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Mutation Prediction for Coronaviruses Using genome sequence and Recurrent Neural Networks

Computers, Materials & Continua 2022年第10期73卷 1601-1619页

作者： Pranav Pushkar Christo Ananth Preeti Nagrath Jehad F.Al-Amri Vividha Anand Nayyar Bharati Vidyapeeth’s College of Engineering New Delhi110063India Department of Natural and Exact Sciences Samarkand State UniversitySamarkandUzbekistan Graduate School Duy Tan UniversityDa Nang550000Viet Nam Faculty of Information Technology Duy Tan UniversityDa Nang550000Viet Nam Department of Information Technology College of Computers and Information TechnologyTaif UniversityTaif21944Saudi Arabia

The study of viruses and their genetics has been an opportunity as well as a challenge for the scientific community.The recent ongoing SARSCov2(Severe Acute Respiratory Syndrome)pandemic proved the unpreparedness for these situations.Not only the countermeasures for the effect caused by virus need to be tackled but the mutation taking place in the very genome of the virus is needed to be kept in check frequently.One major way to find out more information about such pathogens is by extracting the genetic data of such viruses.Though genetic data of viruses have been cultured and stored as well as isolated in form of their genome sequences,there is still limited methods on what new viruses can be generated in future due to mutation.This research proposes a deep learning model to predict the genome sequences of the SARS-Cov2 virus using only the previous viruses of the coronaviridae family with the help of RNN-LSTM(Recurrent Neural Network-Long ShortTerm Memory)and RNN-GRU(Gated Recurrent Unit)so that in the future,several counter measures can be taken by predicting possible changes in the genome with the help of existing mutations in the virus.After the process of testing the model,the F1-recall came out to be more than 0.95.The mutation detection’s accuracy of both the models come out about 98.5%which shows the capability of the recurrent neural network to predict future changes in the genome of virus.

关键词： COVID-19 genome sequence coronaviridae RNN-LSTM RNN-GRU

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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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Complete genome sequence and proteomic analysis of a thermophilic bacteriophage BV1

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Acta Oceanologica Sinica 2010年第3期29卷 84-89页

作者： LIU Bin WU Suijie XIE Lianhui Institute of Plant Virology Fujian Agriculture and Forestry University Fuzhou 350002 China College of Food Science Fujian Agriculture and Forestry University Fuzhou 350002 China Key Laboratory of Marine Biogenetic Resources Third Institute of Oceanography State Oceanic Administration Xiamen 361005 China

Viruses of thermophiles are of great interest due to their roles in gene transfer, global geochemical cycle and evolution of life on earth. However, the thermophilic bacteriophages have not been studied extensively. In this investigation, a typical bacteriophage BV1 was obtained from a thermophilic bacterium Geobacillus sp. 6k512, which was isolated from an inshore hot spring in Xiamen of China. The BV1 contained a double-stranded linear DNA of 35 055 bp, which encodes 54 open reading frames （ORFs）. Interestingly, eight of the 54 BV1 ORFs shared sequence similarities to genes from human disease-relevant bacteria. Seven proteins of the purified BV1 virions were identified by proteomic analysis. Determination of BV1 functional genomics would facilitate the better understanding of the mechanism for virus-thermophile interaction.

关键词： thermophile bacteriophage genome sequence proteomic analysis

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genome sequence,FUNCTIONAL GENOMICS AND GENETIC LINKAGE ANALYSIS OF SHIITAKE MUSHROOM LENTINULA EDODES

GENOME SEQUENCE,FUNCTIONAL GENOMICS AND GENETIC LINKAGE ANAL...

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海峡两岸第十届菌物学暨第三届食药用菌学术研讨会

作者： KWANH.S. AUC.H. WONG M.C. KWOK I.S.W. CHUM W.W.Y. YIP P.Y. WONG K.S. School of Life Sciences and Food Research Centre The Chinese University of Hong Kong The Chinese University of Hong Kong ShatinN.THong Kong SARPRC

＜正＞Lentinula edodes（Shiitake/Xianggu） is a popular cultivated mushroom species.Understanding the genomics and functional genomics of L.edodes is essential to improve its cultivation and quality.genome sequencing of L.edodes provides numerous molecular genetic markers for breeding and genetic manipulation.We sequenced the genome of L.edodes monokaryon L54A using Roche 454 and ABI SOLiD.Sequencing reads of about 1011 Mb were de novo assembled into a 39.8 Mb genome.We compiled the genome sequences into a searchable database with which we have been annotating the genes and analyzing the metabolic pathways.Over 13,000 gene models were predicted from the genome sequence.The gene models were annotated by BLASTX and categorized according to Gene Ontology（GO） and Kyoto Encyclopedia of Genes and genomes（KEGG）.For functional genomics,we have been using many molecular techniques including SAGE and massive cDNA sequencing to analyze genes differentially expressed during development.Using a mapping population of haploid basidiospores of dikaryon L54,we constructed a high-density genetic linkage map with their high-quality genetic variations including single nucleotide polymorphisms, insertions,and deletions.The Shiitake community will benefit from these resources for genetic studies and breeding.

