Complete genome sequencing and characterization of a potential new genotype of Citrus tristeza virus in Iran.
Citrus tristeza virus (CTV) is one of the economically destructive viruses affecting citrus trees worldwide, causing significant losses in fruit production. Comparative genomic studies have shown genetic diversity in various regions of the genome of CTV isolates, which has classified the virus into...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2023-01-01
|
| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0288068&type=printable |
| _version_ | 1797394484439285760 |
|---|---|
| author | Abozar Ghorbani Mohammad Mehdi Faghihi Faezeh Falaki Keramatollah Izadpanah |
| author_facet | Abozar Ghorbani Mohammad Mehdi Faghihi Faezeh Falaki Keramatollah Izadpanah |
| author_sort | Abozar Ghorbani |
| collection | DOAJ |
| description | Citrus tristeza virus (CTV) is one of the economically destructive viruses affecting citrus trees worldwide, causing significant losses in fruit production. Comparative genomic studies have shown genetic diversity in various regions of the genome of CTV isolates, which has classified the virus into several genotypes. In recent years, some orange citrumelo-tolerant rootstocks showed yellowing, decline, and vein clearing in northern Iran (Mazandaran province, Sari). We confirmed the presence of CTV in the symptomatic trees by reverse transcription PCR (RT-PCR). The complete genome of a Sari isolate of CTV (Sari isolate) was sequenced using next-generation sequencing (NGS) technology. In addition, phylogenetic analysis, differential gene expression of the virus and identification of its variants in a population were studied. We obtained the final contigs of the virus (nt) and annotated all genomes to viral ORFs, untranslated regions (UTRs), intergenic regions, and 5' and 3' ends of the genome. Phylogenetic analysis of the Sari isolate and other genotypes of CTV showed that the Sari isolates were placed in a distinct cluster without a sister group. Based on the number of specific transcripts (TPM) in CTV RNA -Seq, P13 was the most highly expressed gene related to the host range of the virus and its systemic infection. The ORFs of the polyprotein, P33, and P18 showed variation in a single population of the sari isolate. The CTV has a potential for variation in a population in a host, and these variations may contribute to the best fit of the CTV in different situations. In Iran, whole genome sequencing of the CTV was performed for the first time, and we gained new insights into CTV variation in a population. |
| first_indexed | 2024-03-09T00:20:27Z |
| format | Article |
| id | doaj.art-7aa5a16dd26d439ab51282a070e055c7 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-03-09T00:20:27Z |
| publishDate | 2023-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-7aa5a16dd26d439ab51282a070e055c72023-12-12T05:35:34ZengPublic Library of Science (PLoS)PLoS ONE1932-62032023-01-01186e028806810.1371/journal.pone.0288068Complete genome sequencing and characterization of a potential new genotype of Citrus tristeza virus in Iran.Abozar GhorbaniMohammad Mehdi FaghihiFaezeh FalakiKeramatollah IzadpanahCitrus tristeza virus (CTV) is one of the economically destructive viruses affecting citrus trees worldwide, causing significant losses in fruit production. Comparative genomic studies have shown genetic diversity in various regions of the genome of CTV isolates, which has classified the virus into several genotypes. In recent years, some orange citrumelo-tolerant rootstocks showed yellowing, decline, and vein clearing in northern Iran (Mazandaran province, Sari). We confirmed the presence of CTV in the symptomatic trees by reverse transcription PCR (RT-PCR). The complete genome of a Sari isolate of CTV (Sari isolate) was sequenced using next-generation sequencing (NGS) technology. In addition, phylogenetic analysis, differential gene expression of the virus and identification of its variants in a population were studied. We obtained the final contigs of the virus (nt) and annotated all genomes to viral ORFs, untranslated regions (UTRs), intergenic regions, and 5' and 3' ends of the genome. Phylogenetic analysis of the Sari isolate and other genotypes of CTV showed that the Sari isolates were placed in a distinct cluster without a sister group. Based on the number of specific transcripts (TPM) in CTV RNA -Seq, P13 was the most highly expressed gene related to the host range of the virus and its systemic infection. The ORFs of the polyprotein, P33, and P18 showed variation in a single population of the sari isolate. The CTV has a potential for variation in a population in a host, and these variations may contribute to the best fit of the CTV in different situations. In Iran, whole genome sequencing of the CTV was performed for the first time, and we gained new insights into CTV variation in a population.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0288068&type=printable |
| spellingShingle | Abozar Ghorbani Mohammad Mehdi Faghihi Faezeh Falaki Keramatollah Izadpanah Complete genome sequencing and characterization of a potential new genotype of Citrus tristeza virus in Iran. PLoS ONE |
| title | Complete genome sequencing and characterization of a potential new genotype of Citrus tristeza virus in Iran. |
| title_full | Complete genome sequencing and characterization of a potential new genotype of Citrus tristeza virus in Iran. |
| title_fullStr | Complete genome sequencing and characterization of a potential new genotype of Citrus tristeza virus in Iran. |
| title_full_unstemmed | Complete genome sequencing and characterization of a potential new genotype of Citrus tristeza virus in Iran. |
| title_short | Complete genome sequencing and characterization of a potential new genotype of Citrus tristeza virus in Iran. |
| title_sort | complete genome sequencing and characterization of a potential new genotype of citrus tristeza virus in iran |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0288068&type=printable |
| work_keys_str_mv | AT abozarghorbani completegenomesequencingandcharacterizationofapotentialnewgenotypeofcitrustristezavirusiniran AT mohammadmehdifaghihi completegenomesequencingandcharacterizationofapotentialnewgenotypeofcitrustristezavirusiniran AT faezehfalaki completegenomesequencingandcharacterizationofapotentialnewgenotypeofcitrustristezavirusiniran AT keramatollahizadpanah completegenomesequencingandcharacterizationofapotentialnewgenotypeofcitrustristezavirusiniran |