangzhouZhejiang 310053China Sanya Nanfan Research Institute from Hainan University Hainan Yazhou Bay Seed LaboratorySanya 572025China Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing 100700China Department of Biology Hong Kong Baptist UniversityKowloon TongHong KongChina College of Horticulture Academy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjing 210095China Department of Postharvest Science Agricultural Research OrganizationVolcani CenterP.O.Box 15159HaMaccabim Road 68Rishon LeZion 7505101Israel

Tropane alkaloids(TAs),which are anticholinergic agents,are an essential class of natural compounds,and there is a growing demand for TAs with anesthetic,analgesic,and spasmolytic *** acutan-gulus(Solanaceae)is a TA-producing plant that was used as an anesthetic in ancient *** this study,we assembled a high-quality,chromosome-scale genome of *** with a contig N50 of 7.4 Mb.A recent whole-genome duplication occurred in *** after its divergence from other Solanaceae species,which resulted in the duplication of ADC1 and UGT genes involved in TA *** catalytic activities of H6H enzymes were determined for three Solanaceae *** the basis of evolution and co-expressed genes,AaWRKY11 was selected for further analyses,which revealed that its encoded tran-scription factor promotes TA biosynthesis by activating AaH6H1 *** provide useful insights into genome evolution related to TA biosynthesis and have potential implications for genetic manipulation of TA-producing plants.

关键词： Anisodus acutangulus tropane alkaloid biosynthesis hyoscyamine 6 b-hydroxylase AaWRKY11

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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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Sequence Information on Simple Sequence Repeats and Single Nucleotide Polymorphisms through Transcriptome Analysis of Mungbean

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Journal of Integrative plant Biology 2011年第1期53卷 63-73页

作者： Kyaw Thu Moe Jong-Wook Chung Young-Il Cho Jung-Kyung Moon Ja-Hwan Ku Jin-Kyo Jung Jungran Lee Yong-Jin Park Department of plant resources College of Industrial SciencesKongju National University The Rural Development Administration(RDA) Legume Bio-resource center of Green Manure(LBRCGM) Kongju National University

Mungbean （Vigna radiata （L.） Wilczek） is a unique species in its ability to fix atmospheric nitrogen, with early maturity, and relatively good drought resistance. We used 454 sequencing technology for transcriptome sequencing. A total of 150 159 and 142 993 reads produced 5 254 and 6 374 large contigs （〉_500 bp） with an average length of 833 and 853 for Sunhwa and Jangan, respectively. Functional annotation to known sequences yielded 41.34% and 41.74% unigenes for Jangan and Sunhwa. A higher number of simple sequence repeat （SSR） motifs was identified in Jangan （1 630） compared with that of Sunhwa （1 334）. A similar SSR distribution pattern was observed in both varieties. A total of 8 249 single nucleotide polymorphisms （SNPs） and indels with 2 098 high-confidence candidates were identified in the two mungbean varieties. The average distance between individual SNPs was -860 bp. Our report demonstrates the utility of transcriptomic data for implementing a functional annotation and development of genetic markers. We also provide large resource sequence data for mungbean improvement programs.

关键词： Sequence Information on Simple Sequence Repeats and Single Nucleotide Polymorphisms through Transcriptome Analysis of Mungbean SNPs

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Germacrone Induces Apoptosis in Human Hepatoma HepG2 Cells through Inhibition of the JAK2/STAT3 Signalling Pathway

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Journal of Huazhong University of Science and Technology(Medical Sciences) 2013年第3期33卷 339-345页

作者：柳昀熠郑倩方斌王维马凤云 Sadia Roshan Amal Banafa 陈明洁常俊丽邓小敏李克秀杨广笑何光源 The genetic Engineering International Cooperation base of Chinese Ministry of Science and Technology Chinese National Center of Plant Gene Research (Wuhan) HUST PartKey Laboratory of Molecular Biophysics of Chinese Ministry of EducationCollege of Life Science and TechnologyHuazhong University of Science and Technology

Summary： Previous studies have shown that STAT3 plays a vital role in the genesis and progression of cancer. In this study, we investigated the relationship between the JAK2/STAT3 signalling pathway and germacrone-induced apoptosis in HepG2 cells. HepG2 cells were incubated with germacrone for 24 h, the protein expression of p-STAT3, STAT3, p-JAK2 and JAK2 was detected by Westem Blotting, and RT-PCR was used to determine the expression of STAT3, p53, Bcl-2 and Bax at transcriptional levels. Besides that, HepG2 cells were pre-treated with AG490 or IL-6 for 2 h, and then incubated with ger- macrone for 24 h. The expression ofp-JAK2, JAK2, p-STAT3, STAT3, p53, Bax and Bcl-2 was detected by Western blotting. The activity of HepG2 cells was tested by MTT assay. The apoptosis of HepG2 cells and levels of reactive oxygen species （ROS） were flow cytometrically measured. The results showed that germacrone exposure decreased p-STAT3 and p-JAK2 and regulated expression of p53 and Bcl-2 family members at the same time. Moreover, IL-6 enhanced the activation of the JAK2/STAT3 signalling pathway and therefore attenuated the germacrone-induced apoptosis. Suppression of JAK2/STAT3 signalling pathway by AG490, an inhibitor of JAK2, resulted in apoptosis and an increase in ROS in response to germacrone exposure. We therefore conclude that germacrone induces apoptosis through the JAK2/STAT3 signalling pathway.

关键词： germacrone JAK2/STAT3 apoptosis HepG2 ceils

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genetic Variation of the Novel Badnaviruses Infecting Nelumbo Nucifera based on the RT/RNase H Coding Region Sequences

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Horticultural plant Journal 2020年第5期6卷 335-342页

作者： Zhen He Tingting Dong Tielin Wang Wen Chen Xian Liu Liangjun Li School of Horticulture and plant Protection Yangzhou UniversityYangzhouJiangsu 225009China State Key Laboratory Breeding base of Dao-di Herbs National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijing 100700China

Lotus(Nelumbo nucifera Gaertn.)is an economically important perennial aquatic herb plant in ***,viral diseases caused by Cucumber mosaic virus(CMV)and Dasheen mosaic virus(DsMV)are detected in *** this study,the putatively novel badnaviruses from lotus plants(LBVs)were identified using next-generation sequencing of siRNAs and conventional Sanger sequencing based on the RT/RNase H coding region *** plants infected by LBVs harbored virus quasispecies.A unique recombination event of LBVs was found in a single lotus *** inoculation showed that LBVs could actively replicate in the lotus plants,but without a wide host *** field survey of 43 lotus plants in Jiangsu Province showed a prevalence of 62.8%for LBVs,confirming that it is widely distributed in Jiangsu Province of China.

关键词： Nelumbo nucifera Badnaviruses mixed infection genetic variation

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A High-Throughput Screening System for Arabidopsis Transcription Factors and Its Application to Med25-Dependent Transcriptional Regulation

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Molecular plant 2011年第3期4卷 546-555页

作者： Bin Oua Kang-Quan Yin Sai-Nan Liu Yan Yang Tren Gu Jennifer Man Wing Hui Li Zhang Jin Miao Youichi Kondou Minami Matsui Hong-Ya Gu Li-Jia Qu national Laboratory for Protein Engineering and plant genetic Engineering College of Life Sciences Peking University Beijing 100871 People's Republic ofChina plant Science center RIKEN Yokohama Institute 1-7-22 Suehiro-cho Tsurumi-ku Yokohama City Kanagawa 230-0045 Japan The national plant Gene Research center (Beijing) Beijing 100101 People's Republic of China

The activities of transcription factors （TFs） require interactions with specific DNA sequences and other reg- ulatory proteins. To detect such interactions in Arabidopsis, we developed a high-throughput screening system with a Gateway-compatible Gal4-AD-TF library of 1589 Arabidopsis TFs, which can be easily screened by mating-based yeast-one-hybrid （YIH） and yeast-two-hybrid （Y2H） methods. The efficiency of the system was validated by examining two well-characterized TF-DNA and TF-protein interactions： the CHE-CCA1 promoter interaction by YIH and NPR1-TGAs interactions by Y2H. We used this system to identify eight TFs that interact with a Mediator subunit, Med25, a key reg- ulator in JA signaling. We identified five TFs that interacted with the GCC-box cis-element in the promoter of PDF1.2, a downstream gene of Med25. We found that three of these TFs, all from the AP2-EREBP family, interact directly both with Med25 and the GCC-box of PDF1.2, suggesting that Med25 regulates PDF1.2 expression through these three TFs. These results demonstrate that this high-throughput Y1H/Y2H screening system is an efficient tool for studying transcrip- tional regulation networks in Arabidopsis. This system will be available for other Arabidopsis researchers, and thus it provides a vital resource for the Arabidopsis community.

关键词： Transcription factors Arabidopsis yeast-one-hybrid yeast-two-hybrid Med25.

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Genomic selection in plant breeding:Key factors shaping two decades of progress

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Molecular plant 2024年第4期17卷 552-578页

作者： Admas Alemu Johanna Astrand Osval A.Montesinos-López Julio Isidro y Sanchez Javier Fernandez-Gónzalez Wuletaw Tadesse Ramesh R.Vetukuri Anders S.Carlsson Alf Ceplitis JoséCrossa Rodomiro Ortiz Aakash Chawade Department of plant Breeding Swedish University of Agricultural SciencesAlnarpSweden Lantmannen Lantbruk SvalövSweden Facultad de Telematica University de ColimaColimaColima 28040Mexico Centro de Biotecnología y Genómica de plantas(CBGP UPM-INIA)Universidad Politécnica de Madrid(UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria(INIA)Campus de Montegancedo-UPM28223 MadridSpain International center for Agricultural Research in the Dry Areas(icarDA) RabatMorocco International Maize and Wheat Improvement center(CIMMYT) Km 45Carretera México-VeracruzTexcocoMéxico 52640Mexico

Genomic selection,the application of genomic prediction(GP)models to select candidate individuals,has significantly advanced in the past two decades,effectively accelerating genetic gains in plant *** article provides a holistic overview of key factors that have influenced GP in plant breeding during this *** delved into the pivotal roles of training population size and genetic diversity,and their relationship with the breeding population,in determining GP *** emphasis was placed on optimizing training population *** explored its benefits and the associated diminishing returns beyond an optimum *** was done while considering the balance between resource allocation and maximizing prediction accuracy through current optimization *** density and distribution of single-nucleotide polymorphisms,level of linkage disequilibrium,genetic complexity,trait heritability,statistical machine-learning methods,and non-additive effects are the other vital *** wheat,maize,and potato as examples,we summarize the effect of these factors on the accuracy of GP for various *** search for high accuracy in GP—theoretically reaching one when using the Pearson’s correlation as a metric—is an active research area as yet far from optimal for various *** hypothesize that with ultra-high sizes of genotypic and phenotypic datasets,effective training population optimization methods and support from other omics approaches(transcriptomics,metabolomics and proteomics)coupled with deep-learning algorithms could overcome the boundaries of current limitations to achieve the highest possible prediction accuracy,making genomic selection an effective tool in plant breeding.

关键词： genomic selection genetic gain genomic prediction optimization deep learning training population optimization

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Phylogenetically diverse,acetaldehyde-degrading bacterial community in the deep sea water of the West Pacific Ocean

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Acta Oceanologica Sinica 2018年第8期37卷 54-64页

作者： GAO Boliang SHANG Xiexie LI Li DI Wenjie ZENG Runying School of Life Sciences Xiamen UniversityXiamen 361102China State Key Laboratory Breeding base of Marine genetic resource Third Institute of OceanographyState Oceanic AdministrationXiamen 361005China Fujian Collaborative Innovation center for Exploitation and Utilization of Marine Biological resources Xiamen 361005China

As a major aldehyde pollutant widely existing in industry and our daily life, acetaldehyde is more and more harmful to human health. As characteristic habitat niche, bacteria from deep sea environments are abundant and distinctive in heredity, physiology and ecological functions. Thus, the development of acetaldehyde-degrading bacteria from deep sea provides a new method to harness acetaldehyde pollutant. Firstly, in this study,acetaldehyde-degrading bacteria in the deep sea water of the West Pacific Ocean were enriched in situ and in the laboratory respectively, and then the diversity of uncultured bacteria was studied by using 16 S r RNA genes. Then acetaldehyde-degrading strains were isolated from two samples, including enrichment in situ and enrichment in laboratory samples of deep sea water from the West Pacific Ocean using acetaldehyde as the sole carbon source,and then the ability of acetaldehyde degradation was detected. Our results showed that the main uncultured bacteria of two samples with different enrichment approaches were similar, including Proteobacteria,Actinobacteria, Firmicutes, Cyanobacteria, but the structure of bacterial community were significant *** subgroups, α, γ, δ and ε, were found in Proteobacteria group. The γ-Proteobacteria was dominant（63.5%clones in laboratory enriched sample, 75% clones in situ enriched sample）. The species belonged to γ-Proteobacteria and their proportion was nearly identical between the two enrichment samples, and Vibrio was the predominant genus（45% in laboratory enriched sample, 48.5% in situ enriched sample）, followed by Halomonas（9% in situ enriched sample） and Streptococcus（6% in laboratory enriched sample）. A total of 12 acetaldehyde-degrading strains were isolated from the two samples, which belonged to Vibrio, Halomonas,Pseudoalteromonas, Pseudomonas and Bacillus of γ-Proteobacteria. Strains ACH-L-5, ACH-L-8 and ACH-S-12,belonging to Vibrio and Halomonas, have strong ability of acetaldehyde degr

关键词： acetaldehyde-degrading bacteria ALDH deep sea in situ

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