Mycovirus Hunting Revealed the Presence of Diverse Viruses in a Single Isolate of the Phytopathogenic Fungus Diplodia seriata From Pakistan
Diplodia seriata in the family Botryosphaeriaceae is a cosmopolitan phytopathogenic fungus and is responsible for causing cankers, fruit rot and leaf spots on economically important plants. In this study, we characterized the virome of a single Pakistani strain (L3) of D. seriata. Several viral-like...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-06-01
|
| Series: | Frontiers in Cellular and Infection Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fcimb.2022.913619/full |
| _version_ | 1811236928463306752 |
|---|---|
| author | Haris Ahmed Khan Paul Telengech Hideki Kondo Muhammad Faraz Bhatti Nobuhiro Suzuki |
| author_facet | Haris Ahmed Khan Paul Telengech Hideki Kondo Muhammad Faraz Bhatti Nobuhiro Suzuki |
| author_sort | Haris Ahmed Khan |
| collection | DOAJ |
| description | Diplodia seriata in the family Botryosphaeriaceae is a cosmopolitan phytopathogenic fungus and is responsible for causing cankers, fruit rot and leaf spots on economically important plants. In this study, we characterized the virome of a single Pakistani strain (L3) of D. seriata. Several viral-like contig sequences were obtained via a previously conducted next-generation sequencing analysis. Multiple infection of the L3 strain by eight RNA mycoviruses was confirmed through RT-PCR using total RNA samples extracted from this strain; the entire genomes were determined via Sanger sequencing of RT-PCR and RACE clones. A BLAST search and phylogenetic analyses indicated that these eight mycoviruses belong to seven different viral families. Four identified mycoviruses belong to double-stranded RNA viral families, including Polymycoviridae, Chrysoviridae, Totiviridae and Partitiviridae, and the remaining four identified mycoviruses belong to single-stranded RNA viral families, i.e., Botourmiaviridae, and two previously proposed families “Ambiguiviridae” and “Splipalmiviridae”. Of the eight, five mycoviruses appear to represent new virus species. A morphological comparison of L3 and partially cured strain L3ht1 suggested that one or more of the three viruses belonging to Polymycoviridae, “Splipalmiviridae” and “Ambiguiviridae” are involved in the irregular colony phenotype of L3. To our knowledge, this is the first report of diverse virome characterization from D. seriata. |
| first_indexed | 2024-04-12T12:16:32Z |
| format | Article |
| id | doaj.art-36ae6205c6b249dcad549a5ad8e9ffe5 |
| institution | Directory Open Access Journal |
| issn | 2235-2988 |
| language | English |
| last_indexed | 2024-04-12T12:16:32Z |
| publishDate | 2022-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Cellular and Infection Microbiology |
| spelling | doaj.art-36ae6205c6b249dcad549a5ad8e9ffe52022-12-22T03:33:24ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882022-06-011210.3389/fcimb.2022.913619913619Mycovirus Hunting Revealed the Presence of Diverse Viruses in a Single Isolate of the Phytopathogenic Fungus Diplodia seriata From PakistanHaris Ahmed Khan0Paul Telengech1Hideki Kondo2Muhammad Faraz Bhatti3Nobuhiro Suzuki4Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, PakistanInstitute of Plant Science and Resources, Okayama University, Kurashiki, JapanInstitute of Plant Science and Resources, Okayama University, Kurashiki, JapanAtta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, PakistanInstitute of Plant Science and Resources, Okayama University, Kurashiki, JapanDiplodia seriata in the family Botryosphaeriaceae is a cosmopolitan phytopathogenic fungus and is responsible for causing cankers, fruit rot and leaf spots on economically important plants. In this study, we characterized the virome of a single Pakistani strain (L3) of D. seriata. Several viral-like contig sequences were obtained via a previously conducted next-generation sequencing analysis. Multiple infection of the L3 strain by eight RNA mycoviruses was confirmed through RT-PCR using total RNA samples extracted from this strain; the entire genomes were determined via Sanger sequencing of RT-PCR and RACE clones. A BLAST search and phylogenetic analyses indicated that these eight mycoviruses belong to seven different viral families. Four identified mycoviruses belong to double-stranded RNA viral families, including Polymycoviridae, Chrysoviridae, Totiviridae and Partitiviridae, and the remaining four identified mycoviruses belong to single-stranded RNA viral families, i.e., Botourmiaviridae, and two previously proposed families “Ambiguiviridae” and “Splipalmiviridae”. Of the eight, five mycoviruses appear to represent new virus species. A morphological comparison of L3 and partially cured strain L3ht1 suggested that one or more of the three viruses belonging to Polymycoviridae, “Splipalmiviridae” and “Ambiguiviridae” are involved in the irregular colony phenotype of L3. To our knowledge, this is the first report of diverse virome characterization from D. seriata.https://www.frontiersin.org/articles/10.3389/fcimb.2022.913619/fullphytopathogenic fungimycoviromenext-generation sequencingDiplodia seriataBotryosphaeriaceaessRNA virus |
| spellingShingle | Haris Ahmed Khan Paul Telengech Hideki Kondo Muhammad Faraz Bhatti Nobuhiro Suzuki Mycovirus Hunting Revealed the Presence of Diverse Viruses in a Single Isolate of the Phytopathogenic Fungus Diplodia seriata From Pakistan Frontiers in Cellular and Infection Microbiology phytopathogenic fungi mycovirome next-generation sequencing Diplodia seriata Botryosphaeriaceae ssRNA virus |
| title | Mycovirus Hunting Revealed the Presence of Diverse Viruses in a Single Isolate of the Phytopathogenic Fungus Diplodia seriata From Pakistan |
| title_full | Mycovirus Hunting Revealed the Presence of Diverse Viruses in a Single Isolate of the Phytopathogenic Fungus Diplodia seriata From Pakistan |
| title_fullStr | Mycovirus Hunting Revealed the Presence of Diverse Viruses in a Single Isolate of the Phytopathogenic Fungus Diplodia seriata From Pakistan |
| title_full_unstemmed | Mycovirus Hunting Revealed the Presence of Diverse Viruses in a Single Isolate of the Phytopathogenic Fungus Diplodia seriata From Pakistan |
| title_short | Mycovirus Hunting Revealed the Presence of Diverse Viruses in a Single Isolate of the Phytopathogenic Fungus Diplodia seriata From Pakistan |
| title_sort | mycovirus hunting revealed the presence of diverse viruses in a single isolate of the phytopathogenic fungus diplodia seriata from pakistan |
| topic | phytopathogenic fungi mycovirome next-generation sequencing Diplodia seriata Botryosphaeriaceae ssRNA virus |
| url | https://www.frontiersin.org/articles/10.3389/fcimb.2022.913619/full |
| work_keys_str_mv | AT harisahmedkhan mycovirushuntingrevealedthepresenceofdiversevirusesinasingleisolateofthephytopathogenicfungusdiplodiaseriatafrompakistan AT paultelengech mycovirushuntingrevealedthepresenceofdiversevirusesinasingleisolateofthephytopathogenicfungusdiplodiaseriatafrompakistan AT hidekikondo mycovirushuntingrevealedthepresenceofdiversevirusesinasingleisolateofthephytopathogenicfungusdiplodiaseriatafrompakistan AT muhammadfarazbhatti mycovirushuntingrevealedthepresenceofdiversevirusesinasingleisolateofthephytopathogenicfungusdiplodiaseriatafrompakistan AT nobuhirosuzuki mycovirushuntingrevealedthepresenceofdiversevirusesinasingleisolateofthephytopathogenicfungusdiplodiaseriatafrompakistan |