Search and characterization of genomic elements of interest in the zebra mussel's genome

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