Luận văn : XÂY DỰNG QUY TRÌNH PHÁT HIỆN VIRUS PMWaV-1 GÂY BỆNH HÉO ĐỎ ĐẦU LÁ (Mealybug wilt) TRÊN CÂY DỨA CAYENNE BẰNG PHƯƠNG PHÁP RT-PCR part 7 doc
Bạn đang xem bản rút gọn của tài liệu. Xem và tải ngay bản đầy đủ của tài liệu tại đây (217.24 KB, 6 trang )
61
24. Sether D.M., Hu J.S., 2002. Closterovirus infection and mealybug
exposure are necessary for the development of mealybug wilt of pineapple
disease. Phytopathology 92: 928 – 935.
25. Ullman D.E., German T.L., Gunashinge U.B., and Ebesu R.H., 1989.
Serology of a closteroviruslike particle associated with mealybug wilt of
pineapple. Phytopathology 79: 1341 - 1345.
26. Wakman W., Teakle D., Thomas J.E., and Dietzgen R.G., 1995. Presence
of closterolike – virus and a bacilliform virus in pineapple plants in
Queensland. Aust. J. Agric. Sci. 46: 947 – 958.
CÁC TRANG WEB
t-star/mealybug.htm
/>
/>
62
PHỤ LỤC 1
Các cấu trúc thứ cấp của cặp primer 225, 226 kiểm tra bằng phần mềm
Oligo Analyzer
1. Các cấu trúc kẹp tóc (hairpin)
Primer
Delta G
(kcal/mole)
Base
pair
Cấu trúc hairpin
225 -0,14 2 ACAGGAAGG
|| :A
CACTCACAAC
226 -0,21 2 CGCACAAA
|| ::C
CTAACGAACTT
2. Các cấu trúc hetero dimer
Delta G
(kcal/mole)
Base
pair
Cấu trúc hetero dimer
-5.12
-1,94
-1,6
-1,6
-1,57
-1,57
-1,57
4
2
2
2
2
2
2
5' ACAGGAAGGACAACACTCAC
: ||||
3' CTAACGAACTTCAAACACGC
5' ACAGGAAGGACAACACTCAC
|| :
3' CTAACGAACTTCAAACACGC
5' ACAGGAAGGACAACACTCAC
|| : :
3' CTAACGAACTTCAAACACGC
5' ACAGGAAGGACAACACTCAC
: ||
3' CTAACGAACTTCAAACACGC
5' ACAGGAAGGACAACACTCAC
: || :
3' CTAACGAACTTCAAACACGC
5' ACAGGAAGGACAACACTCAC
|| : : :
3' CTAACGAACTTCAAACACGC
5' ACAGGAAGGACAACACTCAC
|| : :
3' CTAACGAACTTCAAACACGC
63
3. Các cấu trúc homo dimer
Primer
Delta G
(kcal/mole)
Base
pair
Cấu trúc homo dimer
225
-1.6
-1.6
-1,57
-1,57
2
2
2
2
5' ACAGGAAGGACAACACTCAC
|| : : ::
3' CACTCACAACAGGAAGGACA
5' ACAGGAAGGACAACACTCAC
: || :: :
3' CACTCACAACAGGAAGGACA
5' ACAGGAAGGACAACACTCAC
|| : : ::
3' CACTCACAACAGGAAGGACA
5' ACAGGAAGGACAACACTCAC
|| ::
3' CACTCACAACAGGAAGGACA
226
-3.54
-3.54
-3.14
-3.14
-3,14
-1,94
2
2
2
2
2
2
5' CGCACAAACTTCAAGCAATC
||
3' CTAACGAACTTCAAACACGC
5' CGCACAAACTTCAAGCAATC
||| :::
3' CTAACGAACTTCAAACACGC
5' CGCACAAACTTCAAGCAATC
||
3' CTAACGAACTTCAAACACGC
5' CGCACAAACTTCAAGCAATC
|| :: :: ::
3' CTAACGAACTTCAAACACGC
5' CGCACAAACTTCAAGCAATC
||
3' CTAACGAACTTCAAACACGC
5' CGCACAAACTTCAAGCAATC
|| ::
3' CTAACGAACTTCAAACACGC
64
-1,94
-1,47
2
2
5' CGCACAAACTTCAAGCAATC
|| ::
3' CTAACGAACTTCAAACACGC
5' CGCACAAACTTCAAGCAATC
||
3' CTAACGAACTTCAAACACGC
PHỤ LỤC 2
Kết quả BLAST của cặp primer 225, 226
Score E
Sequences producing significant alignments: (Bits) Value
gi|18253957|gb|AF414119.1|AF414119
Pineapple mealybug wilt-as 40.1 0.48
gi|22227|emb|X63205.1|ZMCAB48
Zea mays cab48 gene for chlorop 36.2 7.5
