The core region of the coat protein gene is highly useful for establishing the provisional identification and classification of begomoviruses

The core region of the coat protein gene is highly useful for establishing the provisional... Polymerase chain reaction (PCR) was applied to detect and establish provisional identity of begomoviruses through amplification of a ∼ 575 bp fragment of the begomoviral coat protein gene ( CP ), referred to as the ‘core’ region of the CP gene (core CP ). The core CP fragment contains conserved and unique regions, and was hypothesized to constitute a sequence useful for begomovirus classification. Virus relationships were predicted by distance and parsimony analyses using the A component (bipartite viruses) or full genome (monopartite viruses), CP gene, core CP , or the 200 5′-nucleotides (nt) of the CP . Reconstructed trees and sequence divergence estimates yielded very similar conclusions for all sequence sets, while the CP 5′-200 nt was the best strain discriminator. Alignment of the core CP region for 52 field isolates with reference begomovirus sequences permitted provisional virus identification based on tree position and extent of sequence divergence. Geographic origin of field isolates was predictable based on phylogenetic separation of field isolates examined here. A ‘closest match’ or genus-level identification could be obtained for previously undescribed begomoviruses using the BLAST program to search a reference core CP database located at our website and/or in GenBank. Here, we describe an informative molecular marker that permits provisional begomovirus identification and classification using a begomoviral sequence that is smaller than the presently accepted, but less accessible CP sequence. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Archives of Virology Springer Journals

The core region of the coat protein gene is highly useful for establishing the provisional identification and classification of begomoviruses

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Publisher
Springer-Verlag
Copyright
Copyright © 2001 by Springer-Verlag/Wien
Subject
Legacy
ISSN
0304-8608
eISSN
1432-8798
D.O.I.
10.1007/s007050170080
Publisher site
See Article on Publisher Site

Abstract

Polymerase chain reaction (PCR) was applied to detect and establish provisional identity of begomoviruses through amplification of a ∼ 575 bp fragment of the begomoviral coat protein gene ( CP ), referred to as the ‘core’ region of the CP gene (core CP ). The core CP fragment contains conserved and unique regions, and was hypothesized to constitute a sequence useful for begomovirus classification. Virus relationships were predicted by distance and parsimony analyses using the A component (bipartite viruses) or full genome (monopartite viruses), CP gene, core CP , or the 200 5′-nucleotides (nt) of the CP . Reconstructed trees and sequence divergence estimates yielded very similar conclusions for all sequence sets, while the CP 5′-200 nt was the best strain discriminator. Alignment of the core CP region for 52 field isolates with reference begomovirus sequences permitted provisional virus identification based on tree position and extent of sequence divergence. Geographic origin of field isolates was predictable based on phylogenetic separation of field isolates examined here. A ‘closest match’ or genus-level identification could be obtained for previously undescribed begomoviruses using the BLAST program to search a reference core CP database located at our website and/or in GenBank. Here, we describe an informative molecular marker that permits provisional begomovirus identification and classification using a begomoviral sequence that is smaller than the presently accepted, but less accessible CP sequence.

Journal

Archives of VirologySpringer Journals

Published: Aug 1, 2001

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