Genomes of Poaceae sisters reveal key metabolic innovations preceding the emergence of grasses

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 7, 2024

SUMMARY The grass family (Poaceae, Poales) holds immense economic and ecological significance, exhibiting unique metabolic traits, including dual starch lignin biosynthetic pathways. To investigate when how the innovations known in grasses evolved, we sequenced genomes of a non-core grass, Pharus latifolius , non-grass graminids, Joinvillea ascendens Ecdeiocolea monostachya representing sister clade to Poaceae, Typha latifolia remaining Poales. rho whole genome duplication (ρWGD) ancestral lineage for all contributed gene expansions underlying cytosolic biosynthesis, whereas an earlier tandem phenylalanine ammonia lyase ( PAL ) gave rise phenylalanine/tyrosine PTAL responsible biosynthesis. Two mutations were sufficient expand function into PTAL. integrated genomic biochemical analyses relatives Poales revealed evolutionary molecular basis key grasses. Abstract Figure

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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Accurately Inferring Ancient Auto and Allopolyploidization Events using Forward-time Simulations

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 21, 2024

Abstract Multiple rounds of whole-genome duplication (WGD) followed by diploidization have occurred throughout the evolutionary history angiosperms. To understand how these cycles occur, much work has been done to model genomic consequences and significance WGD. The machinations are strongly influenced mode speciation (allo or autopolyploidy). However, there is no discrete boundary between allo autopolyploidy, which best described as a continuum. Here we present forward-time polyploid genome evolution simulator called SpecKS. SpecKS models originating from 2D continuum, whose dimensions account for both level genetic differentiation ancestral parental genomes, well time lag their subsequent reunion in derived polyploid. Using extensive simulations, demonstrate that changes initial conditions along either dimension continuum deterministically affect shape Ks histogram. Our findings indicate error common method estimating WGD histogram peak scales with degree allopolyploidy, an alternative, accurate estimation independent allopolyploidy. Lastly, use derive tests infer divergence time, diversity species, input We apply latter test transcriptomic data over 200 species across plant kingdom, results concordant prevailing theory majority angiosperm lineages diverse genomes may be allopolyploid origin.

Language: Английский

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Polyploidy and genome evolution in the common cordgrass Spartina anglica : an enigmatic evolution of allopolyploidy

Systematics and Biodiversity, Journal Year: 2024, Volume and Issue: 22(1)

Published: June 21, 2024

Hybridization and polyploidy represent major features of Spartina (cordgrass) evolution, the recent formation common cordgrass anglica is one most striking examples allopolyploidy speciation. S. originated in nineteenth century Western Europe through hybridization between alterniflora (an American native) maritima (a European native). The resulting F1 hybrid, x townsendii, underwent genome doubling, leading to anglica. species has attracted much interest as a useful model system context polyploid evolution biological invasion. However, several aspects are complicated poorly understood. In this review, we examine evolutionary history after nearly half since its discovery. We provide current state knowledge regarding history, origin, dynamics following polyploidization. Recent findings using molecular approaches have demonstrated that undergone rapid structural transcriptomic changes. This realization shattered earlier perceptions genetically depauperate species, thus showing more than previously thought raising questions species. discussed these issues depth will continue unique exceptional avenue for gaining valuable insight into early stages evolution.

Language: Английский

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Homoeologs in Allopolyploids: Navigating Redundancy as Both an Evolutionary Opportunity and a Technical Challenge—A Transcriptomics Perspective

Genes, Journal Year: 2024, Volume and Issue: 15(8), P. 977 - 977

Published: July 24, 2024

Allopolyploidy in plants involves the merging of two or more distinct parental genomes into a single nucleus, significant evolutionary process plant kingdom. Transcriptomic analysis provides invaluable insights allopolyploid by elucidating fate duplicated genes, revealing novelties and uncovering their environmental adaptations. By examining gene expression profiles, scientists can discern how genes have evolved to acquire new functions regulatory roles. This often leads development novel traits adaptive strategies that leverage thrive diverse ecological niches. Understanding these molecular mechanisms not only enhances our appreciation genetic complexity underlying allopolyploidy but also underscores importance agriculture ecosystem resilience. However, transcriptome profiling is challenging due genomic redundancy, which further complicated presence multiple chromosomes sets variations among homoeologs allelic genes. Prior analysis, sub-genome phasing homoeology inference are essential for obtaining comprehensive view expression. review aims clarify terminology this field, identify most aspects explain inherent difficulties, suggest reliable analytic strategies. Furthermore, bulk RNA-seq highlighted as primary method studying expression, focusing on critical steps like read mapping normalization differential analysis. approach effectively captures from both genomes, facilitating combined profiles. Its sensitivity detecting low-abundance transcripts allows subtle differences between be identified, crucial understanding dynamics balance allopolyploids.

Language: Английский

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