Big Secrets of Small Creatures: A Genomic Journey in Metamonad
Metamonad
The Metamonad group is a category within the realm of single-celled eukaryotes that encompasses various subgroups. This group includes subgroups such as Fornicata and Parabasalia. The Parabasalia subgroup contains parasitic species like Trichomonas vaginalis, Histomonas meleagridis, and Tritrichomonas foetus, as well as organisms like Trichomonas tenax which, though not parasitic, are opportunistic. Within the Metamonad group, the Fornicata subgroup includes free-living species such as Carpediemonas membranifera. The relationship of the genus Kipferlia with these groups plays a crucial role in deciphering the phylogenetic structure of Metamonad. This diversity provides significant data for studies in evolutionary biology and microbiology.
Kipferlia: This genus is less known and less researched. Specific details and species information are comparatively scarce.
Trichomonas vaginalis: A protozoan species known to cause sexually transmitted infections in humans. Known as trichomoniasis, it can lead to infections in the urogenital system of both men and women. Trichomonas vaginalis is a typical parasite.
Trichomonas tenax: A protozoan found in the human oral cavity, proliferating in cases of poor oral hygiene. Generally harmless, it can contribute to respiratory infections under certain circumstances. While not parasitic, it is considered an opportunistic organism.
Carpediemonas membranifera: This species is free-living, often found in anaerobic environments, especially in aquatic ecosystems. Carpediemonas membranifera is a non-parasitic organism and can live in oxygen-deprived environments.
Histomonas meleagrides: A protozoan species that causes disease, particularly among poultry. It leads to a disease known as histomoniasis, notably affecting birds like turkeys. Histomonas meleagrides has a parasitic life cycle and is contagious.
Tritrichomonas foetus: This species causes sexually transmitted diseases in cattle, leading to reproductive issues and miscarriages. Tritrichomonas foetus is defined as a parasitic organism and lives in the reproductive systems of animals.
Each species possesses characteristics that are studied in microbiology and parasitology, noted for their presence in various habitats.
When conducting genomic comparisons, the selection of “Target/db” and “Query” species depends on the objectives and hypotheses of your study. We will focus on various species within the Metamonad group, and the selection should be based on their similarities, differences, and research goals.
Similarity-Based Approach: Examining the genetic differences between Trichomonas vaginalis and Trichomonas tenax helps to understand the different effects of similar species on humans.
Difference-Based Approach: Comparing Histomonas meleagrides and Carpediemonas membranifera reveals the genetic adaptations of species with different life cycles and environments.
Evolutionary Approach: Comparing the genetic data of species from different groups enables a broad evolutionary perspective and the creation of a phylogenetic tree.
In my genomic comparison study, I plan to select one “target” and two “query” species; you can find which species these are and the reasons for their selection in the explanation below.
Target (Reference): Trichomonas vaginalis
Reason for Selection: Trichomonas vaginalis is a well-known protozoan causing sexually transmitted diseases in humans. There has been extensive research on this species, so its genetic information may be more detailed and accessible. Additionally, its direct relation to human health may attract more research interest.
Query 1: Tritrichomonas foetus
Reason for Selection: Tritrichomonas foetus is a protozoan that causes sexually transmitted diseases in cattle. Compared to Trichomonas vaginalis, it is important for animal health and serves as a good choice to understand the genetic structure of a similar pathogen living in a different host.
Query 2: Histomonas meleagrides
Reason for Selection: Histomonas meleagrides is another protozoan that causes diseases in poultry. Choosing this species can provide an interesting comparison to reveal genetic similarities and differences with human and cattle pathogens.
These selections allow for a comparative analysis between pathogens affecting human health and those impacting animal health. Thus, you can study the genetic adaptations and evolutionary differences of similar protozoan species living in different hosts. This comparison can provide valuable information about the evolution of pathogens and disease mechanisms.
In my upcoming Medium article, we will embark on a journey into the depths of our genetic and comparative genomic research. I have previously shared with you the sources from which we obtain the genomes for these exciting studies. Now, I wish to share with you small visuals that step-by-step illustrate how these genomes are downloaded.
When downloading genomes for our species, we utilize taxonomic information to determine which species’ genomes are accessible. With this information in hand, we can then proceed with the downloading process.
We go directly to the genome section, select the genome of the species we want to download, and then perform the download by choosing the fasta format. This downloaded file is then added to the resources section of PyCharm.
Now that we have completed our downloading processes, we can create a folder with your chosen name in the resources section of our project, or directly place the downloaded genomes there. It’s time to move on to the comparative genomics analysis.
I will cover this in another write-up. Looking forward to our next discussion!
NOTE:
In our studies, we will frequently use multifasta files; this format consolidates multiple DNA or protein sequences into a single file. This is a fundamental tool for bioinformatics analyses.
A multifasta file is a text file containing one or more protein or nucleotide sequences. Each sequence starts with an identification line beginning with the “>” symbol. This line can include the name of the sequence, its species, and other information. The sequence follows the identification line and consists of one or more lines where each amino acid or nucleotide is represented by a letter code.
Multifasta files are commonly used for storing and sharing biological data. For example, a researcher can store the sequences of all members of a protein family in a multifasta file. This can help the researcher study the evolutionary history and function of the protein family.
Multifasta files can also be used for the analysis of biological data. For example, a researcher can compare sequences in a multifasta file to identify similarities and differences. This can help the researcher determine the function or evolutionary relationships of proteins or nucleotide sequences.
Multifasta files are typically saved in the following format:
>protein1
AAAGGGTTTT
>protein2
AAAGGGTTTT
>protein3
AAAGGGTTTTIn this example, three protein sequences are recorded. The names of each sequence are “protein1,” “protein2,” and “protein3.” Each sequence consists of 10 amino acids represented by the letters “A,” “G,” “T,” and “C.”
Various software can be used to create and read multifasta files. For example, BioEdit for Windows and EMBOSS for Linux are commonly used software for creating and reading multifasta files.
Multifasta files are an important tool for the storage and analysis of biological data. These files help researchers more efficiently examine proteins, nucleotide sequences, and other biological data.
This Medium article was created as a part of my ongoing education in the Miuul Bioinformatics Bootcamp, under the guidance of my instructor Zeynep Akdeniz. Her approach has significantly contributed to my learning process. I would like to thank her for the knowledge and experiences I have gained during this training. For those who wish to acquire more information in the field of bioinformatics, I recommend visiting the Miuul Bioinformatics Bootcamp website.
