Multiple polyploidizations inArabidopsis lyratastabilized by long-range adaptive introgression across Eurasia DOI Creative Commons
Alison Scott, Uliana Kolesnikova, Anna Glushkevich

et al.

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

Published: Aug. 27, 2024

Abstract Abundance of polyploidy varies across lineages, evolutionary time and geography, suggesting both genetics environment play a role in polyploid persistence. Arabidopsis lyrata appears to be the most polyploidy-rich species-complex genus, with multiple origins autotetraploidy. This is revealed by genomic data from over 400 samples Eurasia. We found 30 previously undescribed autotetraploid populations Siberia minimum two separate origins, independent those reported Central Europe. The establishment Siberian tetraploids mediated meiotic adaptation at same genes as European tetraploid A. arenosa, despite high divergence geographical separation. Haplotype analysis based on synthetic long-read assemblies supports long-range introgression adaptive alleles interspecific pool arenosa . Once evolved, promotes new lineages through inter– intraspecific introgression.

Language: Английский

Defining autopolyploidy: Cytology, genetics, and taxonomy DOI Creative Commons

Zhenling Lv,

Charles Addo Nyarko, Vinita Ramtekey

et al.

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

Published: March 4, 2024

Autopolyploidy is taxonomically defined as the presence of more than two copies each genome within an organism or species, where genomes present must all originate same species. Alternatively, "genetic" "cytological" autopolyploidy by polysomic inheritance: random pairing and segregation four (or more) homologous chromosomes present, with no preferential partners. In this review, we provide overview methods used to categorize species taxonomic cytological autopolyploids, including both modern obsolete methods, marker-segregation-based genomics methods. Subsequently, also investigated how frequently inheritance has been reliably documented in autopolyploids. Pure predominantly was 39 43 putative autopolyploid data available (91%) seven eight synthetic several cases mixed We found clear autopolyploids disomic inheritance, which likely a function our search methodology. Interestingly, purely another five partial predominant that appear be allopolyploids. Our results suggest observations can lead relabeling allopolyploid highlight need for further cytogenetic genomic investigation into polyploid origins types.

Language: Английский

Citations

8
Unveiling the Mysteries of Non-Mendelian Heredity in Plant Breeding DOI Creative Commons
Mohsen Yoosefzadeh-Najafabadi, Mohsen Hesami, Istvan Rajcan

et al.

Plants, Journal Year: 2023, Volume and Issue: 12(10), P. 1956 - 1956

Published: May 11, 2023

Mendelian heredity is the cornerstone of plant breeding and has been used to develop new varieties plants since 19th century. However, there are several cases, such as cytoplasmic inheritance, methylation, epigenetics, hybrid vigor, loss heterozygosity (LOH), where not applicable, known non-Mendelian heredity. This type inheritance can be influenced by factors besides genetic architecture its potential. Therefore, exploring various mechanisms, their prevalence in plants, implications for paramount importance accelerate pace crop improvement. In this review, we examine current understanding including patterns, applications breeding, provide an overview forms (including epigenetic LOH), explore insight into potential it holds future research.

Language: Английский

Citations

8
Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants DOI Creative Commons
Gillian Reynolds, Brendan Mumey,

Veronika Strnadová-Neeley

et al.

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

Published: April 29, 2024

Abstract Premise The genomes of polyploid plants archive the evolutionary events leading to their present forms. However, plant numerous hurdles genome comparison algorithms for classification types and exploring dynamics. Methods Here, problem intra‐ inter‐genome examining is reframed as a metagenomic problem, enabling use rapid scalable MinHashing approach. To determine how polyploidy are described by this approach, were examined from across spectrum both k ‐mer composition frequency with range sizes. In no subgenome‐specific ‐mers identified; rather, whole‐chromosome subspaces utilized. Results Given chromosome‐scale assemblies sufficient repetitive element content, literature‐verified subgenomic genomic relationships revealed, including distinguishing auto‐ allopolyploidy putative progenitor assignment. sequences responsible rapidly evolving landscape transposable elements. An investigation into parameters revealed that downsampled space (genomic signatures) produced excellent approximations sequence similarity. Furthermore, clustering approach used signatures scrutinized ensure applicability metagenomics‐based method. Discussion easily implementable highly computationally efficient MinHashing‐based strategy enables comparative subgenomics genomics large complex genomes. Such comparisons provide evidence polyploidy‐type assignments. cases where repeat signal may not be adequate given chromosomes' global profile, alternative methods more specific but outperform

