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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 various Melicytus species based on their ITS sequences and the DGGE band patterns of the RT fragments from M. alpinus. For M. alpinus, two predominant fragment patterns are distinguishable in the gel (designated type 1 (lanes 1–9) and type 2 (lanes 10–11)). 1: M. alpinus Akatore Creek 1; 2: M. alpinus Akatore Creek 2; 3: M. alpinus Hooper's Inlet; 4: M. alpinus Middlemarch; 5: M. alpinus Nugget Point 1; 6: M. alpinus Nugget Point 2; M. alpinus Pyramids 1; 8: M. alpinus Pyramids 2; 9: M. alpinus Taiaroa Head; 10: M. alpinus Ida Range; 11: M. alpinus Pisa Range 1; 12: M. alpinus Pisa Range 2; 13: M. alpinus Pisa Range 3.
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PLR008F3: Phylogenetic tree showing the relationships of various Melicytus species based on their ITS sequences and the DGGE band patterns of the RT fragments from M. alpinus. For M. alpinus, two predominant fragment patterns are distinguishable in the gel (designated type 1 (lanes 1–9) and type 2 (lanes 10–11)). 1: M. alpinus Akatore Creek 1; 2: M. alpinus Akatore Creek 2; 3: M. alpinus Hooper's Inlet; 4: M. alpinus Middlemarch; 5: M. alpinus Nugget Point 1; 6: M. alpinus Nugget Point 2; M. alpinus Pyramids 1; 8: M. alpinus Pyramids 2; 9: M. alpinus Taiaroa Head; 10: M. alpinus Ida Range; 11: M. alpinus Pisa Range 1; 12: M. alpinus Pisa Range 2; 13: M. alpinus Pisa Range 3.

Mentions: Analysis of badnavirus fragment patterns for the M. alpinus collections showed considerable variation within the species (Fig. 3). Plants identified in the field as M. alpinus collected from six coastal sites in eastern Otago (Akatore Creek, Hooper's Inlet, Nugget Point, Pyramids, Sandymount and Taiaroa Head) and from four inland sites (Swampy Summit, Middlemarch, Ida Range and Pisa Range) were subjected to PCR and DGGE analysis. DNA samples from the Swampy Summit plants (4/4) and Sandymount plants (2/2) did not amplify with the HafF and HafR primers. The remaining DNA samples all gave PCR products of the expected size. When the corresponding GC clamped primers were used for the amplification of the RT fragment, the plants collected from the coastal sites (Akatore Creek, Hooper's Inlet, Nugget Point, Pyramids, Sandymount and Taiaroa Head) and one inland site (Middlemarch) showed identical DGGE band profiles (Fig. 3, type 1). Two of the inland plants, Pisa Range 1 and Ida Range, shared a second unique DGGE band profile (Fig. 3, type 2). The two remaining plants collected from the Pisa Range showed band profiles that were different from each other and from the other two groups. The two specimens of M. chathamicus examined gave identical DGGE patterns (results not shown).Fig. 3.


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 various Melicytus species based on their ITS sequences and the DGGE band patterns of the RT fragments from M. alpinus. For M. alpinus, two predominant fragment patterns are distinguishable in the gel (designated type 1 (lanes 1–9) and type 2 (lanes 10–11)). 1: M. alpinus Akatore Creek 1; 2: M. alpinus Akatore Creek 2; 3: M. alpinus Hooper's Inlet; 4: M. alpinus Middlemarch; 5: M. alpinus Nugget Point 1; 6: M. alpinus Nugget Point 2; M. alpinus Pyramids 1; 8: M. alpinus Pyramids 2; 9: M. alpinus Taiaroa Head; 10: M. alpinus Ida Range; 11: M. alpinus Pisa Range 1; 12: M. alpinus Pisa Range 2; 13: M. alpinus Pisa Range 3.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

PLR008F3: Phylogenetic tree showing the relationships of various Melicytus species based on their ITS sequences and the DGGE band patterns of the RT fragments from M. alpinus. For M. alpinus, two predominant fragment patterns are distinguishable in the gel (designated type 1 (lanes 1–9) and type 2 (lanes 10–11)). 1: M. alpinus Akatore Creek 1; 2: M. alpinus Akatore Creek 2; 3: M. alpinus Hooper's Inlet; 4: M. alpinus Middlemarch; 5: M. alpinus Nugget Point 1; 6: M. alpinus Nugget Point 2; M. alpinus Pyramids 1; 8: M. alpinus Pyramids 2; 9: M. alpinus Taiaroa Head; 10: M. alpinus Ida Range; 11: M. alpinus Pisa Range 1; 12: M. alpinus Pisa Range 2; 13: M. alpinus Pisa Range 3.
Mentions: Analysis of badnavirus fragment patterns for the M. alpinus collections showed considerable variation within the species (Fig. 3). Plants identified in the field as M. alpinus collected from six coastal sites in eastern Otago (Akatore Creek, Hooper's Inlet, Nugget Point, Pyramids, Sandymount and Taiaroa Head) and from four inland sites (Swampy Summit, Middlemarch, Ida Range and Pisa Range) were subjected to PCR and DGGE analysis. DNA samples from the Swampy Summit plants (4/4) and Sandymount plants (2/2) did not amplify with the HafF and HafR primers. The remaining DNA samples all gave PCR products of the expected size. When the corresponding GC clamped primers were used for the amplification of the RT fragment, the plants collected from the coastal sites (Akatore Creek, Hooper's Inlet, Nugget Point, Pyramids, Sandymount and Taiaroa Head) and one inland site (Middlemarch) showed identical DGGE band profiles (Fig. 3, type 1). Two of the inland plants, Pisa Range 1 and Ida Range, shared a second unique DGGE band profile (Fig. 3, type 2). The two remaining plants collected from the Pisa Range showed band profiles that were different from each other and from the other two groups. The two specimens of M. chathamicus examined gave identical DGGE patterns (results not shown).Fig. 3.

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