De novo characterization of Phenacoccus solenopsis transcriptome and analysis of gene expression profiling during development and hormone biosynthesis View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-05-15

AUTHORS

Surjeet Kumar Arya, Yogeshwar Vikram Dhar, Santosh Kumar Upadhyay, Mehar Hasan Asif, Praveen Chandra Verma

ABSTRACT

The cotton mealybug Phenacoccus solenopsis is a devastating pest of cotton causing tremendous loss in the yield of crops each year. Widespread physiological and biological studies on P. solenopsis have been carried out, but the lack of genetic information has constrained our understanding of the molecular mechanisms behind its growth and development. To understand and characterize the different developmental stages, RNA-Seq platform was used to execute de-novo transcriptome assembly and differential gene expression profiling for the eggs, first, second, third instar and adult female stages. About 182.67 million reads were assembled into 93,781 unigenes with an average length of 871.4 bp and an N50 length of 1899 bp. These unigenes sequences were annotated and classified by performing NCBI non-redundant (Nr) database, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG), Gene ontology (GO), the Swiss-Prot protein database (Swiss-Prot), and nearest related organism Acyrthosiphon pisum (pea aphid) database. To get more information regarding the process of metamorphosis, we performed a pairwise comparison of four developmental stages and obtained 29,415 differentially expressed genes. Some of the differentially expressed genes were associated with functional protein synthesis, anti-microbial protection, development and hormone biosynthesis. Functional pathway enrichment analysis of differentially expressed genes showed the positive correlation with specific physiological activities of each stage, and these results were confirmed by qRT-PCR experiments. This study gives a valuable genomics resource of P. solenopsis covering all its developmental stages and will promote future studies on biological processes at the molecular level. More... »

PAGES

7573

References to SciGraph publications

  • 2011-10-26. Identification of genes associated with nitrogen-use efficiency by genome-wide transcriptional analysis of two soybean genotypes in BMC GENOMICS
  • 2017-05-02. Lipidomics and RNA-Seq Study of Lipid Regulation in Aphis gossypii parasitized by Lysiphlebia japonica in SCIENTIFIC REPORTS
  • 2017-07-03. Comparative transcriptome analysis on the synthesis pathway of honey bee (Apis mellifera) mandibular gland secretions in SCIENTIFIC REPORTS
  • 2016-06-09. Identification of G protein-coupled receptors required for vitellogenin uptake into the oocytes of the red flour beetle, Tribolium castaneum in SCIENTIFIC REPORTS
  • 2016-09-05. Expression of an insecticidal fern protein in cotton protects against whitefly in NATURE BIOTECHNOLOGY
  • 2011-08-04. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome in BMC BIOINFORMATICS
  • 2011-05-15. Full-length transcriptome assembly from RNA-Seq data without a reference genome in NATURE BIOTECHNOLOGY
  • 2011-09-07. Next-generation transcriptome assembly in NATURE REVIEWS GENETICS
  • 2009-12. Biochemical characteristics of immune-associated phospholipase A2 and its inhibition by an entomopathogenic bacterium, Xenorhabdus nematophila in JOURNAL OF MICROBIOLOGY
  • 2017-10-19. Reference genes validation in Phenacoccus solenopsis under various biotic and abiotic stress conditions in SCIENTIFIC REPORTS
  • 2016-10-31. How multi-partner endosymbioses function in NATURE REVIEWS MICROBIOLOGY
  • 2010-06-24. De novo characterization of a whitefly transcriptome and analysis of its gene expression during development in BMC GENOMICS
  • 2012-01. The convergent evolution of defensive polyacetylenic fatty acid biosynthesis genes in soldier beetles in NATURE COMMUNICATIONS
  • 2017-01-10. Fatty acid synthase 2 contributes to diapause preparation in a beetle by regulating lipid accumulation and stress tolerance genes expression in SCIENTIFIC REPORTS
  • 2014-02-10. G-protein-coupled receptor participates in 20-hydroxyecdysone signaling on the plasma membrane in CELL COMMUNICATION AND SIGNALING
  • 2011-03. RNA interference for the control of whiteflies (Bemisia tabaci) by oral route in JOURNAL OF BIOSCIENCES
  • 2015-12-11. Deltamethrin resistance in the cotton mealybug, Phenacoccus solenopsis Tinsley: Cross-resistance to other insecticides, fitness cost analysis and realized heritability in PHYTOPARASITICA
  • 2017-01-03. The transcriptome of the mosquito Aedes fluviatilis (Diptera: Culicidae), and transcriptional changes associated with its native Wolbachia infection in BMC GENOMICS
  • 2002-03. The snail superfamily of zinc-finger transcription factors in NATURE REVIEWS MOLECULAR CELL BIOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41598-018-25845-3

