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Halophytophthoras
Halophytophthoras
They are saprophytic oomyces, fungus-like microrganisms
Samples Cu27 and Cu97 from mangroves
Data: genetic sequences
Tools: Geneious, MG-RAST and MicrobiomeAnalyst
Objectives: identify species, analyse genetic capacity and recontruct mitogenome
Geneious
Geneious
Geneious is a bioinformatics software platform for molecular biology and sequence analysis. As it is a closed-source programme, I used the 14-day free trial to run my analyses.
Firstly, I built phylogenetic trees using six molecular markers (CoxI, ITS, LSU, HSP90, NADH1 and beta-tubulin); to test if Cu27 and Cu97 contained the same species. Then, I identified the species using the BLAST function from the National Center for Biotechnology Information (NCBI).
Unfortunately I did not have enough time in the free trial to construct the mitogenome.
MG-RAST
MG-RAST
MG-RAST is an open source server that suggests automatic phylogenetic and functional analysis of metagenomes.
In order to compare the genomic and metabolic functions of the microbiome and its host, I manually reorganized the sequence files. After this industrious task, the upload of the microbiome data was not accepted by the software, so a comparison was not possible.
Nonetheless, I learnt how to create and interpret Krona graphs and KEGG pathways.
MicrobiomeAnalyst
MicrobiomeAnalyst
MicrobiomeAnalyst is an open-source statistical and visual tool for meta-analysis of microbiome data. In order to use the Marker Data Profiling (MDP) function, I created marker gene abundance data by restructuring the data with Excel.
Through MicrobiomeAnalyst I obtained different types of outputs, including abundance barplots, alfa-/beta-diversity PCAs, rarefraction curves, heat trees and heatmaps. I was able to compare the host eukatyote and the microbiome by running the same analyses on both datasets.
Results
Results
Using Geneious I verified that both samples contained the same species: Halophytophthora vesicula. The metabolic and functional analysis did not yield positive results, as it was limited by the issues I had with MG-RAST. MicrobiomeAnalyst fournished interesting results and excellent graphical outputs, which will be utilized by my supervisor for further analysis.
During my Professional Practice I was able to fulfil my personal objectives: I learnt how to use three new programmes, I improved my communication, time-management and organizational skills and I created valuable personal connections for my future career.
This website was developed under the International Master of Science in Marine Biological Resources (IMBRSea), during an internship partnered by the University of Algarve and Cientro de Ciencias de Mar (CCMAR). Neither the student nor the master are the owners of the information included in this website.
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