Metatranscriptomic Analysis and In Silico Approach Identified Mycoviruses in the Arbuscular Mycorrhizal Fungus Rhizophagus spp.
Identifieur interne : 000636 ( Main/Corpus ); précédent : 000635; suivant : 000637Metatranscriptomic Analysis and In Silico Approach Identified Mycoviruses in the Arbuscular Mycorrhizal Fungus Rhizophagus spp.
Auteurs : Achal Neupane ; Chenchen Feng ; Jiuhuan Feng ; Arjun Kafle ; Heike Bücking ; Shin-Yi Lee MarzanoSource :
- Viruses [ 1999-4915 ] ; 2018.
English descriptors
- KwdEn :
- MESH :
- genetics : Fungal Viruses, Plant Roots.
- isolation & purification : Fungal Viruses.
- microbiology : Plant Roots, Plants.
- virology : Mycorrhizae.
- Gene Expression Profiling, Genome, Viral, Symbiosis.
Abstract
Arbuscular mycorrhizal fungi (AMF), including Rhizophagus spp., can play important roles in nutrient cycling of the rhizosphere. However, the effect of virus infection on AMF's role in nutrient cycling cannot be determined without first knowing the diversity of the mycoviruses in AMF. Therefore, in this study, we sequenced the R. irregularis isolate-09 due to its previously demonstrated high efficiency in increasing the N/P uptake of the plant. We identified one novel mitovirus contig of 3685 bp, further confirmed by reverse transcription-PCR. Also, publicly available Rhizophagus spp. RNA-Seq data were analyzed to recover five partial virus sequences from family Narnaviridae, among which four were from R. diaphanum MUCL-43196 and one was from R. irregularis strain-C2 that was similar to members of the Mitovirus genus. These contigs coded genomes larger than the regular mitoviruses infecting pathogenic fungi and can be translated by either a mitochondrial translation code or a cytoplasmic translation code, which was also reported in previously found mitoviruses infecting mycorrhizae. The five newly identified virus sequences are comprised of functionally conserved RdRp motifs and formed two separate subclades with mitoviruses infecting Gigasporamargarita and Rhizophagusclarus, further supporting virus-host co-evolution theory. This study expands our understanding of virus diversity. Even though AMF is notably hard to investigate due to its biotrophic nature, this study demonstrates the utility of whole root metatranscriptome.
DOI: 10.3390/v10120707
PubMed: 30545059
PubMed Central: PMC6316171
Links to Exploration step
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Feng</name><affiliation><nlm:affiliation>Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA. jiuhuan.feng@sdstate.edu.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Agronomy, Horticulture, and Plant Sciences, South Dakota State University, Brookings, SD 57007, USA. jiuhuan.feng@sdstate.edu.</nlm:affiliation></affiliation></author><author><name sortKey="Kafle, Arjun" sort="Kafle, Arjun" uniqKey="Kafle A" first="Arjun" last="Kafle">Arjun Kafle</name><affiliation><nlm:affiliation>Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA. arjun.kafle@sdstate.edu.</nlm:affiliation></affiliation></author><author><name sortKey="Bucking, Heike" sort="Bucking, Heike" uniqKey="Bucking H" first="Heike" last="Bücking">Heike Bücking</name><affiliation><nlm:affiliation>Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA. heike.bucking@sdstate.edu.</nlm:affiliation></affiliation></author><author><name sortKey="Lee Marzano, Shin Yi" sort="Lee Marzano, Shin Yi" uniqKey="Lee Marzano S" first="Shin-Yi" last="Lee Marzano">Shin-Yi Lee Marzano</name><affiliation><nlm:affiliation>Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA. shinyi.marzano@sdstate.edu.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Agronomy, Horticulture, and Plant Sciences, South Dakota State University, Brookings, SD 57007, USA. shinyi.marzano@sdstate.edu.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2018">2018</date><idno type="RBID">pubmed:30545059</idno><idno type="pmid">30545059</idno><idno type="doi">10.3390/v10120707</idno><idno type="pmc">PMC6316171</idno><idno type="wicri:Area/Main/Corpus">000636</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000636</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Metatranscriptomic Analysis and In Silico Approach Identified Mycoviruses in the Arbuscular Mycorrhizal Fungus <i>Rhizophagus</i> spp.</title><author><name sortKey="Neupane, Achal" sort="Neupane, Achal" uniqKey="Neupane A" first="Achal" last="Neupane">Achal Neupane</name><affiliation><nlm:affiliation>Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA. achal.neupane@sdstate.edu.</nlm:affiliation></affiliation></author><author><name sortKey="Feng, Chenchen" sort="Feng, Chenchen" uniqKey="Feng C" first="Chenchen" last="Feng">Chenchen Feng</name><affiliation><nlm:affiliation>Department of Agronomy, Horticulture, and Plant Sciences, South Dakota State University, Brookings, SD 57007, USA. chenchen.feng@sdstate.edu.</nlm:affiliation></affiliation></author><author><name sortKey="Feng, Jiuhuan" sort="Feng, Jiuhuan" uniqKey="Feng J" first="Jiuhuan" last="Feng">Jiuhuan Feng</name><affiliation><nlm:affiliation>Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA. jiuhuan.feng@sdstate.edu.