Charting the course for new discoveries in polyploid lineages DOI Creative Commons
Michael R. McKain, Ya Yang, Agnieszka A. Golicz

et al.

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

Published: July 1, 2024

Methods for generating and analyzing data from polyploid species are not new to Applications in Plant Sciences, yet a special issue on the topic still presents an exciting opportunity explore newly emerging research techniques. The complexity associated with existence of multiple genomes single nucleus has meant that despite decades research, there unexplored frontiers at molecular, phylogenetic, ecological, evolutionary levels. Some uncharted areas persist forays excellent by dedicated scientists, some remain unmapped because community avoids due lack tools or data. eight articles this provide waypoints allow us push boundaries our knowledge lineages. applications offered here range critical techniques determining ploidy level organism, through synthetic reviews optimal treatment phylogenomics population genomics, leveraging developing further understanding genome dynamics whole-plant responses polyploidy. We look forward impact these innovative approaches will have accelerating expansion into nature polyploidy across plant taxa coming years. Despite generally acknowledged prevalence plants, any given specimen is far trivial. Techniques answering question include direct chromosome counts, but also indirect measures flow cytometry (Smith et al., 2018), measurements spore sizes (Kuo 2021), even spectroscopy (Buono Albach, 2023). This features two facilitate accurate assessment ploidy—one method long tradition science, another takes advantage modern sequencing Ramirez-Castillo al. (2024) developed using croziers, fiddleheads, count chromosomes different fern species. Although roots typically used mitotic ability incorporate croziers as potential sources material allows wider array availability samples. use enzyme pretreatment cellulose–pectinase solution improve permeability tissue uptake colchicine arrest metaphase. Chromosome counting original which was first described plants (reviewed Soltis 2014), continues legacy. Moving sequence data, Gaynor present nQuack, R package estimation ranging whole-genome resequencing target enrichment. Building methodology nQuire (Weiß nQuack implements expectation maximization three distributions—normal, beta, beta-binomial—to identify diploid hexaploid. expands capacity opening up ploidy-level DNA can be adequately isolated sequenced, including herbarium specimens. generation high-throughput reads polyploids increased total amount genetic information available, researchers face significant challenges processing conceptualized organisms. remains enthusiastic about unlocking discoveries approaches, they rightfully wary pitfalls incorrect read mapping correctly identifying homeologs. guide genomic phylogenetic exploration Phillips explores variant identification provides detailed recommendations modifying standard calling pipelines accommodate analysis. paper highlights process, necessity accounting genotype dosage, paralogy between subgenomes, other polyploid-specific bias estimation. Ning review limitations inferring relationships phylogenomic transcriptomic approaches. They conclude that, improvements polyploid-rich genera, certain remain, reliable orthologous genes sorting all homoeologous copies allopolyploids. Both insights foundational analytical required unraveling complexities much-needed practical grappling Once allopolyploids been identified perhaps placed context, it becomes compelling examine interaction subgenomes. Authors took tackling subgenome assignment exchange, applying were originally very purposes questions around genomes. Ortiz Sharbrough modified ABBA-BABA test (Durand 2011)—developed patterns interspecific hybridization—in order assess gene tests whether one become more like vice versa. To method, authors explored Coffea arabica L. genome, known allopolyploid maternal donor C. eugenioides S. Moore paternal canephora Pierre ex A. Froehner. able both subgenomes being overwritten other. Interestingly, pattern extended plastids driven maternal-like, suggesting nuclear–plastid incompatibility genome. better Reynolds take similarity metagenomics. k-mer profiles rapidly evolving repetitive elements assemblies assign auto- vs. progenitors computationally efficient scalable, recreate well-studied lineages approach. reveal power existing expand origins dynamics. While interacting assigned understood level, ultimate expression traits organismal represents its own challenges. How do integrate phenotypic, physiological, ecological understand evolution organisms beyond their dynamics? offer ways approaching question, careful examination integrated phenotypic changes within lineage systematic comparison hybrid dimensions. Baker methods co-expression analyses build networks anatomical, morphological, physiological traits. then compared Brassica, key affect network structure, found had larger connected than diploids. framework considering instead individual variables applicable go simple bivariate comparisons, help develop deeper impacts selection non-target integration diverse polyploids, niche space morphology, historically challenging. address this, Krieg divergence index (DI), investigation interpretation hybrids types studies. DI novel how hybrid/allopolyploid differs parents quantitative manner works scales, phenotypes divergence. standardized approach comprehensive formation specifically generally. pathways fully consequences hybridization lineages, we findings result implementation taxa. As noted American Journal Botany companion (Barker 2024), scope ask answer vastly past decade. papers set stage next round empirical innovations, addressing broad challenging, exciting, chart territory fundamental complex networks. emphasize impressive progress field, synthesizing previously possible. At same time, actually (Gaynor 2024; 2024) extremely valuable, providing without cannot embark downstream analyses. Between extremes (Ortiz Sharbrough, well interrogate (Baker systematically comparing progenitor (Krieg, 2024). Reflecting advances featured here, hope continue rapid traditional study systems geographies. conceived authors. M.R.M., Y.Y., A.G. carried out editorial duties manuscripts included issue. B.L.G. led writing editing manuscript, contributing text edits final version. All approved version manuscript. editors sincere thanks publications thank reviewers effort, intellectual contributions during peer-review process improved quality clarity manuscripts.

Language: Английский

Polyploid plants take cytonuclear perturbations in stride DOI Creative Commons
Daniel B. Sloan, Justin L. Conover, Corrinne E. Grover

et al.