gi|62630081|gb|AC122311.6|
Mus musculus BAC clone RP23-298B23 36.2 7.5
> gi|18253957|gb|AF414119.1|AF414119 Pineapple mealybug wilt-associated virus-
1 methyltransferase/helicase protein gene, partial sequence; RNA-dependent RNA
polymerase (RdRp), small hydrophobic protein, heat shock protein 70 (hsp70), p46,
and putative coat protein genes, complete cds. Length=10038
Score = 40.1 bits (20), Expect = 0.48
Identities = 20/20 (100%), Gaps = 0/20 (0%)
Strand=Plus/Plus
Primer 225 ACAGGAAGGACAACACTCAC 20
||||||||||||||||||||
Sbjct 5958 ACAGGAAGGACAACACTCAC 5977
Score = 40.1 bits (20), Expect = 0.48
Identities = 20/20 (100%), Gaps = 0/20 (0%)
Strand=Plus/Minus
Primer 226 CGCACAAACTTCAAGCAATC 59
||||||||||||||||||||
Sbjct 6547 CGCACAAACTTCAAGCAATC 6528
> gi|22227|emb|X63205.1|ZMCAB48 Zea mays cab48 gene for chlorophyll a/b binding
protein precursor. Length=2780
Score = 36.2 bits (18), Expect = 7.5
Identities = 18/18 (100%), Gaps = 0/18 (0%)
Strand=Plus/Plus
Primer 225 ACAGGAAGGACAACACTC 18
||||||||||||||||||
Sbjct 781 ACAGGAAGGACAACACTC 798
65
> gi|62630081|gb|AC122311.6| Mus musculus BAC clone RP23-298B23 from
chromosome 6, complete sequence. Length=209435
Score = 36.2 bits (18), Expect = 7.5
Identities = 18/18 (100%), Gaps = 0/18 (0%)
Strand=Plus/Minus
Primer 226 CACAAACTTCAAGCAATC 59
||||||||||||||||||
Sbjct 49897 CACAAACTTCAAGCAATC 49880
PHỤ LỤC 3
Kết quả BLAST của trình tự D1, D2.
Score E
Sequences producing significant alignments: (Bits) Value
gi|18253957|gb|AF414119.1|AF414119
Pineapple mealybug wilt-as 969 0.0
gi|8977608|emb|AL137017.9|
Human DNA sequence from clone RP11 44.1 0.41
gi|34495171|gb|AC140307.3|
Mus musculus BAC clone RP23-389D15 40.1 6.4
gi|62659432|ref|XM_579802.1|
PREDICTED: Rattus norvegicus LOC498 40.1 6.4
gi|15487179|emb|AL589706.13|
Human DNA sequence from clone RP 40.1 6.4
gi|19068404|emb|AL391737.2|CNS06C8G
chromosome I of strain GB 40.1 6.4
gi|61656697|emb|BX088713.8|
Zebrafish DNA sequence from clone 40.1 6.4
gi|52627220|gb|AC097087.13|
Rattus norvegicus BAC CH230-140P 40.1 6.4
gi|20334517|gb|AC106726.3|
Homo sapiens 3 BAC RP11-450I19 (Ro 40.1 6.4
gi|26108544|gb|AE016762.1|
Escherichia coli CFT073 section 8 of 40.1 6.4
gi|146881|gb|J01652.1|ECOMOTAB
E. coli mocha promoter, motA a 40.1 6.4
gi|48994873|gb|U00096.2|
Escherichia coli K-12 MG1655 complete g 40.1 6.4
gi|47118301|dbj|BA000007.2| Escherichia coli O157:H7 DNA, comple 40.1 6.4
gi|1736542|dbj|D90831.1|
E.coli genomic DNA, Kohara clone #339(4 40.1 6.4
>
gi|18253957|gb|AF414119.1|AF414119 Pineapple mealybug wilt-associated
virus-1 methyltransferase/helicase protein gene, partial sequence; RNA-
dependent RNA polymerase (RdRp), small hydrophobic protein, heat shock
protein 70 (hsp70), p46, and putative coat protein genes, omplete cds.
