Difference between revisions of "Mike N"
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Click [[Media: Floral_Timing.pptx]] for a PowerPoint summarizing what I have done, and briefly what I found. | Click [[Media: Floral_Timing.pptx]] for a PowerPoint summarizing what I have done, and briefly what I found. | ||
| − | The following is a complete list of what I found for the eleven genes I investigated. Genes are ordered in decending confidence, determined by the e-value of the results of the BLASTn | + | The following is a complete list of what I found for the eleven genes I investigated. Genes are ordered in decending confidence, determined by the e-value of the top hit from the results of the BLASTn (and also decending confidence for the top hits among scaffolds, for genes that had multiple good scaffold hits). The primers are listed in sequential order. |
== '''Crytochrome 1 (CRY1)''' == | == '''Crytochrome 1 (CRY1)''' == | ||
| Line 13: | Line 13: | ||
-'''Scaffold 000331''' 122,000-129,000 | -'''Scaffold 000331''' 122,000-129,000 | ||
| − | tc | + | (tc)x5 at 120,300 product size: 251bp forward primer: CATTTTGGGACAGAGGGAGTAG reverse primer: CAGTAACCAACATGCAAAAGGA |
-'''Scaffold 01561''' 18,500-23,800 | -'''Scaffold 01561''' 18,500-23,800 | ||
| − | ta | + | (ta)x5 at 11,000 product size: 291bp forward primer: TACCTTAAGGCTCCGTTTGTTT reverse primer: TCCATTTGTTTCGATGTACTGG |
| − | ga | + | (ga)x8 at 37,500 product size: 153bp forward primer: ATCTCCCTACGGTGGGATAAGT reverse primer: AACCTATCGATCCACTCCTTCA |
-'''Scaffold 00649''' 28,300-28,600 | -'''Scaffold 00649''' 28,300-28,600 | ||
| − | ga | + | (ga)x6 at 27,600 product size: 245bp forward primer: TTAATTTTGTCCCACCCAAGAC reverse primer: TGAGGGTTCAAAGGACAAAACT |
| − | tc | + | (tc)x5 at 30,800 product size: 162bp forward primer: CTCATTGTCAAACGCAGACTTC reverse primer: TGGTAGTCATCAGGATGGTTTG |
| Line 38: | Line 38: | ||
-'''Scaffold 00100''' 192,000-200,600 | -'''Scaffold 00100''' 192,000-200,600 | ||
| − | ct | + | (ct)x5 at 190,600 product size: 201bp forward primer: ATGATAAAACAATCACCAGCCC reverse primer: GCTTTCGCCTCTACGATCTTTA |
| − | ta | + | (ta)x5 at 207,900 product size: 225bp forward primer: TTTCGCTCAGTTATCTCTCTCTGA reverse primer: CCATCTTTAACTGCACAAACCA |
| Line 47: | Line 47: | ||
-'''Scaffold 00649''' 16,000-30,000 (Note this scaffold was also a hit for CRY1) | -'''Scaffold 00649''' 16,000-30,000 (Note this scaffold was also a hit for CRY1) | ||
| − | tc | + | (tc)x5 at 30,800 product size: 162bp forward primer: CTCATTGTCAAACGCAGACTTC reverse primer: TGGTAGTCATCAGGATGGTTTG |
-'''Scaffold 01561''' 20,000-21,000 (Note this scaffold was also a hit for CRY1) | -'''Scaffold 01561''' 20,000-21,000 (Note this scaffold was also a hit for CRY1) | ||
| − | ta | + | (ta)x5 at 11,000 product size: 291bp forward primer: TACCTTAAGGCTCCGTTTGTTT reverse primer: TCCATTTGTTTCGATGTACTGG |
| − | ga | + | (ga)x8 at 37,500 product size: 153bp forward primer: ATCTCCCTACGGTGGGATAAGT reverse primer: AACCTATCGATCCACTCCTTCA |
| Line 61: | Line 61: | ||
-'''Scaffold 00751''' 84,000-89,200 | -'''Scaffold 00751''' 84,000-89,200 | ||
| − | aga | + | (aga)x8 at 81,900 product size: 265bp forward primer: CCCGAAAATACCCTTTCTCTCT reverse primer: GGCAATTACCAATTACGTGTCA |
| − | ag | + | (ag)x10 at 92,400 product size: 262bp forward primer: AAGAGGGGTAGACCAAAATTGA reverse primer: AATTTCACTCCAACCAAGAAGG |
| Line 70: | Line 70: | ||
-'''Scaffold 01843''' 40,900-41,000 | -'''Scaffold 01843''' 40,900-41,000 | ||
| − | ac | + | (ac)x6 at 31,800 product size: 285bp forward primer: CCAAGATCCTTCCAAACTAACG reverse primer: TTCTTCTTCTTCTTCGTTTGCC |
| − | gaa | + | (gaa)x5 at 32,000 product size: 133bp forward primer: AGGGGTTAACAAAACATACCCC reverse primer: TCTCTGGTTCAATTTAGGGCTC |
| − | tc | + | (tc)x11 at 48,300 product size: 275bp forward primer: GAAACAGATGGCATGGTGAGTA reverse primer: CTCCAAAACCCTATGAAAGTGC |
| Line 81: | Line 81: | ||
-'''Scaffold 00752''' 17,000-24,800 | -'''Scaffold 00752''' 17,000-24,800 | ||
| − | ga | + | (ga)x6 at 14,800 product size: 277bp forward primer: CTCCAACTCTGAACTGATTCCC reverse primer: GAAACGCGTCCTTGATTATCTC |
-'''Scaffold 00111''' 154,000-162,000 | -'''Scaffold 00111''' 154,000-162,000 | ||
| − | ct | + | (ct)x9 at 144,800 product size: 164bp forward primer: GTGGAAAATGTAAAGACACGCA reverse primer: AAAGCTTTCTAACCTCCGATCC |
| − | at | + | (at)x5 at 165,400 product size: 300bp forward primer: CTTTCTTCCACTCAAGCCCTAA reverse primer: GAATCTTGTGCACCACACACTT |
| Line 95: | Line 95: | ||
-'''Scaffold 00079''' 69,000-69,200 | -'''Scaffold 00079''' 69,000-69,200 | ||
| − | ta | + | (ta)x6 at 61,500 product size: 217bp forward primer: GCTCTCTTTCTCCATGCCTTTA reverse primer: CCCCCAATAACCCTCATTTATT |
| − | aat | + | (aat)x6 at 69,900 product size: 292bp forward primer: GTTTGACATATCGAGCTTGCAC reverse primer: TTGGTTGTAGAGGAGTGGGATT |
-'''Scaffold 00651''' 19,900-20,100 | -'''Scaffold 00651''' 19,900-20,100 | ||
| − | ac | + | (ac)x6 at 14,200 product size: 192bp forward primer: AACTCTTAAAAAGGGACGGAGG reverse primer: CTTTCCCGGTTTCTTGTTTGTA |
| − | ag | + | (ag)x6 at 22,300 product size: 276bp forward primer: CGTCTTCCCAAAGAGCTTAATG reverse primer: TTCTAAGGCCACAAAACCAACT |
-'''Scaffold 01102''' 51,500-51,700 | -'''Scaffold 01102''' 51,500-51,700 | ||
| − | tg | + | (tg)x7 at 45,400 product size: 253bp forward primer: AGGATGAGTGAAAGAGCGTACC reverse primer: CCAGATTTTTCAGAGAATTGGC |
| − | ga | + | (ga)x5 at 66,700 product size: 129bp forward primer: ACCATATTATTGGACCCAGGTG reverse primer: ATAGCACAAACTCCCAAAATGG |
-'''Scaffold 00292''' 195,200-195,300 | -'''Scaffold 00292''' 195,200-195,300 | ||
| − | ac | + | (ac)x8 at 179,200 product size: 282bp forward primer: GATCCATGTTGTTGTGGATTTG reverse primer: TTCTCGAAGATCATTGGAGGTT |
| − | ct | + | (ct)x6 at 197,600 product size: 299bp forward primer: AGCCATTTGAGTTTTCAGGTGT reverse primer: TCACCCTCCACTAGGACTTGTT |
| Line 122: | Line 122: | ||
-'''Scaffold 00988''' 71,100-71,200 | -'''Scaffold 00988''' 71,100-71,200 | ||
| − | tc | + | (tc)x5 at 70,500 product size: 221bp forward primer: AAGAGCAAGAGACATGACGGAT reverse primer: GTTTTTGGGTCTTGATGGGATA |
| − | tc | + | (tc)x7 at 71,200 product size: 198bp forward primer: CAACCTCAGCATCACAGAGAAG reverse primer: GGGGAAGAATTGAACAACAGAG |
| Line 131: | Line 131: | ||
-'''Scaffold 00357''' 56,800-58,200 | -'''Scaffold 00357''' 56,800-58,200 | ||
| − | ga | + | (ga)x6 at 53,400 product size: 250bp forward primer: TCATTACTCCTTTGCCCATTCT reverse primer: CTTTCTCGGGTGATTCAATGAT |
| − | ag | + | (ag)x5 at 54,300 product size: 130bp forward primer: GATTTCTGGATGGATTCTCAGC reverse primer: ATCCCAAATACAAAACCCACTC |
Revision as of 16:54, 15 March 2012
In order to investigate the timing of blooming in blueberries, I found a paper discussing floral timing in Arabidopsis (Amasino, Richard. (2010) Seasonal and Developmental Timing of Flowering. The Plant Journal, 61, 1001-1013.). In this paper, I found a figure describing the known major genes in the blooming pathway (see below, edited).
