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Long-read sequencing(method of the year 2022):The way forward for plant omics research

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Molecular Plant 2023年第5期16卷 791-793页

作者： sunil kumar sahu Huan Liu State Key Laboratory of Agricultural Genomics BGI-ShenzhenShenzhen 518083China College of Life Sciences University of Chinese Academy of SciencesBejing 100049China

Long-read sequencing(LRS)technology along with the recent development of computational tools,crowned the“method of the year 2022”(Marx,2023),have made it possible to sequence and assemble the genomes of practically every representative species(Kovaka et al.,2023).By considering its immense role and potential in advancing scientific research,the LRS market was valued at$1.35 billion in 2021 and is anticipated to reach$4.4 billion by 2031,growing at a compound annual growth rate of 14.4%from 2022 to 2031(***).Here,we discuss the current state and advantages of LRS technologies,the successful cases and novel discoveries with LRS,potential broad applications in plant genomics research,and the challenges that still need to be overcome in the future.

关键词： overcome crown method

Guardians of the fragrance:Uncovering the genetics behind citrus oil glands

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Plant Communications 2024年第5期5卷 97-99页

作者： sunil kumar sahu Muhammad Imran State Key Laboratory of Agricultural Genomics Key Laboratory of GenomicsMinistry of AgricultureBGI ResearchShenzhen 518083China BGI Research Wuhan 430074China State Key Laboratory for Conservation and Utilization of Subtropical AgroBioresources College of AgricultureSouth China Agriculture UniversityGuangzhou 510642China Center for Plant Biology School of Life SciencesTsinghua UniversityBeijing 100084China

The colorful,nutrient-rich peels of citrus fruits have long been valued for their tangy flavors and aromatic *** oils are produced and stored in special secretory structures called oil glands,which are prevalent across citrus varieties(Knight et al.,2001).Oil glands serve as"reservoirs"for diverse metabolites such as terpenes and flavonoids that give citrus fruits their characteristic aroma(Mahato et al.,2019;Voo et al.,2012;Xian et al.,2022).Many of these compounds also act as chemical defenses against pest and pathogens(Fisher and Phillips,2008).

关键词： citrus Guard reservoirs

Spatially resolved transcriptomics: a comprehensive review of their technological advances, applications, and challenges

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Journal of Genetics and Genomics 2023年第9期50卷 625-640页

作者： Mengnan Cheng Yujia Jiang Jiangshan Xu Alexios-Fotios AMentis Shuai Wang Huiwen Zheng sunil kumar sahu Longqi Liu Xun Xu BGI-Hangzhou HangzhouZhejiang 310012China BGI-Shenzhen ShenzhenGuangdong 518103China College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China State Key Laboratory of Agricultural Genomics BGI-ShenzhenShenzhenGuangdong 518083China Guangdong Provincial Key Laboratory of Genome Read and Write ShenzhenGuangdong 518120China

The ability to explore life kingdoms is largely driven by innovations and breakthroughs in technology,from the invention of the microscope 350 years ago to the recent emergence of single-cell sequencing,by which the scientific community has been able to visualize life at an unprecedented *** recently,the Spatially Resolved Transcriptomics(SRT)technologies have filled the gap in probing the spatial or even three-dimensional organization of the molecular foundation behind the molecular mysteries of life,including the origin of different cellular populations developed from totipotent cells and human *** this review,we introduce recent progresses and challenges on SRT from the perspectives of technologies and bioinformatic tools,as well as the representative SRT *** the currently fast-moving progress of the SRT technologies and promising results from early adopted research projects,we can foresee the bright future of such new tools in understanding life at the most profound analytical level.

关键词： Spatially resolved transcriptomics Bioinformatic tools Spatial single-cell Cell communications Tissue dissection Three-dimensional organ

Dissecting the genome of star fruit(Averrhoa carambola L.)

