All Outputs (38)

Local cryptic diversity in salinity adaptation mechanisms in the wild outcrossing Brassica fruticulosa (2024)
Journal Article
Busoms, S., da Silva, A. C., Escolà, G., Abdilzadeh, R., Curran, E., Bollmann-Giolai, A., Bray, S., Wilson, M., Poschenrieder, C., & Yant, L. (2024). Local cryptic diversity in salinity adaptation mechanisms in the wild outcrossing Brassica fruticulosa. Proceedings of the National Academy of Sciences, 121(40), Article e2407821121. https://doi.org/10.1073/pnas.2407821121

It is normally supposed that populations of the same species should evolve shared mechanisms of adaptation to common stressors due to evolutionary constraint. Here, we describe a system of within-species local adaptation to coastal habitats, Brassica... Read More about Local cryptic diversity in salinity adaptation mechanisms in the wild outcrossing Brassica fruticulosa.

Kinetochore and ionomic adaptation to whole-genome duplication in Cochlearia shows evolutionary convergence in three autopolyploids (2024)
Journal Article
Bray, S. M., Hämälä, T., Zhou, M., Busoms, S., Fischer, S., Desjardins, S. D., Mandáková, T., Moore, C., Mathers, T. C., Cowan, L., Monnahan, P., Koch, J., Wolf, E. M., Lysak, M. A., Kolar, F., Higgins, J. D., Koch, M. A., & Yant, L. (2024). Kinetochore and ionomic adaptation to whole-genome duplication in Cochlearia shows evolutionary convergence in three autopolyploids. Cell Reports, 43(8), Article 114576. https://doi.org/10.1016/j.celrep.2024.114576

Whole-genome duplication (WGD) occurs in all kingdoms and impacts speciation, domestication, and cancer outcome. However, doubled DNA management can be challenging for nascent polyploids. The study of within-species polyploidy (autopolyploidy) permit... Read More about Kinetochore and ionomic adaptation to whole-genome duplication in Cochlearia shows evolutionary convergence in three autopolyploids.

Impact of whole-genome duplications on structural variant evolution in Cochlearia (2024)
Journal Article
Hämälä, T., Moore, C., Cowan, L., Carlile, M., Gopaulchan, D., K. Brandrud, M., Birkeland, S., Loose, M., Kolář, F., A. Koch, M., & Yant, L. (2024). Impact of whole-genome duplications on structural variant evolution in Cochlearia. Nature Communications, 15, Article 5377. https://doi.org/10.1038/s41467-024-49679-y

Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. Yet WGDs are hugely disruptive mutations, and we still lack a clear understanding of their fitness consequences. Here, we study whether WGDs result in... Read More about Impact of whole-genome duplications on structural variant evolution in Cochlearia.

Chromosome-scale genome assembly of bread wheat’s wild relative Triticum timopheevii (2024)
Journal Article
Grewal, S., Yang, C.-Y., Scholefield, D., Ashling, S., Ghosh, S., Swarbreck, D., Collins, J., Yao, E., Sen, T. Z., Wilson, M., Yant, L., King, I. P., & King, J. (2024). Chromosome-scale genome assembly of bread wheat’s wild relative Triticum timopheevii. Scientific Data, 11(1), Article 420. https://doi.org/10.1038/s41597-024-03260-w

Wheat (Triticum aestivum) is one of the most important food crops with an urgent need for increase in its production to feed the growing world. Triticum timopheevii (2n = 4x = 28) is an allotetraploid wheat wild relative species containing the At and... Read More about Chromosome-scale genome assembly of bread wheat’s wild relative Triticum timopheevii.

The evolution of the duckweed ionome mirrors losses in structural complexity (2024)
Journal Article
Smith, K. E., Zhou, M., Flis, P., Jones, D. H., Bishopp, A., & Yant, L. (2024). The evolution of the duckweed ionome mirrors losses in structural complexity. Annals of Botany, 133(7), 997-1006. https://doi.org/10.1093/aob/mcae012

• Background and Aims The duckweeds (Lemnaceae) consist of 36 species exhibiting impressive phenotypic variation, including the progressive evolutionary loss of a fundamental plant organ, the root. Loss of roots and reduction of vascular tissues in r... Read More about The evolution of the duckweed ionome mirrors losses in structural complexity.

