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Journal articles on the topic 'Arabidopsis suecica'

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Published: 25 January 2025

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1

SÄLL, TORBJÖRN, CHRISTINA LIND-HALLDÉN, MATTIAS JAKOBSSON, and CHRISTER HALLDÉN. "Mode of reproduction in Arabidopsis suecica." Hereditas 141, no. 3 (February 8, 2005): 313–17. http://dx.doi.org/10.1111/j.1601-5223.2004.01833.x.

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2

Solhaug, Erik M., Jacie Ihinger, Maria Jost, Veronica Gamboa, Blaine Marchant, Denise Bradford, R. W. Doerge, Anand Tyagi, Amy Replogle, and Andreas Madlung. "Environmental Regulation of Heterosis in the Allopolyploid Arabidopsis suecica." Plant Physiology 170, no. 4 (February 19, 2016): 2251–63. http://dx.doi.org/10.1104/pp.16.00052.

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3

McCullough, Erin, Kirsten M. Wright, Aurelia Alvarez, Chanel P. Clark, Wayne L. Rickoll, and Andreas Madlung. "Photoperiod-dependent floral reversion in the natural allopolyploid Arabidopsis suecica." New Phytologist 186, no. 1 (January 13, 2010): 239–50. http://dx.doi.org/10.1111/j.1469-8137.2009.03141.x.

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4

Sall, T., M. Jakobsson, C. Lind-Hallden, and C. Hallden. "Chloroplast DNA indicates a single origin of the allotetraploid Arabidopsis suecica." Journal of Evolutionary Biology 16, no. 5 (September 2003): 1019–29. http://dx.doi.org/10.1046/j.1420-9101.2003.00554.x.

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5

Ali, Hoda B. M., Martin A. Lysak, and Ingo Schubert. "Genomic in situ hybridization in plants with small genomes is feasible and elucidates the chromosomal parentage in interspecific Arabidopsis hybrids." Genome 47, no. 5 (October 1, 2004): 954–60. http://dx.doi.org/10.1139/g04-041.

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Genomic in situ hybridization (GISH) is a useful tool to analyse natural polyploids, hybrid plants, and their backcross progenies as to their origin, genomic composition, and intergenomic rearrangements. However, in angiosperms with very small genomes (<0.6 pg/1 C), often only heterochromatic regions were found to be labeled. We have modified the GISH technique to label entire mitotic and meiotic chromosomes of Arabidopsis thaliana (2n = 10) and closely related species with very small genomes by using high concentrations of DNA (7.5–15 µg per probe per slide) or 5 µg of probe and long hybridization times (>60 h). According to our GISH data, Cardaminopsis carpatica (2n = 16) is most likely the diploid ancestor of the autotetraploid Arabidopsis arenosa (2n = 32). Furthermore, within the allotetraploid species Arabidopsis suecica (2n = 26), it was possible to elucidate the origin of chromosomes contributed by the parental species A. thaliana and A. arenosa for a specimen with 2n = 26 or a deviating chromosome number.Key words: genomic in situ hybridization (GISH), Arabidopsis, Brassicaceae, allopolyploids, synthetic hybrids.
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6

O'Kane, Steve L., Barbara A. Schaal, and Ihsan A. Al-Shehbaz. "The Origins of Arabidopsis suecica (Brassicaceae) as Indicated by Nuclear rDNA Sequences." Systematic Botany 21, no. 4 (October 1996): 559. http://dx.doi.org/10.2307/2419615.

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7

Mummenhoff, Klaus, and Herbert Hurka. "Subunit polypeptide composition of rubisco and the origin of allopolyploid Arabidopsis suecica (Brassicaceae)." Biochemical Systematics and Ecology 22, no. 8 (December 1994): 807–11. http://dx.doi.org/10.1016/0305-1978(94)90084-1.

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8

LIND-HALLDEN, C., C. HALLDEN, and T. SALL. "Genetic variation in Arabidopsis suecica and its parental species A. arenosa and A. thaliana." Hereditas 136, no. 1 (April 2002): 45–50. http://dx.doi.org/10.1034/j.1601-5223.2002.1360107.x.

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9

JAKOBSSON, M., T. SÄLL, C. LIND-HALLDÉN, and C. HALLDÉN. "The evolutionary history of the common chloroplast genome of Arabidopsis thaliana and A. suecica." Journal of Evolutionary Biology 20, no. 1 (January 2007): 104–21. http://dx.doi.org/10.1111/j.1420-9101.2006.01217.x.

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10

Pontes, O., N. Neves, M. Silva, M. S. Lewis, A. Madlung, L. Comai, W. Viegas, and C. S. Pikaard. "Chromosomal locus rearrangements are a rapid response to formation of the allotetraploid Arabidopsis suecica genome." Proceedings of the National Academy of Sciences 101, no. 52 (December 16, 2004): 18240–45. http://dx.doi.org/10.1073/pnas.0407258102.

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11

Jakobsson, Mattias, Jenny Hagenblad, Simon Tavaré, Torbjörn Säll, Christer Halldén, Christina Lind-Halldén, and Magnus Nordborg. "A Unique Recent Origin of the Allotetraploid Species Arabidopsis suecica: Evidence from Nuclear DNA Markers." Molecular Biology and Evolution 23, no. 6 (March 20, 2006): 1217–31. http://dx.doi.org/10.1093/molbev/msk006.

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12

Asbe, Amelia, Starr C. Matsushita, Spencer Gordon, H. E. Kirkpatrick, and Andreas Madlung. "Floral Reversion in Arabidopsis suecica Is Correlated with the Onset of Flowering and Meristem Transitioning." PLOS ONE 10, no. 5 (May 26, 2015): e0127897. http://dx.doi.org/10.1371/journal.pone.0127897.

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13

Madlung, Andreas, Natalie Henkhaus, Leigh Jurevic, Emanual A. Kahsai, and James Bernhard. "Natural variation and persistent developmental instabilities in geographically diverse accessions of the allopolyploid Arabidopsis suecica." Physiologia Plantarum 144, no. 2 (November 10, 2011): 123–33. http://dx.doi.org/10.1111/j.1399-3054.2011.01526.x.

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14

Chang, Peter L., Brian P. Dilkes, Michelle McMahon, Luca Comai, and Sergey V. Nuzhdin. "Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners." Genome Biology 11, no. 12 (2010): R125. http://dx.doi.org/10.1186/gb-2010-11-12-r125.

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15

"Arabidopsis suecica." CABI Compendium CABI Compendium (January 7, 2022). http://dx.doi.org/10.1079/cabicompendium.112387.

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16

Burns, Robin, Terezie Mandáková, Joanna Gunis, Luz Mayela Soto-Jiménez, Chang Liu, Martin A. Lysak, Polina Yu Novikova, and Magnus Nordborg. "Gradual evolution of allopolyploidy in Arabidopsis suecica." Nature Ecology & Evolution, August 19, 2021. http://dx.doi.org/10.1038/s41559-021-01525-w.

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AbstractMost diploid organisms have polyploid ancestors. The evolutionary process of polyploidization is poorly understood but has frequently been conjectured to involve some form of ‘genome shock’, such as genome reorganization and subgenome expression dominance. Here we study polyploidization in Arabidopsis suecica, a post-glacial allopolyploid species formed via hybridization of Arabidopsis thaliana and Arabidopsis arenosa. We generated a chromosome-level genome assembly of A. suecica and complemented it with polymorphism and transcriptome data from all species. