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Barragan AC, Collenberg M, Schwab R, Kersten S, Kerstens MHL, Požárová D, Bezrukov I, Bemm F, Kolár F, Weigel D. Deleterious phenotypes in wild Arabidopsis arenosa populations are common and linked to runs of homozygosity. G3 (Bethesda) 2024; 14:jkad290. [PMID: 38124484 PMCID: PMC10917499 DOI: 10.1093/g3journal/jkad290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/07/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023]
Abstract
In this study, we aimed to systematically assess the frequency at which potentially deleterious phenotypes appear in natural populations of the outcrossing model plant Arabidopsis arenosa, and to establish their underlying genetics. For this purpose, we collected seeds from wild A. arenosa populations and screened over 2,500 plants for unusual phenotypes in the greenhouse. We repeatedly found plants with obvious phenotypic defects, such as small stature and necrotic or chlorotic leaves, among first-generation progeny of wild A. arenosa plants. Such abnormal plants were present in about 10% of maternal sibships, with multiple plants with similar phenotypes in each of these sibships, pointing to a genetic basis of the observed defects. A combination of transcriptome profiling, linkage mapping and genome-wide runs of homozygosity patterns using a newly assembled reference genome indicated a range of underlying genetic architectures associated with phenotypic abnormalities. This included evidence for homozygosity of certain genomic regions, consistent with alleles that are identical by descent being responsible for these defects. Our observations suggest that deleterious alleles with different genetic architectures are segregating at appreciable frequencies in wild A. arenosa populations.
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Affiliation(s)
- A Cristina Barragan
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
- The Sainsbury Laboratory, Norwich NR4 7UH, UK
| | - Maximilian Collenberg
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
- Catalent, 73614 Schorndorf, Germany
| | - Rebecca Schwab
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
| | - Sonja Kersten
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
- Institute of Plant Breeding, University of Hohenheim, 70599 Stuttgart, Germany
| | - Merijn H L Kerstens
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
- Department of Plant Developmental Biology, Wageningen University and Research, 6708 PB, Wageningen, Netherlands
| | - Doubravka Požárová
- Department of Botany, Faculty of Science, Charles University, 128 01 Prague, Czech Republic
- The MAMA AI, 100 00 Prague, Czech Republic
| | - Ilja Bezrukov
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
| | - Felix Bemm
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
- KWS Saat, 37574 Einbeck, Germany
| | - Filip Kolár
- Department of Botany, Faculty of Science, Charles University, 128 01 Prague, Czech Republic
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
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Wlodzimierz P, Rabanal FA, Burns R, Naish M, Primetis E, Scott A, Mandáková T, Gorringe N, Tock AJ, Holland D, Fritschi K, Habring A, Lanz C, Patel C, Schlegel T, Collenberg M, Mielke M, Nordborg M, Roux F, Shirsekar G, Alonso-Blanco C, Lysak MA, Novikova PY, Bousios A, Weigel D, Henderson IR. Cycles of satellite and transposon evolution in Arabidopsis centromeres. Nature 2023:10.1038/s41586-023-06062-z. [PMID: 37198485 DOI: 10.1038/s41586-023-06062-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 04/06/2023] [Indexed: 05/19/2023]
Abstract
Centromeres are critical for cell division, loading CENH3 or CENPA histone variant nucleosomes, directing kinetochore formation and allowing chromosome segregation1,2. Despite their conserved function, centromere size and structure are diverse across species. To understand this centromere paradox3,4, it is necessary to know how centromeric diversity is generated and whether it reflects ancient trans-species variation or, instead, rapid post-speciation divergence. To address these questions, we assembled 346 centromeres from 66 Arabidopsis thaliana and 2 Arabidopsis lyrata accessions, which exhibited a remarkable degree of intra- and inter-species diversity. A. thaliana centromere repeat arrays are embedded in linkage blocks, despite ongoing internal satellite turnover, consistent with roles for unidirectional gene conversion or unequal crossover between sister chromatids in sequence diversification. Additionally, centrophilic ATHILA transposons have recently invaded the satellite arrays. To counter ATHILA invasion, chromosome-specific bursts of satellite homogenization generate higher-order repeats and purge transposons, in line with cycles of repeat evolution. Centromeric sequence changes are even more extreme in comparison between A. thaliana and A. lyrata. Together, our findings identify rapid cycles of transposon invasion and purging through satellite homogenization, which drive centromere evolution and ultimately contribute to speciation.
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Affiliation(s)
- Piotr Wlodzimierz
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Fernando A Rabanal
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Robin Burns
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Matthew Naish
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Elias Primetis
- School of Life Sciences, University of Sussex, Brighton, UK
| | - Alison Scott
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Terezie Mandáková
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Nicola Gorringe
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Andrew J Tock
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Daniel Holland
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Katrin Fritschi
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Anette Habring
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Christa Lanz
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Christie Patel
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Theresa Schlegel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Maximilian Collenberg
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Miriam Mielke
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Magnus Nordborg
- Gregor Mendel Institute, Vienna, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Fabrice Roux
- LIPME, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Gautam Shirsekar
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Martin A Lysak
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Polina Y Novikova
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
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Röseler W, Collenberg M, Yoshida K, Lanz C, Sommer RJ, Rödelsperger C. The improved genome of the nematode Parapristionchus giblindavisi provides insights into lineage-specific gene family evolution. G3 Genes|Genomes|Genetics 2022; 12:6671220. [PMID: 35980151 PMCID: PMC9526060 DOI: 10.1093/g3journal/jkac215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/08/2022] [Indexed: 11/24/2022]
Abstract
Nematodes such as Caenorhabditis elegans and Pristionchus pacificus are extremely successful model organisms for comparative biology. Several studies have shown that phenotypic novelty but also conserved processes are controlled by taxon-restricted genes. To trace back the evolution of such new or rapidly evolving genes, a robust phylogenomic framework is indispensable. Here, we present an improved version of the genome of Parapristionchus giblindavisi which is the only known member of the sister group of Pristionchus. Relative to the previous short-read assembly, the new genome is based on long reads and displays higher levels of contiguity, completeness, and correctness. Specifically, the number of contigs dropped from over 7,303 to 735 resulting in an N50 increase from 112 to 791 kb. We made use of the new genome to revisit the evolution of multiple gene families. This revealed Pristionchus-specific expansions of several environmentally responsive gene families and a Pristionchus-specific loss of the de novo purine biosynthesis pathway. Focusing on the evolution of sulfatases and sulfotransferases, which control the mouth form plasticity in P. pacificus, reveals differences in copy number and genomic configurations between the genera Pristionchus and Parapristionchus. Altogether, this demonstrates the utility of the P. giblindavisi genome to date and polarizes lineage-specific patterns.