    DOI

    http://dx.doi.org/10.1038/s41598-018-25845-3

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1103911357

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/29765069


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0601", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biochemistry and Cell Biology", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Genetics", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Animals", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Female", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Gene Expression Profiling", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Gene Expression Regulation, Developmental", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Gene Ontology", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Hemiptera", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "High-Throughput Nucleotide Sequencing", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Insect Hormones", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Insect Proteins", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Sequence Analysis, RNA", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, Room No: 310, 2-Rafi Marg, New Delhi, India", 
              "id": "http://www.grid.ac/institutes/grid.469887.c", 
              "name": [
                "CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, UP-226001, Lucknow, India", 
                "Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, Room No: 310, 2-Rafi Marg, New Delhi, India"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Arya", 
            "givenName": "Surjeet Kumar", 
            "id": "sg:person.013320347573.81", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013320347573.81"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, Room No: 310, 2-Rafi Marg, New Delhi, India", 
              "id": "http://www.grid.ac/institutes/grid.469887.c", 
              "name": [
                "CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, UP-226001, Lucknow, India", 
                "Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, Room No: 310, 2-Rafi Marg, New Delhi, India"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Dhar", 
            "givenName": "Yogeshwar Vikram", 
            "id": "sg:person.01213505101.97", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01213505101.97"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Botany, Panjab University, 160014, Chandigarh, India", 
              "id": "http://www.grid.ac/institutes/grid.261674.0", 
              "name": [
                "Department of Botany, Panjab University, 160014, Chandigarh, India"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Upadhyay", 
            "givenName": "Santosh Kumar", 
            "id": "sg:person.01224640607.03", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01224640607.03"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, Room No: 310, 2-Rafi Marg, New Delhi, India", 
              "id": "http://www.grid.ac/institutes/grid.469887.c", 
              "name": [
                "CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, UP-226001, Lucknow, India", 
                "Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, Room No: 310, 2-Rafi Marg, New Delhi, India"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Asif", 
            "givenName": "Mehar Hasan", 
            "id": "sg:person.01073737755.10", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01073737755.10"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, Room No: 310, 2-Rafi Marg, New Delhi, India", 
              "id": "http://www.grid.ac/institutes/grid.469887.c", 
              "name": [
                "CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, UP-226001, Lucknow, India", 
                "Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, Room No: 310, 2-Rafi Marg, New Delhi, India"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Verma", 
            "givenName": "Praveen Chandra", 
            "id": "sg:person.0635677533.38", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0635677533.38"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1186/1471-2164-11-400", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1024648987", 
              "https://doi.org/10.1186/1471-2164-11-400"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1478-811x-12-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011615037", 
              "https://doi.org/10.1186/1478-811x-12-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s12600-015-0500-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035038910", 
              "https://doi.org/10.1007/s12600-015-0500-3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrg3068", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1003128522", 
              "https://doi.org/10.1038/nrg3068"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.1883", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015803168", 
              "https://doi.org/10.1038/nbt.1883"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrm757", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007237018", 
              "https://doi.org/10.1038/nrm757"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ncomms2147", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051507865", 
              "https://doi.org/10.1038/ncomms2147"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41598-017-01546-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1085105123", 
              "https://doi.org/10.1038/s41598-017-01546-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrmicro.2016.151", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1024262276", 
              "https://doi.org/10.1038/nrmicro.2016.151"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s12864-016-3441-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1031303723", 
              "https://doi.org/10.1186/s12864-016-3441-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2164-12-525", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000637556", 
              "https://doi.org/10.1186/1471-2164-12-525"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2105-12-323", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1021902674", 
              "https://doi.org/10.1186/1471-2105-12-323"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41598-017-13925-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1092212973", 
              "https://doi.org/10.1038/s41598-017-13925-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.3665", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1031548133", 
              "https://doi.org/10.1038/nbt.3665"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41598-017-04879-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1090333400", 
              "https://doi.org/10.1038/s41598-017-04879-z"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s12275-009-0145-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007664859", 