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Agronomy, Horticulture, and Plant Sciences, South Dakota State University, Brookings, SD 57007, USA. jiuhuan.feng@sdstate.edu.</nlm:affiliation></affiliation></author><author><name sortKey="Kafle, Arjun" sort="Kafle, Arjun" uniqKey="Kafle A" first="Arjun" last="Kafle">Arjun Kafle</name><affiliation><nlm:affiliation>Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA. arjun.kafle@sdstate.edu.</nlm:affiliation></affiliation></author><author><name sortKey="Bucking, Heike" sort="Bucking, Heike" uniqKey="Bucking H" first="Heike" last="Bücking">Heike Bücking</name><affiliation><nlm:affiliation>Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA. heike.bucking@sdstate.edu.</nlm:affiliation></affiliation></author><author><name sortKey="Lee Marzano, Shin Yi" sort="Lee Marzano, Shin Yi" uniqKey="Lee Marzano S" first="Shin-Yi" last="Lee Marzano">Shin-Yi Lee Marzano</name><affiliation><nlm:affiliation>Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA. shinyi.marzano@sdstate.edu.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Agronomy, Horticulture, and Plant Sciences, South Dakota State University, Brookings, SD 57007, USA. shinyi.marzano@sdstate.edu.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Viruses</title><idno type="eISSN">1999-4915</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Fungal Viruses (genetics)</term><term>Fungal Viruses (isolation & purification)</term><term>Gene Expression Profiling (MeSH)</term><term>Genome, Viral (MeSH)</term><term>Mycorrhizae (virology)</term><term>Plant Roots (genetics)</term><term>Plant Roots (microbiology)</term><term>Plants (microbiology)</term><term>Symbiosis (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Fungal Viruses</term><term>Plant Roots</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Fungal Viruses</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Plant Roots</term><term>Plants</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Mycorrhizae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Profiling</term><term>Genome, Viral</term><term>Symbiosis</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Arbuscular mycorrhizal fungi (AMF), including <i>Rhizophagus</i> spp., can play important roles in nutrient cycling of the rhizosphere. However, the effect of virus infection on AMF's role in nutrient cycling cannot be determined without first knowing the diversity of the mycoviruses in AMF. Therefore, in this study, we sequenced the <i>R</i>. <i>irregularis</i> isolate-09 due to its previously demonstrated high efficiency in increasing the N/P uptake of the plant. We identified one novel mitovirus contig of 3685 bp, further confirmed by reverse transcription-PCR. Also, publicly available <i>Rhizophagus</i> spp. RNA-Seq data were analyzed to recover five partial virus sequences from family <i>Narnaviridae</i>, among which four were from <i>R. diaphanum</i> MUCL-43196 and one was from <i>R. irregularis</i> strain-C2 that was similar to members of the <i>Mitovirus</i> genus. These contigs coded genomes larger than the regular mitoviruses infecting pathogenic fungi and can be translated by either a mitochondrial translation code or a cytoplasmic translation code, which was also reported in previously found mitoviruses infecting mycorrhizae. The five newly identified virus sequences are comprised of functionally conserved RdRp motifs and formed two separate subclades with mitoviruses infecting <i>Gigaspora</i><i>margarita</i> and <i>Rhizophagus</i><i>clarus</i>, further supporting virus-host co-evolution theory. This study expands our understanding of virus diversity. Even though AMF is notably hard to investigate due to its biotrophic nature, this study demonstrates the utility of whole root metatranscriptome.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30545059</PMID><DateCompleted><Year>2019</Year><Month>04</Month><Day>08</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>09</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1999-4915</ISSN><JournalIssue CitedMedium="Internet"><Volume>10</Volume><Issue>12</Issue><PubDate><Year>2018</Year><Month>12</Month><Day>12</Day></PubDate></JournalIssue><Title>Viruses</Title><ISOAbbreviation>Viruses</ISOAbbreviation></Journal><ArticleTitle>Metatranscriptomic Analysis and In Silico Approach Identified Mycoviruses in the Arbuscular Mycorrhizal Fungus <i>Rhizophagus</i> spp.