Organellar transcripts dominate the cellular mRNA pool across plants of varying ploidy levels

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(30)

Published: July 19, 2022

Mitochondrial and plastid functions depend on coordinated expression of proteins encoded by genomic compartments that have radical differences in copy number organellar nuclear genomes. In polyploids, doubling the genome may add challenges to maintaining balanced involved cytonuclear interactions. Here, we use ribo-depleted RNA sequencing (RNA-seq) analyze transcript abundance for genomes leaf tissue from four different polyploid angiosperms their close diploid relatives. We find even though contain <1% genes genome, they generate majority (69.9 82.3%) messenger (mRNA) transcripts cell. are responsible a much smaller percentage (1.3 3.7%) mRNA pool but still produce higher abundances per gene compared genome. Nuclear encoding functionally interact with mitochondrial or products exhibit levels consistently more than 10-fold lower counterparts, indicating an extreme imbalance at level despite predominance equimolar interactions protein level. Nevertheless, interacting show strongly correlated across functional categories, suggesting observed stoichiometric does not preclude coordination expression. Finally, alter ratios relatives consistent systematic ways, successful plants able compensate perturbations associated doubling.

Language: Английский

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Cytonuclear interplay in auto‐ and allopolyploids: a multifaceted perspective from the Festuca‐Lolium complex

The Plant Journal, Journal Year: 2024, Volume and Issue: 118(4), P. 1102 - 1118

Published: Feb. 7, 2024

Restoring cytonuclear stoichiometry is necessary after whole-genome duplication (WGD) and interspecific/intergeneric hybridization in plants. We investigated this phenomenon auto- allopolyploids of the Festuca-Lolium complex providing insights into mechanisms governing interactions early polyploid hybrid generations. Our study examined main processes potentially involved restoring balance WGD comparing diploids new well-established autopolyploids. uncovered that both number chloroplasts chloroplast genome copies were significantly higher newly established autopolyploids grew further more The increase copy exceeded rise fully compensated for doubling nuclear genome. In addition, changes organelle gene expression insignificant. Allopolyploid Festuca × Lolium hybrids displayed potential structural conflicts parental protein variants within complexes. While biased maternal allele has been observed numerous hybrids, our results suggest its role stabilization limited. This provides restoration stoichiometry, yet it emphasizes need future research to explore post-transcriptional regulation impact on stoichiometry. findings may enhance understanding plant evolution, with broader implications diverse biological contexts.

Language: Английский

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Maternal dominance contributes to subgenome differentiation in allopolyploid fishes

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Dec. 15, 2023

Teleost fishes, which are the largest and most diverse group of living vertebrates, have a rich history ancient recent polyploidy. Previous studies allotetraploid common carp goldfish (cyprinids) reported dominant subgenome, is more expressed exhibits biased gene retention. However, underlying mechanisms contributing to observed 'subgenome dominance' remains poorly understood. Here we report high-quality genomes twenty-one cyprinids investigate origin subsequent subgenome evolution patterns following three independent allopolyploidy events. We identify closest extant relatives diploid progenitor species, genetic epigenetic differences among subgenomes, conclude that dominance likely due combination maternal transposable element densities in each polyploid. These findings provide an important foundation understanding teleost ultimately role polyploidy evolutionary innovations.

Language: Английский

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Polyploid plants take cytonuclear perturbations in stride

The Plant Cell, Journal Year: 2024, Volume and Issue: 36(4), P. 829 - 839

Published: Jan. 24, 2024

Hybridization in plants is often accompanied by nuclear genome doubling (allopolyploidy), which has been hypothesized to perturb interactions between and organellar (mitochondrial plastid) genomes creating imbalances the relative copy number of these producing genetic incompatibilities maternally derived half allopolyploid from paternal progenitor. Several evolutionary responses have predicted ameliorate effects, including selection for changes protein sequences that restore cytonuclear interactions; biased gene retention/expression/conversion favoring maternal copies; fine-tuning numbers expression levels. Numerous recent studies, however, found are inconsistent rarely scale genome-wide generalities. The apparent robustness plant allopolyploidy may reflect features general allopolyploids such as lack F2 hybrid breakdown under disomic inheritance, others more plant-specific, slow sequence divergence preexisting regulatory cell size endopolyploidy during development. Thus, only act main barrier establishment lineages, perhaps helping explain why so pervasive evolution.

