search and characterization of genomic elements of interest in the zebra mussel's genome
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Search and characterization of genomic elements of interest in the zebra mussel's genomeTRANSCRIPT
University of GironaScience Faculty
Genetics Department
Search and characterization of genomic elements of interest in the
zebra mussel’s genome (Dreissena polymorpha)
Isaac Noguera GuixàTutor: Dr. Núria Sanz
Final Project of Biology Degree2012 - 2013 term
01/07/2013
Source: Dean Messer, Department of water recurses, West Sacramento
Introductiono 100 of the World's Worst Invasive Alien Species in the Global Invasive Species Database
o Background of the research:
Colonization routes and contamination levels in invaded waters.
Source: Steve Wells, Center for Lakes and Reservoirs, Portland State University.
Objectives1) Search and identify genomic elements of interest in the
Dreissena polymorpha’s genome
2) Identify the main gene regions
3) Design specific PCR primers
Methodology
Promoter (Neural Network
Promoter Prediction)
Coding region (ORF finder)
UnTranslated Regions
Identify the gene regions
Delimit the gene sequence inside the
whole contig
Blast contig - gene
Drosophila melanogaster
Mytilus galloprovincialis
Search of the predicted genes in
other species
Blast2GO
1st bioinformatics analysis
3885 contigs of genomic DNA obtained from Roche
454 sequencing of 2 individuals
Samples
Source: whyevolutionistrue.wordpress.com
Results
3715 contigs
Blast2GO results
Unannotated Annotated
3815 contigs
70 contigs
?
DNA replication origin-binding helicaseThree prime repair exonuclease 1Transposon Ty3-I Gag-Pol polyproteinPutative tick transposonSerine/threonine kinase PINK1TPA: endonuclease-reverse transcriptasePutative zinc finger proteinORF 99Proto-oncogene serine/threonine-protein kinase pim 1Deoxycytidine KinasePutative RNA-directed DNA polymerase from transposon BSSodium- and chloride-dependent GABA transporterMethionine-tRNA ligaseThrombospondin 1 Histone H1 Histone H2A Histone H2BHistone H3 Histone H4 …
(Contig nº 76) (Contig nº 70) (Contig nº 1276)(Contig nº 102)(Contig nº 76)
High degree of evolutionary conservatism ( / )
Seq. description
ResultsBlast gene-contig results
ResultsIdentification of gene regions
Conclusions1. Use of bioinformatics methods has allowed the identification and
characterization of 5 genes in the Dreissena polymorpha’s genome. These are H1, H2A, H2B, H3 and H4 histone genes.
2. The paper of this genes as molecular markers in zebra mussel population studies may not be valid due to its evolutionarily conserved sequence.
On the other hand, they could be used in studies about DNA quantification to estimate the contamination levels in invaded waters.
3. The main regions of this genes have been correctly identified, except in the case of histone H2A gene.
4. The design of specific primers would have to focus on the flanking regions of these genes.
Thank you for your attention