To address some of these major genes I first found their sequences in Arabidopsis. Then, using these sequences as queries, I ran a BLASTn against the blueberry 454 scaffolds on the Genome Database site for blueberry we were given access to ([1]). If the matches were relatively weak, a tBLASTx was also run between the ortholog and database, and the top hits were compared to confirm similarity. I then submitted the scaffold(s) that best match(ed) to the 'SSR finder tool' also on the Genome Database site ([2]). The primers were generated by the 'SSR finder tool' and represent those given that were closest to the location of the orthologs, either bi- or tri- nucleotide repeats with at least 5 repeating units, and that produce a product ranging from 100 to 700 base pairs in length.
Click Media: Floral_Timing.pptx for a PowerPoint summarizing what I have done, and briefly what I found.
The following is a complete list of what I found for the eleven genes I investigated. Genes are ordered in decending confidence, determined by the e-value of the top hit from the results of the BLASTn (and also decending confidence for the top hits among scaffolds, for genes that had multiple good scaffold hits). The primers are listed in sequential order.
Contents
Crytochrome 1 (CRY1)
-Scaffold 000331 122,000-129,000
(tc)x5 at 120,300 product size: 251bp forward primer: CATTTTGGGACAGAGGGAGTAG reverse primer: CAGTAACCAACATGCAAAAGGA
-Scaffold 01561 18,500-23,800
(ta)x5 at 11,000 product size: 291bp forward primer: TACCTTAAGGCTCCGTTTGTTT reverse primer: TCCATTTGTTTCGATGTACTGG
(ga)x8 at 37,500 product size: 153bp forward primer: ATCTCCCTACGGTGGGATAAGT reverse primer: AACCTATCGATCCACTCCTTCA
-Scaffold 00649 28,300-28,600
(ga)x6 at 27,600 product size: 245bp forward primer: TTAATTTTGTCCCACCCAAGAC reverse primer: TGAGGGTTCAAAGGACAAAACT
(tc)x5 at 30,800 product size: 162bp forward primer: CTCATTGTCAAACGCAGACTTC reverse primer: TGGTAGTCATCAGGATGGTTTG
Phytochrome A (PHYA)
-Scaffold 03861' 3,400-5,800
Unfortunately, the scaffold length is only 7,403bp long, so no adequate SSRs were detected and appropriate primers could not be found.
