Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree DOI Creative Commons
David Dylus, Adrian Altenhoff, Sina Majidian

и другие.

Nature Biotechnology, Год журнала: 2023, Номер 42(1), С. 139 - 147

Опубликована: Апрель 20, 2023

Abstract Current methods for inference of phylogenetic trees require running complex pipelines at substantial computational and labor costs, with additional constraints in sequencing coverage, assembly annotation quality, especially large datasets. To overcome these challenges, we present Read2Tree, which directly processes raw reads into groups corresponding genes bypasses traditional steps phylogeny inference, such as genome assembly, all-versus-all sequence comparisons, while retaining accuracy. In a benchmark encompassing broad variety datasets, Read2Tree is 10–100 times faster than assembly-based approaches most cases more accurate—the exception being when coverage high reference species very distant. Here, to illustrate the applicability tool, reconstruct yeast tree life 435 spanning 590 million years evolution. We also apply >10,000 Coronaviridae samples, accurately classifying highly diverse animal samples near-identical severe acute respiratory syndrome coronavirus 2 sequences on single tree. The speed, accuracy versatility enable comparative genomics scale.

Язык: Английский

Biological sequence analysis DOI

Samvedna Shukla,

Bhawana Mishra, Himanshu Avashthi

и другие.

Elsevier eBooks, Год журнала: 2021, Номер unknown, С. 33 - 47

Опубликована: Окт. 22, 2021

Язык: Английский

Процитировано

1263
ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference DOI Creative Commons
Jacob L. Steenwyk, Thomas J. Buida, Yuanning Li

и другие.

PLoS Biology, Год журнала: 2020, Номер 18(12), С. e3001007 - e3001007

Опубликована: Дек. 2, 2020

Highly divergent sites in multiple sequence alignments (MSAs), which can stem from erroneous inference of homology and saturation substitutions, are thought to negatively impact phylogenetic inference. Thus, several different trimming strategies have been developed for identifying removing these prior However, a recent study reported that doing so worsen inference, underscoring the need alternative alignment strategies. Here, we introduce ClipKIT, an software that, rather than putatively phylogenetically uninformative sites, instead aims identify retain parsimony-informative known be informative. To test efficacy examined accuracy support phylogenies inferred 14 strategies, including those implemented across nearly 140,000 broad sampling evolutionary histories. Phylogenies ClipKIT-trimmed accurate, robust, time saving. Furthermore, ClipKIT consistently outperformed other methods diverse datasets, suggesting based on retaining provide robust framework trimming.

Язык: Английский

Процитировано

437
Ancient gene linkages support ctenophores as sister to other animals DOI Creative Commons
Darrin T. Schultz, Steven H. D. Haddock, Jessen V. Bredeson

и другие.

Nature, Год журнала: 2023, Номер 618(7963), С. 110 - 117

Опубликована: Май 17, 2023

Abstract A central question in evolutionary biology is whether sponges or ctenophores (comb jellies) are the sister group to all other animals. These alternative phylogenetic hypotheses imply different scenarios for evolution of complex neural systems and animal-specific traits 1–6 . Conventional approaches based on morphological characters increasingly extensive gene sequence collections have not been able definitively answer this 7–11 Here we develop chromosome-scale linkage, also known as synteny, a character resolving 12 We report new genomes ctenophore two marine sponges, three unicellular relatives animals (a choanoflagellate, filasterean amoeba an ichthyosporean) that serve outgroups analysis. find ancient syntenies conserved between their close relatives. Ctenophores eukaryotes share ancestral metazoan patterns, whereas bilaterians, cnidarians derived chromosomal rearrangements. Conserved syntenic unite with cnidarians, placozoans monophyletic clade exclusion ctenophores, placing The patterns synteny shared by result rare irreversible chromosome fusion-and-mixing events provide robust unambiguous support ctenophore-sister hypothesis. findings framework deep, recalcitrant problems implications our understanding animal evolution.

Язык: Английский

Процитировано

232
Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes DOI
Raúl Riesco, Martha E. Trujillo

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Год журнала: 2024, Номер 74(3)

Опубликована: Март 21, 2024

The field of microbial taxonomy is dynamic, aiming to provide a stable and contemporary classification system for prokaryotes. Traditionally, reliance on phenotypic characteristics limited the comprehensive understanding diversity evolution. introduction molecular techniques, particularly DNA sequencing genomics, has transformed our perception prokaryotic diversity. In past two decades, advancements in genome have transitioned from traditional methods genome-based taxonomic framework, not only define species, but also higher ranks. As technology databases rapidly expand, maintaining updated standards crucial. This work seeks revise 2018 guidelines applying data taxonomy, adapting minimal recommendations reflect technological progress during this period.

Язык: Английский

Процитировано

182
Cyanobacteria and biogeochemical cycles through Earth history DOI
Patricia Sánchez‐Baracaldo, Giorgio Bianchini, Jamie D. Wilson

и другие.

Trends in Microbiology, Год журнала: 2021, Номер 30(2), С. 143 - 157

Опубликована: Июль 4, 2021

Язык: Английский

Процитировано

179
PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data DOI
Jacob L. Steenwyk, Thomas J. Buida, Abigail L. LaBella

и другие.

Bioinformatics, Год журнала: 2021, Номер 37(16), С. 2325 - 2331

Опубликована: Фев. 5, 2021

Diverse disciplines in biology process and analyze multiple sequence alignments (MSAs) phylogenetic trees to evaluate their information content, infer evolutionary events processes predict gene function. However, automated processing of MSAs remains a challenge due the lack unified toolkit. To fill this gap, we introduce PhyKIT, toolkit for UNIX shell environment with 30 functions that trees, including but not limited estimation mutation rate, evaluation composition biases, calculation degree violation molecular clock collapsing bipartitions (internal branches) low support.To demonstrate utility detail three use cases: (1) summarizing content diagnosing potential biases or tree data; (2) evaluating gene-gene covariation rates identify functional relationships, novel ones, among genes (3) resolution polytomies which are suggestive rapid radiation data. We anticipate PhyKIT will be useful processing, examining deriving biological meaning from increasingly large phylogenomic datasets.PhyKIT is freely available on GitHub (https://github.com/JLSteenwyk/PhyKIT), PyPi (https://pypi.org/project/phykit/) Anaconda Cloud (https://anaconda.org/JLSteenwyk/phykit) under MIT license extensive documentation user tutorials (https://jlsteenwyk.com/PhyKIT).Supplementary data at Bioinformatics online.

Язык: Английский

Процитировано

158
Integrating gene annotation with orthology inference at scale DOI
Bogdan Kirilenko, Chetan Munegowda, Ekaterina Osipova

и другие.

Science, Год журнала: 2023, Номер 380(6643)

Опубликована: Апрель 27, 2023

Annotating coding genes and inferring orthologs are two classical challenges in genomics evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method integrates structural gene annotation orthology inference. implements different paradigm orthologous loci, improves ortholog detection of conserved compared with state-of-the-art methods, handles even highly fragmented assemblies. scales hundreds genomes, which we demonstrate by applying it 488 placental mammal 501 bird assemblies, creating the largest comparative resources so far. Additionally, detects losses, enables selection screens, automatically provides superior measure mammalian genome quality. is powerful scalable annotate compare genomic era.

Язык: Английский

Процитировано

92
Sustainable Design of Structural and Functional Polymers for a Circular Economy DOI Creative Commons
Bernhard von Vacano, Hannah Mangold,

Guido W. M. Vandermeulen

и другие.

Angewandte Chemie International Edition, Год журнала: 2022, Номер 62(12)

Опубликована: Окт. 5, 2022

To achieve a sustainable circular economy, polymer production must start transitioning to recycled and biobased feedstock accomplish CO2 emission neutrality. This is not only true for structural polymers, such as in packaging or engineering applications, but also functional polymers liquid formulations, adhesives, lubricants, thickeners dispersants. At their end of life, be either collected via technical pathway, biodegradable if they are collectable. Advances chemistry aided by computational material science, open the way addressing these issues comprehensively designing recyclability biodegradability. Review explores how scientific progress, together with emerging regulatory frameworks, societal expectations economic boundary conditions, paint pathways transformation towards economy polymers.

Язык: Английский

Процитировано

78
MEGA12: Molecular Evolutionary Genetic Analysis version 12 for adaptive and green computing DOI Creative Commons
Sudhir Kumar,

Glen Stecher,

Michael Suleski

и другие.

Molecular Biology and Evolution, Год журнала: 2024, Номер 41(12)

Опубликована: Дек. 1, 2024

Abstract We introduce the 12th version of Molecular Evolutionary Genetics Analysis (MEGA12) software. This latest brings many significant improvements by reducing computational time needed for selecting optimal substitution models and conducting bootstrap tests on phylogenies using maximum likelihood (ML) methods. These are achieved implementing heuristics that minimize likely unnecessary computations. Analyses empirical simulated datasets show substantial savings these without compromising accuracy results. MEGA12 also links-in an evolutionary sparse learning approach to identify fragile clades associated sequences in trees inferred through phylogenomic analyses. In addition, this includes fine-grained parallelization ML analyses, support high-resolution monitors, enhanced Tree Explorer. can be downloaded from https://www.megasoftware.net.

Язык: Английский

Процитировано

77
The promise and pitfalls of synteny in phylogenomics DOI Creative Commons
Jacob L. Steenwyk,

Nicole King

PLoS Biology, Год журнала: 2024, Номер 22(5), С. e3002632 - e3002632

Опубликована: Май 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.

Язык: Английский

Процитировано

20