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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

(A) Denaturing gradient gel electrophoresis analysis of RT fragments from different collections of M. ramiflorus from different geographic localities. 1: Marker: Otago Peninsula (Mel1); 2: Evansdale Glen; 3: Akatore; 4: Karamea (West Coast); 5: Nichols Creek (Dunedin); 6: Rangitoto Island (Auckland); 7: Otago Peninsula (OP-1); 8: Otago Peninsula (OP-2); 9: Otago Peninsula (OP-3); 10: Otago Peninsula (OP-4); 11: Waitati (Wa1); 12: Waitati (Wa2); 13: Waitati (Wa3); 14: Waitati (Wa4); 15: Waitati (Wa5); 16: Waitati (Wa6). (B) Denaturing gradient gel electrophoresis of RT fragments from different collections of M. ramiflorus from one maternal and six progeny plants. The parent plant contained a complete set of fragments (labelled groups A, B and C). Progeny P1, P3 and P5 also contained the complete set, whereas progeny P2 contained only group C, progeny P4 contained groups B and C, and progeny P6 contained groups A and B. 1: Waitati (Mel-3) female parent; 2: Marker: Waitati (Mel-4); 3–8: Progeny plants: 3: Waitati (P1); 4: Waitati (P2); 5: Waitati (P3); 6: Waitati (P4); 7: Waitati (P5); 8: Waitati (P6).
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PLR008F2: (A) Denaturing gradient gel electrophoresis analysis of RT fragments from different collections of M. ramiflorus from different geographic localities. 1: Marker: Otago Peninsula (Mel1); 2: Evansdale Glen; 3: Akatore; 4: Karamea (West Coast); 5: Nichols Creek (Dunedin); 6: Rangitoto Island (Auckland); 7: Otago Peninsula (OP-1); 8: Otago Peninsula (OP-2); 9: Otago Peninsula (OP-3); 10: Otago Peninsula (OP-4); 11: Waitati (Wa1); 12: Waitati (Wa2); 13: Waitati (Wa3); 14: Waitati (Wa4); 15: Waitati (Wa5); 16: Waitati (Wa6). (B) Denaturing gradient gel electrophoresis of RT fragments from different collections of M. ramiflorus from one maternal and six progeny plants. The parent plant contained a complete set of fragments (labelled groups A, B and C). Progeny P1, P3 and P5 also contained the complete set, whereas progeny P2 contained only group C, progeny P4 contained groups B and C, and progeny P6 contained groups A and B. 1: Waitati (Mel-3) female parent; 2: Marker: Waitati (Mel-4); 3–8: Progeny plants: 3: Waitati (P1); 4: Waitati (P2); 5: Waitati (P3); 6: Waitati (P4); 7: Waitati (P5); 8: Waitati (P6).

Mentions: The 530 bp RT fragment from M. ramiflorus was resolved into >25 distinct bands by DGGE (Fig. 2A). Overall, band patterns from different individuals were very similar in appearance and showed many bands in common. However, differences were apparent as some individuals contained additional bands or conversely lacked other bands. For example, the DGGE band pattern from a plant collected from Karamea (lane 4) was similar though distinct from eastern coastal Otago plants (lanes 2, 3) although fewer bands were observed overall. A plant from Rangitoto Island, Auckland (lane 6) showed three distinctive strong bands in the lower part of the gel but otherwise was similar to the remaining collections. Four plants collected from the same locality on the Otago Peninsula (lanes 7, 8, 9, 10) showed individual differences but contained many common bands. There were no consistent differences in the band patterns from plants collected from the southern part of the South Island (Dunedin), the northern part of the South Island (Karamea) and the northern part of the North Island (Auckland) that could be attributed to geographic location.Fig. 2.


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

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

(A) Denaturing gradient gel electrophoresis analysis of RT fragments from different collections of M. ramiflorus from different geographic localities. 1: Marker: Otago Peninsula (Mel1); 2: Evansdale Glen; 3: Akatore; 4: Karamea (West Coast); 5: Nichols Creek (Dunedin); 6: Rangitoto Island (Auckland); 7: Otago Peninsula (OP-1); 8: Otago Peninsula (OP-2); 9: Otago Peninsula (OP-3); 10: Otago Peninsula (OP-4); 11: Waitati (Wa1); 12: Waitati (Wa2); 13: Waitati (Wa3); 14: Waitati (Wa4); 15: Waitati (Wa5); 16: Waitati (Wa6). (B) Denaturing gradient gel electrophoresis of RT fragments from different collections of M. ramiflorus from one maternal and six progeny plants. The parent plant contained a complete set of fragments (labelled groups A, B and C). Progeny P1, P3 and P5 also contained the complete set, whereas progeny P2 contained only group C, progeny P4 contained groups B and C, and progeny P6 contained groups A and B. 1: Waitati (Mel-3) female parent; 2: Marker: Waitati (Mel-4); 3–8: Progeny plants: 3: Waitati (P1); 4: Waitati (P2); 5: Waitati (P3); 6: Waitati (P4); 7: Waitati (P5); 8: Waitati (P6).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

PLR008F2: (A) Denaturing gradient gel electrophoresis analysis of RT fragments from different collections of M. ramiflorus from different geographic localities. 1: Marker: Otago Peninsula (Mel1); 2: Evansdale Glen; 3: Akatore; 4: Karamea (West Coast); 5: Nichols Creek (Dunedin); 6: Rangitoto Island (Auckland); 7: Otago Peninsula (OP-1); 8: Otago Peninsula (OP-2); 9: Otago Peninsula (OP-3); 10: Otago Peninsula (OP-4); 11: Waitati (Wa1); 12: Waitati (Wa2); 13: Waitati (Wa3); 14: Waitati (Wa4); 15: Waitati (Wa5); 16: Waitati (Wa6). (B) Denaturing gradient gel electrophoresis of RT fragments from different collections of M. ramiflorus from one maternal and six progeny plants. The parent plant contained a complete set of fragments (labelled groups A, B and C). Progeny P1, P3 and P5 also contained the complete set, whereas progeny P2 contained only group C, progeny P4 contained groups B and C, and progeny P6 contained groups A and B. 1: Waitati (Mel-3) female parent; 2: Marker: Waitati (Mel-4); 3–8: Progeny plants: 3: Waitati (P1); 4: Waitati (P2); 5: Waitati (P3); 6: Waitati (P4); 7: Waitati (P5); 8: Waitati (P6).
Mentions: The 530 bp RT fragment from M. ramiflorus was resolved into >25 distinct bands by DGGE (Fig. 2A). Overall, band patterns from different individuals were very similar in appearance and showed many bands in common. However, differences were apparent as some individuals contained additional bands or conversely lacked other bands. For example, the DGGE band pattern from a plant collected from Karamea (lane 4) was similar though distinct from eastern coastal Otago plants (lanes 2, 3) although fewer bands were observed overall. A plant from Rangitoto Island, Auckland (lane 6) showed three distinctive strong bands in the lower part of the gel but otherwise was similar to the remaining collections. Four plants collected from the same locality on the Otago Peninsula (lanes 7, 8, 9, 10) showed individual differences but contained many common bands. There were no consistent differences in the band patterns from plants collected from the southern part of the South Island (Dunedin), the northern part of the South Island (Karamea) and the northern part of the North Island (Auckland) that could be attributed to geographic location.Fig. 2.

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