Genome evolution and diversity of wild and cultivated potatoes

Nature, Journal Year: 2022, Volume and Issue: 606(7914), P. 535 - 541

Published: June 8, 2022

Potato (Solanum tuberosum L.) is the world's most important non-cereal food crop, and vast majority of commercially grown cultivars are highly heterozygous tetraploids. Advances in diploid hybrid breeding based on true seeds have potential to revolutionize future potato production1-4. So far, relatively few studies examined genome evolution diversity wild cultivated landrace potatoes, which limits application their breeding. Here we assemble 44 high-quality genomes from 24 20 accessions that representative Solanum section Petota, tuber-bearing clade, as well 2 neighbouring section, Etuberosum. Extensive discordance phylogenomic relationships suggests complexity evolution. We find substantially expanded its repertoire disease-resistance genes when compared with closely related seed-propagated solanaceous crops, indicative effect tuber-based propagation strategies genome. discover a transcription factor determines tuber identity interacts mobile tuberization inductive signal SP6A. also identify 561,433 high-confidence structural variants construct map large inversions, provides insights for improving inbred lines precluding linkage drag, exemplified by 5.8-Mb inversion associated carotenoid content tubers. This study will accelerate enrich our understanding biology global staple crop.

Language: Английский

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Phylogenomics and the flowering plant tree of life

Journal of Integrative Plant Biology, Journal Year: 2022, Volume and Issue: 65(2), P. 299 - 323

Published: Nov. 23, 2022

Abstract The advances accelerated by next‐generation sequencing and long‐read technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of studies adopting hundreds thousands genes across wealth clades have emerged ushered phylogenetics evolution into new era. meantime, roadmap researchers when making decisions different approaches their phylogenomic research design is imminent. This review focuses on utility genomic data (from organelle genomes, both reduced representation whole‐genome sequencing) in evolutionary investigations, describes baseline methodology experimental analytical procedures, summarizes recent progress flowering phylogenomics at ordinal, familial, tribal, lower levels. We also discuss challenges, such as adverse impact orthology inference reconstruction raised from systematic errors, underlying biological factors, duplication, hybridization/introgression, incomplete lineage sorting, together suggesting that bifurcating tree may not be best model life. Finally, we promising avenues future studies.

Language: Английский

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Deep reticulation: the long legacy of hybridization in vascular plant evolution

The Plant Journal, Journal Year: 2023, Volume and Issue: 114(4), P. 743 - 766

Published: Feb. 13, 2023

Hybridization has long been recognized as a fundamental evolutionary process in plants but, until recently, our understanding of its phylogenetic distribution and biological significance across deep scales largely obscure. Over the past decade, genomic phylogenomic datasets have revealed, perhaps not surprisingly, that hybridization, often associated with polyploidy, common throughout history plants, particularly various lineages flowering plants. However, studies also highlighted challenges disentangling signals ancient hybridization from other sources conflict (in particular, incomplete lineage sorting). Here, we provide critical review vascular outlining well-documented cases plant phylogeny, well unique to documenting versus recent hybridization. We definition for which, knowledge, explicitly attempted before. Further extent reticulation should remain an important research focus, especially because published examples likely represent tip iceberg terms total future increasingly explore macroevolutionary this process, impact on trajectories (e.g. how does influence trait evolution or generation biodiversity over time scales?), life ecological factors shape, shaped, frequency geologic phylogeny. Finally, consider implications ubiquitous conceptualize, analyze, classify Networks, opposed bifurcating trees, more accurate representations many cases, although ability infer, visualize, use networks comparative analyses is highly limited. Developing improved methods generation, visualization, represents direction biology. Current classification systems do generally allow recognition reticulate lineages, classifications themselves are based evidence chloroplast genome. Updating better reflect nuclear phylogenies, considering whether recognize systems, will challenge systematics community.