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Affiliation(s)
- Waltraud Röseler
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology , 72076 Tübingen, Germany
| | - Maximilian Collenberg
- Department for Molecular Biology, Max Planck Institute for Biology , 72076 Tübingen, Germany
| | - Kohta Yoshida
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology , 72076 Tübingen, Germany
| | - Christa Lanz
- Department for Molecular Biology, Max Planck Institute for Biology , 72076 Tübingen, Germany
| | - Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology , 72076 Tübingen, Germany
| | - Christian Rödelsperger
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology , 72076 Tübingen, Germany
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Barragan AC, Collenberg M, Wang J, Lee RRQ, Cher WY, Rabanal FA, Ashkenazy H, Weigel D, Chae E. A Truncated Singleton NLR Causes Hybrid Necrosis in Arabidopsis thaliana. Mol Biol Evol 2021; 38:557-574. [PMID: 32966577 PMCID: PMC7826191 DOI: 10.1093/molbev/msaa245] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Hybrid necrosis in plants arises from conflict between divergent alleles of immunity genes contributed by different parents, resulting in autoimmunity. We investigate a severe hybrid necrosis case in Arabidopsis thaliana, where the hybrid does not develop past the cotyledon stage and dies 3 weeks after sowing. Massive transcriptional changes take place in the hybrid, including the upregulation of most NLR (nucleotide-binding site leucine-rich repeat) disease-resistance genes. This is due to an incompatible interaction between the singleton TIR-NLR gene DANGEROUS MIX 10 (DM10), which was recently relocated from a larger NLR cluster, and an unlinked locus, DANGEROUS MIX 11 (DM11). There are multiple DM10 allelic variants in the global A. thaliana population, several of which have premature stop codons. One of these, which has a truncated LRR-PL (leucine-rich repeat [LRR]-post-LRR) region, corresponds to the DM10 risk allele. The DM10 locus and the adjacent genomic region in the risk allele carriers are highly differentiated from those in the nonrisk carriers in the global A. thaliana population, suggesting that this allele became geographically widespread only relatively recently. The DM11 risk allele is much rarer and found only in two accessions from southwestern Spain-a region from which the DM10 risk haplotype is absent-indicating that the ranges of DM10 and DM11 risk alleles may be nonoverlapping.
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Affiliation(s)
- Ana Cristina Barragan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Maximilian Collenberg
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jinge Wang
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Rachelle R Q Lee
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Wei Yuan Cher
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Fernando A Rabanal
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Haim Ashkenazy
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Eunyoung Chae
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Department of Biological Sciences, National University of Singapore, Singapore
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Frei H, Everts R, von Ammon K, Kaufmann F, Walther D, Schmitz SFH, Collenberg M, Steinlin M, Lim C, Thurneysen A. Randomised controlled trials of homeopathy in hyperactive children: treatment procedure leads to an unconventional study design. Experience with open-label homeopathic treatment preceding the Swiss ADHD placebo controlled, randomised, double-blind, cross-over trial. HOMEOPATHY 2007; 96:35-41. [PMID: 17227746 DOI: 10.1016/j.homp.2006.11.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Revised: 11/02/2006] [Accepted: 11/06/2006] [Indexed: 11/15/2022]
Abstract
BACKGROUND Treatment of patients with attention deficit hyperactivity disorder (ADHD) with homeopathy is difficult. The Swiss randomised, placebo controlled, cross-over trial in ADHD patients (Swiss ADHD trial) was designed with an open-label screening phase prior to the randomised controlled phase. During the screening phase, the response of each child to successive homeopathic medications was observed until the optimal medication was identified. Only children who reached a predefined level of improvement participated in the randomised, cross-over phase. Although the randomised phase revealed a significant beneficial effect of homeopathy, the cross-over caused a strong carryover effect diminishing the apparent difference between placebo and verum treatment. METHODS This retrospective analysis explores the screening phase data with respect to the risk of failure to demonstrate a specific effect of a randomised controlled trial (RCT) with randomisation at the start of the treatment. RESULTS During the screening phase, 84% (70/83) of the children responded to treatment and reached eligibility for the randomised trial after a median time of 5 months (range 1-18), with a median of 3 different medications (range 1-9). Thirteen children (16%) did not reach eligibility. Five months after treatment start, the difference in Conners Global Index (CGI) rating between responders and non-responders became highly significant (p = 0.0006). Improvement in CGI was much greater following the identification of the optimal medication than in the preceding suboptimal treatment period (p < 0.0001). CONCLUSIONS Because of the necessity of identifying an optimal medication before response to treatment can be expected, randomisation at the start of treatment in an RCT of homeopathy in ADHD children has a high risk of failure to demonstrate a specific treatment effect, if the observation time is shorter than 12 months.
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Affiliation(s)
- H Frei
- Swiss Association of Homeopathic Physicians, Lucerne, Switzerland.
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