The evolutionary landscape of prokaryotic chromosome/plasmid balance

Communications Biology, Journal Year: 2024, Volume and Issue: 7(1)

Published: Nov. 4, 2024

The balance between chromosomal and plasmid DNAs determines the genomic plasticity of prokaryotes. Natural selections, acting on level organisms or plasmids, shape abundances in prokaryotic genomes. Despite importance plasmids health engineering, there have been rare systematic attempts to quantitatively model predict determinants underlying strength different selection forces. Here, we develop a metabolic flux that describes intracellular resource competition plasmid-encoded reactions. By coarse graining, this predicts landscape natural selections chromosome/plasmid balance, which is featured by tradeoff phenotypic non-phenotypic pressures. This further validated observed pattern distributions vast collection genomes retrieved from NCBI database. Our results establish universal paradigm understand interplay provide insights into evolutionary origin diversity. An sheds light forces govern

Language: Английский

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Founder events and subsequent genetic bottlenecks underlie karyotype evolution in the Ibero-North African endemic Carex helodes

Annals of Botany, Journal Year: 2023, Volume and Issue: 133(5-6), P. 871 - 882

Published: July 3, 2023

Despite chromosomal evolution being one of the major drivers diversification in plants, we do not yet have a clear view how new chromosome rearrangements become fixed within populations, which is crucial step forward for understanding speciation.

Language: Английский

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Genome size variation and whole-genome duplications in the monocot order Poales

Research Square (Research Square), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 12, 2023

Abstract Nuclear genome sizes of 54 representative species from 44 genera the monocot order Poales were investigated by flow cytometry (FCM). Small holoploid genomes with < 2 pg/2C are characteristic Poales, only some families have larger 2C values, although this is not consistently case. The monoploid as well mean DNA content per chromosome (MC) show a similar pattern. A comparison size data current molecular phylogenetic suggests that small (1Cx 0.4 pg) and chromosomes (MC ≤ 0.05 pg), found in families, likely ancestral features Poales. Conspicuous increases occurred particularly Poaceae (grasses) to lesser extent xyrid clade restios. According previous phylogenomic studies, characterized whole-genome duplication (WGDs) called ρ, which absent all other families. However, it clear 1Cx ρ event not, or no longer, associated significant increase minimum grasses compared Future studies need clarify whether smallest values due secondary reduction nuclear after relatively large minimal caused further WGD within

Language: Английский

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Chromosome-Scale Genome Assembly for Soft-Stem Bulrush (Schoenoplectus tabernaemontani) Confirms a Clade-Specific Whole-Genome Duplication in Cyperaceae

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(7)

Published: July 1, 2024

Schoenoplectus tabernaemontani (C. C. Gmelin) Palla is a typical macrophyte in diverse wetland ecosystems. This species holds great potential decontamination applications and carbon sequestration. Previous studies have shown that this may experienced recent polyploidization. would make S. unique model to study the processes consequences of whole-genome duplications context well-documented holocentric chromosomes dysploidy events Cyperaceae. However, inference was not completely solid because it lacked homology information essential ascertain polyploidy. We present here first chromosome-level genome assembly for tabernaemontani. By combining Oxford Nanopore Technologies (ONT) long reads Illumina short reads, plus chromatin conformation via Hi-C method, we assembled spanning 507.96 Mb, with 99.43% data accurately mapped assembly. The contig N50 value 3.62 Mb. overall BUSCO score 94.40%. About 68.94% comprised repetitive elements. A total 36,994 protein-coding genes were predicted annotated. Long terminal repeat retrotransposons accounted ∼26.99% genome, surpassing content observed most sequenced Cyperid genomes. Our well-supported haploid 21 pseudochromosomes, each harboring putative centromeres. findings corroborated karyotype 2n = 2X 42. also confirmed duplication occurring after divergence between Schoenoplecteae Bolboschoeneae. expands scope genomes within Cyperaceae family, encompassing fifth genus. It provides research resources on evolution conservation.

Language: Английский

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Chromosome numbers in Bolboschoenus (Cyperaceae) correspond to main morphotypes at a worldwide scale

Plant Systematics and Evolution, Journal Year: 2024, Volume and Issue: 311(1)

Published: Dec. 14, 2024

Language: Английский

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Macroevolutionary inference of complex modes of chromosomal speciation in a cosmopolitan plant lineage

New Phytologist, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 25, 2024

The effects of single chromosome number change-dysploidy - mediating diversification remain poorly understood. Dysploidy modifies recombination rates, linkage, or reproductive isolation, especially for one-fifth all eukaryote lineages with holocentric chromosomes. on have not been estimated because modeling numbers linked to heterogeneity along phylogenies is quantitatively challenging. We propose a new state-dependent model evolution that links rates dysploidy considering and differentiates between anagenetic cladogenetic changes. apply this Carex (Cyperaceae), cosmopolitan flowering plant clade recover two distinct modes chromosomal speciation in Carex. In one mode, occurs frequently drives faster rates. the other rare, driven by hidden, unmeasured factors. When we use excludes hidden states, mistakenly infer strong, uniformly positive effect diversification, showing standard models may lead confident but incorrect conclusions about diversification. This study demonstrates can significant role large despite presence factors simultaneously affect

Language: Английский

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Macroevolutionary inference of complex modes of chromosomal speciation in a cosmopolitan plant lineage

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

Published: Sept. 7, 2023

Summary The effects of single chromosome number change—dysploidy—mediating diversification remain poorly understood. Dysploidy modifies recombination rates, linkage, or reproductive isolation, especially for one-fifth all eukaryote lineages with holocentric chromosomes. on have not been estimated because modeling numbers linked to heterogeneity along phylogenies is quantitatively challenging. We propose a new state-dependent model evolution that links rates dysploidy considering and differentiates between anagenetic cladogenetic changes. apply this Carex (Cyperaceae), cosmopolitan flowering plant clade recover two distinct modes chromosomal speciation in . In one mode, occurs frequently drives faster rates. the other rare driven by hidden, unmeasured factors. When we use excludes hidden states, mistakenly infer strong, uniform positive effect diversification, showing standard models may lead confident but incorrect conclusions about diversification. This study demonstrates can significant role large despite presence factors simultaneously affect

Language: Английский

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The global distribution of angiosperm genome size is shaped by climate

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Dec. 8, 2022

Summary Angiosperms, which inhabit diverse environments across all continents, exhibit significant variation in genome sizes, making them an excellent model system for examining hypotheses about the global distribution of size. These include previously proposed large-genome-constraint, mutational-hazard, polyploidy-mediated, and climate-mediated hypotheses. We compiled largest size dataset to date, encompassing >5% known angiosperm species, analyzed using a comprehensive geographic angiosperms. observed that angiosperms with large range sizes generally had small genomes, supporting large-genome-constraint hypothesis. Climate was shown exert strong influence on along latitudinal gradient, while frequency polyploidy type growth form negligible effects. In contrast unimodal patterns gradient by plant traits polyploid proportions, increase from equator 40-50°N/S is probably mediated different (mostly climatic) mechanisms than decrease 40–50°N northwards. Our analysis suggests mainly shaped climatically-mediated purifying selection, genetic drift, relaxed environmental filtering.

Language: Английский

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Evolução dos estudos acerca dos cromossomos holocêntricos: uma revisão de literatura

Research Society and Development, Journal Year: 2022, Volume and Issue: 11(17), P. e213111739082 - e213111739082

Published: Dec. 26, 2022

A principal fonte de estudo da citogenética é o cromossomo, cujo uma estrutura celular composta por material genético e proteínas. Os cromossomos podem ser divididos em holocêntricos que são não apresentam centrômeros localizados ao longo sua estrutura, diferentemente dos monocêntricos, os quais possuem centrômero localizado, qual tipo cromossomo mais comum nas espécies geral. O presente buscou revisar bibliograficamente estudos acerca afim acompanhar a evolução das pesquisas dessa temática. revisão literatura foi feita partir dados bibliográficos sites busca como Google Acadêmico, Scielo, PubMed Lilacs. Foram achados todo 5.024 artigos científicos, onde apenas dez deles foram dispostos numa tabela acordo com critérios metodologia. Ainda existam bastante holocêntricos, necessárias para esclarecer algumas dúvidas evolutivas, especiação comparações taxonômicas entre as do mesmo gênero.

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