Length=10038
Score = 969 bits (489), Expect = 0.0
Identities = 510/517 (98%), Gaps = 0/517 (0%)
Strand=Plus/Plus
Query 31 TTATCGTGATATAAAAAGGTATTTCGGACTCAACAAGTTCAACAAAGATGTGTATCTCGA 90
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 6019 TTATCGTGATATAAAAAGGTATTTCGGACTCAACAAGTTCAACAAAGATGTGTATCTCGA 6078
Query 91 TAAATTGAAACCCACAATCGAGGTAGTGGTTGACGACTGGGGTTGTTCTATAGGACCAGT 150
|||||||||||||||||||||||||||| ||||||||||||||||| |||||||||||||
Sbjct 6079 TAAATTGAAACCCACAATCGAGGTAGTGATTGACGACTGGGGTTGTCCTATAGGACCAGT 6138
Query 151 AGACGGTGCGAGAGGGAAAGCCAAATCAGTTCTCACTTTAGCCTCTGATTTTATAACGGG 210
|||||||||| | |||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 6139 AGACGGTGCGCGCGGGAAAGCCAAATCAGTTCTCACTTTAGCCTCTGATTTTATAACGGG 6198
Query 211 ATTGGTACAACTAGCGATCAAGATGACGAATCAACAAGTATCTGTGTCTGTTTGTTCAGT 270
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 6199 ATTGGTACAACTAGCGATCAAGATGACGAATCAACAAGTATCTGTGTCTGTTTGTTCAGT 6258
Query 271 ACCAGCAGCTTACAATTCTTATCAAAGGGGTTTTATTTTTGAAAGTTGTAAGTTGAGCTC 330
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 6259 ACCAGCAGCTTACAATTCTTATCAAAGGGGTTTTATTTTTGAAAGTTGTAAGTTGAGCTC 6318
66
Query 331 TATAAATGTGCAGGCGGTAGTAAACGAACCGACCGCAGCTGGATTGAGTGCTTTCATAAC 390
|||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 6319 TATAGATGTGCAGGCGGTAGTAAACGAACCGACCGCAGCTGGATTGAGTGCTTTCATAAC 6378
Query 391 TACCCCGAAAGCTTCTGTGAATTATTTGTTAGTCTACGATTTCGGAGGAGGCACTTTTGA 450
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 6379 TACCCCGAAAGCTTCTGTGAATTATTTGTTAGTCTACGATTTCGGAGGAGGCACTTTTGA 6438
Query 451 TAGTTCCTTACTCGTGGTTGGGCCTGCGTACGTGGGAGTACTGGATTCGATGGGAGATAA 510
|||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct 6439 TAGTTCCTTACTCGTGGTTGGGGGTGCGTACGTGGGAGTACTGGATTCGATGGGAGATAA 6498
Query 511 CTATCTGGGAGGCAGGGACGTAGATAACAGATTGCTT 547
|||||||||||||||||||||||||||||||||||||
Sbjct 6499 CTATCTGGGAGGCAGGGACGTAGATAACAGATTGCTT 6535
>
gi|8977608|emb|AL137017.9| Human DNA sequence from clone RP11-120J1 on
chromosome 9 Contains the 3' end of a novel gene and a CpG island,
complete sequence. Length=167585
Score = 44.1 bits (22), Expect = 0.41
Identities = 28/30 (93%), Gaps = 0/30 (0%)
Strand=Plus/Plus
Query 250 ATCTGTGTCTGTTTGTTCAGTACCAGCAGC 279
||||||||||||| |||||||||||||||
Sbjct 31275 ATCTGTGTCTGTTACTTCAGTACCAGCAGC 31304
>
gi|34495171|gb|AC140307.3| Mus musculus BAC clone RP23-389D15 from
chromosome 19, complete sequence. Length=187731
Score = 40.1 bits (20), Expect = 6.4
Identities = 20/20 (100%), Gaps = 0/20 (0%)
Strand=Plus/Plus
Query 511 CTATCTGGGAGGCAGGGACG 530
||||||||||||||||||||
Sbjct 120588 CTATCTGGGAGGCAGGGACG 120607
……………
……………
……………
