Dosage-sensitivity shapes how genes transcriptionally respond to allopolyploidy and homoeologous exchange in resynthesized Brassica napus

Genetics, Journal Year: 2023, Volume and Issue: 225(1)

Published: June 20, 2023

The gene balance hypothesis proposes that selection acts on the dosage (i.e. copy number) of genes within dosage-sensitive portions networks, pathways, and protein complexes to maintain balanced stoichiometry interacting proteins, because perturbations stoichiometric can result in reduced fitness. This has been called selection. Dosage is also hypothesized constrain expression responses changes, making (those encoding members proteins) experience more similar changes. In allopolyploids, where whole-genome duplication involves hybridization diverged lineages, organisms often homoeologous exchanges recombine, duplicate, delete regions genome alter pairs. Although makes predictions about response exchanges, they have not empirically tested. We used genomic transcriptomic data from 6 resynthesized, isogenic Brassica napus lines over 10 generations identify analyzed responses, tested for patterns imbalance. Groups had less variable than dosage-insensitive genes, a sign their relative constrained. difference was absent pairs whose biased toward B. A subgenome. Finally, duplication, suggesting create These findings expand our knowledge impact evolution potentially connect polyploid genomes time, homoeolog bias duplicate retention.

Language: Английский

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Genome‐wide patterns of homoeologous gene flow in allotetraploid coffee

Applications in Plant Sciences, Journal Year: 2024, Volume and Issue: 12(4)

Published: June 14, 2024

Allopolyploidy-a hybridization-induced whole-genome duplication event-has been a major driver of plant diversification. The extent to which chromosomes pair with their proper homolog vs. homoeolog in allopolyploids varies across taxa, and methods detect homoeologous gene flow (HGF) are needed understand how HGF has shaped polyploid lineages.

Language: Английский

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Variation in cytonuclear expression accommodation among allopolyploid plants

Genetics, Journal Year: 2022, Volume and Issue: 222(2)

Published: Aug. 11, 2022

Cytonuclear coevolution is a common feature among plants, which coordinates gene expression and protein products between the nucleus organelles. Consequently, lineage-specific differences may result in incompatibilities cytoplasm hybrid taxa. Allopolyploidy also phenomenon plant evolution. The nature of allopolyploids cytonuclear incompatibilities, but massive nuclear redundancy created during polyploidy affords additional avenues for resolving conflict (i.e. accommodation). Here we evaluate changes organelle-targeted genes 6 allopolyploid lineages that represent 4 genera Arabidopsis, Arachis, Chenopodium, Gossypium) encompass range polyploid ages. Because could potentially biases toward maternal homoeolog and/or level, patterns usage, bias, expression-level dominance relative to background noncytonuclear diploid parents. Although find subsets most match our expectations preference, these observations are not consistent either or categories genes. Our results indicate evolution be subtle variable genes, likely reflecting diversity mechanisms resolve nuclear-cytoplasmic species.

Language: Английский

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Genome-wide patterns of homoeologous gene flow in allotetraploid coffee

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

Published: Sept. 12, 2023

ABSTRACT Premise Allopolyploidy – a hybridization-induced whole-genome duplication event has been major driver of plant diversification. The extent to which chromosomes pair with their proper homolog vs. homoeolog in allopolyploids varies across taxa, and methods detect homoeologous gene flow (HGF) are needed understand how HGF shaped polyploid lineages. Methods ABBA-BABA test represents classic method for detecting introgression between closely related species, but here we developed modified use the characterize direction allotetraploid Coffea arabica . Results We found that is abundant C. genome, both subgenomes serving as donors recipients variation. also highly maternally biased plastid-targeted not mitochondrial-targeted genes, would be expected if plastid-nuclear incompatibilities exist two parent species. Discussion Together our analyses provide simple framework new evidence consistent selection favoring overwriting paternally derived alleles by ameliorate incompatibilities. Natural therefore appears shape intensity allopolyploid coffee, indicating cytoplasmic inheritance long-term consequences

Language: Английский

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Genome diploidization associates with cladogenesis, trait disparity, and plastid gene evolution

PLANT PHYSIOLOGY, Journal Year: 2022, Volume and Issue: 190(1), P. 403 - 420

Published: June 7, 2022

Abstract Angiosperm genome evolution was marked by many clade-specific whole-genome duplication events. The Microlepidieae is one of the monophyletic clades in mustard family (Brassicaceae) formed after an ancient allotetraploidization. Postpolyploid cladogenesis has resulted extant c. 17 genera and 60 species endemic to Australia New Zealand (10 species). As postpolyploid diploidization a trial-and-error process under natural selection, it may proceed with different intensity be associated speciation In Microlepidieae, extents homoeologous recombination between two parental subgenomes generated slow (“cold”) versus fast (“hot”) diploidization. To gain deeper understanding we analyzed phylogenetic relationships this tribe using complete chloroplast sequences, entire 35S rDNA units, abundant repetitive sequences. four recovered intra-tribal mirror varied genomes, suggesting that intrinsic genomic features underlying extent are shared among within clade. Nevertheless, even congeneric exert considerable morphological disparity (e.g. fruit shape), whereas some experience extensive convergence despite pace their We showed faster positively mean genes (plastid–nuclear coevolution). Higher rates perennials than annual were observed. Altogether, our results confirm potential as promising subject for analysis Brassicaceae.

Language: Английский

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Comparison of ONT and CCS sequencing technologies on the polyploid genome of a medicinal plant showed that high error rate of ONT reads are not suitable for self-correction

Chinese Medicine, Journal Year: 2022, Volume and Issue: 17(1)

Published: Aug. 9, 2022

Many medicinal plants are known for their complex genomes with high ploidy, heterozygosity, and repetitive content which pose severe challenges genome sequencing of those species. Long reads from Oxford nanopore technology (ONT) or Pacific Biosciences Single Molecule, Real-Time (SMRT) offer great advantages in de novo assembly, especially heterozygosity content. Currently, multiple allotetraploid species have sequenced by long-read sequencing. However, we found that a considerable proportion these (7.9% on average, maximum 23.7%) could not be covered NGS (Next Generation Sequencing) (uncovered region reads, UCR) suggesting the questionable low-quality area genomic areas can't due to bias. The underlying causes UCR assembly solutions this problem never been studied.

Language: Английский

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Population genomics and subgenome evolution of the allotetraploid frog Xenopus laevis in southern Africa

G3 Genes Genomes Genetics, Journal Year: 2022, Volume and Issue: 13(2)

Published: Dec. 16, 2022

Allotetraploid genomes have two distinct genomic components called subgenomes that are derived from separate diploid ancestral species. Many characteristics such as gene function, expression, recombination, and transposable element mobility may differ significantly between subgenomes. To explore the possibility subgenome population structure flow well, we examined genetic variation in an allotetraploid frog-the African clawed frog (Xenopus laevis)-over dynamic varied habitat of its native range southern Africa. Using reduced representation genome sequences 91 samples 12 localities, found no strong evidence differed substantially by subgenome. We then compared patterns nuclear to mitochondrial using Sanger 455 183 localities. Our results provide further resolution geographic distribution diversity this species illustrate both corresponds roughly with seasonal rainfall topography

Language: Английский

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Compensatory Genetic and Transcriptional Cytonuclear Coordination in Allopolyploid Lager Yeast (Saccharomyces pastorianus)

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(11)

Published: Oct. 19, 2022

Abstract Cytonuclear coordination between biparental-nuclear genomes and uniparental-cytoplasmic organellar in plants is often resolved by genetic transcriptional cytonuclear responses. Whether this mechanism also acts allopolyploid members of other kingdoms not clear. Additionally, interleaved cells/individuals within the same population underexplored. The yeast Saccharomyces pastorianus provides opportunity to explore coevolution during different growth stages from novel dimensions. Using S. cells multiple environment, we show that nuclear mitochondria-targeted genes have undergone both asymmetric gene conversion stage-specific biased expression favoring mitochondrial genome donor (Saccharomyces eubayanus). Our results suggest lager species entails an orchestrated compensatory evolutionary regulatory shift. common as well unique properties underlying allopolyploidy unicellular yeasts higher offers insights into mechanisms evolution associated with speciation.

Language: Английский

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Genome Evolution and Introgression in the New Zealand mud Snails Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(5)

Published: May 1, 2024

Abstract We have sequenced, assembled, and analyzed the nuclear mitochondrial genomes transcriptomes of Potamopyrgus estuarinus kaitunuparaoa, two prosobranch snail species native to New Zealand that together span continuum from estuary freshwater. These are closest known relatives freshwater antipodarum—a model for studying evolution sex, host–parasite coevolution, biological invasiveness—and thus provide key evolutionary context understanding its unusual biology. The P. kaitunuparaoa very similar in size overall gene content. Comparative analyses genome content indicate these harbor a near-identical set genes involved meiosis sperm functions, including seven with meiosis-specific functions. results consistent obligate sexual reproduction framework future comprising both obligately asexual lineages, each separately derived ancestor. Genome-wide multigene phylogenetic is likely relative antipodarum. nevertheless show there has been considerable introgression between kaitunuparaoa. That does not extend genome, which appears serve as barrier hybridization Nuclear-encoded whose products function joint mitochondrial-nuclear enzyme complexes exhibit patterns nonintrogression, indicating incompatibilities may prevented more extensive flow species.

Language: Английский

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Little Evidence for Homoeologous Gene Conversion and Homoeologous Exchange Events inGossypiumAllopolyploids

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

Published: Nov. 12, 2023

ABSTRACT A complicating factor in analyzing allopolyploid genomes is the possibility of physical interactions between homoeologous chromosomes during meiosis, resulting either crossover (homoeologous exchanges) or non-crossover products gene conversion). This latter process was first described cotton by comparing SNP patterns sequences from two diploid progenitors with those subgenomes. These analyses, however, did not explicitly account for autapomorphic SNPs that may lead to similar as conversion, creating uncertainties about reality inferred conversion events. Here, we use an expanded phylogenetic sampling high-quality genome assemblies seven Gossypium species (all derived same polyploidy event), four (two closely related each subgenome), and a outgroup derive robust method identifying potential genomic regions exchange. Using this new method, find little evidence cottons only forty best-supported events are shared more than one species. We do, reveal single, exchange event at end chromosome 1, which occurred shortly after allopolyploidization but prior divergence descendant Overall, our analyses demonstrate exchanges uncommon , affecting zero 24 genes per subgenome (0.0 - 0.065%) across More generally, highlight problems using simple four-taxon tests investigate established allopolyploids. SIGNIFICANCE STATEMENT Allopolyploidy prominent plant diversification, involving union divergent single nucleus via interspecific hybridization doubling. The merger sets motion variety inter-genomic epigenomic thought origin phenotypes. Among these recombinational duplicated chromosomes, can involve sequence lengths ranging several bases entire arms, be reciprocal unidirectional their effects. Here present analytical framework detecting processes allopolyploids, they have been rare group genus.

Language: Английский

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