Molecular mechanisms of adaptive evolution in wild animals and plants

Science China Life Sciences, Journal Year: 2023, Volume and Issue: 66(3), P. 453 - 495

Published: Jan. 13, 2023

Language: Английский

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The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Nature Genetics, Journal Year: 2024, Volume and Issue: 56(4), P. 721 - 731

Published: April 1, 2024

Abstract Coffea arabica , an allotetraploid hybrid of eugenioides and canephora is the source approximately 60% coffee products worldwide, its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies a di-haploid C. accession modern representatives diploid progenitors, . The three species exhibit largely conserved genome structures between parents descendant subgenomes, with no obvious global subgenome dominance. find evidence for founding polyploidy event 350,000–610,000 years ago, followed by pre-domestication bottlenecks, resulting in narrow genetic variation. A split wild cultivar progenitors occurred ~30.5 thousand period migration two populations. Analysis varieties, including lines historically introgressed highlights their breeding histories loci that may contribute to pathogen resistance, laying groundwork future genomics-based

Language: Английский

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Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences

Nature Ecology & Evolution, Journal Year: 2024, Volume and Issue: 8(3), P. 519 - 535

Published: Jan. 12, 2024

Polyploidy or whole-genome duplication (WGD) is a major event that drastically reshapes genome architecture and often assumed to be causally associated with organismal innovations radiations. The 2R hypothesis suggests two WGD events (1R 2R) occurred during early vertebrate evolution. However, the timing of relative divergence gnathostomes (jawed vertebrates) cyclostomes (jawless hagfishes lampreys) unresolved whether these underlie phenotypic diversification remains elusive. Here we present inshore hagfish, Eptatretus burgeri. Through comparative analysis lamprey gnathostome genomes, reconstruct in cyclostome evolution, leveraging insights into ancestral genome. Genome-wide synteny phylogenetic analyses support scenario which 1R stem-lineage Cambrian, stem-lineage, maximally late Cambrian-earliest Ordovician, after its from cyclostomes. We find stem-cyclostomes experienced an additional independent triplication. Functional genomic morphospace demonstrate generally contribute developmental evolution similar changes regulatory both groups. appreciable morphological only but not lineage, calling question general expectation WGDs lead leaps bodyplan complexity.

Language: Английский

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Gradual evolution of allopolyploidy in Arabidopsis suecica

Nature Ecology & Evolution, Journal Year: 2021, Volume and Issue: 5(10), P. 1367 - 1381

Published: Aug. 19, 2021

Abstract Most diploid organisms have polyploid ancestors. The evolutionary process of polyploidization is poorly understood but has frequently been conjectured to involve some form ‘genome shock’, such as genome reorganization and subgenome expression dominance. Here we study in Arabidopsis suecica , a post-glacial allopolyploid species formed via hybridization thaliana arenosa . We generated chromosome-level assembly A. complemented it with polymorphism transcriptome data from all species. Despite divergence around 6 million years ago (Ma) between the ancestral differences their composition, see no evidence shock: colinear genomes; there dominance expression; transposon dynamics appear stable. However, find changes suggesting gradual adaptation polyploidy. In particular, shows upregulation meiosis-related genes, possibly prevent aneuploidy undesirable homeologous exchanges that are observed synthetic cyto-nuclear processes, response new cytoplasmic environment plastids maternally inherited These not seen hybrids, thus likely represent subsequent evolution.

Language: Английский

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Patterns, mechanisms, and consequences of homoeologous exchange in allopolyploid angiosperms: a genomic and epigenomic perspective

New Phytologist, Journal Year: 2023, Volume and Issue: 238(6), P. 2284 - 2304

Published: April 3, 2023

Summary Allopolyploids result from hybridization between different evolutionary lineages coupled with genome doubling. Homoeologous chromosomes (chromosomes common shared ancestry) may undergo recombination immediately after allopolyploid formation and continue over successive generations. The outcome of this meiotic pairing behavior is dynamic complex. exchanges (HEs) lead to the unbalanced gametes, reduced fertility, selective disadvantage. By contrast, HEs could act as sources novel substrates, shifting relative dosage parental gene copies, generating phenotypic diversity, helping establishment neo‐allopolyploids. However, HE patterns vary among lineages, across generations, even within individual genomes chromosomes. causes consequences variation are not fully understood, though interest in phenomenon has increased last decade. Recent technological advances show promise uncovering mechanistic basis HEs. Here, we describe recent observations angiosperm underlying genomic epigenomic features, We identify critical research gaps discuss future directions far‐reaching implications understanding evolution applying them development important traits polyploid crops.