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

Citations

5
Charting the course for new discoveries in polyploid lineages DOI Creative Commons
Michael R. McKain, Ya Yang, Agnieszka A. Golicz

et al.

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

Published: July 1, 2024

Methods for generating and analyzing data from polyploid species are not new to Applications in Plant Sciences, yet a special issue on the topic still presents an exciting opportunity explore newly emerging research techniques. The complexity associated with existence of multiple genomes single nucleus has meant that despite decades research, there unexplored frontiers at molecular, phylogenetic, ecological, evolutionary levels. Some uncharted areas persist forays excellent by dedicated scientists, some remain unmapped because community avoids due lack tools or data. eight articles this provide waypoints allow us push boundaries our knowledge lineages. applications offered here range critical techniques determining ploidy level organism, through synthetic reviews optimal treatment phylogenomics population genomics, leveraging developing further understanding genome dynamics whole-plant responses polyploidy. We look forward impact these innovative approaches will have accelerating expansion into nature polyploidy across plant taxa coming years. Despite generally acknowledged prevalence plants, any given specimen is far trivial. Techniques answering question include direct chromosome counts, but also indirect measures flow cytometry (Smith et al., 2018), measurements spore sizes (Kuo 2021), even spectroscopy (Buono Albach, 2023). This features two facilitate accurate assessment ploidy—one method long tradition science, another takes advantage modern sequencing Ramirez-Castillo al. (2024) developed using croziers, fiddleheads, count chromosomes different fern species. Although roots typically used mitotic ability incorporate croziers as potential sources material allows wider array availability samples. use enzyme pretreatment cellulose–pectinase solution improve permeability tissue uptake colchicine arrest metaphase. Chromosome counting original which was first described plants (reviewed Soltis 2014), continues legacy. Moving sequence data, Gaynor present nQuack, R package estimation ranging whole-genome resequencing target enrichment. Building methodology nQuire (Weiß nQuack implements expectation maximization three distributions—normal, beta, beta-binomial—to identify diploid hexaploid. expands capacity opening up ploidy-level DNA can be adequately isolated sequenced, including herbarium specimens. generation high-throughput reads polyploids increased total amount genetic information available, researchers face significant challenges processing conceptualized organisms. remains enthusiastic about unlocking discoveries approaches, they rightfully wary pitfalls incorrect read mapping correctly identifying homeologs. guide genomic phylogenetic exploration Phillips explores variant identification provides detailed recommendations modifying standard calling pipelines accommodate analysis. paper highlights process, necessity accounting genotype dosage, paralogy between subgenomes, other polyploid-specific bias estimation. Ning review limitations inferring relationships phylogenomic transcriptomic approaches. They conclude that, improvements polyploid-rich genera, certain remain, reliable orthologous genes sorting all homoeologous copies allopolyploids. Both insights foundational analytical required unraveling complexities much-needed practical grappling Once allopolyploids been identified perhaps placed context, it becomes compelling examine interaction subgenomes. Authors took tackling subgenome assignment exchange, applying were originally very purposes questions around genomes. Ortiz Sharbrough modified ABBA-BABA test (Durand 2011)—developed patterns interspecific hybridization—in order assess gene tests whether one become more like vice versa. To method, authors explored Coffea arabica L. genome, known allopolyploid maternal donor C. eugenioides S. Moore paternal canephora Pierre ex A. Froehner. able both subgenomes being overwritten other. Interestingly, pattern extended plastids driven maternal-like, suggesting nuclear–plastid incompatibility genome. better Reynolds take similarity metagenomics. k-mer profiles rapidly evolving repetitive elements assemblies assign auto- vs. progenitors computationally efficient scalable, recreate well-studied lineages approach. reveal power existing expand origins dynamics. While interacting assigned understood level, ultimate expression traits organismal represents its own challenges. How do integrate phenotypic, physiological, ecological understand evolution organisms beyond their dynamics? offer ways approaching question, careful examination integrated phenotypic changes within lineage systematic comparison hybrid dimensions. Baker methods co-expression analyses build networks anatomical, morphological, physiological traits. then compared Brassica, key affect network structure, found had larger connected than diploids. framework considering instead individual variables applicable go simple bivariate comparisons, help develop deeper impacts selection non-target integration diverse polyploids, niche space morphology, historically challenging. address this, Krieg divergence index (DI), investigation interpretation hybrids types studies. DI novel how hybrid/allopolyploid differs parents quantitative manner works scales, phenotypes divergence. standardized approach comprehensive formation specifically generally. pathways fully consequences hybridization lineages, we findings result implementation taxa. As noted American Journal Botany companion (Barker 2024), scope ask answer vastly past decade. papers set stage next round empirical innovations, addressing broad challenging, exciting, chart territory fundamental complex networks. emphasize impressive progress field, synthesizing previously possible. At same time, actually (Gaynor 2024; 2024) extremely valuable, providing without cannot embark downstream analyses. Between extremes (Ortiz Sharbrough, well interrogate (Baker systematically comparing progenitor (Krieg, 2024). Reflecting advances featured here, hope continue rapid traditional study systems geographies. conceived authors. M.R.M., Y.Y., A.G. carried out editorial duties manuscripts included issue. B.L.G. led writing editing manuscript, contributing text edits final version. All approved version manuscript. editors sincere thanks publications thank reviewers effort, intellectual contributions during peer-review process improved quality clarity manuscripts.

Language: Английский

Citations

1