              "https://doi.org/10.1007/s12275-009-0145-3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/srep40509", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050259773", 
              "https://doi.org/10.1038/srep40509"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s12038-011-9009-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015221730", 
              "https://doi.org/10.1007/s12038-011-9009-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/srep27648", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1039122295", 
              "https://doi.org/10.1038/srep27648"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2018-05-15", 
        "datePublishedReg": "2018-05-15", 
        "description": "The cotton mealybug Phenacoccus solenopsis is a devastating pest of cotton causing tremendous loss in the yield of crops each year. Widespread physiological and biological studies on P. solenopsis have been carried out, but the lack of genetic information has constrained our understanding of the molecular mechanisms behind its growth and development. To understand and characterize the different developmental stages, RNA-Seq platform was used to execute de-novo transcriptome assembly and differential gene expression profiling for the eggs, first, second, third instar and adult female stages. About 182.67 million reads were assembled into 93,781 unigenes with an average length of 871.4\u2009bp and an N50 length of 1899 bp. These unigenes sequences were annotated and classified by performing NCBI non-redundant (Nr) database, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG), Gene ontology (GO), the Swiss-Prot protein database (Swiss-Prot), and nearest related organism Acyrthosiphon pisum (pea aphid) database. To get more information regarding the process of metamorphosis, we performed a pairwise comparison of four developmental stages and obtained 29,415 differentially expressed genes. Some of the differentially expressed genes were associated with functional protein synthesis, anti-microbial protection, development and hormone biosynthesis. Functional pathway enrichment analysis of differentially expressed genes showed the positive correlation with specific physiological activities of each stage, and these results were confirmed by qRT-PCR experiments. This study gives a valuable genomics resource of P. solenopsis covering all its developmental stages and will promote future studies on biological processes at the molecular level.", 
        "genre": "article", 
        "id": "sg:pub.10.1038/s41598-018-25845-3", 
        "isAccessibleForFree": true, 
        "isPartOf": [
          {
            "id": "sg:journal.1045337", 
            "issn": [
              "2045-2322"
            ], 
            "name": "Scientific Reports", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "8"
          }
        ], 
        "keywords": [
          "developmental stages", 
          "Gene Ontology", 
          "hormone biosynthesis", 
          "P. solenopsis", 
          "NCBI non-redundant database", 
          "Swiss-Prot protein database", 
          "valuable genomic resource", 
          "cotton mealybug Phenacoccus solenopsis", 
          "novo transcriptome assembly", 
          "functional protein synthesis", 
          "functional pathway enrichment analysis", 
          "De novo characterization", 
          "RNA-seq platforms", 
          "non-redundant database", 
          "differential gene expression", 
          "qRT-PCR experiments", 
          "pathway enrichment analysis", 
          "adult female stage", 
          "gene expression profiling", 
          "different developmental stages", 
          "mealybug Phenacoccus solenopsis", 
          "anti-microbial protection", 
          "genomic resources", 
          "orthologous groups", 
          "N50 length", 
          "specific physiological activities", 
          "transcriptome assembly", 
          "unigene sequences", 
          "yield of crops", 
          "devastating pest", 
          "Kyoto Encyclopedia", 
          "protein database", 
          "expression profiling", 
          "genetic information", 
          "enrichment analysis", 
          "female stage", 
          "gene expression", 
          "Phenacoccus solenopsis", 
          "biological processes", 
          "molecular mechanisms", 
          "protein synthesis", 
          "genes", 
          "solenopsis", 
          "molecular level", 
          "process of metamorphosis", 
          "third instar", 
          "physiological activity", 
          "biosynthesis", 
          "biological studies", 
          "BP", 
          "unigenes", 
          "transcriptome", 
          "genome", 
          "pests", 
          "pairwise comparisons", 
          "Encyclopedia", 
          "tremendous loss", 
          "instars", 
          "reads", 
          "metamorphosis", 
          "crops", 
          "profiling", 
          "eggs", 
          "sequence", 
          "expression", 
          "cotton", 
          "stage", 
          "assembly", 
          "future studies", 
          "development", 
          "average length", 
          "growth", 
          "mechanism", 
          "positive correlation", 
          "characterization", 
          "activity", 
          "clusters", 
          "length", 
          "analysis", 
          "understanding", 
          "yield", 
          "study", 
          "process", 
          "database", 
          "synthesis", 
          "loss", 
          "ontology", 
          "levels", 
          "more information", 
          "protection", 
          "information", 
          "experiments", 
          "resources", 
          "lack", 
          "comparison", 
          "results", 
          "correlation", 
          "platform", 
          "group", 
          "years"
        ], 
        "name": "De novo characterization of Phenacoccus solenopsis transcriptome and analysis of gene expression profiling during development and hormone biosynthesis", 
        "pagination": "7573", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1103911357"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1038/s41598-018-25845-3"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "29765069"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1038/s41598-018-25845-3", 
          "https://app.dimensions.ai/details/publication/pub.1103911357"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-08-04T17:05", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20220804/entities/gbq_results/article/article_763.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1038/s41598-018-25845-3"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/s41598-018-25845-3'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/s41598-018-25845-3'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s41598-018-25845-3'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/s41598-018-25845-3'