关键词： Shiitake Mushroom genome sequence transcriptome fruiting body development

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Complete genome sequence of a Divergent Strain of Lettuce Chlorosis Virus from Periwinkle in China

Complete Genome Sequence of a Divergent Strain of Lettuce Ch...

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中国植物病理学会2017年学术年会

作者： Tian Xin Shen Pan Zhang Song Zhou Changyong Cao Mengji National Citrus Engineering Research Center Citrus Research InstituteSouthwest University

A novel strain of Lettuce chlorosis virus（LCV） was identified from periwinkle（PW）with foliar interveinal chlorosis and plant dwarf in China.Complete nucleotide（nt） sequences of genomic RNA1 and RNA2 of the virus are 8 602 nt and 8 456 nt,respectively.The genomic organization of LCVPW resembles that of a California isolate（LCV-CA）,but its RNA2 only encodes 8 open reading frames.The LCV-PWRNA2 is shorter than that of LCV-CA,mainly due to two large deletions.Phylogenetic analyses were performed using the amino acid sequences of the RdRp（ORFlb）,HSP70 h,coat protein（CP） and minor coat protein（CPm） of the two LCV isolates and representative members of the genus Crinivirus.Neighbor-joining trees show that the two LCV isolates are grouped together in a cluster containing Cucurbit chlorotic yellows virus（CCYV）,Bean yellow disorder virus（BnYDV）,Cucurbit yellow stunting disorder virus（CYSDV） and Tetterwort vein chlorosis virus（TVCV）.LCV-PWis different from LCV-CA by 84%（RNA1） and 89%（RNA2） at the genomic sequences and the bean isolate by 84.0%at the 421-nt HSP70 h sequence（KC602375,RNA2）,respectively.More recently,a tomato isolate of LCV（KX158863） was identified from Shandong province.Comparison of a 446-nt partial la polyprotein sequence of the two Chinese isolates showed that they were 99.8%identical withone another,suggesting that they might bethe same variant.

关键词： Lettuce chlorosis virus genome sequence Crinivirus Periwinkle

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Biological characterization and genome sequence of phages of Staphylococcus aureus

Biological characterization and genome sequence of phages of...

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2017中国长三角遗传学大会

Objective:Staphylococcus aureus is a widely-spread gram-positive pathogen causing endocarditis,osteomyelitis,pneumonia and food poisoning.In recent years,due to the large-scale use and abuse of antibiotics,Staphylococcus aureus resistance bacteria have been emerging.From MRSA(methicillin resistant Staphylococcus aureus) to VISA(vancomycin resistant Staphylococcus aureus),Staphylococcus aureus resistant bacterias emerge very quickly.But the cost of antibiotic research is high,the cycle is long,and it can not keep pace with the speed of bacterial resistance.It is urgent to find new treatment methods for drug-resistant bacteria.Two strains of phages named big phage and small phage of Staphylococcus aureus were isolated from the cattle farm in Shanghai.Samples contain cow manure,washing water and milk.our research aims to study the classification and biological characterization and genome sequence of two bacteriophages and provide new idea for phage therapy of Staphylococcus aureus.Methods:Two Staphylococcus aureus bacteriophages were isolated from the dairy farm environment by the standard strain ATCC25923 of Staphylococcus aureus,which is presented by laboratory teacher Conghui Zhang.The morphology and size of bacteriophages were observed by transmission electron microscope with negative staining.The pH and temperature stability were studied as well,the optimal multiplication of infection,the one-step growth curve,adsoution curve and infection curve were plotted.The phage DNA were extracted for genome sequence and bioinformatics analysis.Results:Two phages were screened by Staphylococcus aureus ATCC25923,named big phage and small phage respectively,and were identified as Myoviridaeby transmission electron microscopy.big phage belongs to the family of Myoviridaeby with head diameter of about 95 nm,tail length of about230 nm and tail width of about 16 nm.The big phage genome is linear double-stranded DNA with a full-length 142.978 bp and a GC content of 29.799%.This phage had high activity with PH from 6 to9 and temp