Language: Английский

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Cytonuclear Interactions and Subgenome Dominance Shape the Evolution of Organelle-Targeted Genes in the Brassica Triangle of U

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(3)

Published: Feb. 23, 2024

Abstract The interaction and coevolution between nuclear cytoplasmic genomes are one of the fundamental hallmarks eukaryotic genome evolution and, 2 billion yr later, still major contributors to formation new species. Although many studies have investigated role cytonuclear interactions following allopolyploidization, relative magnitude effect subgenome dominance versus on remains unclear. Brassica triangle U features 3 diploid species that together formed separate allotetraploid similar evolutionary timescales, providing an ideal system for understanding contribution donor hybrid polyploid. Here, we pattern organelle-targeted genes in carinata (BBCC) varieties juncea (AABB) at whole-genome level, with particular focus enzyme complexes. We found partial evidence plastid-targeted experience selection match plastid genomes, but no obvious corresponding signal mitochondria-targeted from these separately allopolyploids. Interestingly, acting always reduced retention rate encoded by B subgenome, regardless whether nigra (BB) was contributed paternal or maternal progenitor. More broadly, this study illustrates distinct selective pressures experienced plastid- genes, despite a shared inheritance natural history. Our also highlights important allopolyploid evolution, even whose function depends inherited molecules.

Language: Английский

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Incorporating genetic load contributes to predicting Arabidopsis thaliana’s response to climate change

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: March 20, 2025

Understanding how species respond to climate change can facilitate conservation and crop breeding. Current prediction frameworks about population vulnerability focused on predicting range shifts or local adaptation but ignored genetic load, which is also crucial for adaptation. By analyzing 1115 globally distributed Arabidopsis thaliana natural accessions, we find that effective size (Ne) the major contributor of load variation, both along genome among populations, explain 74-94% variation in populations. Intriguingly, Ne affects by changing effectiveness purifying selection GC biased gene conversion strength. In particular, incorporating offset distribution models (SDM), predict that, populations at species' edge are generally higher risk. The eastern perform poorer all aspects, southern have lower SDM suitability, while northern load. Among diverse Yangtze River basin most vulnerable under future change. Overall, here deciphered driving forces A. thaliana, incorporated SDM, fate Genetic often overlooked predictions response This study found was determinant helps

Language: Английский

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Plastid-encoded RNA polymerase variation in Pelargonium sect Ciconium

Horticulture Advances, Journal Year: 2024, Volume and Issue: 2(1)

Published: Jan. 10, 2024

Abstract Cyto-Nuclear Incompatibility (CNI), in which there is a mismatch the interaction between organelles and nucleus, impacts plant species evolution as it has direct effect on fitness of plants. It can reduce fertility and/or result bleached plants devoid functional chloroplasts. Understanding processes leading to CNI could help improve breeding efforts, especially cases where with desirable traits need be crossed into existing cultivars. To better understand occurrence its effects phenotype, we combined near comprehensive crossing series across clade from Pelargonium section Ciconium comparative genomics protein modelling for plastid-encoded RNA polymerase (PEP), rpo genes encoding PEP subunits were found unusually highly divergent, two length-variable regions. Of all plastome-encoded genes, these contain more variation than observed angiosperms that this underlies structural inferred P. sect. . This variation, resulting differing physico-chemical properties rpo-encoded peptides, provides possible explanation CNI, but cannot directly correlate plastid related phenotypes genotypes. suggests one nuclear genome plastome are needed fully explain patterns.

Language: Английский

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Little evidence for homoeologous gene conversion and homoeologous exchange events in Gossypium allopolyploids

American Journal of Botany, Journal Year: 2024, Volume and Issue: 111(8)

Published: Aug. 1, 2024

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). Homoeologous conversion was first described cotton by comparing SNP patterns sequences from two diploid progenitors with those subgenomes. These analyses, however, did not explicitly consider other evolutionary scenarios that may give rise to similar as conversion, creating uncertainties about reality inferred events.

Language: Английский

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Identification, characteristics, and cytological analysis of three disomic alien addition lines of Brassica napus- Raphanus sativus

New Crops, Journal Year: 2025, Volume and Issue: unknown, P. 100078 - 100078

Published: April 1, 2025

Language: Английский

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The binding pocket properties were fundamental to functional diversification of the GDSL-type esterases/lipases gene family in cotton

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 13

Published: Jan. 18, 2023

Cotton is one of the most important crops in world. GDSL-type esterases/lipases (GELPs) are widely present all kingdoms and play an essential role regulating plant growth, development, responses to abiotic biotic stresses. However, molecular mechanisms underlying this functional diversity remain unclear. Here, based on identification GELP gene family, we applied genetic evolution simulation techniques explore cotton species. A total 1502 genes were identified 10 Segmental duplication differences evolutionary rates leading causes increase number during for ecological adaptation. Structural analysis revealed that family has high structural diversity. Moreover, studies have demonstrated significant properties binding pockets among GELPs. In process adapting environment, GELPs not only segmental but also different rates, resulting This leads 3D structure pocket and, finally, These findings provide a reference further analyses

Language: Английский

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