Gigantea (GI)
-Scaffold 00100 192,000-200,600
(ct)x5 at 190,600 product size: 201bp forward primer: ATGATAAAACAATCACCAGCCC reverse primer: GCTTTCGCCTCTACGATCTTTA
(ta)x5 at 207,900 product size: 225bp forward primer: TTTCGCTCAGTTATCTCTCTCTGA reverse primer: CCATCTTTAACTGCACAAACCA
Cryptochrome 2 (CRY2)
-Scaffold 00649 16,000-30,000 (Note this scaffold was also a hit for CRY1)
(tc)x5 at 30,800 product size: 162bp forward primer: CTCATTGTCAAACGCAGACTTC reverse primer: TGGTAGTCATCAGGATGGTTTG
-Scaffold 01561 20,000-21,000 (Note this scaffold was also a hit for CRY1)
(ta)x5 at 11,000 product size: 291bp forward primer: TACCTTAAGGCTCCGTTTGTTT reverse primer: TCCATTTGTTTCGATGTACTGG
(ga)x8 at 37,500 product size: 153bp forward primer: ATCTCCCTACGGTGGGATAAGT reverse primer: AACCTATCGATCCACTCCTTCA
Phytochrome B (PHYB)
-Scaffold 00751 84,000-89,200
(aga)x8 at 81,900 product size: 265bp forward primer: CCCGAAAATACCCTTTCTCTCT reverse primer: GGCAATTACCAATTACGTGTCA
(ag)x10 at 92,400 product size: 262bp forward primer: AAGAGGGGTAGACCAAAATTGA reverse primer: AATTTCACTCCAACCAAGAAGG
Constans (CO)
-Scaffold 01843 40,900-41,000
(ac)x6 at 31,800 product size: 285bp forward primer: CCAAGATCCTTCCAAACTAACG reverse primer: TTCTTCTTCTTCTTCGTTTGCC
(gaa)x5 at 32,000 product size: 133bp forward primer: AGGGGTTAACAAAACATACCCC reverse primer: TCTCTGGTTCAATTTAGGGCTC
(tc)x11 at 48,300 product size: 275bp forward primer: GAAACAGATGGCATGGTGAGTA reverse primer: CTCCAAAACCCTATGAAAGTGC
Constitutive Photomorphogenisis 1 (COP1)
-Scaffold 00752 17,000-24,800
(ga)x6 at 14,800 product size: 277bp forward primer: CTCCAACTCTGAACTGATTCCC reverse primer: GAAACGCGTCCTTGATTATCTC
-Scaffold 00111 154,000-162,000
(ct)x9 at 144,800 product size: 164bp forward primer: GTGGAAAATGTAAAGACACGCA reverse primer: AAAGCTTTCTAACCTCCGATCC
(at)x5 at 165,400 product size: 300bp forward primer: CTTTCTTCCACTCAAGCCCTAA reverse primer: GAATCTTGTGCACCACACACTT
Cycling DOF Factor (CDF)
-Scaffold 00079 69,000-69,200
(ta)x6 at 61,500 product size: 217bp forward primer: GCTCTCTTTCTCCATGCCTTTA reverse primer: CCCCCAATAACCCTCATTTATT
(aat)x6 at 69,900 product size: 292bp forward primer: GTTTGACATATCGAGCTTGCAC reverse primer: TTGGTTGTAGAGGAGTGGGATT
-Scaffold 00651 19,900-20,100
(ac)x6 at 14,200 product size: 192bp forward primer: AACTCTTAAAAAGGGACGGAGG reverse primer: CTTTCCCGGTTTCTTGTTTGTA
(ag)x6 at 22,300 product size: 276bp forward primer: CGTCTTCCCAAAGAGCTTAATG reverse primer: TTCTAAGGCCACAAAACCAACT
-Scaffold 01102 51,500-51,700
(tg)x7 at 45,400 product size: 253bp forward primer: AGGATGAGTGAAAGAGCGTACC reverse primer: CCAGATTTTTCAGAGAATTGGC
(ga)x5 at 66,700 product size: 129bp forward primer: ACCATATTATTGGACCCAGGTG reverse primer: ATAGCACAAACTCCCAAAATGG
-Scaffold 00292 195,200-195,300
(ac)x8 at 179,200 product size: 282bp forward primer: GATCCATGTTGTTGTGGATTTG reverse primer: TTCTCGAAGATCATTGGAGGTT
(ct)x6 at 197,600 product size: 299bp forward primer: AGCCATTTGAGTTTTCAGGTGT reverse primer: TCACCCTCCACTAGGACTTGTT
Apetala 1 (AP1)
-Scaffold 00988 71,100-71,200
(tc)x5 at 70,500 product size: 221bp forward primer: AAGAGCAAGAGACATGACGGAT reverse primer: GTTTTTGGGTCTTGATGGGATA
(tc)x7 at 71,200 product size: 198bp forward primer: CAACCTCAGCATCACAGAGAAG reverse primer: GGGGAAGAATTGAACAACAGAG
Flowering Locus T (FT)
-Scaffold 00357 56,800-58,200
(ga)x6 at 53,400 product size: 250bp forward primer: TCATTACTCCTTTGCCCATTCT reverse primer: CTTTCTCGGGTGATTCAATGAT
(ag)x5 at 54,300 product size: 130bp forward primer: GATTTCTGGATGGATTCTCAGC reverse primer: ATCCCAAATACAAAACCCACTC
Leafy (LFY)
No ortholog could be found in Vaccinium when a BLASTn was run in the 454 scaffold database when the Arabidopsis sequence was used as the query.
