Genomic characterization and expression profiles of stress-associated proteins(SAPs)in castor bean(Ricinus communis)

Stress-associated proteins(SAPs)are known as response factors to multiple abiotic and biotic stresses in plants.However,the potential physiological and molecular functions of SAPs remain largely unclear.Castor bean(Ricinus communis L.)is one of the most economically valuable non-edible woody oilseed crops,able to be widely cultivated in marginal lands worldwide because of its broad adaptive capacity to soil and climate conditions.Whether SAPs in castor bean plays a key role in adapting diverse soil conditions and stresses remains unknown.In this study,we used the castor bean genome to identify and characterize nine castor bean SAP genes(RcSAP).Structural analysis showed that castor bean SAP gene structures and functional domain types vary greatly,differing in intron number,protein sequence,and functional domain type.Notably,the AN1-C2H2eC2H2 zinc finger domain within RcSAP9 has not been often observed in other plant families.High throughput RNA-seq data showed that castor bean SAP gene profiles varied among different tissues.In addition,castor bean SAP gene expression varied in response to different stresses,including salt,drought,heat,cold and ABA and MeJA,suggesting that the transcriptional regulation of castor bean SAP genes might operate independently of each other,and at least partially independent from ABA and MeJA signal pathways.Cis-element analyses for each castor bean SAP gene showed that no common cis-elements are shared across the nine castor bean SAP genes.Castor bean SAPs were localized to different regions of cells,including the cytoplasm,nucleus,and cytomembrane.This study provides a comprehensive profile of castor bean SAP genes that advances our understanding of their potential physiological and molecular functions in regulating growth and development and their responses to different abiotic stresses.

The Genomic Characterization of Enterovirus D68 from 2011 to 2015 in Beijing, China

A retrospective surveillance study on enterovirus D68 was performed in Beijing, China, following the largest and most widespread EV-D68 infection, which occurred in the USA. From January 2011 to July 2015, EV-D68 was identified in 12 individuals with respiratory infections in Beijing, China. The phylogenetic relationships based on the genomic sequence alignment showed that there were two lineages circulating in Beijing from 2011 to 2015. Eight EV-D68 strains belonged to group 1 and four belonged to group 3. All EV-D68 strains from Beijing in 2014 were separately clustered into subgroup II of group 1. Based on these results, we concluded that the Beijing EV-D68 strains had little association with the EV-D68 strains circulating in the 2014 USA outbreak.

Genomic characterization reveals distinctmutation landscapes and therapeutic implications in neuroendocrine carcinomas of the gastrointestinal tract

Background:Neuroendocrine carcinomas of the gastrointestinal tract(GINECs)remain a disease of grim prognosis with limited therapeutic options.Their molecular characteristics are still undefined.This study aimed to explore the underlying genetic basis and heterogeneity of GI-NECs.Methods:Comprehensive genomic analysis using whole-exome sequencing was performed on 143 formalin-fixed,paraffin-embedded samples of surgically resected GI-NEC with a thorough histological evaluation.Mutational signatures,somatic mutations,and copy number aberrations were analyzed and compared across anatomic locations and histological subtypes.Survival analysis was conducted to identify the independent factors.Results:In total,143GI-NECswere examined:the stomach,87 cases(60.8%);the esophagus,29 cases(20.3%);the colorectum,20 cases(14.0%);and the small intestine,7 cases(4.9%).Eighty-three(58.0%)and 60(42.0%)cases were subclassified into small cell and large cell subtypes,respectively.GI-NECs showed distinct genetic alterations from their lung counterparts and non-neuroendocrine carcinomas in the same locations.Obvious heterogeneity of mutational signatures,somatic mutations,and copy number variations was revealed across anatomic locations rather than histological subtypes.Except for tumor protein p53(TP53)and retinoblastoma 1(RB1),the most frequently mutated genes in the stomach,esophagus,colorectum,and small intestine were low-density lipoprotein receptor-related protein 1B(LRP1B),notch receptor 1(NOTCH1),adenomatosis polyposis coli(APC),catenin beta 1(CTNNB1),respectively.Mutations in the WNT-β-catenin,NOTCH and erythroblastic leukemia viral oncogene B(ERBB)pathwayswere prevalently identified in gastric,esophageal,and colorectalNECs,respectively.Importantly,104(72.7%)GI-NECs harbored putative clinically relevant alterations,and non-gastric location and RB1 bi-allelic inactivation with copy number alterations were identified as two independent poor prognostic factors.Furthermore,we found that tumor cells in GI-NECs first gain clonal mutations in TP53,RB1,NOTCH1 and APC,followed by subsequent wholegenome doubling(WGD)and post-WGD clonal mutations in LRP1B,CUB and Sushi multiple domains 3(CSMD3),FAT tumor suppressor homolog 4(FAT4)and erb-b2 receptor tyrosine kinase 4(ERBB4),and finally develop subclonal mutations.Conclusions:GI-NECs harbor distinct genomic landscapes and demonstrate significant genetic heterogeneity across different anatomic locations.Moreover,potentially actionable alterations and prognostic factors were revealed for GI-NECs.