关键词： Staphylococcus aureus phage biological characterization genome sequence

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Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis

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Plant Communications 2022年第4期3卷 105-123页

作者： Fuqiang Cui Xiaoxue Ye Xiaoxiao Li Yifan Yang Zhubing Hu Kirk Overmyer Mikael Brosche Hong Yu Jarkko Salojarvi College of Forestry and Biotechnology State Key Laboratory of Subtropical SilvicultureZhejiang A&F UniversityLin’anHangzhou 311300China Key Laboratory of Biology and Genetic Resources of Tropical Crops Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouHainan 571101China School of Biological Sciences Nanyang Technological UniversitySingaporeSingapore Organismal and Evolutionary Biology Research Program Faculty of Biological and Environmental Sciencesand the Viikki Plant Science CentreUniversity of HelsinkiPO Box 65(Viikinkaari 1)00014 HelsinkiFinland Institute of Botany Jiangsu Province and Chinese Academy of SciencesNanjingChina State Key Laboratory of Cotton Biology Department of BiologyInstitute of Plant Stress BiologyHenan UniversityKaifengChina

Vaccinium darrowii is a subtropical wild blueberry species that has been used to breed economically important southern highbush cultivars.The adaptive traits of V.darrowii to subtropical climates can provide valuable information for breeding blueberry and perhaps other plants,especially against the background of global warming.Here,we assembled the V.darrowii genome into 12 pseudochromosomes using Oxford Nanopore long reads complemented with Hi-C scaffolding technologies,and we predicted 41815 genes using RNA-sequencing evidence.Syntenic analysis across three Vaccinium species revealed a highly conserved genome structure,with the highest collinearity between V.darrowii and Vaccinium corymbosum.This conserved genome structure may explain the high fertility observed during crossbreeding of V.darrowii with other blueberry cultivars.Analysis of gene expansion and tandem duplication indicated possible roles for defense-and flowering-associated genes in the adaptation of V.darrowii to the subtropics.Putative SOC1 genes in V.darrowii were identified based on phylogeny and expression analysis.Blueberries are covered in a thick cuticle layer and contain anthocyanins,which confer their powdery blue color.Using RNA sequencing,we delineated the cuticle biosynthesis pathways of Vaccinium species in V.darrowii.This result can serve as a reference for breeding berries whose colors are appealing to customers.The V.darrowii reference genome,together with the unique traits of this species,including its diploid genome,short vegetative phase,and high compatibility in hybridization with other blueberries,make V.darrowii a potential research model for blueberry species.

关键词： Vaccinium darrowii blueberry genome sequence cuticle subtropical adaptation

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The genome sequence of Salix suchowensis,an alternative model system for studying the unique biology of angiosperm woody plants

The genome sequence of Salix suchowensis,an alternative mode...

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遗传学与表观遗传学前沿暨第三届中国青年遗传学家论坛

作者：尹佟明 Xiaogang Dai Kai Feng Yingnan Chen Zhibing Wan Ning Ye Mingxiu Wang Key Lab of Forest Genetics and biotechnology Nanjing Forestry University

In this study,we report the genome sequence of Salix suchowensis,a shrub willow closely related to poplars.A total of 303.2Mb genome sequences were assembled with 23.8-fold of454 single and mate-pair reads and 231.1-fold of Illumina pair-end reads.We predicted 26,599protein-coding genes and the assembled genome was highly collinear to the poplar genome.Compared with Populus trichocarpa,this Salix specieshad substantially smaller genome size and lower gene number.genomesacross the two lineages shared the most recent‘Salicoid’duplication,and the more ancient duplications common to Arabidopsis and other dicots.Gene cluster analysis for these two lineages indicated that more extensive loss of genes underwent in willow than in poplar.GO enrichment further showed that willow retained genes that were generally more pleiotropic than poplar genes to balance its heavier loss in genes number.SalixandPopulus began to divergearound six million years after the’Salicoid’duplication.This study also found that S.suchowensis had higher substitution rate man P.trichocarpa,perhaps due to its earlier sexual maturity.The availability of a Salix genome,alongside that for P.trichocarpa,increases our knowledge of the evolution of the Salicaceae and provides a means for comparative genomics between these woody perennial species and the other sequenced model plants.In total,these resources will be useful for dissecting themechanisms and pathways that control woody traits in Salicaceae,and should help to maximize the efficiency of these genera as woody biofuel crops.

