Genomic analysis of marine Halophythophthoras and comparison of their genetic capacity and gene organization with terrestrial relatives
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 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 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 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
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.