     

    This table displays all metadata directly associated to this object as RDF triples.

    312 TRIPLES      21 PREDICATES      155 URIs      127 LITERALS      17 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1038/s41598-018-25845-3 schema:about N3fb68a596bd9490ea0f262096fbeb7fd
    2 N46a220954ee644b5843f6e98e4d4a646
    3 N49e86150120f4e90aa83458fffb465c5
    4 N52cbccc76b5d48249b085f27c8a81f45
    5 N8de9c68358cd4ffd972151c316155108
    6 Nc5637c4365df4abfa83d4ea78926a776
    7 Ne17b2839f7c3440a82cf43d6f8f3c20e
    8 Nec630bf59c794bbbad9ba8fdb986dd6c
    9 Nfdcd57bd581f4176a0adc98089492009
    10 Nfeff1220978144428fc336af39875435
    11 anzsrc-for:06
    12 anzsrc-for:0601
    13 anzsrc-for:0604
    14 schema:author N2b0e43da04de4199ab82489d57148d82
    15 schema:citation sg:pub.10.1007/s12038-011-9009-1
    16 sg:pub.10.1007/s12275-009-0145-3
    17 sg:pub.10.1007/s12600-015-0500-3
    18 sg:pub.10.1038/nbt.1883
    19 sg:pub.10.1038/nbt.3665
    20 sg:pub.10.1038/ncomms2147
    21 sg:pub.10.1038/nrg3068
    22 sg:pub.10.1038/nrm757
    23 sg:pub.10.1038/nrmicro.2016.151
    24 sg:pub.10.1038/s41598-017-01546-1
    25 sg:pub.10.1038/s41598-017-04879-z
    26 sg:pub.10.1038/s41598-017-13925-9
    27 sg:pub.10.1038/srep27648
    28 sg:pub.10.1038/srep40509
    29 sg:pub.10.1186/1471-2105-12-323
    30 sg:pub.10.1186/1471-2164-11-400
    31 sg:pub.10.1186/1471-2164-12-525
    32 sg:pub.10.1186/1478-811x-12-9
    33 sg:pub.10.1186/s12864-016-3441-4
    34 schema:datePublished 2018-05-15
    35 schema:datePublishedReg 2018-05-15
    36 schema:description The cotton mealybug Phenacoccus solenopsis is a devastating pest of cotton causing tremendous loss in the yield of crops each year. Widespread physiological and biological studies on P. solenopsis have been carried out, but the lack of genetic information has constrained our understanding of the molecular mechanisms behind its growth and development. To understand and characterize the different developmental stages, RNA-Seq platform was used to execute de-novo transcriptome assembly and differential gene expression profiling for the eggs, first, second, third instar and adult female stages. About 182.67 million reads were assembled into 93,781 unigenes with an average length of 871.4 bp and an N50 length of 1899 bp. These unigenes sequences were annotated and classified by performing NCBI non-redundant (Nr) database, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG), Gene ontology (GO), the Swiss-Prot protein database (Swiss-Prot), and nearest related organism Acyrthosiphon pisum (pea aphid) database. To get more information regarding the process of metamorphosis, we performed a pairwise comparison of four developmental stages and obtained 29,415 differentially expressed genes. Some of the differentially expressed genes were associated with functional protein synthesis, anti-microbial protection, development and hormone biosynthesis. Functional pathway enrichment analysis of differentially expressed genes showed the positive correlation with specific physiological activities of each stage, and these results were confirmed by qRT-PCR experiments. This study gives a valuable genomics resource of P. solenopsis covering all its developmental stages and will promote future studies on biological processes at the molecular level.
    37 schema:genre article
    38 schema:isAccessibleForFree true
    39 schema:isPartOf N79493570a5354cafbad040f0af2e6df1
    40 Nd3157b6c7f3243248e15ba96636f182a
    41 sg:journal.1045337
    42 schema:keywords BP
    43 De novo characterization
    44 Encyclopedia
    45 Gene Ontology
    46 Kyoto Encyclopedia
    47 N50 length
    48 NCBI non-redundant database
    49 P. solenopsis
    50 Phenacoccus solenopsis
    51 RNA-seq platforms
    52 Swiss-Prot protein database
    53 activity
    54 adult female stage
    55 analysis
    56 anti-microbial protection
    57 assembly
    58 average length