关键词： shrub willow genome sequence woody plants genome evolution

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Enhanced cobalamin biosynthesis in Ensifer adhaerens by regulation of key genes with gradient promoters

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Synthetic and Systems Biotechnology 2022年第3期7卷 941-948页

作者： Sha Xu Zhiqiang Xiao Shiqin Yu Weizhu Zeng Yongming Zhu Jingwen Zhou National Engineering Laboratory for Cereal Fermentation Technology Jiangnan University1800 Lihu RoadWuxiJiangsu214122China School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of EducationJiangnan University1800 Lihu RoadWuxiJiangsu214122China Science Center for Future Foods Jiangnan University1800 Lihu RoadWuxiJiangsu214122China Jiangsu Provisional Research Center for Bioactive Product Processing Technology Jiangnan University1800 Lihu RoadWuxiJiangsu214122China Hunan Hongying Biotechnology Co.Ltd. 10 Hongying RoadJinshiHunan415400China

Cobalamin is an essential human vitamin widely used in the pharmaceutical,food,and feed additive industries and currently produced by bacteria or archaea.Ensifer adhaerens HY-1 is an industrial strain that also produces cobalamin.However production outputs are poor and the specific synthesis pathways require characterization.In this study,the whole genome sequence of E.adhaerens HY-1 was generated and annotated,and genes associated with cobalamin biosynthesis were identified.Then,three genes,CobSV,CobQ,and CobW were identified as the most efficient ones for enhancing cobalamin synthesis.By transcriptome sequencing of E.adhaerens HY-1 cells at different growth stages,65 endogenous promoters with different gradient strengths were identified.After combined expression of different strength promoters and key genes,a high cobalamin-producing recombinant strain,‘hmm’(genotype:PmetH-CobSV-PibpA-CobQ-Pmdh-CobW),was generated.Cobalamin production was 143.8 mg/L in shaking flasks,which was 41.0%higher than the original strain.Cobalamin production was further enhanced to 171.2 mg/L using fed-batch fermentation.Importantly,our data and novel approach provide important references for the analysis of cobalamin synthesis and other metabolites in complex metabolic pathways.

关键词： Ensifer adhaerens Cobalamin genome sequence Transcriptome sequence Promoter Overexpression Combinations

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Apple stem grooving virus is associated with leaf yellow mottle mosaic disease on Citrus grandis cv. Huangjinmiyou in China

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Journal of Integrative Agriculture 2022年第7期21卷 2031-2041页

作者： XUAN Zhi-you ZHANG Song LI Ping YANG Fang-yun CHEN Hong-ming LIU Ke-hong ZHOU Yan LI Zhong-an ZHOU Chang-yong CAO Meng-ji National Citrus Engineering and Technology Research Center Citrus Research InstituteSouthwest UniversityChongqing 400712P.R.China State Cultivation Base of Crop Stress Biology for Southern Mountainous Land Academy of Agricultural SciencesSouthwest UniversityChongqing 400715P.R.China

Although it is usually latent on citrus, apple, and pear, apple stem grooving virus(ASGV) poses a great risk to many sensitive cultivars. Since severe leaf yellow mottle mosaic(LYMM) symptoms have been observed on Huangjinmiyou(HJY) pummelos(Citrus grandis cv. Huangjinmiyou), a commercial variety that is widely cultivated in South China, high throughput sequencing(HTS) was used to find potential pathogens and only three divergent ASGV variants were identified. The three ASGV variants shared 81.03–82.34% genome-wide pairwise identities with each other, and were separately closest to other ASGV variants from different hosts and/or geographical regions, as indicated by viral phylogenies. However, these new variants may have developed from viral interstrain interactions, based on the results of recombination analysis. A large-scale survey using reverse transcription-PCR(RT-PCR) protocols designed for the three ASGV variants revealed a high incidence(92.7–100%) of ASGV in symptomatic HJY trees from 11 major citrusproducing regions in China. None of ASGV were detected in asymptomatic trees. Temperature treatments applied to the symptomatic HJY plants showed that ASGV is sensitive to high temperatures(30–35°C), at which not only the plants recovered, but also the viruses were not detected by RT-PCR, while at low temperatures(20–24°C), both the symptoms and viruses remained detectable. These data show that ASGV is associated with the LYMM disease prevalent on HJY in China, and this is the significant basis especially of taking appropriate measures timely to manage the disease.

关键词： citrus pummelo apple stem grooving virus genome sequence thermotherapy

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