Next Article in Journal
Cross-Kingdom Analysis of Diversity, Evolutionary History, and Site Selection within the Eukaryotic Macrophage Migration Inhibitory Factor Superfamily
Previous Article in Journal
Molecular Therapies for Choroideremia
Open AccessArticle

Genomic Analyses Identify Novel Molecular Signatures Specific for the Caenorhabditis and other Nematode Taxa Providing Novel Means for Genetic and Biochemical Studies

1
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L9H 6K5, Canada
2
Department of Biology, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Genes 2019, 10(10), 739; https://doi.org/10.3390/genes10100739
Received: 26 July 2019 / Revised: 6 September 2019 / Accepted: 17 September 2019 / Published: 24 September 2019
(This article belongs to the Special Issue C. elegans - A tribute to the legendary worm)
The phylum Nematoda encompasses numerous free-living as well as parasitic members, including the widely used animal model Caenorhabditis elegans, with significant impact on human health, agriculture, and environment. In view of the importance of nematodes, it is of much interest to identify novel molecular characteristics that are distinctive features of this phylum, or specific taxonomic groups/clades within it, thereby providing innovative means for diagnostics as well as genetic and biochemical studies. Using genome sequences for 52 available nematodes, a robust phylogenetic tree was constructed based on concatenated sequences of 17 conserved proteins. The branching of species in this tree provides important insights into the evolutionary relationships among the studied nematode species. In parallel, detailed comparative analyses on protein sequences from nematodes (Caenorhabditis) species reported here have identified 52 novel molecular signatures (or synapomorphies) consisting of conserved signature indels (CSIs) in different proteins, which are uniquely shared by the homologs from either all genome-sequenced Caenorhabditis species or a number of higher taxonomic clades of nematodes encompassing this genus. Of these molecular signatures, 39 CSIs in proteins involved in diverse functions are uniquely present in all Caenorhabditis species providing reliable means for distinguishing this group of nematodes in molecular terms. The remainder of the CSIs are specific for a number of higher clades of nematodes and offer important insights into the evolutionary relationships among these species. The structural locations of some of the nematodes-specific CSIs were also mapped in the structural models of the corresponding proteins. All of the studied CSIs are localized within the surface-exposed loops of the proteins suggesting that they may potentially be involved in mediating novel protein–protein or protein–ligand interactions, which are specific for these groups of nematodes. The identified CSIs, due to their exclusivity for the indicated groups, provide reliable means for the identification of species within these nematodes groups in molecular terms. Further, due to the predicted roles of these CSIs in cellular functions, they provide important tools for genetic and biochemical studies in Caenorhabditis and other nematodes. View Full-Text
Keywords: genome sequences; molecular markers (synapomorphies); phylogenetic trees; conserved signature indels; Caenorhabditis elegans; Chromadorea; structural analysis of Caenorhabditis/nematodes-specific indels; evolutionary relationships among nematodes genome sequences; molecular markers (synapomorphies); phylogenetic trees; conserved signature indels; Caenorhabditis elegans; Chromadorea; structural analysis of Caenorhabditis/nematodes-specific indels; evolutionary relationships among nematodes
Show Figures

Figure 1

MDPI and ACS Style

Khadka, B.; Chatterjee, T.; Gupta, B.P.; Gupta, R.S. Genomic Analyses Identify Novel Molecular Signatures Specific for the Caenorhabditis and other Nematode Taxa Providing Novel Means for Genetic and Biochemical Studies. Genes 2019, 10, 739.

Show more citation formats Show less citations formats
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop