Horizontal gene transfer in eukaryotes: aligning theory with data

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: 25(6), P. 416 - 430

Published: Jan. 23, 2024

Language: Английский

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Mechanisms That Shape Microbial Pangenomes

Trends in Microbiology, Journal Year: 2021, Volume and Issue: 29(6), P. 493 - 503

Published: Jan. 9, 2021

Language: Английский

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Global patterns and rates of habitat transitions across the eukaryotic tree of life

Nature Ecology & Evolution, Journal Year: 2022, Volume and Issue: 6(10), P. 1458 - 1470

Published: Aug. 4, 2022

Abstract The successful colonization of new habitats has played a fundamental role during the evolution life. Salinity is one strongest barriers for organisms to cross, which resulted in distinct marine and non-marine (including both freshwater soil) communities. Although microbes represent by far vast majority eukaryote diversity, salt barrier shaping diversity across eukaryotic tree poorly known. Traditional views suggest rare ancient marine/non-marine transitions but this view being challenged discovery several recently transitioned lineages. Here, we investigate habitat eukaryotes using unique set taxon-rich phylogenies inferred from combination long-read short-read environmental metabarcoding data spanning ribosomal DNA operon. Our results show that, overall, microbial communities are phylogenetically have occurred directions almost all major lineages, with hundreds transition events detected. Some groups experienced relatively high rates transitions, most notably fungi crossing probably been an important aspect their diversification. At deepest phylogenetic levels, ancestral reconstruction analyses that may first evolved two largest known assemblages (TSAR Amorphea) arose different habitats. Overall, our findings indicate provide global perspective on domain

Language: Английский

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Diatom heterotrophy on brown algal polysaccharides emerged through horizontal gene transfer, gene duplication, and neofunctionalization

PLoS Biology, Journal Year: 2025, Volume and Issue: 23(4), P. e3003038 - e3003038

Published: April 1, 2025

A major goal of evolutionary biology is to identify the genetic basis for emergence complex adaptive traits. Diatoms are ancestrally photosynthetic microalgae. However, in genus Nitzschia , loss photosynthesis led a group free-living secondary heterotrophs whose manner acquiring chemical energy unclear. Here, we sequence genome non-photosynthetic diatom sing1 and its catabolism brown algal cell wall polysaccharide alginate. N . obtained an endolytic alginate lyase enzyme by horizontal gene transfer (HGT) from marine bacterium. Subsequent duplication through unequal crossing over transposition 91 genes three distinct families. One family retains ancestral function. By contrast, two others underwent domain duplication, gain, loss, rearrangement, mutation encode novel functions that can account oligosaccharide import endomembrane system exolytic production monosaccharides. Together, our results show how single HGT event followed substantial neofunctionalization access new ecological niche.

Language: Английский

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The fate of artificial transgenes in Acanthamoeba castellanii

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: April 13, 2025

The soil amoeba Acanthamoeba castellanii is an emerging model organism with which to study a wide range of biomedical, microbiological, and evolutionary phenomena. While transformation systems were established for this more than two decades ago, the fate artificial transgenes has not been well characterized. In study, experiments performed investigate how A. genome responds foreign DNA presented in both circular linear plasmid form. Nanopore sequencing was used as high throughput method screen transgene resulting transformant cultures, candidate integrations identified. Molecular biology validate sequence data provide additional context on transgenes. A devised estimate rate read chimerism nanopore runs accurately account effects identifying putative integrations. Based experimental hand, potential mechanism maintenance proposed, one incoming tandemly duplicated telomeres are added ends. Our results suggest that leads molecules maintained telomere-containing, transgene-bearing minichromosomes, may facilitate chromosomal integration. This process allow lateral gene transfer by expanding window opportunity exogenous be taken up integrated into genome. Similar mechanisms exist other eukaryote groups, suggesting widespread feature biology.

Language: Английский

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Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(4)

Published: Jan. 8, 2021

Significance The ochrophytes are an ancient and important group of eukaryotic algae, including diatoms, the most photosynthesisers in modern ocean, a wide range other species. Throughout their history, have exchanged genes with bacteria eukaryotes through horizontal gene transfer (HGT), diversifying cell biology. Here, we profile thousands phylogenetic trees, showing that HGTs from contribute particularly to recent evolution occurring more frequently than and, potentially, diatoms ochrophytes. Using experimental computational techniques, show bacterial predominantly impact diatom secreted proteome, which may striking evolutionary success diatoms.

Language: Английский

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Endogenous giant viruses contribute to intraspecies genomic variability in the model green alga Chlamydomonas reinhardtii

Virus Evolution, Journal Year: 2022, Volume and Issue: 8(2)

Published: July 1, 2022

Chlamydomonas reinhardtii is a unicellular eukaryotic alga that has been studied as model organism for decades. Despite an extensive history system, phylogenetic and genetic characteristics of viruses infecting this have remained elusive. We analyzed high-throughput genome sequence data C. field isolates, in six we discovered sequences belonging to endogenous giant reach up several 100 kb length. In addition, also the entire closely related virus endogenized within incerta, closest sequenced relative reinhardtii. Endogenous add hundreds new gene families host strains, highlighting their contribution pangenome dynamics interstrain genomic variability Our findings suggest endogenization may important implications structuring population ecology protists environment.

Language: Английский

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Extreme genome diversity and cryptic speciation in a harmful algal-bloom-forming eukaryote

Current Biology, Journal Year: 2023, Volume and Issue: 33(11), P. 2246 - 2259.e8

Published: May 23, 2023

Harmful algal blooms of the toxic haptophyte Prymnesium parvum are a recurrent problem in many inland and estuarine waters around world. Strains P. vary toxins they produce other physiological traits associated with harmful blooms, but genetic basis for this variation is unknown. To investigate genome diversity morphospecies, we generated assemblies 15 phylogenetically geographically diverse strains parvum, including Hi-C guided, near-chromosome-level two strains. Comparative analysis revealed considerable DNA content between strains, ranging from 115 to 845 Mbp. included haploids, diploids, polyploids, not all differences were due copy number. Haploid size different chemotypes differed by as much 243 Syntenic phylogenetic analyses indicate that UTEX 2797, common laboratory strain Texas, hybrid retains distinct haplotypes. Investigation gene families variably present across identified several functional categories metabolic genes biosynthesis metabolites proliferation transposable elements. Together, our results comprises multiple cryptic species. These genomes provide robust genomic framework investigations into eco-physiological consequences intra- inter-specific demonstrate need similar resources algal-bloom-forming morphospecies.

Language: Английский

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Reconstructing the last common ancestor of all eukaryotes

PLoS Biology, Journal Year: 2024, Volume and Issue: 22(11), P. e3002917 - e3002917

Published: Nov. 25, 2024

Understanding the origin of eukaryotic cells is one most difficult problems in all biology. A key challenge relevant to question eukaryogenesis reconstructing gene repertoire last common ancestor (LECA). As data sets grow, sketching an accurate genomics-informed picture early cellular complexity requires provision analytical resources and a commitment sharing. Here, we summarise progress towards understanding biology LECA outline community approach inferring its wider repertoire. Once assembled, robust set will be useful tool for evaluating alternative hypotheses about eukaryotes evolution traits descendant lineages, with relevance diverse fields such as cell biology, microbial ecology, biotechnology, agriculture, medicine. In this Consensus View, put forth status quo agreed path forward reconstruct LECA's content.

Language: Английский

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Diversity of electron transport chains in anaerobic protists

Biochimica et Biophysica Acta (BBA) - Bioenergetics, Journal Year: 2020, Volume and Issue: 1862(1), P. 148334 - 148334

Published: Nov. 5, 2020

Eukaryotic microbes (protists) that occupy low-oxygen environments often have drastically different mitochondrial metabolism compared to their aerobic relatives. A common theme among many anaerobic protists is the serial loss of components electron transport chain (ETC). Here, we discuss diversity ETC across tree eukaryotes and review hypotheses for how ETCs are modified, ultimately lost, in protists. We find while converged some same as animals, there clear protist-specific strategies thrive without oxygen.

Language: Английский

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