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Horticulture Research 2020年第1期7卷 1626-1635页

作者： Yannan Fan sunil kumar sahu Ting Yang Weixue Mu Jinpu Wei Le Cheng Jinlong Yang Ranchang Mu Jie Liu Jianming Zhao Yuxian Zhao Xun Xu Xin Liu Huan Liu State Key Laboratory of Agricultural Genomics China National GeneBankBGIShenzhen518120 ShenzhenChina BGI-Yunnan BGI-Shenzhen650106 KunmingChina Forestry Bureau of Ruili Yunnan Dehong678600 RuiliChina Chinese Academy of Forestry BeijingChina Guangdong Provincial Key Laboratory of Genome Read and Write 518120 ShenzhenChina BGI-Fuyang BGI-Shenzhen236009 FuyangChina Department of Biology University of CopenhagenCopenhagenDenmark

Averrhoa carambola is commonly known as star fruit because of its peculiar shape,and its fruit is a rich source of minerals and *** is also used in traditional medicines in countries such as India,China,the Philippines,and Brazil for treating various ailments,including fever,diarrhea,vomiting,and skin ***,we present the first draft genome of the Oxalidaceae family,with an assembled genome size of 470.51 *** total,24,726 protein-coding genes were identified,and 16,490 genes were annotated using various well-known *** phylogenomic analysis confirmed the evolutionary position of the Oxalidaceae *** on the gene functional annotations,we also identified enzymes that may be involved in important nutritional pathways in the star fruit ***,the data from this first sequenced genome in the Oxalidaceae family provide an essential resource for nutritional,medicinal,and cultivational studies of the economically important star-fruit plant.

关键词： vitamin Brazil cultivation

Polyunsaturated fatty acid-producing marine thraustochytrids:A potential source for antimicrobials

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Journal of Coastal Life Medicine 2015年第11期 848-851页

作者： Kaliyamoorthy Kalidasan sunil kumar sahu Kasinathan Kayalvizhi Kandasamy Kathiresan Centre of Advanced Study in Marine Biology Faculty of Marine SciencesAnnamalai UniversityParangipettai-608502Tamil NaduIndia

Objective:To evaluate the antimicrobial activity of marine thraustochytrids extracted from different ***:Crude extracts were derived from marine thraustochytrids,isolated from decaying mangrove leaf *** extracts were tested for antibacterial activity by using agar disc diffusion method against 10 clinical bacterial *** extracts were also analysed for presence of functional chemical groups by using Fourier transform infrared ***:Thraustochytrid extracts exhibited potent antibacterial activity against both Gramnegative and-positive *** antibacterial activity was observed prominently in butanol extract,followed by petroleum ether,methanol and chloroform *** antibacterial activity was maximum[(21.33±1.52)mm]against Staphylococcus aureus and minimum[(7.00±2.00)]mm against Klebsiella pneumonia and Salmonella ***:Thraustochytrids isolated from decaying mangrove leaf litter are potential sources of antibacterial compounds against clinical pathogens,which are called for further investigation of thraustochytrids as natural antibiotics.

关键词： Mangrove Leaf litter Thraustochytrids Polyunsaturated fatty acid Antibacterial activity

Antimicrobial and anticoagulant activities of the spine of stingray Himantura imbricata

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Journal of Coastal Life Medicine 2014年第2期 89-93页

作者： Kaliyamoorthy Kalidasan Velayudham Ravi sunil kumar sahu Murugan Lakshmi Maheshwaran Kathiresan Kandasamy Centre of Advanced Study in Marine Biology Faculty of Marine SciencesAnnamalai UniversityParangipettai-608502Tamil NaduIndia