Language: Английский

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Learning to tango with four (or more): the molecular basis of adaptation to polyploid meiosis

Plant Reproduction, Journal Year: 2022, Volume and Issue: 36(1), P. 107 - 124

Published: Sept. 23, 2022

Abstract Polyploidy, which arises from genome duplication, has occurred throughout the history of eukaryotes, though it is especially common in plants. The resulting increased size, heterozygosity, and complexity can be an evolutionary opportunity, facilitating diversification, adaptation evolution functional novelty. On other hand, when they first arise, polyploids face a number challenges, one biggest being meiotic pairing, recombination segregation suddenly more than two copies each chromosome, limit their fertility. Both for developing polyploidy as crop improvement tool (which holds great promise due to high lasting multi-stress resilience polyploids), well our basic understanding meiosis plant evolution, we need know both specific nature challenges face, how overcome evolution. In recent years there been dramatic uptick molecular basis polyploid adaptations that focus this review.

Language: Английский

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Alkaline Stress Induces Different Physiological, Hormonal and Gene Expression Responses in Diploid and Autotetraploid Rice

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(10), P. 5561 - 5561

Published: May 16, 2022

Saline−alkaline stress is a critical abiotic that negatively affects plants’ growth and development. Considerably higher enhancements in plant tolerance to saline−alkaline have often been observed polyploid plants compared their diploid relatives, the underlying mechanism of which remains elusive. In this study, we explored variations morphological physiological characteristics, phytohormones, genome-wide gene expression between an autotetraploid rice its relative response alkaline stress. It was polyploidization imparted level than relative. An eclectic array parameters commonly used for stress, such as proline, soluble sugars, malondialdehyde, together with activities some selected antioxidant enzymes, analyzed at five time points first 24 h following treatment rice. Phytohormones, abscisic acid indole-3-acetic were also comparatively evaluated two types different ploidy levels under Transcriptomic analysis revealed patterns altered accordance cellular phytohormones upon particular, genes related peroxide transcription factors substantially upregulated treatment. essence, exhibited differential may shed more light on underpinning ameliorated genome duplication.

Language: Английский

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Global Patterns of Subgenome Evolution in Organelle-Targeted Genes of Six Allotetraploid Angiosperms

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(4)

Published: April 1, 2022

Abstract Whole-genome duplications (WGDs) are a prominent process of diversification in eukaryotes. The genetic and evolutionary forces that WGD imposes on cytoplasmic genomes not well understood, despite the central role cytonuclear interactions play eukaryotic function fitness. Cellular respiration photosynthesis depend successful interaction between 3,000+ nuclear-encoded proteins destined for mitochondria or plastids gene products multi-subunit complexes such as OXPHOS, organellar ribosomes, Photosystems I II, Rubisco. Allopolyploids thus faced with critical task coordinating nuclear genes were inherited from different species. Because share more recent history common descent maternal subgenome than paternal subgenome, “mismatches” allopolyploids might lead to accelerated rates evolution homoeologs allopolyploids, either through relaxed purifying selection strong directional rectify these mismatches. We report evidence six independently formed allotetraploids subgenomes exhibit unequal protein-sequence evolution, but we found no incompatibilities result altered trajectories organelle-targeted genes. analyses content revealed mixed whether lost rapidly non-organelle-targeted Together, global provide insights into complex dynamics showing allopolyploid have separate sharing same nucleus, generation time, ecological context.

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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Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles

Systematic Biology, Journal Year: 2024, Volume and Issue: 73(2), P. 392 - 418

Published: March 1, 2024

Abstract Introgression allows polyploid species to acquire new genomic content from diploid progenitors or other unrelated lineages, contributing genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement large numbers alleles inherited polyploid’s ancestral species, profoundly reshaping composition. such complex polyploids, it is often difficult determine which taxa were progenitor provided additional introgressive blocks through subsequent hybridization. Here, we use population-level data reconstruct phylogenetic history Betula pubescens (downy birch), a tetraploid assumed be allopolyploid origin known hybridize with at least four birch species. This was achieved by modeling polyploidization events under multispecies coalescent then using an approximate Bayesian computation rejection algorithm evaluate compare competing models. We provide evidence that B. outcome autoploid genome doubling event in common ancestor pendula its extant sister platyphylla, took place approximately 178,000–188,000 generations ago. Extensive hybridization pendula, nana, humilis followed aftermath autopolyploidization, relative contribution each these varying markedly across species’ range. Functional analysis loci containing introgressed nana identified multiple genes involved climate adaptation, while derived revealed several regulation meiotic stability pollen viability plant

Language: Английский

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