Biology subjects

Klimov, P. B.

Publications and source records attributed to Klimov, P. B..

3 recordsLinked to original sources

bioRxiv2026

GeneFamHunter: annotation-independent recovery of divergent and tandemly arrayed gene-family members from genome assemblies

Motivation: Gene families expand by tandem duplication, diverge and decay, so their members are often missing, fragmented or fused in automated genome annotations, and divergent copies escape pairwise similarity searches. These challenges are particularly pronounced in non-model organisms, for which well-annotated genomes and reference proteomes are often unavailable, limiting the applicability of protein-based gene family recovery methods. Results: We developed GeneFamHunter to recover gene-family members directly from nucleotide assemblies. It searches continuous six-frame translations of overlapping genomic windows using four complementary domain- and profile-based methods, clusters hits while distinguishing tandem paralogs, predicts and validates gene models, and constructs gene trees. Across six Quest for Orthologs genomes, window-based HMMER searches recovered all 130 reference papain-like (C1A) loci, with 21 off-target hits, compared with 45 for stop-to-stop ORF searches; whole-contig HMMER searches recovered 108 (83.1%). With 11 distantly related queries, PSI-BLAST and DELTA-BLAST recovered all reference loci, whereas RPSTBLASTN recovered 98.5-99.2% and TBLASTN, as used by BITACORA, recovered 94.6-95.4%. Across six mite genomes, GeneFamHunter recovered all 209 previously reported C1 loci and identified 37 additional candidate loci. In a separate comparison, it recovered all 128 reference UniProt C1A proteins and identified five additional loci without annotated gene models; OrthoFinder included 35 non-C1A proteins, whereas OMA recovered 98 reference proteins. Availability and implementation: GeneFamHunter is implemented in Bash for Linux and SLURM clusters and is freely available at https://github.itap.purdue.edu/HeLab/GeneFamHunter (MIT license). Benchmark code and data: https://github.itap.purdue.edu/HeLab/GeneFamHunter_benchmarks and Zenodo (DOI: 10.5281/zenodo.23744704).

genomics↗

bioRxiv2023

Predicting Blomia tropicalis allergens using a multiomics approach

The domestic mite Blomia tropicalis is a major source of allergens in tropical and subtropical regions. Despite its great medical importance, the allergome of this mite is not sufficiently studied. Only 14 allergen groups have been identified in B. tropicalis so far, even though early radioimmunoelectrophoresis techniques (27 uncharacterized allergen complexes) and comparative data based on 40 allergen groups officially recognized by WHO/IUIS in domestic astigmatid mites, suggest that a large set of additional allergens may be present. Here, we use a multiomics approach to assess the allergome of B. tropicalis using genomic, transcriptomic sequence data, and a highly sensitive protein abundance quantification. Out of 14 known allergen groups, we confirmed 13 (one WHO/IUIS allergen, Blo t 19, was found to be a contaminant originated from a nematode) and identified 16 potentially novel allergens using sequence similarity. These data indicate that B. tropicalis shares 27 known/deduced allergen groups with pyroglyphid house dust mites (genus Dermatophagoides). Among them, five allergen-encoding genes were highly expressed at the transcript level: Blo t 1, Blo t 5, Blo t 21 (known), Blo t 15, and Blo t 18 (predicted). However, at the protein level, a different set of most abundant allergens was found: Blo t 2, 10, 11, 20 and 21 (mite bodies) or Blo t 3, 4, 6 and predicted Blo t 13, 14 and 36 (mite feces). We show the use of an integrated omics method to identify and predict an array of mite allergens and advanced, label-free proteomics to determine allergen protein abundance. Our research identifies a large set of novel putative allergens and shows that expression levels of allergen-encoding genes may not be strictly correlated with the actual allergenic protein abundance in the mite bodies.

molecular biology↗

bioRxiv2019

Evaluating the boundaries of marine biogeographic regions of the Southwestern Atlantic using halacarid mites (Halacaridae), meiobenthic organisms with a low dispersal potential

AimWe evaluated traditional biogeographic boundaries of coastal marine regions in SW Atlantic using DNA sequence data from common, rocky-shore inhabiting, marine mites of the genera Agauopsis and Rhombognathus, family Halacaridae.\n\nMethodsWe investigated geographic population genetic structure using CO1 gene sequences, estimated divergence times using a multigene dataset and absolute time-calibrated molecular clock analyses, and performed environmental niche modeling (ENM) of common marine mite species.\n\nResultsAgauopsis legionium has a shallow history (2.01 Ma) with four geographically differentiated groups. Two of them corresponded to the traditional Amazonian and Northeastern ecoregions, but the boundary between the two other groups was inferred at the Abrolhos Plateau, not Cabo Frio. Rhombognathus levigatoides s. lat. was represented by two cryptic species that diverged 7.22 (multilocus data) or 10.01 Ma (CO1-only analyses), with their boundary, again at the Abrolhos Plateau. ENM showed that A. legionium has suitable habitats scattered along the coast, while the two R. levigatoides cryptic species differ considerably in their niches, especially in parameters related to upwelling. This indicates that genetic isolation associated with the Abrolhos Plateau occurred in both lineages, but for the R. levigatoides species complex, ecological niche specialization was also an important factor.\n\nMain conclusionsOur study suggests that the major biogeographic boundary in the Southwestern Atlantic lies not at Cabo Frio but at the Abrolhos Plateau. There, two biogeographically relevant factors meet: (i) changes in current directions (which limit dispersal) and (ii) abrupt changes in environmental parameters associated with the South Atlantic Central Waters (SACW) upwelling (offering distinct ecological niches). We suggest that our result represents a general biogeographic pattern because a barrier at the Abrolhos Plateau was found previously for the fish genus Macrodon (phylogeographic data), prosobranch mollusks, ascidians, and reef fishes (community-level data).

evolutionary biology↗