Objective:To study the spine structure of stingray Himantura imbricata(***)and to evaluate the anticoagulant properties of the spine extract obtained through various solvents extracts followed by antibacterial activity against human ***:Spines of *** were collected from Nagappattinam coast,Tamil Nadu,India and their spines were observed under the light *** grounded spines were subjected to extraction of metabolites using methanol,ethanol,chloroform and *** activity was evaluated by disc diffusion technique against 10 human ***,anticoagulant activity was also assessed by following United States Pharmacopeia ***:Light microscopic observation of spine revealed that the venom apparatus of the stingray *** consisted of two to three spines,glandular tissue and a *** spine extract showed potent antibacterial activity against all tested *** activity(14 mm)was found against Staphylococcus *** extract showed 91.50 USP units/mg of anticoagulant ***:Microscopic observations gave new insight about the spine structure of the *** spine extracts of *** showed potent activity against human pathogens revealed by the good zone of *** extracts conferred the most prominent antibacterial *** anticoagulant activity was also comparable with that of standard heparin.

关键词： Stingrays Himantura imbricata Spine Antimicrobial activity Anticoagulant activity

Population Dynamics of Colonizing Fauna and Its Effect on Growth Rates of the Farmed Red Alga Alsidium triquetrum (S. G. Gmelin) Trevisan

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Natural Science 2022年第2期14卷 42-55页

作者： Ruben Cabrera Arsenio J. Areces Jhoana Díaz-Larrea sunil kumar sahu Juan Ricardo Cruz-Aviña Laura G. Nuñez García Gabinete de Arqueología Oficina del Historiador de la Ciudad Habana Vieja Cuba Instituto de Geografía Tropical Ministerio de Ciencia Tecnología y Medio Ambiente Municipio Playa Ciudad Habana Cuba Departamento de Hidrobiología Universidad Autónoma Metropolitana Unidad Iztapalapa CBS Cd de México México State Key Laboratory of Biocontrol Guangdong Key Laboratory of Plant Resources School of Life Science Sun Yat-Sen University Guangzhou China Facultad de Medicina Veterinaria y Zootecnia BUAP Laboratorio de Medicina de la Conservación Licenciatura en Medicina Veterinaria y Fauna Silvestre Km. 7.5 Carretera Ca&ntilde ada Morelos El Salado Tecamachalco Puebla Mexico

Herbivores can drastically alter the morphology of macroalgae by directly consuming tissue and by inflicting structural wounds. Macroalgae host abundant and diverse epibiont communities, the dynamics of which tend to be mostly unknown in space and time. As the cultivation of macroalgae gains momentum worldwide, it is key to measure how epibionts could affect algal performance. We examined the epibiont community associated with farmed Alsidium triquetrum, a red macroalga with growing pharmacological interest. Measurements were conducted over two independent 60-day periods, one in summer and one in winter. Epibionts showed different patterns of succession in both seasons. Crustaceans, mainly amphipods, showed the highest overall density, with deleterious effects on daily growth rates of A. triquetrum in winter. Adverse effects as a function of epibionts were not detected in summer. A. triquetrum is a perennial alga. However, its performance as a crop in the nearshore can be significantly affected by the epibiont community structure that persists in winter. Amphipods and ascoglossan molluscs were risk factors in the mariculture of this agarophyte. In winter, they can destroy plants when they reach more than five individuals per gram of fresh biomass. Results highlight that commercial farming of A. triquetrum would be successful if grown throughout the summer.

关键词： Cultivation Epifauna Macroalgae Macroinvertebrates Seaweed Mariculture

Haplotype-resolved and chromosome-scale genomes provide insights into co-adaptation between the Amur tiger and Amur leopard

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Zoological Research 2024年第3期45卷 464-467页

作者： Hai-Meng Li Bo-Yang Liu Min-Hui Shi Le Zhang Shang-Chen Yang sunil kumar sahu Liang-Yu Cui Shan-Lin Liu Nicolas Dussex Yue Ma Dan Liu Wei-Yao Kong Hao-Rong Lu Yue Zhao Love Dalén Huan Liu Tian-Ming Lan Guang-Shun Jiang Yan-Chun Xu College of Wildlife and Protected Area Northeast Forestry UniversityHarbinHeilongjiang 150040China State Key Laboratory of Agricultural Genomics BGI ResearchShenzhenGuangdong 518083China College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China College of Life Sciences Zhejiang UniversityHangzhouZhejiang 310058China BGI Research WuhanHubei 430074China Department of Entomology College of Plant ProtectionChina Agricultural UniversityBeijing 100193China Centre for Palaeogenetics Svante Arrhenius väg 20CStockholm 10691Sweden Department of Zoology Stockholm UniversityStockholm 10691Sweden Department of Bioinformatics and Genetics Swedish Museum of Natural HistoryStockholm 10691Sweden Heilongjiang Siberian Tiger Park HarbinHeilongjiang 150000China Jinlin Provincial Academy of Forestry Science ChangchunJilin 130033China China National GeneBank BGI ResearchShenzhenGuangdong 518120China Guangdong Provincial Key Laboratory of Genome Read and Write BGI ResearchShenzhenGuangdong 518083China BGI Life Science Joint Research Center Northeast Forestry UniversityHarbinHeilongjiang 150040China Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected AreaNortheast Forestry UniversityHarbinHeilongjiang 150040China National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization HarbinHeilongjiang 150040China

DEAR EDITOR,Big cats,such as Amur tigers(Panthera tigris altaica)and Amur leopards(*** orientalis),are apex predator and have evolved specialized traits for hunting and carnivory(Moya et al.,2022),thus playing a crucial role in maintaining biodiversity and ecosystem integrity by regulating prey-predator ***,human-induced pressures,habitat fragmentation,and environmental alterations have restricted these species in small and isolated ***,all extant big cats are categorized as endangered or threatened according to their conservation *** tigers and Amur leopards share overlapping geographic ranges,habitats,and certain prey species in the forests of Northeast Asia(Jiang et al.,2015).To reduce interspecies conflict,these carnivores exhibit differentiated dietary and temporal *** tigers predominantly prey on large ungulates,while Amur leopards hunt small to medium-sized animals(Sugimoto et al.,2016).Additionally,they occupy different temporal niches,with tigers being active at night and leopards more active during the *** spatial and temporal niche partitioning,interspecific competition between these two species is ***,benefiting from their greater size,have a competitive advantage over leopards,which can manifest in occasional leopard predation by tigers and declines in leopard populations with increasing tiger density(Jiang et al.,2015).Tigers also displace leopards from marginal habitats in nature reserves where they coexist.

关键词： habitat Panthera resolved

QM/MM Based Study of Electronic Structure of Platinum Dihalides

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Open Journal of Applied Sciences 2025年第1期15卷 305-328页

作者： Anil kumar Soni Swati Vishnu kumar sahu Department of Chemistry Shia Post Graduate College Lucknow India Academy of Scientific and Innovative Research NPL Chemical and Food BND Division CSIR-National Physical Laboratory New Delhi India Department of Chemistry Maharani Lal Kunwari Post Graduate College Balrmpur India

In this research work, atomic and molecular orbitals based analysis has been made to see electronic structure of platinum halides (platinum dichloride, platinum dibromide, platinum diiodide and platinum difluride). The geometry optimization and three dimensional (3D) modeling of the above mentioned species have been made on CAChe pro software. The results show: (i) The involvement of three p atomic orbitals is negligible as their summation values are very low in comparison to d orbital and considerably low with respect to s orbital. (ii) The study well support the Landis concepts of sdn-hybridation (here n = 1) as bond angle and contributions of s-orbital and d-orbital of Pt(II) are maximum with negligible contribution of p-orbitals. (iii) These halides also support the cloud-expanding effect with experimental data and also follow the nephelauxetic effect. The result is in good agreement with experiment results that covalent character increases in the order: PtI2 > PtBr2 > PtCl2 > PtF2. (iv) And thus the study will help to fine tune the existing complexes of these halides.

关键词： Platinum Dhalides Mulliken Population Analysis sd-Hybridization Molecular Orbital Diagram