Near-complete genome sequence of cowpea severe mosaic virus in South America and reduced yardlong bean production due to the viral infection
The sequence of a near-complete genome (two RNA segments) of cowpea severe mosaic virus (CpSMV) in the Comovirus genus is revealed in South America. High-throughput sequencing (HTS) was performed using total RNA extracted from partially purified virus preparations obtained from infected yardlong bea...
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| creator | Boari, Alessandra J. Quadros, Ayane F. F. Kauffmann, Caterynne M. Pantoja, Késsia F. C. Gomes Junior, Rui A. Freire Filho, Francisco R. Oliveira, Raimundo P. Cordovil, Gabriele A. Gavinho, Brenda E. S. Kitajima, Elliot W. Blawid, Rosana Nagata, Tatsuya |
| description | The sequence of a near-complete genome (two RNA segments) of cowpea severe mosaic virus (CpSMV) in the
Comovirus
genus is revealed in South America. High-throughput sequencing (HTS) was performed using total RNA extracted from partially purified virus preparations obtained from infected yardlong bean leaves (
Vigna unguiculata
subsp.
sesquipedalis
), collected in Santa Izabel, state of Pará, Brazil. The YLB (yardlong bean) isolate has an RNA-1 with 5896 nucleotides (nt) and an RNA-2 with 3515 nt, showing 74.2% and 67.9% identity, respectively, with the CpSMV-DG isolate sequences from the USA, the only complete genome available so far. Despite the low percentage in nt identity, the amino acid (aa) sequence of the viral protease together with the RNA-dependent RNA polymerase (Pro/RdRp) and the large and small coat proteins (CP-L/CP-S), used as species demarcation criteria of the
Secoviridae
family, showed 92.2% (Pro-RdRp) and 85.6% (CP-L/CL-S) identities between DG and YLB isolates sequences. The nucleotide identity of partial RNA-1 sequences of 2199 nt (part of the helicase, VPg, Pro, and 2/3 of the RdRP) varied from 95.1 to 95.3% among YLB and eleven isolates from Brazil available on GenBank. Phylogenetic analysis based on this 2199 nt sequence revealed that the YLB isolate was positioned in a different clade compared to other CpSMV isolates. An estimate of damage caused by CpSMV under experimental conditions revealed a reduction of 39.4% in the total number of pods and 54.3% in the total number of grains, regardless of the yardlong bean cultivar evaluated. The reduction of total weight of the grains by CpSMV infection was dependent on the cultivar and was higher in cv. De metro (66.2%) than in cv. Slin (38.9%). |
| doi_str_mv | 10.1007/s40858-021-00420-w |
| format | Article |
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Comovirus
genus is revealed in South America. High-throughput sequencing (HTS) was performed using total RNA extracted from partially purified virus preparations obtained from infected yardlong bean leaves (
Vigna unguiculata
subsp.
sesquipedalis
), collected in Santa Izabel, state of Pará, Brazil. The YLB (yardlong bean) isolate has an RNA-1 with 5896 nucleotides (nt) and an RNA-2 with 3515 nt, showing 74.2% and 67.9% identity, respectively, with the CpSMV-DG isolate sequences from the USA, the only complete genome available so far. Despite the low percentage in nt identity, the amino acid (aa) sequence of the viral protease together with the RNA-dependent RNA polymerase (Pro/RdRp) and the large and small coat proteins (CP-L/CP-S), used as species demarcation criteria of the
Secoviridae
family, showed 92.2% (Pro-RdRp) and 85.6% (CP-L/CL-S) identities between DG and YLB isolates sequences. The nucleotide identity of partial RNA-1 sequences of 2199 nt (part of the helicase, VPg, Pro, and 2/3 of the RdRP) varied from 95.1 to 95.3% among YLB and eleven isolates from Brazil available on GenBank. Phylogenetic analysis based on this 2199 nt sequence revealed that the YLB isolate was positioned in a different clade compared to other CpSMV isolates. An estimate of damage caused by CpSMV under experimental conditions revealed a reduction of 39.4% in the total number of pods and 54.3% in the total number of grains, regardless of the yardlong bean cultivar evaluated. The reduction of total weight of the grains by CpSMV infection was dependent on the cultivar and was higher in cv. De metro (66.2%) than in cv. Slin (38.9%).</description><identifier>ISSN: 1983-2052</identifier><identifier>ISSN: 1982-5676</identifier><identifier>EISSN: 1983-2052</identifier><identifier>DOI: 10.1007/s40858-021-00420-w</identifier><language>eng</language><publisher>Cham: Springer International Publishing</publisher><subject>Amino acid sequence ; Amino acids ; Analysis ; Beans ; Biomedical and Life Sciences ; Cowpeas ; Cultivars ; DNA helicase ; DNA-directed RNA polymerase ; Gene sequencing ; Genetic aspects ; Genomes ; Genomics ; Health aspects ; Life Sciences ; Next-generation sequencing ; Nucleotide sequence ; Nucleotides ; Phylogeny ; Plant Pathology ; Proteins ; Reduction ; RNA ; RNA polymerase ; RNA-directed RNA polymerase ; Short Communication ; Vigna unguiculata ; Vigna unguiculata sesquipedalis ; Viral infections ; Viruses</subject><ispartof>Tropical Plant Pathology, 2021-08, Vol.46 (4), p.487-491</ispartof><rights>Sociedade Brasileira de Fitopatologia 2021</rights><rights>COPYRIGHT 2021 Springer</rights><rights>Sociedade Brasileira de Fitopatologia 2021.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c309t-36845614bce6b7bf1e135f3e94e7e4b302ccaf3e8d066eca0714631bfd72df223</cites><orcidid>0000-0003-3514-7232</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s40858-021-00420-w$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s40858-021-00420-w$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids></links><search><creatorcontrib>Boari, Alessandra J.</creatorcontrib><creatorcontrib>Quadros, Ayane F. F.</creatorcontrib><creatorcontrib>Kauffmann, Caterynne M.</creatorcontrib><creatorcontrib>Pantoja, Késsia F. C.</creatorcontrib><creatorcontrib>Gomes Junior, Rui A.</creatorcontrib><creatorcontrib>Freire Filho, Francisco R.</creatorcontrib><creatorcontrib>Oliveira, Raimundo P.</creatorcontrib><creatorcontrib>Cordovil, Gabriele A.</creatorcontrib><creatorcontrib>Gavinho, Brenda E. S.</creatorcontrib><creatorcontrib>Kitajima, Elliot W.</creatorcontrib><creatorcontrib>Blawid, Rosana</creatorcontrib><creatorcontrib>Nagata, Tatsuya</creatorcontrib><title>Near-complete genome sequence of cowpea severe mosaic virus in South America and reduced yardlong bean production due to the viral infection</title><title>Tropical Plant Pathology</title><addtitle>Trop. plant pathol</addtitle><description>The sequence of a near-complete genome (two RNA segments) of cowpea severe mosaic virus (CpSMV) in the
Comovirus
genus is revealed in South America. High-throughput sequencing (HTS) was performed using total RNA extracted from partially purified virus preparations obtained from infected yardlong bean leaves (
Vigna unguiculata
subsp.
sesquipedalis
), collected in Santa Izabel, state of Pará, Brazil. The YLB (yardlong bean) isolate has an RNA-1 with 5896 nucleotides (nt) and an RNA-2 with 3515 nt, showing 74.2% and 67.9% identity, respectively, with the CpSMV-DG isolate sequences from the USA, the only complete genome available so far. Despite the low percentage in nt identity, the amino acid (aa) sequence of the viral protease together with the RNA-dependent RNA polymerase (Pro/RdRp) and the large and small coat proteins (CP-L/CP-S), used as species demarcation criteria of the
Secoviridae
family, showed 92.2% (Pro-RdRp) and 85.6% (CP-L/CL-S) identities between DG and YLB isolates sequences. The nucleotide identity of partial RNA-1 sequences of 2199 nt (part of the helicase, VPg, Pro, and 2/3 of the RdRP) varied from 95.1 to 95.3% among YLB and eleven isolates from Brazil available on GenBank. Phylogenetic analysis based on this 2199 nt sequence revealed that the YLB isolate was positioned in a different clade compared to other CpSMV isolates. An estimate of damage caused by CpSMV under experimental conditions revealed a reduction of 39.4% in the total number of pods and 54.3% in the total number of grains, regardless of the yardlong bean cultivar evaluated. The reduction of total weight of the grains by CpSMV infection was dependent on the cultivar and was higher in cv. De metro (66.2%) than in cv. Slin (38.9%).