A Comprehensive Analysis of Citrus Tristeza Variants of Bhutan and Across the World
Mandarin orange is economically one of the most important fruit crops in Bhutan. However, in recent years, orange productivity has dropped due to severe infection of citrus tristeza virus (CTV) associated with the gradual decline of citrus orchards. Although the disease incidence has been reported,...
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Frontiers Media S.A.
2022-04-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2022.797463/full |
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| author | Dilip Kumar Ghosh Amol Kokane Sunil Kokane Krishanu Mukherjee Jigme Tenzin Datta Surwase Dhanshree Deshmukh Mrugendra Gubyad Kajal Kumar Biswas |
| author_facet | Dilip Kumar Ghosh Amol Kokane Sunil Kokane Krishanu Mukherjee Jigme Tenzin Datta Surwase Dhanshree Deshmukh Mrugendra Gubyad Kajal Kumar Biswas |
| author_sort | Dilip Kumar Ghosh |
| collection | DOAJ |
| description | Mandarin orange is economically one of the most important fruit crops in Bhutan. However, in recent years, orange productivity has dropped due to severe infection of citrus tristeza virus (CTV) associated with the gradual decline of citrus orchards. Although the disease incidence has been reported, very limited information is available on genetic variability among the Bhutanese CTV variants. This study used reverse transcription PCR (RT-PCR) to detect CTV in collected field samples and recorded disease incidence up to 71.11% in Bhutan’s prominent citrus-growing regions. To elucidate the extent of genetic variabilities among the Bhutanese CTV variants, we targeted four independent genomic regions (5′ORF1a, p25, p23, and p18) and analyzed a total of 64 collected isolates. These genomic regions were amplified and sequenced for further comparative bioinformatics analysis. Comprehensive phylogenetic reconstructions of the GenBank deposited sequences, including the corresponding genomic locations from 53 whole-genome sequences, revealed unexpected and rich diversity among Bhutanese CTV variants. A resistant-breaking (RB) variant was also identified for the first time from the Asian subcontinent. Our analyses unambiguously identified five (T36, T3, T68, VT, and HA16-5) major, well-recognized CTV strains. Bhutanese CTV variants form two additional newly identified distinct clades with higher confidence, B1 and B2, named after Bhutan. The origin of each of these nine clades can be traced back to their root in the north-eastern region of India and Bhutan. Together, our study established a definitive framework for categorizing global CTV variants into their distinctive clades and provided novel insights into multiple genomic region-based genetic diversity assessments, including their pathogenicity status. |
| first_indexed | 2024-04-13T11:06:53Z |
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| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-13T11:06:53Z |
| publishDate | 2022-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-b9eded7ef1f34aac829ab2c46c55dd7a2022-12-22T02:49:14ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2022-04-011310.3389/fmicb.2022.797463797463A Comprehensive Analysis of Citrus Tristeza Variants of Bhutan and Across the WorldDilip Kumar Ghosh0Amol Kokane1Sunil Kokane2Krishanu Mukherjee3Jigme Tenzin4Datta Surwase5Dhanshree Deshmukh6Mrugendra Gubyad7Kajal Kumar Biswas8Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, IndiaPlant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, IndiaPlant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, IndiaWhitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, United StatesNational Citrus Program, Department of Agriculture, Royal Government of Bhutan, Thimpu, BhutanPlant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, IndiaPlant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, IndiaPlant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, IndiaDepartment of Plant Pathology, Indian Agricultural Research Institute, New Delhi, IndiaMandarin orange is economically one of the most important fruit crops in Bhutan. However, in recent years, orange productivity has dropped due to severe infection of citrus tristeza virus (CTV) associated with the gradual decline of citrus orchards. Although the disease incidence has been reported, very limited information is available on genetic variability among the Bhutanese CTV variants. This study used reverse transcription PCR (RT-PCR) to detect CTV in collected field samples and recorded disease incidence up to 71.11% in Bhutan’s prominent citrus-growing regions. To elucidate the extent of genetic variabilities among the Bhutanese CTV variants, we targeted four independent genomic regions (5′ORF1a, p25, p23, and p18) and analyzed a total of 64 collected isolates. These genomic regions were amplified and sequenced for further comparative bioinformatics analysis. Comprehensive phylogenetic reconstructions of the GenBank deposited sequences, including the corresponding genomic locations from 53 whole-genome sequences, revealed unexpected and rich diversity among Bhutanese CTV variants. A resistant-breaking (RB) variant was also identified for the first time from the Asian subcontinent. Our analyses unambiguously identified five (T36, T3, T68, VT, and HA16-5) major, well-recognized CTV strains. Bhutanese CTV variants form two additional newly identified distinct clades with higher confidence, B1 and B2, named after Bhutan. The origin of each of these nine clades can be traced back to their root in the north-eastern region of India and Bhutan. Together, our study established a definitive framework for categorizing global CTV variants into their distinctive clades and provided novel insights into multiple genomic region-based genetic diversity assessments, including their pathogenicity status.https://www.frontiersin.org/articles/10.3389/fmicb.2022.797463/fullcitrus tristeza virusgenomic diversitysequencing and phylogenetic analysisRT-PCRgenomic regions |
| spellingShingle | Dilip Kumar Ghosh Amol Kokane Sunil Kokane Krishanu Mukherjee Jigme Tenzin Datta Surwase Dhanshree Deshmukh Mrugendra Gubyad Kajal Kumar Biswas A Comprehensive Analysis of Citrus Tristeza Variants of Bhutan and Across the World Frontiers in Microbiology citrus tristeza virus genomic diversity sequencing and phylogenetic analysis RT-PCR genomic regions |
| title | A Comprehensive Analysis of Citrus Tristeza Variants of Bhutan and Across the World |
| title_full | A Comprehensive Analysis of Citrus Tristeza Variants of Bhutan and Across the World |
| title_fullStr | A Comprehensive Analysis of Citrus Tristeza Variants of Bhutan and Across the World |
| title_full_unstemmed | A Comprehensive Analysis of Citrus Tristeza Variants of Bhutan and Across the World |
| title_short | A Comprehensive Analysis of Citrus Tristeza Variants of Bhutan and Across the World |
| title_sort | comprehensive analysis of citrus tristeza variants of bhutan and across the world |
| topic | citrus tristeza virus genomic diversity sequencing and phylogenetic analysis RT-PCR genomic regions |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2022.797463/full |
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