Revisiting Y-chromosome detection methods: R-CQ and KAMY efficiently identify Y chromosome sequences in Tephritidae insect pests DOI Creative Commons
Dimitris Rallis, Konstantina T. Tsoumani, Flávia Krsticevic

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 1, 2023

Abstract The detection and characterization of sex chromosome sequences is particularly important for major pest families, like the Tephritidae, whereas alternative management approaches, mainly involving male-only release programs, rely on ability to target manipulate sex-specific genomic regions, those Y chromosome. However, resolving detecting X at level requires careful consideration algorithmic outputs, especially in species where extensive markers are not available. Here, we present R-CQ KAMY, two computational methods developed chromosome-linked sequences. We evaluate their performance newly generated chromosome-level assemblies four Tephritid species: Ceratitis capitata, Bactrocera dorsalis, zonata Anastrepha ludens . By combining predictions with a manual curation process, assess strengths limitations each method provide robust dataset curated X- Y-linked Overall, our results establish framework studying poorly characterized lineages identifying supporting broader development chromosome-based managements systems.

Language: Английский

GENA-LM: a family of open-source foundational DNA language models for long sequences DOI Creative Commons
Veniamin Fishman, Yuri Kuratov, Aleksei Shmelev

et al.

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(2)

Published: Jan. 11, 2025

Abstract Recent advancements in genomics, propelled by artificial intelligence, have unlocked unprecedented capabilities interpreting genomic sequences, mitigating the need for exhaustive experimental analysis of complex, intertwined molecular processes inherent DNA function. A significant challenge, however, resides accurately decoding which inherently involves comprehending rich contextual information dispersed across thousands nucleotides. To address this need, we introduce GENA language model (GENA-LM), a suite transformer-based foundational models capable handling input lengths up to 36 000 base pairs. Notably, integrating newly developed recurrent memory mechanism allows these process even larger segments. We provide pre-trained versions GENA-LM, including multispecies and taxon-specific models, demonstrating their capability fine-tuning addressing spectrum complex biological tasks with modest computational demands. While already achieved breakthroughs protein biology, GENA-LM showcases similarly promising potential reshaping landscape genomics multi-omics data analysis. All are publicly available on GitHub (https://github.com/AIRI-Institute/GENA_LM) HuggingFace (https://huggingface.co/AIRI-Institute). In addition, web service (https://dnalm.airi.net/) allowing user-friendly annotation models.

Language: Английский

Citations

3
Positive correlations in susceptibility to a diverse panel of viruses across Drosophilidae host species DOI Creative Commons
Ryan M. Imrie, Megan A. Wallace, Ben Longdon

et al.

Evolution Letters, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 5, 2025

Our ability to predict the emergence of novel viruses relies on there being generalisable patterns in susceptibilities hosts infections. Studies investigating variation susceptibility among host species have consistently shown that closely related share similar a given virus. However, extent which such phylogenetic are correlated amongst diverse sets is unclear. Here, we investigate correlations Drosophilidae panel eleven different invertebrate viruses, comprising seven unique virus species, six families, and both RNA DNA viruses. The each pair tested was either positively across or did not show evidence correlation. No negative correlations, indicative evolutionary trade-offs were detected between any pairs. strength generally higher same family, consistent with infectivity. results suggest generalised can result positive even highly diverged while specialised interactions individual cause stepwise decrease correlation from within-species, within-family, across-family level.

Language: Английский

Citations

1
Analysis of 30 chromosome-level Drosophila genome assemblies reveals dynamic evolution of centromeric satellite repeats DOI Creative Commons
Daniel Gebert, Amir D. Hay,

Jennifer P. Hoang

et al.

Genome biology, Journal Year: 2025, Volume and Issue: 26(1)

Published: March 18, 2025

Abstract Background The Drosophila genus is ideal for studying genome evolution due to its relatively simple chromosome structure and small size, with rearrangements mainly restricted within arms, such as Muller elements. However, work on the rapidly evolving repetitive genomic regions, composed of transposons tandem repeats, have been hampered by lack genus-wide chromosome-level assemblies. Results Integrating long-read sequencing capture technology, here we produce annotate 30 assemblies genus. Based this dataset, reveal evolutionary dynamics across phylogeny, including identification regions that show comparatively high structural stability throughout evolution. Moreover, ananassae subgroup, uncover emergence new conformations rapid expansion novel satellite DNA sequence families, which form large continuous pericentromeric domains higher-order repeat structures are reminiscent those observed in human Arabidopsis genomes. Conclusions These present a valuable resource future research, power demonstrated our analysis In addition, based findings, propose subgroup an model system centromere structure.

