A De Novo Transcriptome Assembly ofCeratopteris richardiiProvides Insights into the Evolutionary Dynamics of Complex Gene Families in Land Plants

Genome Biology and Evolution, Год журнала: 2021, Номер 13(3)

Опубликована: Март 1, 2021

As the closest extant sister group to seed plants, ferns are an important reference point study origin and evolution of plant genes traits. One bottleneck use in phylogenetic genetic studies is fact that genome-level sequence information this limited, due extreme genome sizes most ferns. Ceratopteris richardii (hereafter Ceratopteris) has been widely used as a model system for In study, we generated transcriptome Ceratopteris, through de novo assembly RNA-seq data from 17 sequencing libraries derived two sexual types gametophytes five different sporophyte tissues. The transcriptome, together with 38 genomes transcriptomes other species across Viridiplantae, were uncover evolutionary dynamics orthogroups (predicted gene families using OrthoFinder) within euphyllophytes identify proteins associated major shifts morphology physiology occurred last common ancestors euphyllophytes, ferns, plants. Furthermore, resource was classify GRAS domain transcriptional regulators many developmental processes Through analysis each 15 orthogroups, uncovered which family members conserved or have diversified Taken together, database analyses reported here provide platform exploring land plants studying function seed-free vascular

Язык: Английский

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Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection

Molecular Systems Biology, Год журнала: 2021, Номер 17(10)

Опубликована: Окт. 1, 2021

Yeasts are known to have versatile metabolic traits, while how these traits evolved has not been elucidated systematically. We performed integrative evolution analysis investigate genomic determines trait generation by reconstructing genome-scale models (GEMs) for 332 yeasts. These GEMs could comprehensively characterize diversity and predict enzyme functionality, thereby signifying that sequence-level shaped reaction networks towards new functions. Strikingly, using GEMs, we can mechanistically map different evolutionary events, e.g. horizontal gene transfer duplication, onto relevant subpathways explain plasticity. This demonstrates family expansion promiscuity prominent mechanisms gains, GEM simulations reveal additional factors, such as loss from distant pathways, contribute losses. Furthermore, our pinpoint specific genes pathways under positive selection the formulation of complex i.e. thermotolerance Crabtree effect. Our findings illustrate multidimensional in both network structure individual enzymes drives phenotypic variations.

Язык: Английский

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Horizontal gene transfer in yeasts

Current Opinion in Genetics & Development, Год журнала: 2022, Номер 76, С. 101950 - 101950

Опубликована: Июль 13, 2022

Язык: Английский

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Microbial Dynamics in Sour–Sweet Wine Vinegar: Impacts on Chemical and Sensory Composition

Applied Sciences, Год журнала: 2023, Номер 13(13), С. 7366 - 7366

Опубликована: Июнь 21, 2023

The most known and traditional vinegar is the one that made from wine. For its production, grape must undergo alcohol fermentation posterior oxidation of ethanol to acetic acid. Yeasts acid bacteria (AAB) carry out biochemical processes in sequence. process wine acetification can be achieved by slow (the Orléans or French methods) a quick submerged industrial process. High-quality usually produced methods using oak casks, once wood allows continuous aeration culture. Sour–sweet presents balance both bitter/sour sweet flavors. sourness typically comes acid, while sweetness come type fruit amount sugar present at end production. In general, sour-sweet has more complex nuanced flavor profile compared regular vinegar, which often simply sour. One kind where yeasts co-exist produce savory balsamic (TBV), Italy. Spain, fortified sherry also been used for Portugal, some companies have port since 2018. These three distinctive products common found, well balanced with sourness. this review, we analyze sour-sweat process, bearing mind possible interactions between AAB occur during production considering symbiotic competitive features diverse microbiota.

Язык: Английский

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Multilayered horizontal operon transfers from bacteria reconstruct a thiamine salvage pathway in yeasts

Proceedings of the National Academy of Sciences, Год журнала: 2019, Номер 116(44), С. 22219 - 22228

Опубликована: Окт. 14, 2019

Horizontal acquisition of bacterial genes is presently recognized as an important contribution to the adaptation and evolution eukaryotic genomes. However, mechanisms underlying expression consequent selection fixation prokaryotic in new setting are largely unknown. Here we show that composing pathway for synthesis essential vitamin B1 (thiamine) were lost ancestor a yeast lineage, Wickerhamiella/Starmerella (W/S) clade, known harbor unusually large number alien origin. The thiamine was subsequently reassembled, at least twice, by multiple HGT events from different donors involving both single entire operons. In W/S-clade species Starmerella bombicola obtained direct genetic evidence all functional. reconstructed composed operating coordinately scavenge derivatives environment. newly acquired operons involved repertoire until now only sparsely documented, namely longer intergenic regions, post-horizontal gene transfer (HGT) fusions fostering coordinated expression, relocation, possibly recombination generating mosaic genes. results provide additional occurred recurrently this lineage crucial reestablishment functions similar used across broad range microbes promote their

Язык: Английский

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