Combined genomics to discover genes associated with tolerance to soil carbonate (2023)
Journal Article
Busoms, S., Pérez‐Martín, L., Terés, J., Huang, X., Yant, L., Tolrà, R., Salt, D. E., & Poschenrieder, C. (2023). Combined genomics to discover genes associated with tolerance to soil carbonate. Plant, Cell and Environment, 46(12), 3986-3998. https://doi.org/10.1111/pce.14691

Carbonate‐rich soils limit plant performance and crop production. Previously, local adaptation to carbonated soils was detected in wild Arabidopsis thaliana accessions, allowing the selection of two demes with contrasting phenotypes: A1 (carbonate to... Read More about Combined genomics to discover genes associated with tolerance to soil carbonate.

Transition to Self-compatibility Associated With Dominant S-allele in a Diploid Siberian Progenitor of Allotetraploid Arabidopsis kamchatica Revealed by Arabidopsis lyrata Genomes (2023)
Journal Article
Kolesnikova, U. K., Scott, A. D., Van de Velde, J. D., Burns, R., Tikhomirov, N. P., Pfordt, U., Clarke, A. C., Yant, L., Seregin, A. P., Vekemans, X., Laurent, S., & Novikova, P. Y. (2023). Transition to Self-compatibility Associated With Dominant S-allele in a Diploid Siberian Progenitor of Allotetraploid Arabidopsis kamchatica Revealed by Arabidopsis lyrata Genomes. Molecular Biology and Evolution, 40(7), Article msad122. https://doi.org/10.1093/molbev/msad122

A transition to selfing can be beneficial when mating partners are scarce, for example, due to ploidy changes or at species range edges. Here, we explain how self-compatibility evolved in diploid Siberian Arabidopsis lyrata, and how it contributed to... Read More about Transition to Self-compatibility Associated With Dominant S-allele in a Diploid Siberian Progenitor of Allotetraploid Arabidopsis kamchatica Revealed by Arabidopsis lyrata Genomes.

Loss of ancestral function in duckweed roots is accompanied by progressive anatomical reduction and a re-distribution of nutrient transporters (2023)
Journal Article
Ware, A., Jones, D. H., Flis, P., Chrysanthou, E., Smith, K. E., Kümpers, B. M., Yant, L., Atkinson, J. A., Wells, D. M., Bhosale, R., & Bishopp, A. (2023). Loss of ancestral function in duckweed roots is accompanied by progressive anatomical reduction and a re-distribution of nutrient transporters. Current Biology, 33(9), 1795-1802. https://doi.org/10.1016/j.cub.2023.03.025

Organ loss occurs frequently during plant and animal evolution. Sometimes, non-functional organs are retained through evolution. Vestigial organs are defined as genetically determined structures that have lost their ancestral (or salient) function. D... Read More about Loss of ancestral function in duckweed roots is accompanied by progressive anatomical reduction and a re-distribution of nutrient transporters.

Chasing the mechanisms of ecologically adaptive salinity tolerance (2023)
Journal Article
Busoms, S., Fischer, S., & Yant, L. (2023). Chasing the mechanisms of ecologically adaptive salinity tolerance. Plant Communications, 4(6), Article 100571. https://doi.org/10.1016/j.xplc.2023.100571

Plants adapted to challenging environments offer fascinating models of evolutionary change. Importantly, they also give information to meet our pressing need to develop resilient, low-input crops. With mounting environmental fluctuation—including tem... Read More about Chasing the mechanisms of ecologically adaptive salinity tolerance.

Genomics and biochemical analyses reveal a metabolon key to β-L-ODAP biosynthesis in Lathyrus sativus (2023)
Journal Article
Edwards, A., Njaci, I., Sarkar, A., Jiang, Z., Kaithakottil, G. G., Moore, C., Cheema, J., Stevenson, C. E. M., Rejzek, M., Novák, P., Vigouroux, M., Vickers, M., Wouters, R. H. M., Paajanen, P., Steuernagel, B., Moore, J. D., Higgins, J., Swarbreck, D., Martens, S., Kim, C. Y., …Emmrich, P. M. F. (2023). Genomics and biochemical analyses reveal a metabolon key to β-L-ODAP biosynthesis in Lathyrus sativus. Nature Communications, 14, Article 876. https://doi.org/10.1038/s41467-023-36503-2

Grass pea (Lathyrus sativus L.) is a rich source of protein cultivated as an insurance crop in Ethiopia, Eritrea, India, Bangladesh, and Nepal. Its resilience to both drought and flooding makes it a promising crop for ensuring food security in a chan... Read More about Genomics and biochemical analyses reveal a metabolon key to β-L-ODAP biosynthesis in Lathyrus sativus.

