Comparative Genomics

Comparative genomics involves comparing the genetic material of one organism to many others, including gene-encoded functions, content, number, and location. This technique has diverse applications, including selecting microorganisms with desirable characteristics for compound production by identifying genes responsible for specific traits. Additionally, comparative genomics can be used to identify genes responsible for undesirable traits, such as toxin production, to select against them. Engineers can also use comparative genomics to establish strategies for improving microorganisms, leading to the development of safer, more efficient, and higher-yielding organisms for compound production. Moreover, comparative genomics can help identify specific genes or gene clusters responsible for unique traits that can be patented for use in compound production.

TAXON delivers cutting-edge comparative genomics services designed to aid researchers in their studies. Our services are equipped with state-of-the-art technologies and expert knowledge, and we offer a wide range of deliverables to meet various research needs. Our services include the production of phylogenetic trees and user-friendly plots, which enable data analysis to highlight exceptional characteristics of genomic regions of interest. Additionally, we provide gene abundance and clustering analysis to offer evolutionary context for gene discovery, uniqueness or taxonomic analyses. With TAXON's comparative genomics service, researchers can better understand the relationships between different organisms or proteins, leading to new discoveries in the field of genomics.

Deliverables of Comparative Genomics service:

Phylogenic trees of organism or protein of interest (in Newick and svg formats)
The sequence of regions of interest (in Genbank format)
Comparison of the region of interest (in svg format)
Table of the abundance of gene of interest abundance in all analyzed species (in csv, tsv and/or xlxs formats).
Absence/presence table of the gene of interest in all analyzed organisms analyzed (in csv, tsv and/or xlxs formats).
Hierarchical clustering of analyzed organisms based on functional profile (in svg format).
Comparison of hierarchical clustering and phylogenetic tree of organism/ proteins of interest (in svg format).
A complete report describing methods and comparative analyses results (in PDF format)

See Our Services in Practice

The figure presented in this study displays the inferred phylogenomic relationships among more than 1,500 E. faecalis members. The inner circle indicates the source of isolation and the red points indicate the presence of kdp genes within the strains. The clusters of strains with high phylogenetic signals were observed to have similar kdp occurrences. Nevertheless, it was found that using phylogeny-aware methods resulted in a significantly positive correlation between the presence of kdp genes and E. faecalis of clinical origin (p-value of 2.76E-11). This highlights the importance of considering phylogenetic signals in statistical analysis, as failure to do so can result in misleadingly low p-values and false conclusions.

Reference: Acciarri G, Gizzi FO, Torres Manno MA, Stülke J, Espariz M, Blancato VS and Magni C (2023) Redundant potassium transporter systems guarantee the survival of Enterococcus faecalis under stress conditions. Front. Microbiol. 14:1117684. doi: 10.3389 fmicb.2023.1117684

In this case, we explored the specific features related to cheese production in four strains: IQ23, GM70, GM75, and IQ110. The figure illustrates full genomic alignments and synteny of these strains against reference strains, where each colored block represents a conserved genomic region, and different positions of the same block indicate rearrangement. The figure also highlights unique sequences as blank spaces and features of interest, including lactose utilization operon, citrate metabolism genes, and bile salt tolerance genes, with colored arrows. Overall, the figure provides an overview of the genomic features of the strains studied and their relationship to reference strains.

Reference: Martino, G. P., Espariz, M., Gallina Nizo, G., Esteban, L., Blancato, V. S., & Magni, C. (2018). Safety assessment and functional properties of four enterococci strains isolated from regional Argentinean cheese. International journal of food microbiology, 277, 1–9. https://doi.org/10.1016/j.ijfoodmicro.2018.04.012

In this case, information available from public databases was used to resolve the identity of B. pumilus group strains at a species level. The figure shows the comparison of phylogenomic and functional dendrograms of Bacillus pumilus group strains. The evolutionary history of the indicated strains was inferred using core genes. On the other hand, the biological functions of proteins encoded in the genome were used as a binary score for hierarchical cluster analysis. In this case, coherence between the phylogenic tree and functional dendrograms was used to reinforce bacterial species circumscriptions whereas different topologies were used to recognize ecologically distinct strains.

Reference: Espariz M, Zuljan FA, Esteban L, Magni C (2016) Taxonomic Identity Resolution of Highly Phylogenetically Related Strains and Selection of Phylogenetic Markers by Using Genome-Scale Methods: The Bacillus pumilus Group Case. PLoS ONE 11(9): e0163098. doi:10.1371/journal. pone.0163098

Salmonella, a food-borne pathogen, developed modified cell envelope mechanisms to counteract copper toxicity and enable virulence. In this case, it compares both of the genomic regions containing the residual fragments of the cus locus among representative Salmonella strains. In the Figure, the coding sequences are represented by blue arrows, except for those encoding the cus genes (or their residuary fragments). The fim genes, encoding a type 1 fimbria, next to the cus locus, are colored yellow. The BLAST hits are colored on a green gradient according to their shared identity as determined by BLASTn.

Reference: Checa, S. K., Giri, G. F., Espariz, M., Argüello, J. M., & Soncini, F. C. (2021). Copper Handling in the Salmonella Cell Envelope and Its Impact on Virulence. Trends in microbiology, 29(5), 384–387. https://doi.org/10.1016/j.tim.2021.01.004