Language: Английский

Citations

1
Double trouble: two retrotransposons triggered a cascade of invasions in Drosophila species within the last 50 years DOI Creative Commons

Almorò Scarpa,

Riccardo Pianezza, Hannah R. Gellert

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 9, 2025

Abstract Horizontal transfer of genetic material in eukaryotes has rarely been documented over short evolutionary timescales. Here, we show that two retrotransposons, Shellder and Spoink , invaded the genomes multiple species melanogaster subgroup within last 50 years. Through horizontal transfer, spread D. during 1980s, while both simulans 1990s. Possibly following hybridization, infected island endemic mauritiana (Mauritius) sechellia (Seychelles) with TEs after 1995. In same approximate time-frame, also teissieri a confined to sub-Saharan Africa. We find donors are likely American Drosophila from willistoni cardini repleta groups. Thus, described cascade TE invasions could only become feasible extended their distributions into Americas 200 years ago, aided by human activity. Our work reveals cascades invasions, initiated human-mediated range expansions, have an impact on genomic phenotypic evolution geographically dispersed species. Within few decades, invade many species, including endemics, very distant donor TE.

Language: Английский

Citations

0
Temperature affects conspecific and heterospecific mating rates in Drosophila DOI
Jonathan A. Rader, Daniel R. Matute

Animal Behaviour, Journal Year: 2025, Volume and Issue: unknown, P. 123168 - 123168

Published: April 1, 2025

Language: Английский

Citations

0
Comparative gene annotation of 304 species of Drosophilidae DOI Creative Commons

P. K. Dhakad,

Bernard Kim, Dmitri A. Petrov

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 15, 2025

Abstract High-quality genome annotations are essential if we to address central questions in comparative genomics, such as the origin of new genes, drivers size variation, and evolutionary forces shaping gene content structure. Here, present protein-coding for 304 species family Drosophilidae, generated using Comparative Annotation Toolkit (CAT) BRAKER3, incorporating available RNA-seq protein evidence. We take a phylogenetic approach annotation, with aim improving consistency accuracy, generate robust set orthology assignments. analyze our mixed-model find that number CDS length exhibit moderate heritability (43.3% 12.3%, respectively). This suggests while history contributes variation these traits, species-specific factors, including assembly error, play substantial role observed differences. To illustrate utility analyses, investigate codon usage bias amino acid composition across Drosophilidae. is correlated overall GC evolves slowly, but it also strongly shaped by selection, that, general, strongest selection on synonymous show lowest third positions. annotation dataset forms part an on-going collaborative project sequence annotate all data being made rapidly freely basis. hope this effort will serve foundation studies functional genomics biology

Language: Английский

Citations

0
Phylogenomic Insights into the Evolution and Origin of Nematoda DOI Creative Commons
Xue Qing, Y. Miles Zhang,

Sidi Sun

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 14, 2023

Abstract The phylum Nematoda represents one of the most cosmopolitan and abundant metazoan groups on Earth. In this study, we reconstructed phylogenomic tree for Nematoda. A total 60 genomes, belonging to eight nematode orders, were newly sequenced, providing first low-coverage genomes orders Dorylaimida, Mononchida, Monhysterida, Chromadorida, Triplonchida, Enoplida. resulting phylogeny is well-resolved across clades, with topologies remaining consistent various reconstruction parameters. subclass Enoplia placed as a sister group rest Nematoda, agrees previous published phylogenies. While order Triplonchida monophyletic, it not well-supported, Enoplida paraphyletic. Taxa possessing stomatostylet form monophyletic group; however, superfamily Aphelenchoidea does constitute clade. genera Trichinella Trichuris are inferred have shared common ancestor approximately 202 mya, considerably later period than previously suggested. All stomatostylet-bearing nematodes proposed originated ∼305 corresponding transition from Devonian Permian period. genus Thornia outside Dorylaimina Nygolaimina, disagreeing its position in studies. Additionally, tested whole genome amplification method demonstrated that promising strategy obtaining sufficient DNA studies microscopic eukaryotes. This study significantly expanded current dataset, enhances our understanding evolution

Language: Английский

Citations

6
Genomics of a sexually selected sperm ornament and female preference in Drosophila DOI
Zeeshan Ali Syed, R. Antonio Gómez, Kirill Borziak

et al.

Nature Ecology & Evolution, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 22, 2024

Language: Английский

Citations

1
Whole genome phylogenomics helps to resolve the phylogenetic position of the Zygothrica genus group (Diptera, Drosophilidae) and the causes of previous incongruences DOI
Maiara Hartwig Bessa, Marco Silva Gottschalk, Lizandra Jaqueline Robe

et al.

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 199, P. 108158 - 108158

Published: July 17, 2024

Language: Английский

Citations

1
Molecular phylogeny and species diversity of the genus Dichaetophora Duda and related taxa (Diptera: Drosophilidae) DOI
Takehiro K. Katoh,

Chen Ji-min,

Jin-Hua Yang

et al.

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 201, P. 108194 - 108194

Published: Sept. 12, 2024

Language: Английский

Citations

1