Circular RNA in disease: Basic properties and biomedical relevance (2022)
Journal Article
Chen, X., Zhou, M., Yant, L., & Huang, C. (2022). Circular RNA in disease: Basic properties and biomedical relevance. Wiley Interdisciplinary Reviews: RNA, 13(6), Article e1723. https://doi.org/10.1002/wrna.1723

Circular RNAs (circRNAs) represent a class of covalently closed RNA molecules with great diversity in molecular features, functions, and regulatory mechanisms. Emerging advances in our understanding of circRNA biogenesis, nuclear export, and stabilit... Read More about Circular RNA in disease: Basic properties and biomedical relevance.

Evolutionary footprints of a cold relic in a rapidly warming world (2021)
Journal Article
Wolf, E., Gaquerel, E., Scharmann, M., Yant, L., & Koch, M. A. (2021). Evolutionary footprints of a cold relic in a rapidly warming world. eLife, 10, Article e71572. https://doi.org/10.7554/elife.71572

With accelerating global warming, understanding the evolutionary dynamics of plant adaptation to environmental change is increasingly urgent. Here we reveal the enigmatic history of the genus Cochlearia (Brassicaceae), a Pleistocene relic that origin... Read More about Evolutionary footprints of a cold relic in a rapidly warming world.

Transposable element annotation in non‐model species: The benefits of species‐specific repeat libraries using semi‐automated EDTA and DeepTE de novo pipelines (2021)
Journal Article
Bell, E. A., Butler, C. L., Oliveira, C., Marburger, S., Yant, L., & Taylor, M. I. (2022). Transposable element annotation in non‐model species: The benefits of species‐specific repeat libraries using semi‐automated EDTA and DeepTE de novo pipelines. Molecular Ecology Resources, 22(2), 823-833. https://doi.org/10.1111/1755-0998.13489

Transposable elements (TEs) are significant genomic components which can be detected either through sequence homology against existing databases or de novo, with the latter potentially reducing the risk of underestimating TE abundance. Here, we descr... Read More about Transposable element annotation in non‐model species: The benefits of species‐specific repeat libraries using semi‐automated EDTA and DeepTE de novo pipelines.

Parallel adaptation in autopolyploid Arabidopsis arenosa is dominated by repeated recruitment of shared alleles (2021)
Journal Article
Konečná, V., Bray, S., Vlček, J., Bohutínská, M., Požárová, D., Choudhury, R. R., Bollmann-Giolai, A., Flis, P., Salt, D. E., Parisod, C., Yant, L., & Kolář, F. (2021). Parallel adaptation in autopolyploid Arabidopsis arenosa is dominated by repeated recruitment of shared alleles. Nature Communications, 12(1), Article 4979. https://doi.org/10.1038/s41467-021-25256-5

Relative contributions of pre-existing vs de novo genomic variation to adaptation are poorly understood, especially in polyploid organisms. We assess this in high resolution using autotetraploid Arabidopsis arenosa, which repeatedly adapted to toxic... Read More about Parallel adaptation in autopolyploid Arabidopsis arenosa is dominated by repeated recruitment of shared alleles.

Polyploidy underlies co-option and diversification of biosynthetic triterpene pathways in the apple tribe (2021)
Journal Article
Su, W., Jing, Y., Lin, S., Yue, Z., Yang, X., Xu, J., Wu, J., Zhang, Z., Xia, R., Zhu, J., An, N., Chen, H., Hong, Y., Yuan, Y., Long, T., Zhang, L., Jiang, Y., Liu, Z., Zhang, H., Gao, Y., …Liu, Z. (2021). Polyploidy underlies co-option and diversification of biosynthetic triterpene pathways in the apple tribe. Proceedings of the National Academy of Sciences, 118(20), 1-11. https://doi.org/10.1073/pnas.2101767118

Whole-genome duplication (WGD) plays important roles in plant evolution and function, yet little is known about how WGD underlies metabolic diversification of natural products that bear significant medicinal properties, especially in nonmodel trees.... Read More about Polyploidy underlies co-option and diversification of biosynthetic triterpene pathways in the apple tribe.

