Difference between revisions of "Vargula tsujii"

Revision as of 15:04, 13 December 2011

Project History

We conducted 454 sequencing on bodies minus eyes. The specimens were collected from Catalina Island, with specific data available on the phylogeny website.

I've made a galaxy history to assemble the transcriptome and look for luciferase genes [1]

There are 8 isotigs retrieved with an E-value of 0.001, when blasting the transcriptome with Vargula hilgendorfii luciferase. When blasted back to GenBank, all 8 of these have strong similarity to known ostracod luciferases.

These luciferase genes are also similar to kielin/crossveinless, which is involved in development.

There is also similarity to vitellogenein, through the VWD similarity.

Project Notes and Ideas

An interesting result is that a truncated luciferase from Vargula hilgendorfii produces bioluminescence, suggesting that one VWD domain is sufficient to catalyze the light reaction. Maeda 1996.

Project Progress

Vargular tsujii consensus sequence: GCAGTCAGTGTCTTCAGTGATCAGTCGAGAAACGAAACGTGATAATGTGGTTAMAAAAMTTATTWATCTTAGCAGTAGGGATCTGCTTTTGTGCAGCTCAAGATTGTTATGAATCAACATGGGCTTCGAATGATTATCCATCTTCATGTGAGGCTCTAAACGGAAGATGTGTAGACTCTGCGTGCGGCAGCTGTGACGAGGTTCTGTTTGGTGATGGATTGTGTGAAAATGCAGGAGGAGCGTCTCCCAAGTGCTGTAGAGATTGCCCAGAAATCGTCAGATGCAGAGCTTCAGCAGCTGGATACTTCCATACATTCTATGGGCAGAGATTCAATCTCCAGGTACCAGGAACCTATCTCTTGAGTGAAGACTGCGTGGGAGGACTATGGTCTCTATACGTTAACCTGGCGAATATTGAAGGAGAGAAGGGAGCAGTTTTGGATTCCGTCAAGATGGTTGTTGGAGACGTAACTGTCGATATTAAACAGAAAGTTGGAGCTGTTACAGTAAATGGAGGTTCCGTTGAAATCGACAGCAA:CCCGTTCTCTATCGGTGACGTCACYATTGCCATCGTACGCACTCCTAACTTTGACGTCTCCGTCATCGAGTTCCTTAAGCTTGTTACATTCGATATCTTACAAGGCAGAGCTTTCAGACTTGCTCCAGATTTCTTATACGCAGACAGGACCTGTGGTTTATGTGGAGTCATGTCCGATGAACCTACTGATTTTATTGACAATCCAGATCAGCTTGCAATCCARGACCAAATGAACCAGGATGTAGACGGCTGCCCACTCTCTGGAAATCCTTCTGACGTCGAATATTGCSTGAATAAGATGCAGCCATATAAGGACGGGTGTGTTAACAAGAACGATGTCCACTTCGGAACCTACCTKTACGCATGCGCACTGGCYTACTGCATGGGCGGMGACGACAGAGTGGAGGATGTTATCTTTGAATACGCTGAAGCCTGCGTTGAACCCATCGGTAGAGCAACCTGCGTCATGAATGGACACACATACTACGATACMTTCGACAAAACAAGTTATCAGTTCCAGGCACCTTGCAAGGTTCTATTYGCCAAAGACTGTACAGATGACGATTGGGAAGTAACCATTACCCATAAAGCAGTTGGAGAATATACTGAAGTAGAGAAGGTCACCGTCCGGTATTTCCAAACCTTGATTGACCTGATAKCGGAGACTAAGAAAGTTTTCGTTAATGGATCGGAAGTGAGCGTCCCTTACAACTATGGAGATACATCTATATACATGTATGATAACTTAATAACCACAGCAGTTCTACCAGGAGCMGTGGTGGTGAAGTACAACTTCGAGCAGATGTTGGCTCTACACATCAGAGATCCATATGAAGCAGACAGCTGTGGTCTGTGTGGTATCTGGGATTTGGATAAATCTAATGAGGGTCCTGATACCCAGTATGTAGATTGTGAACCAACTCCCAACCCTCCAACATGTACTGCTGACAAAGAGGCTGAAGCTAGAGAACTATGTCAGAATATGTTCCCTGCTTCTCTCGACGACGTATGTAACATCTGCTACAAGGCCGACCGTGTTGAGCGTTGCATGTATGAGTATTGTCTTGGTGGTATGGAAGGCTTCTGTCAACAYGCTGGKACCGTCATCGATGAATGCTTCGTGAGACAYGGAGACGATCTACAGTATCCCCCTCAGTGTAAATAAGACGCCTGAGTGAGCTGTAGCAACTACACTATGGTCCATTGAGCATAAAAATGTGTAYTYCTTAAATWTTATAGTTGAGAAGAATGTTGCTATATACATAAACACGACGTAGCATTCAATGTTACTGATATATAAATTGTTATTYAAAATAWATGTATTGATAATATTATATAATAAAGCATTTTGAAGCAAAAAAGAAAAAAG

Primers that sit in gene:

1F- GGGCTTCGAATGATTATCCA

6R- AGCCAACATCTGCTCGAAGT

Primers that amplify the entire fragment:

5UTR FOR- ATCAGTCGAGAAACGAAACGTGATA

3UTR REV- ATAGTGTAGTTGCTACAGCTCACTCA