</description><subject>Amino acid sequence</subject><subject>Amino acids</subject><subject>Analysis</subject><subject>Beans</subject><subject>Biomedical and Life Sciences</subject><subject>Cowpeas</subject><subject>Cultivars</subject><subject>DNA helicase</subject><subject>DNA-directed RNA polymerase</subject><subject>Gene sequencing</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Health aspects</subject><subject>Life Sciences</subject><subject>Next-generation sequencing</subject><subject>Nucleotide sequence</subject><subject>Nucleotides</subject><subject>Phylogeny</subject><subject>Plant Pathology</subject><subject>Proteins</subject><subject>Reduction</subject><subject>RNA</subject><subject>RNA polymerase</subject><subject>RNA-directed RNA polymerase</subject><subject>Short Communication</subject><subject>Vigna unguiculata</subject><subject>Vigna unguiculata sesquipedalis</subject><subject>Viral infections</subject><subject>Viruses</subject><issn>1983-2052</issn><issn>1982-5676</issn><issn>1983-2052</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><recordid>eNp9Uc1u1DAYjBCVKKUvwOmTOKd8_omTHFcVUKQKDsDZcuzP21SJvdhJV30HHhpvU6mckA-2xzPjsaeq3jO8Yojtxyyxa7oaOasRJcf6-Ko6Z30nao4Nf_3P-k31Nud7RMV71Z1Xf76RSbWN82GihWBPIc4EmX6vFCxB9GDj8UCmQA-UCOaYzWjhYUxrhjHAj7gud7CbKY3WgAkOErnVkoNHk9wUwx4GMgEOKRZ4GWMAtxIsEZY7OtmYqdh4ejp6V515M2W6fJ4vql-fP_28vqlvv3_5er27ra3AfqmF6mSjmBwsqaEdPCMmGi-ol9SSHARya03Zdw6VImuwZVIJNnjXcuc5FxfVh823pCoPzYu-j2sK5UrNm6Z8ZM8YFtbVxtqbiXQJGZdkbBmO5tHGQH4s-K7FVjIl5cmWbwKbYs6JvD6kcTbpUTPUp5r0VpMuNemnmvSxiMQmyoUc9pResvxH9RdIKpgm</recordid><startdate>20210801</startdate><enddate>20210801</enddate><creator>Boari, Alessandra J.</creator><creator>Quadros, Ayane F. F.</creator><creator>Kauffmann, Caterynne M.</creator><creator>Pantoja, Késsia F. C.</creator><creator>Gomes Junior, Rui A.</creator><creator>Freire Filho, Francisco R.</creator><creator>Oliveira, Raimundo P.</creator><creator>Cordovil, Gabriele A.</creator><creator>Gavinho, Brenda E. S.</creator><creator>Kitajima, Elliot W.</creator><creator>Blawid, Rosana</creator><creator>Nagata, Tatsuya</creator><general>Springer International Publishing</general><general>Springer</general><general>Springer Nature B.V</general><scope>AAYXX</scope><scope>CITATION</scope><scope>IAO</scope><orcidid>https://orcid.org/0000-0003-3514-7232</orcidid></search><sort><creationdate>20210801</creationdate><title>Near-complete genome sequence of cowpea severe mosaic virus in South America and reduced yardlong bean production due to the viral infection</title><author>Boari, Alessandra J. ; Quadros, Ayane F. F. ; Kauffmann, Caterynne M. ; Pantoja, Késsia F. C. ; Gomes Junior, Rui A. ; Freire Filho, Francisco R. ; Oliveira, Raimundo P. ; Cordovil, Gabriele A. ; Gavinho, Brenda E. S. ; Kitajima, Elliot W. ; Blawid, Rosana ; Nagata, Tatsuya</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c309t-36845614bce6b7bf1e135f3e94e7e4b302ccaf3e8d066eca0714631bfd72df223</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Amino acid sequence</topic><topic>Amino acids</topic><topic>Analysis</topic><topic>Beans</topic><topic>Biomedical and Life Sciences</topic><topic>Cowpeas</topic><topic>Cultivars</topic><topic>DNA helicase</topic><topic>DNA-directed RNA polymerase</topic><topic>Gene sequencing</topic><topic>Genetic aspects</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Health aspects</topic><topic>Life Sciences</topic><topic>Next-generation sequencing</topic><topic>Nucleotide sequence</topic><topic>Nucleotides</topic><topic>Phylogeny</topic><topic>Plant Pathology</topic><topic>Proteins</topic><topic>Reduction</topic><topic>RNA</topic><topic>RNA polymerase</topic><topic>RNA-directed RNA polymerase</topic><topic>Short Communication</topic><topic>Vigna unguiculata</topic><topic>Vigna unguiculata sesquipedalis</topic><topic>Viral infections</topic><topic>Viruses</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Boari, Alessandra J.</creatorcontrib><creatorcontrib>Quadros, Ayane F. F.</creatorcontrib><creatorcontrib>Kauffmann, Caterynne M.</creatorcontrib><creatorcontrib>Pantoja, Késsia F. C.</creatorcontrib><creatorcontrib>Gomes Junior, Rui A.</creatorcontrib><creatorcontrib>Freire Filho, Francisco R.</creatorcontrib><creatorcontrib>Oliveira, Raimundo P.