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">E707</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.3390/v10120707</ELocationID><Abstract><AbstractText>Arbuscular mycorrhizal fungi (AMF), including <i>Rhizophagus</i> spp., can play important roles in nutrient cycling of the rhizosphere. However, the effect of virus infection on AMF's role in nutrient cycling cannot be determined without first knowing the diversity of the mycoviruses in AMF. Therefore, in this study, we sequenced the <i>R</i>. <i>irregularis</i> isolate-09 due to its previously demonstrated high efficiency in increasing the N/P uptake of the plant. We identified one novel mitovirus contig of 3685 bp, further confirmed by reverse transcription-PCR. Also, publicly available <i>Rhizophagus</i> spp. RNA-Seq data were analyzed to recover five partial virus sequences from family <i>Narnaviridae</i>, among which four were from <i>R. diaphanum</i> MUCL-43196 and one was from <i>R. irregularis</i> strain-C2 that was similar to members of the <i>Mitovirus</i> genus. These contigs coded genomes larger than the regular mitoviruses infecting pathogenic fungi and can be translated by either a mitochondrial translation code or a cytoplasmic translation code, which was also reported in previously found mitoviruses infecting mycorrhizae. The five newly identified virus sequences are comprised of functionally conserved RdRp motifs and formed two separate subclades with mitoviruses infecting <i>Gigaspora</i><i>margarita</i> and <i>Rhizophagus</i><i>clarus</i>, further supporting virus-host co-evolution theory. This study expands our understanding of virus diversity. Even though AMF is notably hard to investigate due to its biotrophic nature, this study demonstrates the utility of whole root metatranscriptome.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Neupane</LastName><ForeName>Achal</ForeName><Initials>A</Initials><Identifier Source="ORCID">0000-0003-0371-1177</Identifier><AffiliationInfo><Affiliation>Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA. achal.neupane@sdstate.edu.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Feng</LastName><ForeName>Chenchen</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Department of Agronomy, Horticulture, and Plant Sciences, South Dakota State University, Brookings, SD 57007, USA. chenchen.feng@sdstate.edu.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Feng</LastName><ForeName>Jiuhuan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA. jiuhuan.feng@sdstate.edu.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Agronomy, Horticulture, and Plant Sciences, South Dakota State University, Brookings, SD 57007, USA. jiuhuan.feng@sdstate.edu.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kafle</LastName><ForeName>Arjun</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA. arjun.kafle@sdstate.edu.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bücking</LastName><ForeName>Heike</ForeName><Initials>H</Initials><Identifier Source="ORCID">0000-0002-4040-0944</Identifier><AffiliationInfo><Affiliation>Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA. heike.bucking@sdstate.edu.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lee Marzano</LastName><ForeName>Shin-Yi</ForeName><Initials>SY</Initials><AffiliationInfo><Affiliation>Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA. shinyi.marzano@sdstate.edu.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Agronomy, Horticulture, and Plant Sciences, South Dakota State University, Brookings, SD 57007, USA. shinyi.marzano@sdstate.edu.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>12</Month><Day>12</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Viruses</MedlineTA><NlmUniqueID>101509722</NlmUniqueID><ISSNLinking>1999-4915</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000067148" MajorTopicYN="N">Fungal Viruses</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="Y">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="N">Genome, Viral</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D038821" MajorTopicYN="N">Mycorrhizae</DescriptorName><QualifierName UI="Q000821" MajorTopicYN="Y">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018517" MajorTopicYN="N">Plant Roots</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010944" MajorTopicYN="N">Plants</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013559" MajorTopicYN="N">Symbiosis</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Rhizophagus</Keyword><Keyword MajorTopicYN="Y">mitovirus</Keyword><Keyword MajorTopicYN="Y">mycorrhizal fungi</Keyword><Keyword MajorTopicYN="Y">mycovirus</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>09</Month><Day>22</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2018</Year><Month>12</Month><Day>06</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>12</Month><Day>07</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2018</Year><Month>12</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2018</Year><Month>12</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>4</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">30545059</ArticleId><ArticleId IdType="pii">v10120707</ArticleId><ArticleId IdType="doi">10.3390/v10120707</ArticleId><ArticleId IdType="pmc">PMC6316171</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Genome Biol. 2009;10(3):R25</Citation><ArticleIdList><ArticleId IdType="pubmed">19261174</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Biotechnol. 2011 May 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