Genome copy number predicts extreme evolutionary rate variation in plant mitochondrial DNA

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(10)

Published: March 1, 2024

Nuclear and organellar genomes can evolve at vastly different rates despite occupying the same cell. In most bilaterian animals, mitochondrial DNA (mtDNA) evolves faster than nuclear DNA, whereas this trend is generally reversed in plants. However, some exceptional angiosperm clades, mtDNA substitution have increased up to 5,000-fold compared with closely related lineages. The mechanisms responsible for acceleration are unknown. Because plants rely on homologous recombination repair damage, we hypothesized that copy numbers may predict evolutionary rates, as lower provide fewer templates such mechanisms. support of hypothesis, found number explains 47% variation synonymous across 60 diverse seed plant species representing ~300 million years evolution. Copy was also negatively correlated mitogenome size, which be a cause or consequence mutation rate variation. Both relationships were unique not observed plastid DNA. These results suggest recombinational plays role driving explain evolution more broadly eukaryotes. Our findings contribute broader questions about between genome selection efficiency, drift-barrier hypothesis.

Language: Английский

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The Evolutionary Constraints on Angiosperm Chloroplast Adaptation

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(6)

Published: June 1, 2023

Abstract The chloroplast (plastid) arose via the endosymbiosis of a photosynthetic cyanobacterium by nonphotosynthetic eukaryotic cell ∼1.5 billion years ago. Although plastid underwent rapid evolution genome reduction, its rate molecular is low and organization highly conserved. Here, we investigate factors that have constrained protein-coding genes in genome. Through phylogenomic analysis 773 angiosperm genomes, show there substantial variation between genes. We demonstrate distance gene from likely origin replication influences at which it has evolved, consistent with time distance-dependent nucleotide mutation gradients. In addition, amino acid composition product constraints substitution tolerance, limiting landscape corresponding evolution. Finally, mRNA abundance key factor determining evolution, suggesting an interaction transcription DNA repair plastid. Collectively, location, composition, expression can account for >50% Thus, these three exerted limitation on capacity adaptive plastid-encoded ultimately evolvability chloroplast.

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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When and why are mitochondria paternally inherited?

Current Opinion in Genetics & Development, Journal Year: 2023, Volume and Issue: 80, P. 102053 - 102053

Published: May 26, 2023

In contrast with nuclear genes that are passed on through both parents, mitochondrial maternally inherited in most species, of the time. The genetic conflict stemming from this transmission asymmetry is well-documented, and there an abundance population-genetic theory associated it. While occasional or aberrant paternal inheritance occurs, only a few cases where exclusive genomes evolved state. Why remains poorly understood. By examining commonalities between species inheritance, we discuss what they may tell us about evolutionary forces influencing patterns. We end by discussing recent technological advances make exploring causes consequences feasible.

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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Integrating the Study of Polyploidy Across Organisms, Tissues, and Disease

Annual Review of Genetics, Journal Year: 2024, Volume and Issue: 58(1), P. 297 - 318

Published: Sept. 4, 2024

Polyploidy is a cellular state containing more than two complete chromosome sets. It has largely been studied as discrete phenomenon in either organismal, tissue, or disease contexts. Increasingly, however, investigation of polyploidy across disciplines coalescing around common principles. For example, the recent Across Tree Life meeting considered contribution both organismal evolution over millions years and tumorigenesis much shorter timescales. Here, we build on this newfound integration with unified discussion organisms, cells, disease. We highlight how at multiple biological scales, thus eliminating outdated mindset its specialization. Additionally, discuss rules that are likely to all instances polyploidy. With increasing appreciation pervasive nature displays fascinating commonalities diverse contexts, inquiry related important topic rapidly becoming unified.

Language: Английский

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Plant phase extraction: A method for enhanced discovery of the RNA-binding proteome and its dynamics in plants

The Plant Cell, Journal Year: 2023, Volume and Issue: 35(8), P. 2750 - 2772

Published: May 5, 2023

Abstract RNA-binding proteins (RBPs) play critical roles in posttranscriptional gene regulation. Current methods of systematically profiling RBPs plants have been predominantly limited to interacting with polyadenylated (poly(A)) RNAs. We developed a method called plant phase extraction (PPE), which yielded highly comprehensive proteome (RBPome), uncovering 2,517 from Arabidopsis (Arabidopsis thaliana) leaf and root samples diverse array domains. identified traditional that participate various aspects RNA metabolism plethora nonclassical moonlighting as RBPs. uncovered constitutive tissue-specific essential for normal development and, more importantly, revealed crucial salinity stress responses RBP–RNA dynamics perspective. Remarkably, 40% the are non-poly(A) were not previously annotated RBPs, signifying advantage PPE unbiasedly retrieving propose intrinsically disordered regions contribute their binding provide evidence enzymatic domains metabolic enzymes additional binding. Taken together, our findings demonstrate is an impactful approach identifying complex tissues pave way investigating RBP functions under different physiological conditions at level.

Language: Английский

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Introduction to genomics

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 15 - 30

Published: Jan. 1, 2025

Language: Английский

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Incompatibility and Interchangeability in Molecular Evolution

Genome Biology and Evolution, Journal Year: 2022, Volume and Issue: 15(1)

Published: Dec. 29, 2022

There is remarkable variation in the rate at which genetic incompatibilities molecular interactions accumulate. In some cases, minor changes-even single-nucleotide substitutions-create major when hybridization forces new variants to function a novel background from an isolated population. other genes or even entire functional pathways can be horizontally transferred between anciently divergent evolutionary lineages that span tree of life with little evidence incompatibilities. this review, we explore whether there are general principles explain why certain prone while others maintain interchangeability. We summarize pointing four features may contribute greater resistance replacement: (1) multisubunit enzyme complexes and protein-protein interactions, (2) sensitivity changes gene dosage, (3) rapid sequence evolution, (4) overall importance cell viability, creates small perturbations function. discuss relative levels support for these different hypotheses lay out future directions help striking contrasts patterns incompatibility interchangeability throughout history evolution.

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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