    59 biological processes
    60 biological studies
    61 biosynthesis
    62 characterization
    63 clusters
    64 comparison
    65 correlation
    66 cotton
    67 cotton mealybug Phenacoccus solenopsis
    68 crops
    69 database
    70 devastating pest
    71 development
    72 developmental stages
    73 different developmental stages
    74 differential gene expression
    75 eggs
    76 enrichment analysis
    77 experiments
    78 expression
    79 expression profiling
    80 female stage
    81 functional pathway enrichment analysis
    82 functional protein synthesis
    83 future studies
    84 gene expression
    85 gene expression profiling
    86 genes
    87 genetic information
    88 genome
    89 genomic resources
    90 group
    91 growth
    92 hormone biosynthesis
    93 information
    94 instars
    95 lack
    96 length
    97 levels
    98 loss
    99 mealybug Phenacoccus solenopsis
    100 mechanism
    101 metamorphosis
    102 molecular level
    103 molecular mechanisms
    104 more information
    105 non-redundant database
    106 novo transcriptome assembly
    107 ontology
    108 orthologous groups
    109 pairwise comparisons
    110 pathway enrichment analysis
    111 pests
    112 physiological activity
    113 platform
    114 positive correlation
    115 process
    116 process of metamorphosis
    117 profiling
    118 protection
    119 protein database
    120 protein synthesis
    121 qRT-PCR experiments
    122 reads
    123 resources
    124 results
    125 sequence
    126 solenopsis
    127 specific physiological activities
    128 stage
    129 study
    130 synthesis
    131 third instar
    132 transcriptome
    133 transcriptome assembly
    134 tremendous loss
    135 understanding
    136 unigene sequences
    137 unigenes
    138 valuable genomic resource
    139 years
    140 yield
    141 yield of crops
    142 schema:name De novo characterization of Phenacoccus solenopsis transcriptome and analysis of gene expression profiling during development and hormone biosynthesis
    143 schema:pagination 7573
    144 schema:productId Ndb0f2307e7ca4d45961b8f4f99f80b3d
    145 Ne1ee688607ed4018ac7ae0dbc7964402
    146 Necf86d4981284600b12836bfd346b851
    147 schema:sameAs https://app.dimensions.ai/details/publication/pub.1103911357
    148 https://doi.org/10.1038/s41598-018-25845-3
    149 schema:sdDatePublished 2022-08-04T17:05
    150 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    151 schema:sdPublisher N109b9db4661b4266a54c331619a865a0
    152 schema:url https://doi.org/10.1038/s41598-018-25845-3
    153 sgo:license sg:explorer/license/
    154 sgo:sdDataset articles
    155 rdf:type schema:ScholarlyArticle
    156 N109b9db4661b4266a54c331619a865a0 schema:name Springer Nature - SN SciGraph project
    157 rdf:type schema:Organization
    158 N2b0e43da04de4199ab82489d57148d82 rdf:first sg:person.013320347573.81
    159 rdf:rest Na3ffdbbfe4234af4b7bf62d38421e242
    160 N3fb68a596bd9490ea0f262096fbeb7fd schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    161 schema:name Sequence Analysis, RNA
    162 rdf:type schema:DefinedTerm
    163 N46a220954ee644b5843f6e98e4d4a646 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    164 schema:name Female
    165 rdf:type schema:DefinedTerm
    166 N49e86150120f4e90aa83458fffb465c5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    167 schema:name Animals
    168 rdf:type schema:DefinedTerm
    169 N4f3aa4b5f7944780b0a807a982080644 rdf:first sg:person.0635677533.38
    170 rdf:rest rdf:nil
    171 N52cbccc76b5d48249b085f27c8a81f45 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    172 schema:name Gene Expression Profiling
    173 rdf:type schema:DefinedTerm
    174 N73d031059d7f4a2b8b0d55fdfbf119d9 rdf:first sg:person.01224640607.03
    175 rdf:rest N744297431784436194d82096fd3b9125
    176 N744297431784436194d82096fd3b9125 rdf:first sg:person.01073737755.10