</creatorcontrib><creatorcontrib>Cordovil, Gabriele A.</creatorcontrib><creatorcontrib>Gavinho, Brenda E. S.</creatorcontrib><creatorcontrib>Kitajima, Elliot W.</creatorcontrib><creatorcontrib>Blawid, Rosana</creatorcontrib><creatorcontrib>Nagata, Tatsuya</creatorcontrib><collection>CrossRef</collection><collection>Gale Academic OneFile</collection><jtitle>Tropical Plant Pathology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Boari, Alessandra J.</au><au>Quadros, Ayane F. F.</au><au>Kauffmann, Caterynne M.</au><au>Pantoja, Késsia F. C.</au><au>Gomes Junior, Rui A.</au><au>Freire Filho, Francisco R.</au><au>Oliveira, Raimundo P.</au><au>Cordovil, Gabriele A.</au><au>Gavinho, Brenda E. S.</au><au>Kitajima, Elliot W.</au><au>Blawid, Rosana</au><au>Nagata, Tatsuya</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Near-complete genome sequence of cowpea severe mosaic virus in South America and reduced yardlong bean production due to the viral infection</atitle><jtitle>Tropical Plant Pathology</jtitle><stitle>Trop. plant pathol</stitle><date>2021-08-01</date><risdate>2021</risdate><volume>46</volume><issue>4</issue><spage>487</spage><epage>491</epage><pages>487-491</pages><issn>1983-2052</issn><issn>1982-5676</issn><eissn>1983-2052</eissn><abstract>The sequence of a near-complete genome (two RNA segments) of cowpea severe mosaic virus (CpSMV) in the
Comovirus
genus is revealed in South America. High-throughput sequencing (HTS) was performed using total RNA extracted from partially purified virus preparations obtained from infected yardlong bean leaves (
Vigna unguiculata
subsp.
sesquipedalis
), collected in Santa Izabel, state of Pará, Brazil. The YLB (yardlong bean) isolate has an RNA-1 with 5896 nucleotides (nt) and an RNA-2 with 3515 nt, showing 74.2% and 67.9% identity, respectively, with the CpSMV-DG isolate sequences from the USA, the only complete genome available so far. Despite the low percentage in nt identity, the amino acid (aa) sequence of the viral protease together with the RNA-dependent RNA polymerase (Pro/RdRp) and the large and small coat proteins (CP-L/CP-S), used as species demarcation criteria of the
Secoviridae
family, showed 92.2% (Pro-RdRp) and 85.6% (CP-L/CL-S) identities between DG and YLB isolates sequences. The nucleotide identity of partial RNA-1 sequences of 2199 nt (part of the helicase, VPg, Pro, and 2/3 of the RdRP) varied from 95.1 to 95.3% among YLB and eleven isolates from Brazil available on GenBank. Phylogenetic analysis based on this 2199 nt sequence revealed that the YLB isolate was positioned in a different clade compared to other CpSMV isolates. An estimate of damage caused by CpSMV under experimental conditions revealed a reduction of 39.4% in the total number of pods and 54.3% in the total number of grains, regardless of the yardlong bean cultivar evaluated. The reduction of total weight of the grains by CpSMV infection was dependent on the cultivar and was higher in cv. De metro (66.2%) than in cv. Slin (38.9%).</abstract><cop>Cham</cop><pub>Springer International Publishing</pub><doi>10.1007/s40858-021-00420-w</doi><tpages>5</tpages><orcidid>https://orcid.org/0000-0003-3514-7232</orcidid></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1983-2052 |
| ispartof | Tropical Plant Pathology, 2021-08, Vol.46 (4), p.487-491 |
| issn | 1983-2052 1982-5676 1983-2052 |
| language | eng |
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| source | SpringerNature Journals |
| subjects | Amino acid sequence Amino acids Analysis Beans Biomedical and Life Sciences Cowpeas Cultivars DNA helicase DNA-directed RNA polymerase Gene sequencing Genetic aspects Genomes Genomics Health aspects Life Sciences Next-generation sequencing Nucleotide sequence Nucleotides Phylogeny Plant Pathology Proteins Reduction RNA RNA polymerase RNA-directed RNA polymerase Short Communication Vigna unguiculata Vigna unguiculata sesquipedalis Viral infections Viruses |
| title | Near-complete genome sequence of cowpea severe mosaic virus in South America and reduced yardlong bean production due to the viral infection |
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