Novelty and Convergence in Adaptation to Whole Genome Duplication (2021)
Journal Article
Bohutínská, M., Alston, M., Monnahan, P., Mandáková, T., Bray, S., Paajanen, P., Kolář, F., & Yant, L. (2021). Novelty and Convergence in Adaptation to Whole Genome Duplication. Molecular Biology and Evolution, 38(9), 3910-3924. https://doi.org/10.1093/molbev/msab096

Whole genome duplication (WGD) can promote adaptation but is disruptive to conserved processes, especially meiosis. Studies in Arabidopsis arenosa revealed a coordinated evolutionary response to WGD involving interacting proteins controlling meiotic... Read More about Novelty and Convergence in Adaptation to Whole Genome Duplication.

Population genomic and historical analysis suggests a global invasion by bridgehead processes in Mimulus guttatus (2021)
Journal Article
Vallejo-Marín, M., Friedman, J., Twyford, A. D., Lepais, O., Ickert-Bond, S. M., Streisfeld, M. A., Yant, L., van Kleunen, M., Rotter, M. C., & Puzey, J. R. (2021). Population genomic and historical analysis suggests a global invasion by bridgehead processes in Mimulus guttatus. Communications Biology, 4(1), https://doi.org/10.1038/s42003-021-01795-x

© 2021, The Author(s). Imperfect historical records and complex demographic histories present challenges for reconstructing the history of biological invasions. Here, we combine historical records, extensive worldwide and genome-wide sampling, and de... Read More about Population genomic and historical analysis suggests a global invasion by bridgehead processes in Mimulus guttatus.

Adaptive introgression: how polyploidy reshapes gene flow landscapes (2021)
Journal Article
Schmickl, R., & Yant, L. (2021). Adaptive introgression: how polyploidy reshapes gene flow landscapes. New Phytologist, 230(2), 457-461. https://doi.org/10.1111/nph.17204

© 2021 The Authors. New Phytologist © 2021 New Phytologist Foundation Rare yet accumulating evidence in both plants and animals shows that whole genome duplication (WGD, leading to polyploidy) can break down reproductive barriers, facilitating gene f... Read More about Adaptive introgression: how polyploidy reshapes gene flow landscapes.

De Novo Mutation and Rapid Protein (Co-)evolution during Meiotic Adaptation in Arabidopsis arenosa (2021)
Journal Article
Bohutínská, M., Handrick, V., Yant, L., Schmickl, R., Kolář, F., Bomblies, K., & Paajanen, P. (2021). De Novo Mutation and Rapid Protein (Co-)evolution during Meiotic Adaptation in Arabidopsis arenosa. Molecular Biology and Evolution, 38(5), 1980-1994. https://doi.org/10.1093/molbev/msab001

A sudden shift in environment or cellular context necessitates rapid adaptation. A dramatic example is genome duplication, which leads to polyploidy. In such situations, the waiting time for new mutations might be prohibitive; theoretical and empiric... Read More about De Novo Mutation and Rapid Protein (Co-)evolution during Meiotic Adaptation in Arabidopsis arenosa.

Maintenance of Adaptive Dynamics and No Detectable Load in a Range-Edge Outcrossing Plant Population (2021)
Journal Article
Takou, M., Hämälä, T., Koch, E. M., Steige, K. A., Dittberner, H., Yant, L., Genete, M., Sunyaev, S., Castric, V., Vekemans, X., Savolainen, O., & Meaux, J. D. (2021). Maintenance of Adaptive Dynamics and No Detectable Load in a Range-Edge Outcrossing Plant Population. Molecular Biology and Evolution, 38(5), 1820-1836. https://doi.org/10.1093/molbev/msaa322

During range expansion, edge populations are expected to face increased genetic drift, which in turn can alter and potentially compromise adaptive dynamics, preventing the removal of deleterious mutations and slowing down adaptation. Here, we contras... Read More about Maintenance of Adaptive Dynamics and No Detectable Load in a Range-Edge Outcrossing Plant Population.