Current state and future prospects of Horizontal Gene Transfer detection DOI Creative Commons
Andika Aji Wijaya, Aleksandar Anžel, Hugues Richard

et al.

NAR Genomics and Bioinformatics, Journal Year: 2025, Volume and Issue: 7(1)

Published: Jan. 7, 2025

Artificial intelligence (AI) has been shown to be beneficial in a wide range of bioinformatics applications. Horizontal Gene Transfer (HGT) is driving force evolutionary changes prokaryotes. It widely recognized that it contributes the emergence antimicrobial resistance (AMR), which poses particularly serious threat public health. Many computational approaches have developed study and detect HGT. However, application AI this field not investigated. In work, we conducted review provide information on current trend existing for detecting HGT decipher use field. Here, show growing interest detection, characterized by surge number approaches, including AI-based recent years. We organize into hierarchical structure groups based their methods how each group evolved. make recommendations discuss challenges detection general adoption particular. Moreover, future directions detection.

Language: Английский

The promise and pitfalls of synteny in phylogenomics DOI Creative Commons
Jacob L. Steenwyk,

Nicole King

PLoS Biology, Journal Year: 2024, Volume and Issue: 22(5), P. e3002632 - e3002632

Published: May 20, 2024

Reconstructing the tree of life remains a central goal in biology. Early methods, which relied on small numbers morphological or genetic characters, often yielded conflicting evolutionary histories, undermining confidence results. Investigations based phylogenomics, use hundreds to thousands loci for phylogenetic inquiry, have provided clearer picture life’s history, but certain branches remain problematic. To resolve difficult nodes life, 2 recent studies tested utility synteny, conserved collinearity orthologous more organisms, phylogenetics. Synteny exhibits compelling phylogenomic potential while also raising new challenges. This Essay identifies and discusses specific opportunities challenges that bear value synteny data other rare genomic changes studies. Synteny-based analyses highly contiguous genome assemblies mark chapter era quest reconstruct life.

Language: Английский

Citations

17
Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus DOI Creative Commons
Jacob L. Steenwyk,

Charu Balamurugan,

Huzefa A. Raja

et al.

Microbiology Spectrum, Journal Year: 2024, Volume and Issue: 12(4)

Published: March 6, 2024

Modern taxonomic classification is often based on phylogenetic analyses of a few molecular markers, although single-gene studies are still common. Here, we leverage genome-scale phylogenetics (phylogenomics) species and populations to reconstruct evolutionary relationships in dense data set 710 fungal genomes from the biomedically technologically important genus Aspergillus. To do so, generated novel 1,362 high-quality markers specific for Aspergillus provided profile Hidden Markov Models each, facilitating their use by others. Examining resulting phylogeny helped resolve ongoing controversies, identified new ones, revealed extensive strain misidentification (7.59% strains were previously misidentified), underscoring importance population-level sampling classification. These findings corroborated using current standard, taxonomically informative loci. suggest that phylogenomics can facilitate accurate classifications reconstructions Tree Life.IMPORTANCEIdentification relies markers. Advances genomic technologies have made it possible sequence genome any strain, making assignment (and discovery ones). We examined usefulness limitations large publicly available multiple biomedically, agriculturally, industrially Our nearly 8% misidentified. work highlights systematic biology suggests sequencing strains, including reference (e.g., type strains), will be required reduce errors public databases.

Language: Английский

Citations

14
Common Methods for Phylogenetic Tree Construction and Their Implementation in R DOI Creative Commons

Yue Zou,

Zixuan Zhang, Yujie Zeng

et al.

Bioengineering, Journal Year: 2024, Volume and Issue: 11(5), P. 480 - 480

Published: May 11, 2024

A phylogenetic tree can reflect the evolutionary relationships between species or gene families, and they play a critical role in modern biological research. In this review, we summarize common methods for constructing trees, including distance methods, maximum parsimony, likelihood, Bayesian inference, tree-integration (supermatrix supertree). Here discuss advantages, shortcomings, applications of each method offer relevant codes to construct trees from molecular data using packages algorithms R. This review aims provide comprehensive guidance reference researchers seeking while also promoting further development innovation field. By offering clear concise overview different available, hope enable select most appropriate approach their specific research questions datasets.

Language: Английский

Citations

14
The emerging view on the origin and early evolution of eukaryotic cells DOI
Julian Vosseberg, Jolien J. E. van Hooff, Stephan Köstlbacher

et al.

Nature, Journal Year: 2024, Volume and Issue: 633(8029), P. 295 - 305

Published: Sept. 11, 2024

Language: Английский

Citations

12
The Bryophyte Phylogeny Group: A revised familial classification system based on plastid phylogenomic data DOI
Yunfeng Li,

Lian Luo,

Yang Liu

et al.

Journal of Systematics and Evolution, Journal Year: 2024, Volume and Issue: 62(4), P. 577 - 588

Published: March 12, 2024

Abstract Bryophytes, a monophyletic group comprising three major lineages, diversified soon after the terrestrialization of land plants. However, their internal phylogenetic relationships remain controversial. In this study, we reconstructed ordinal and familial phylogeny bryophytes using largest plastid data set to date, including 549 taxa that represent almost all known orders two‐thirds families. The strongly supported inference enabled us propose in mosses seven newly segregated families, is, Baldwiniellaceae, Calyptrochaetaceae, Ctenidiaceae, Herpetineuraceae, Isodrepaniaceae, Pseudotaxiphyllaceae, Rozeaceae, one reduced family, Climaciaceae. We also transferred liverwort family Calyculariaceae from Fossombroniales Pelliales. Recent advancements molecular have revolutionized bryophyte classification, tending be more fragmental. Hence, further revised classification system for includes 45 142 families mosses, 23 85 liverworts, five hornworts.

Language: Английский

Citations

10
Genetics and Genomics of Infectious Diseases in Key Aquaculture Species DOI Creative Commons
Nguyen Hong Nguyen

Biology, Journal Year: 2024, Volume and Issue: 13(1), P. 29 - 29

Published: Jan. 4, 2024

Diseases pose a significant and pressing concern for the sustainable development of aquaculture sector, particularly as their impact continues to grow due climatic shifts such rising water temperatures. While various approaches, ranging from biosecurity measures vaccines, have been devised combat infectious diseases, efficacy is disease species specific contingent upon multitude factors. The fields genetics genomics offer effective tools control prevent outbreaks in aquatic animal species. In this study, we present key findings our recent research, focusing on genetic resistance three diseases: White Spot Syndrome Virus (WSSV) white shrimp, Bacterial Necrotic Pancreatitis (BNP) striped catfish, skin fluke (a parasitic ailment) yellowtail kingfish. Our investigations reveal that all possess substantial heritable components disease-resistant traits, indicating potential responsiveness artificial selection improvement programs tailored these diseases. Also, observed high association between traits survival rates. Through selective breeding aimed at enhancing pathogens, achieved gains, averaging 10% per generation. These also contributed positively overall production performance productivity Although effects immunological or immune responses were not they yielded favorable results catfish. Furthermore, genomic analyses, including shallow genome sequencing pedigreed populations, enriched understanding architecture underlying traits. are primarily governed by polygenic nature, with numerous genes variants, each small effects. Leveraging range advanced statistical methods, mixed models machine deep learning, developed prediction demonstrated moderate-to-high levels accuracy forecasting disease-related addition genomics, RNA-seq experiments identified several undergo upregulation response infection viral loads within populations. Preliminary microbiome data, while offering limited predictive one studied species, underscore combining data sequence information enhance power Lastly, paper briefly discusses roles precision agriculture systems AI algorithms outlines path future research expedite lines target conclusion, study underscores critical role fortifying sector against threats posed paving way more resilient development.

Language: Английский

Citations

9
Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants DOI Creative Commons
Marek L. Borowiec, Y. Miles Zhang, Karen Neves

et al.

Systematic Biology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 8, 2025

Abstract While some relationships in phylogenomic studies have remained stable since the Sanger sequencing era, many challenging nodes remain, even with genome-scale data. Incongruence or lack of resolution era is frequently attributed to inadequate data modeling and analytical issues that lead systematic biases. However, few investigate potential for random error establish expectations level achievable a given empirical dataset integrate uncertainties across methods when faced conflicting results. Ants are most species-rich lineage social insects one ecologically important terrestrial animals. Consequently, ants garnered significant research attention, including their systematics. Despite this, there has been no comprehensive genus-level phylogeny inferred using genomic thoroughly evaluates both signal strength incongruence. In this study, we provide insight into quantify uncertainty ant tree life by utilizing taxonomically Ultraconserved Elements date, 277 (81%) recognized genera from all 16 extant subfamilies, representing over 98% described species. We use simulations resolution, identify branches less-than-expected concordance, dissect effects model selection on recalcitrant nodes. Simulations show hundreds loci needed resolve our phylogeny. This demonstrates continued role studies. Our analyses picture support incongruence phylogeny, while offering more nuanced depiction significantly expanding generic sampling. consensus approach different find assumptions about root age exert substantial influence divergence dating. results suggest advancing understanding will require not only but also refined phylogenetic models. workflow identifying under-supported concatenation analyses, outline pragmatic way reconcile phylogenomics, introduce user-friendly locus tool

Language: Английский

Citations

1
Genomics of Triatominae, the Chagas Disease Vectors DOI
Antonella Bacigalupo, Sebastián Pita

Published: Jan. 1, 2025

Language: Английский

Citations

1
Disentangling a genome-wide mosaic of conflicting phylogenetic signals in Western Rattlesnakes DOI
Justin M. Bernstein, Yannick Francioli, Drew R. Schield

et al.

Molecular Phylogenetics and Evolution, Journal Year: 2025, Volume and Issue: unknown, P. 108309 - 108309

Published: Feb. 1, 2025

Language: Английский

Citations

1
A genome-based phylogeny for Mollusca is concordant with fossils and morphology DOI Open Access
Zeyuan Chen, J. Antonio Baeza, Chong Chen

et al.

Science, Journal Year: 2025, Volume and Issue: 387(6737), P. 1001 - 1007

Published: Feb. 27, 2025

Extreme morphological disparity within Mollusca has long confounded efforts to reconstruct a stable backbone phylogeny for the phylum. Familiar molluscan groups—gastropods, bivalves, and cephalopods—each represent diverse radiation with myriad morphological, ecological, behavioral adaptations. The phylum further encompasses many more unfamiliar experiments in animal body-plan evolution. In this work, we reconstructed living on basis of metazoan BUSCO (Benchmarking Universal Single-Copy Orthologs) genes extracted from 77 (13 new) genomes, including multiple members all eight classes two high-quality genome assemblies monoplacophorans. Our analyses confirm proposed morphology show widespread genomic variation. flexibility likely explains both historic challenges their genomes evolutionary success.

Language: Английский

Citations

1