    177 rdf:rest N4f3aa4b5f7944780b0a807a982080644
    178 N79493570a5354cafbad040f0af2e6df1 schema:volumeNumber 8
    179 rdf:type schema:PublicationVolume
    180 N8de9c68358cd4ffd972151c316155108 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    181 schema:name Hemiptera
    182 rdf:type schema:DefinedTerm
    183 Na3ffdbbfe4234af4b7bf62d38421e242 rdf:first sg:person.01213505101.97
    184 rdf:rest N73d031059d7f4a2b8b0d55fdfbf119d9
    185 Nc5637c4365df4abfa83d4ea78926a776 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    186 schema:name High-Throughput Nucleotide Sequencing
    187 rdf:type schema:DefinedTerm
    188 Nd3157b6c7f3243248e15ba96636f182a schema:issueNumber 1
    189 rdf:type schema:PublicationIssue
    190 Ndb0f2307e7ca4d45961b8f4f99f80b3d schema:name pubmed_id
    191 schema:value 29765069
    192 rdf:type schema:PropertyValue
    193 Ne17b2839f7c3440a82cf43d6f8f3c20e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    194 schema:name Gene Ontology
    195 rdf:type schema:DefinedTerm
    196 Ne1ee688607ed4018ac7ae0dbc7964402 schema:name doi
    197 schema:value 10.1038/s41598-018-25845-3
    198 rdf:type schema:PropertyValue
    199 Nec630bf59c794bbbad9ba8fdb986dd6c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    200 schema:name Insect Proteins
    201 rdf:type schema:DefinedTerm
    202 Necf86d4981284600b12836bfd346b851 schema:name dimensions_id
    203 schema:value pub.1103911357
    204 rdf:type schema:PropertyValue
    205 Nfdcd57bd581f4176a0adc98089492009 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    206 schema:name Gene Expression Regulation, Developmental
    207 rdf:type schema:DefinedTerm
    208 Nfeff1220978144428fc336af39875435 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    209 schema:name Insect Hormones
    210 rdf:type schema:DefinedTerm
    211 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    212 schema:name Biological Sciences
    213 rdf:type schema:DefinedTerm
    214 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
    215 schema:name Biochemistry and Cell Biology
    216 rdf:type schema:DefinedTerm
    217 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    218 schema:name Genetics
    219 rdf:type schema:DefinedTerm
    220 sg:journal.1045337 schema:issn 2045-2322
    221 schema:name Scientific Reports
    222 schema:publisher Springer Nature
    223 rdf:type schema:Periodical
    224 sg:person.01073737755.10 schema:affiliation grid-institutes:grid.469887.c
    225 schema:familyName Asif
    226 schema:givenName Mehar Hasan
    227 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01073737755.10
    228 rdf:type schema:Person
    229 sg:person.01213505101.97 schema:affiliation grid-institutes:grid.469887.c
    230 schema:familyName Dhar
    231 schema:givenName Yogeshwar Vikram
    232 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01213505101.97
    233 rdf:type schema:Person
    234 sg:person.01224640607.03 schema:affiliation grid-institutes:grid.261674.0
    235 schema:familyName Upadhyay
    236 schema:givenName Santosh Kumar
    237 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01224640607.03
    238 rdf:type schema:Person
    239 sg:person.013320347573.81 schema:affiliation grid-institutes:grid.469887.c
    240 schema:familyName Arya
    241 schema:givenName Surjeet Kumar
    242 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013320347573.81
    243 rdf:type schema:Person
    244 sg:person.0635677533.38 schema:affiliation grid-institutes:grid.469887.c
    245 schema:familyName Verma
    246 schema:givenName Praveen Chandra
    247 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0635677533.38
    248 rdf:type schema:Person
    249 sg:pub.10.1007/s12038-011-9009-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015221730
    250 https://doi.org/10.1007/s12038-011-9009-1
    251 rdf:type schema:CreativeWork
    252 sg:pub.10.1007/s12275-009-0145-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007664859
    253 https://doi.org/10.1007/s12275-009-0145-3
    254 rdf:type schema:CreativeWork
    255 sg:pub.10.1007/s12600-015-0500-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035038910
    256 https://doi.org/10.1007/s12600-015-0500-3
    257 rdf:type schema:CreativeWork
    258 sg:pub.10.1038/nbt.1883 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015803168
    259 https://doi.org/10.1038/nbt.1883
    260 rdf:type schema:CreativeWork
    261 sg:pub.10.1038/nbt.3665 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031548133
    262 https://doi.org/10.1038/nbt.3665
    263 rdf:type schema:CreativeWork
    264 sg:pub.10.1038/ncomms2147 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051507865
    265 https://doi.org/10.1038/ncomms2147
    266 rdf:type schema:CreativeWork
    267 sg:pub.10.1038/nrg3068 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003128522
    268 https://doi.org/10.1038/nrg3068
    269 rdf:type schema:CreativeWork
    270 sg:pub.10.1038/nrm757 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007237018
    271 https://doi.org/10.1038/nrm757
    272 rdf:type schema:CreativeWork
    273 sg:pub.10.1038/nrmicro.2016.151 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024262276
    274 https://doi.org/10.1038/nrmicro.2016.151
    275 rdf:type schema:CreativeWork
    276 sg:pub.10.1038/s41598-017-01546-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1085105123
    277 https://doi.org/10.1038/s41598-017-01546-1
    278 rdf:type schema:CreativeWork
    279 sg:pub.10.1038/s41598-017-04879-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1090333400
    280 https://doi.org/10.1038/s41598-017-04879-z
    281 rdf:type schema:CreativeWork
    282 sg:pub.10.1038/s41598-017-13925-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1092212973
    283 https://doi.org/10.1038/s41598-017-13925-9
    284 rdf:type schema:CreativeWork
    285 sg:pub.10.1038/srep27648 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039122295
    286 https://doi.org/10.1038/srep27648
    287 rdf:type schema:CreativeWork
    288 sg:pub.10.1038/srep40509 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050259773
    289 https://doi.org/10.1038/srep40509
    290 rdf:type schema:CreativeWork
    291 sg:pub.10.1186/1471-2105-12-323 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021902674
    292 https://doi.org/10.1186/1471-2105-12-323
    293 rdf:type schema:CreativeWork
    294 sg:pub.10.1186/1471-2164-11-400 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024648987
    295 https://doi.org/10.1186/1471-2164-11-400
    296 rdf:type schema:CreativeWork
    297 sg:pub.10.1186/1471-2164-12-525 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000637556
    298 https://doi.org/10.1186/1471-2164-12-525
    299 rdf:type schema:CreativeWork
    300 sg:pub.10.1186/1478-811x-12-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011615037
    301 https://doi.org/10.1186/1478-811x-12-9
    302 rdf:type schema:CreativeWork
    303 sg:pub.10.1186/s12864-016-3441-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031303723
    304 https://doi.org/10.1186/s12864-016-3441-4
    305 rdf:type schema:CreativeWork
    306 grid-institutes:grid.261674.0 schema:alternateName Department of Botany, Panjab University, 160014, Chandigarh, India
    307 schema:name Department of Botany, Panjab University, 160014, Chandigarh, India
    308 rdf:type schema:Organization
    309 grid-institutes:grid.469887.c schema:alternateName Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, Room No: 310, 2-Rafi Marg, New Delhi, India
    310 schema:name Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, Room No: 310, 2-Rafi Marg, New Delhi, India
    311 CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, UP-226001, Lucknow, India
    312 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...