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Detection and analysis of endogenous badnaviruses in the New Zealand flora.

Lyttle DJ, Orlovich DA, Guy PL - AoB Plants (2011)

Bottom Line: In a study of the genus Melicytus, internal transcribed spacer (ITS) sequences were compared with the RT data.Analysis of RT sequences revealed the presence of a previously unrecognized species (confirmed using ITS).Analysis of endogenous RT sequences shows potential for the study of systematics, phylogenetics and plant reproductive biology.

View Article: PubMed Central - PubMed

Affiliation: Department of Botany , University of Otago , P.O. Box 56, Dunedin 9054 , New Zealand.

ABSTRACT

Background and aims: Badnaviruses and their host-integrated DNA occur in tropical crops and a few northern temperate species. Following the discovery of a badnavirus on a subantarctic island with floristic links to New Zealand, we postulated that badnaviruses exist in the New Zealand flora. Badnavirus reverse transcriptase (RT) sequences consist of variable regions flanked by highly conserved regions. This study used RT sequences to detect and characterize badnavirus sequences in the New Zealand flora and to investigate their utility for the study of broader aspects of plant biology.

Methodology: Molecular diversity of RT sequences was analysed using polymerase chain reaction and denaturing gradient gel electrophoresis (DGGE). In a study of the genus Melicytus, internal transcribed spacer (ITS) sequences were compared with the RT data.

Principal results: No freely replicating badnaviruses were detected but more than half of the species (37/60) contained RT sequences. Phylogenetic analysis of 21 RT sequences formed monophyletic groups distinct from other species and from badnaviruses. No frameshift mutations occurred in any of the sequences translated in silico. More detailed study of the genus Melicytus indicated broader applications for our approach. Analysis of RT sequences revealed the presence of a previously unrecognized species (confirmed using ITS). Inheritance of DGGE profiles by Melicytus ramiflorus seedlings suggested that this species may undergo apomixis.

Conclusions: The presence of integrated badnavirus sequences in a wide range of taxa from this Southern Hemisphere flora indicates that these sequences may be common in many temperate regions. Potential to activate viruses from these sequences should be considered when placing these species in tissue culture or under other forms of abiotic or genomic stress. Analysis of endogenous RT sequences shows potential for the study of systematics, phylogenetics and plant reproductive biology.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree showing the relationships of New Zealand endogenous badnavirus sequences to known badnaviruses.
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PLR008F1: Phylogenetic tree showing the relationships of New Zealand endogenous badnavirus sequences to known badnaviruses.

Mentions: BLAST searching (Altschul et al. 1997) showed that the sequences reported here did not match any known badnavirus sequence. When the 21 RT DNA sequences from 12 species belonging to four genera (Melicytus 17, Coprosma 7, Parsonsia 2, Chionochloa 1, Myrsine 1) were aligned with known badnavirus sequences from GenBank, each species was shown to contain distinct sequences (Fig. 1).Fig. 1.


Detection and analysis of endogenous badnaviruses in the New Zealand flora.

Lyttle DJ, Orlovich DA, Guy PL - AoB Plants (2011)

Phylogenetic tree showing the relationships of New Zealand endogenous badnavirus sequences to known badnaviruses.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3104934&req=5

PLR008F1: Phylogenetic tree showing the relationships of New Zealand endogenous badnavirus sequences to known badnaviruses.
Mentions: BLAST searching (Altschul et al. 1997) showed that the sequences reported here did not match any known badnavirus sequence. When the 21 RT DNA sequences from 12 species belonging to four genera (Melicytus 17, Coprosma 7, Parsonsia 2, Chionochloa 1, Myrsine 1) were aligned with known badnavirus sequences from GenBank, each species was shown to contain distinct sequences (Fig. 1).Fig. 1.

Bottom Line: In a study of the genus Melicytus, internal transcribed spacer (ITS) sequences were compared with the RT data.Analysis of RT sequences revealed the presence of a previously unrecognized species (confirmed using ITS).Analysis of endogenous RT sequences shows potential for the study of systematics, phylogenetics and plant reproductive biology.

View Article: PubMed Central - PubMed

Affiliation: Department of Botany , University of Otago , P.O. Box 56, Dunedin 9054 , New Zealand.

ABSTRACT

Background and aims: Badnaviruses and their host-integrated DNA occur in tropical crops and a few northern temperate species. Following the discovery of a badnavirus on a subantarctic island with floristic links to New Zealand, we postulated that badnaviruses exist in the New Zealand flora. Badnavirus reverse transcriptase (RT) sequences consist of variable regions flanked by highly conserved regions. This study used RT sequences to detect and characterize badnavirus sequences in the New Zealand flora and to investigate their utility for the study of broader aspects of plant biology.

Methodology: Molecular diversity of RT sequences was analysed using polymerase chain reaction and denaturing gradient gel electrophoresis (DGGE). In a study of the genus Melicytus, internal transcribed spacer (ITS) sequences were compared with the RT data.

Principal results: No freely replicating badnaviruses were detected but more than half of the species (37/60) contained RT sequences. Phylogenetic analysis of 21 RT sequences formed monophyletic groups distinct from other species and from badnaviruses. No frameshift mutations occurred in any of the sequences translated in silico. More detailed study of the genus Melicytus indicated broader applications for our approach. Analysis of RT sequences revealed the presence of a previously unrecognized species (confirmed using ITS). Inheritance of DGGE profiles by Melicytus ramiflorus seedlings suggested that this species may undergo apomixis.

Conclusions: The presence of integrated badnavirus sequences in a wide range of taxa from this Southern Hemisphere flora indicates that these sequences may be common in many temperate regions. Potential to activate viruses from these sequences should be considered when placing these species in tissue culture or under other forms of abiotic or genomic stress. Analysis of endogenous RT sequences shows potential for the study of systematics, phylogenetics and plant reproductive biology.

No MeSH data available.


Related in: MedlinePlus