Toward Molecular Cytogenetical Characterizations in Cotton Genome

Cotton is viewed as the most important cash crop in the world,and sustains the agricultural economies of many nations by providing a sustainable fiber product for the textile industry.Due to

Papaya Ring Spot Virus:An Understanding of a Severe Positive-Sense Single Stranded RNA Viral Disease and Its Management

Viral diseases have been studied in-depth for reducing quality,yield,health and longevity of the fruit,to highlight the economic losses.Positive-sense single-stranded RNA viruses are more devastating among all viruses that infect fruit trees.One of the best examples is papaya ringspot virus(PRSV).It belongs to the genus Potyvirus and it is limited to cause diseases on the family Chenopodiaceae,Cucurbitaceae and Caricaceae.This virus has a serious threat to the production of papaya,which is famous for its high nutritional and pharmaceutical values.The plant parts such as leaves,latex,seeds,fruits,bark,peel and roots may contain the biological compound that can be isolated and used in pharmaceutical industries as a disease control.Viral disease symptoms consist of vein clearing and yellowing of young leaves.Distinctive ring spot patterns with concentric rings and spots on fruit reduce its quality and taste.The virus has two major strains P and W.The former cause disease in papaya and cucurbits while the later one in papaya.Virion comprises 94.4%protein,including a 36 kDa coat protein which is a component responsible for a non-persistent transmission through aphids,and 5.5%nucleic acid.Cross protection,development of transgenic crops,exploring the resistant sources and induction of pathogen derived resistance have been recorded as effective management of PRSV.Along with these practices reduced aphid population through insecticides and plant extracts have been found ecofriendly approaches to minimize the disease incidence.Adoption of transgenic crops is a big challenge for the success of disease resistant papaya crops.The aim of this review is to understand the genomic nature of PRSV,detection methods and the different advanced control methods.This review article will be helpful in developing the best management strategies for controlling PRSV.

Characterization and complete genome sequence of vB_EcoP-Bp4,a novel polyvalent N4-like bacteriophage that infects chicken pathogenic Escherichia coli

Pathogenic Escherichia coli cause chicken colibacillosis, which is economically devastating to the poultry in- dustry worldwide （Bagheri et al., 2014）. Owing to in- creasing antibiotic resistance, phage therapy reagents have been developed to treat bacterial infections （Xu et al., 2015）.

Fur Seal Feces-Associated Circular DNA Virus Identified in Pigs in Anhui, China

Fur seal feces-associated circular DNA virus(FSfa CV)is an unclassified circular replication-associated protein(Rep)-encoding single-stranded(CRESS)DNA virus that has been detected in mammals(fur seals and pigs).The biology and epidemiology of the virus remain largely unknown.To investigate the virus diversity among pigs in Anhui Province,China,we pooled 600 nasal samples in 2017 and detected viruses using viral metagenomic methods.From the assembled contigs,12 showed notably high nucleotide acid sequence similarities to the genome sequences of FSfa CVs.Based on these sequences,a full-length genome sequence of the virus was then obtained using overlapping PCR and sequencing,and the virus was designated as FSfa CV-CHN(Gen Bank No.MK462122).This virus shared 91.3%and 90.9%genome-wide nucleotide sequence similarities with the New Zealand fur seal strain FSfa CV-as50 and the Japanese pig strain FSfa CVJPN1,respectively.It also clustered with the two previously identified FSfa CVs in a unique branch in the phylogenetic tree based on the open reading frame 2(ORF2),Rep-coding gene,and the genome of the reference CRESS DNA viruses.Further epidemiological investigation using samples collected in 2018 showed that the overall positive rate for the virus was 56.4%(111/197)in Anhui Province.This is the first report of FSfa CVs identified in pigs in China,and further epidemiological studies are warranted to evaluate the influence of the virus on pigs.