Language: Английский

Citations

2
Variant calling in polyploids for population and quantitative genetics DOI Creative Commons
Alyssa R. Phillips

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

Published: July 1, 2024

Abstract Advancements in genome assembly and sequencing technology have made whole sequence (WGS) data reference genomes accessible to study polyploid species. Compared popular reduced‐representation approaches, the genome‐wide coverage greater marker density provided by WGS can greatly improve our understanding of species biology. However, biological features that make interesting also pose challenges read mapping, variant identification, genotype estimation. Accounting for characteristics calling like allelic dosage uncertainty, homology between subgenomes, variance chromosome inheritance mode reduce errors. Here, I discuss where potential solutions be integrated into a standard pipeline.

Language: Английский

Citations

2
Ice age‐driven range shifts of diploids and expanding autotetraploids of Biscutella laevigata within a conserved niche DOI Creative Commons
Sandra Grünig, Theofania Patsiou, Christian Parisod

et al.

New Phytologist, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 10, 2024

Summary Early studies of the textbook mixed‐ploidy system Biscutella laevigata highlighted diploids restricted to never‐glaciated lowlands and tetraploids at high elevations across European Alps, promoting hypothesis that whole‐genome duplication (WGD) is advantageous under environmental changes. Here we addressed long‐held hypotheses on role hybridisation origin tetraploids, their single vs multiple origins, whether a shift in climatic niche accompanied WGD. Climatic modelling together with spatial genetics coalescent based ddRAD‐seq genotyping 17 diploid 19 tetraploid populations was used revisit evolution this species complex space time. Diploids differentiated into four genetic lineages corresponding allopatric glacial refugia onset last ice age, whereas displaying tetrasomic inheritance formed uniform group originated from southern before maximum. Derived occurring elevation, autotetraploids likely inherited adaptation elevation rather than having evolved it through or after They further presented considerable postglacial expansion Alps underwent admixture diploids. Although underpinnings successful remain elusive, differentiation B. chiefly driven by history Alps.

Language: Английский

Citations

2
Variant calling in polyploids for population and quantitative genetics DOI Creative Commons
Alyssa R. Phillips

Published: March 15, 2024

Advancements in genome assembly and sequencing technology have made whole sequence (WGS) data reference genomes accessible to study polyploid species. The genome-wide coverage greater marker density provided by WGS data, compared popular reduced-representation approaches, can greatly improve our understanding of species biology. However, biological features that make interesting also pose challenges read mapping, variant identification, genotype estimation. Accounting for characteristics, like allelic dosage uncertainty, homology between subgenomes, variance chromosome inheritance mode, calling reduce errors. Here, I discuss the where potential solutions be integrated into a standard pipeline.

Language: Английский

Citations

0
Multiple polyploidizations inArabidopsis lyratastabilized by long-range adaptive introgression across Eurasia DOI Creative Commons
Alison Scott, Uliana Kolesnikova, Anna Glushkevich

et al.

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

Published: Aug. 27, 2024

Abstract Abundance of polyploidy varies across lineages, evolutionary time and geography, suggesting both genetics environment play a role in polyploid persistence. Arabidopsis lyrata appears to be the most polyploidy-rich species-complex genus, with multiple origins autotetraploidy. This is revealed by genomic data from over 400 samples Eurasia. We found 30 previously undescribed autotetraploid populations Siberia minimum two separate origins, independent those reported Central Europe. The establishment Siberian tetraploids mediated meiotic adaptation at same genes as European tetraploid A. arenosa, despite high divergence geographical separation. Haplotype analysis based on synthetic long-read assemblies supports long-range introgression adaptive alleles interspecific pool arenosa . Once evolved, promotes new lineages through inter– intraspecific introgression.

Language: Английский

Citations

0