Language: Английский

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Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance

Nature Genetics, Journal Year: 2024, Volume and Issue: 56(4), P. 710 - 720

Published: March 15, 2024

Abstract Polyploidy (genome duplication) is a pivotal force in evolution. However, the interactions between parental genomes polyploid nucleus, frequently involving subgenome dominance, are poorly understood. Here we showcase analyses of bamboo system (Poaceae: Bambusoideae) comprising series lineages from diploid (herbaceous) to tetraploid and hexaploid (woody), with 11 chromosome-level de novo genome assemblies 476 transcriptome samples. We find that woody subgenomes exhibit stunning karyotype stability, parallel dominance two clades gradual shift clade. Allopolyploidization have shaped evolution tree-like lignified culms, rapid growth synchronous flowering characteristic bamboos as large grasses. Our work provides insights into remarkable system, including its dependence on genomic context ability switch which dominant over evolutionary time.

Language: Английский

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Genomes, fossils, and the concurrent rise of modern birds and flowering plants in the Late Cretaceous

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(8)

Published: Feb. 12, 2024

The phylogeny and divergence timing of the Neoavian radiation remain controversial despite recent progress. We analyzed genomes 124 species across all orders, using data from 25,460 loci spanning four DNA classes, including 5,756 coding sequences, 12,449 conserved nonexonic elements, 4,871 introns, 2,384 intergenic segments. conducted a comprehensive sensitivity analysis to account for heterogeneity different leading an optimal tree Neoaves with high resolution. This features novel dichotomy comprising two monophyletic clades: previously recognized Telluraves (land birds) newly circumscribed Aquaterraves (waterbirds relatives). Molecular dating analyses 20 fossil calibrations indicate that diversification modern birds began in Late Cretaceous underwent constant steady KPg boundary, concurrent rise angiosperms as well other major Cenozoic animal groups placental multituberculate mammals. catastrophe had limited impact on avian evolution compared Paleocene–Eocene Thermal Maximum, which triggered rapid seabirds. Our findings suggest followed slow process gradualism rather than punctuated equilibrium, interruption by catastrophe. study places bird into new context within vertebrates, ramifications Earth’s biota.

Language: Английский

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Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family

BMC Biology, Journal Year: 2022, Volume and Issue: 20(1)

Published: April 25, 2022

Abstract Background Deep-branching phylogenetic relationships are often difficult to resolve because signals obscured by the long history and complexity of evolutionary processes, such as ancient introgression/hybridization, polyploidization, incomplete lineage sorting (ILS). Phylogenomics has been effective in providing information for resolving both deep- shallow-scale across all branches tree life. The olive family (Oleaceae) is composed 25 genera classified into five tribes with tribe Oleeae consisting four subtribes. Previous analyses showed that ILS and/or hybridization led incongruence family. It was essential distinguish signal conflicts, explore mechanisms uncertainties concerning family, especially at deep-branching nodes. Results We used whole plastid genome nuclear single nucleotide polymorphism (SNP) data infer assess variation rates among main clades also 2608 1865 orthologous genes Oleaceae subtribes Oleeae, respectively. Concatenated coalescence trees based on genome, SNPs multiple suggest events introgression during diversification Oleaceae. Additionally, there extreme heterogeneity substitution tribes. Furthermore, our results supported rather than ILS, factor discordance have originated via polyploidy, its most likely parentages ancestral Jasmineae or sister group, which a “ghost lineage,” Forsythieae. However, mainly responsible Oleeae. Conclusions This study showcases using sequence datasets (plastid genomes, thousands genes) diverse phylogenomic methods partition, heterogeneous models, quantifying branch lengths (QuIBL) analysis, species network analysis can facilitate untangling complex processes introgression, paleopolyploidization, ILS.

