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Vol. 65 No. 7: Issue 7

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Molecular characterization of Chickpea chlorotic dwarf virus strain D in Chickpea (Cicer arietinum) from District Dera Ismail Khan Khyber Pakhtunkhwa, Pakistan

https://doi.org/10.14715/cmb/2019.65.7.7
Kamran Rashid
Department of Bioinformatics and Biotechnology, Government College University Faisalabad Pakistan
Nazia Nahid
Department of Bioinformatics and Biotechnology, Government College University Faisalabad Pakistan
Faiqah Ramzan
Gomal Centre of Biochemistry and Biotechnology, Gomal University Dera Ismail Khan, KP, Pakistan
Muhammad Asaf Khan
Department of Bioinformatics and Biotechnology, Government College University Faisalabad Pakistan
Shabnum Shaheen
Department of Botany, Lahore College for Women University, Lahore Pakistan
Ammara Nasim
Department of Bioinformatics and Biotechnology, Government College University Faisalabad Pakistan
Nazish Masood
Department of Bioinformatics and Biotechnology, Government College University Faisalabad Pakistan
Rob W Briddon
Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad Pakistan
Khadim Hussain
Department of Bioinformatics and Biotechnology, Government College University Faisalabad Pakistan

Corresponding Author(s) : Khadim Hussain

hussaink@gcuf.edu.pk

Cellular and Molecular Biology, Vol. 65 No. 7: Issue 7

Abstract

Chickpea chlorotic dwarf virus (CpCDV), a member of genus Mastrevirus (family Geminiviridae) is an important viral pathogen of chickpea and other legume crops in Middle East, North Africa, India and Pakistan. Among sixteen known strains of CpCDV three are known to infect legume crops in Punjab province of Pakistan. In this study diversity of CpCDV was explored in Khyber Pakhtunkhwa (KP) province of Pakistan. In year 2016, during a survey in the chickpea growing areas of district Dera Ismail Khan, CpCDV infected plants were identified. Leaf samples were collected, and a diagnostic PCR confirmed mastreivrus infection in 4 out of 100 samples. From these samples full-length genome of CpCDV was amplified using specific back-to-back primers. Virus molecules were sequenced to their entirety and sequence analysis of a molecule KRF4 (GenBank accession # KY952837) showed the highest pair wise sequence identity of 97% with a CpCDV molecule (KM229787) isolated from chickpea plant. An SDT analysis revealed it to be the D strain of CpCDV and a recombination detection program (RDP) showed it to be a recombinant between C (KM229780) and L (KT634301) strains of CpCDV. Thus, further supporting the intra-species recombination for CpCDV and presence of the same strain in chickpea growing areas of Pakistan other than Punjab province. This is the first identification of CpCDV (genus Mastrevirus family Geminiviridae) from chickpea (Cicer arietinum) plants in District Dera Ismail Khan, KP province, Pakistan.

Keywords

Chickpea chlorotic dwarf virus (CpCDV) Mastrevirus Geminiviridae Chickpea KP.
Rashid, K., Nahid, N., Ramzan, F., Khan, M. A., Shaheen, S., Nasim, A., Masood, N., Briddon, R. W., & Hussain, K. (2019). Molecular characterization of Chickpea chlorotic dwarf virus strain D in Chickpea (Cicer arietinum) from District Dera Ismail Khan Khyber Pakhtunkhwa, Pakistan. Cellular and Molecular Biology, 65(7), 34–37. https://doi.org/10.14715/cmb/2019.65.7.7
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Author Biography

Khadim Hussain, Department of Bioinformatics and Biotechnology, Government College University Faisalabad Pakistan

Assistant Professor

Department of Bioinformatics and Biotechnology

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