The Sequence Polymorphism And Transcription Features Of Banana Bunchy Top Virus(BBTV) DNA-U3

Banana is one of the most important fruits in the world, as well as important food resources in developing countries. Banana bunchy top disease (BBTD) which caused by Banana bunchy top virus(BBTV) is one of the major diseases, leading to huge production and economic losses. BBTV, the pathogen, belongs to the genus Babuvirus family Nanaviridae. The genome of BBTV consists of six segments of single-stranded DNA of approximately1kb in length. With the exception of DNA-U3, all BBTV components contain a large open reading frame (ORF), encoding different functional proteins:Rep, CP, MP, Clink and NSP, respectively. DNA-U3from some isolates contains a small ORF and encodes a small protein with unknown functions.In order to better understand the diversity of DNA-U3, a survey of banana bunchy top symptom was conducted in13counties of Hainan province in2013. Bunchy top was a common phenomenon in wild banana production areas. However the bunchy top disease is limited in the artificial management field. Cloning and sequencing of43BBTV DNA-U3showed that two types of DNA-U3(homology with the Haikou-2DNA-U3or Haikou-4DNA-U3) were distributed in Hainan province. The DNA-U3has been shown as the high diverse component in our previous studies. Sequence analysis revealed that intra-genomic recombination in DNA-U3is a common phenomenon in Hainan BBTV population. Two restriction enzyme, Nde I and Mfi I, were used to identify intra-genomic recombination. This indicates that like other evolutionary processes including inter-genomic recombination, intra-genomic recombination among the genomic components of the same isolate may also have a significant contribution in the evolution of BBTV genome. To accommodate the changes in the BBTV geographical distribution, the two groups are proposed as the Southeast Asian group and the Pacific-Indian Oceans group. All43BBTV DNA-U3belonged to Southeast Asian group.The sequencing results of HK002sample DNA-U3, we also found that there is two different DNA-U3components in this plants. Sequencing showed that eight Haikou4DNA-U3(HM231314) and11Haikou2DNA-U3(HQ616075) were analyzed in19clones. To point out if two DNA-U3come from one strain or not, the DNA-N component was used to (the big difference between the two strain) do restriction analysis. The result showed that there are two DNA-U3in HK002sample. As our found, the two DNA-U3is just happening the one way recombinant:the sequence moved from Haikou2DNA-U3(HQ616075) to Haikou4DNA-U3(HM231314). Further analysis of the different recombination sites, but there is a recombination hotspot region. For measuring the rate of DNA-U3recombination, the enzyme digestion method was established of HK002clone. By restriction enzyme analysis,48Haikou2DNA-U3(HQ616075) and52Haikou4DNA-U3(HM231314) in100HK002DNA-U3clones. And17recombinant clones, the recombination rate was about17%.Eight different full-length sequence of BBTV were obtained by transcriptome sequencing and reads matching of HK014sample. The reads of DNA-U3(FJ463043) basically positioned within a period of about225nt sequence, but there are still some reads evenly matched other region on DNA-U3, suggesting that the transcription of DNA-U3described not only produces a single transcript of approximately200bp size, but also exists a longer transcript.5’and3’RACE (FJ463043) showed that a transcript length of DNA-U3was not terminate what we expect, sometimes continues to move forward through the transcription initiation site to produce a1226nt mRNA, even more. The presence of this phenomenon or what is the mechanism is still un-know to us that is need to be further studied.