Language: Английский

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Phylogenomics shed light on the complex evolutionary history of a gymnosperm genus showing East Asian–Tethyan disjunction

Journal of Systematics and Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 3, 2025

Abstract When and how disjunct distributions of biological taxa arose has long attracted interest in biogeography, yet the East Asian–Tethyan disjunction is understudied. Cupressus (Cupressaceae) shows this disjunction, with 10 species Asia three Mediterranean region. Here we used target‐capture sequencing obtained 1991 single‐copy nuclear genes, plus complete plastomes, to infer evolutionary history . Our phylogenomic reconstruction resolved four well supported clades , but revealed significant phylogenetic conflicts, inter‐lineage gene flow, incomplete lineage sorting tree estimation error all making important contributions. The Chengiana clade most likely originated by hybridization between ancestors Himalayan–Hengduan Mountains subtropical clades, whereas orogenic climatic changes may have facilitated flow within clade. Molecular dating suggested that recent common ancestor appeared around middle Eocene period then became continuously distributed across Eurasia. when diverged, been driven Eocene/Oligocene declines global temperature, reinforced ecogeographic barrier created uplift Qinghai–Tibet Plateau. Niche shifts clade, signatures selection genes for drought salt tolerance, probably indicate adaptation local conditions. Overall, our study in‐depth analyses are powerful tools deciphering complex origin organisms, especially gymnosperms.

Language: Английский

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The Chloranthus sessilifolius genome provides insight into early diversification of angiosperms

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: Nov. 26, 2021

Abstract Most extant angiosperms belong to Mesangiospermae, which comprises eudicots, monocots, magnoliids, Chloranthales and Ceratophyllales. However, phylogenetic relationships between these five lineages remain unclear. Here, we report the high-quality genome of a member lineage ( Chloranthus sessilifolius ). We detect only one whole duplication within this species find that polyploidization events in different Mesangiospermae are mutually independent. also members all floral development-related gene present C. despite its extremely simplified flower. The AP1 PI genes, however, show weak tissue-specialized expression. Our phylogenomic analyses suggest magnoliids sister groups, both together clade comprising Ceratophyllales while monocot is other Mesangiospermae. findings addition hybridization, incomplete sorting may largely account for inconsistencies observed trees.

Language: Английский

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Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi

Systematic Biology, Journal Year: 2022, Volume and Issue: 71(3), P. 741 - 757

Published: Jan. 31, 2022

Whole genome sequences are beginning to revolutionize our understanding of phylogenetic relationships. Yet, even whole can fail resolve the evolutionary history most rapidly radiating lineages, where incomplete lineage sorting, standing genetic variation, introgression, and other factors obscure group. To overcome such challenges, one emerging strategy is integrate results across different methods. Most approaches have been implemented on reduced representation genomic data sets, but genomes should provide maximum possible evidence approach. Here, we test ability single nucleotide polymorphisms extracted from resequencing data, in an integrative approach, key nodes phylogeny mbuna, rock-dwelling cichlid fishes Lake Malaŵi, which epitomize intractability that often accompanies explosive diversification. This monophyletic radiation has diversified at unparalleled rate into several hundred species less than 2 million years. Using array phylogenomic methods, consistently recovered four major clades a large basal polytomy among them. Although introgression between apparently contributed challenge reconstruction, reduction set nonintrogressed sites still did not help polytomy. On hand, relationships six congeneric pairs were resolved without ambiguity, case existing led us predict resolution would be difficult. We conclude bursts diversification earliest stages mbuna may phylogenetically unresolvable, regions tree clearly supported. Integration multiple will continue increase confidence inferred these whole-genome sets. [Incomplete sorting; introgression; linkage disequilibrium; multispecies coalescence; rapid radiation; soft polytomy.].

Language: Английский

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Genomic insights into zokors’ phylogeny and speciation in China

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(19)

Published: May 5, 2022

Significance Phylogenies are the basis of many ecological and evolutionary studies. However, zokor phylogeny speciation patterns heavily debated. This study disentangled zokors genomically. Six species Eospalax were separated into high-altitude E. baileyi smithi rest four low-altitude by recent Qinghai-Tibet Plateau uplift 3.6 million y ago. rothschildi speciated south Qinling–Huaihe Line, where refuges supplied during glaciation. Introgression incomplete lineage sorting led to complex zokors. Genomic islands formed due ancient polymorphisms divergence hitchhiking. concluded that climatic, geological, tectonic events shaped in China.

Language: Английский

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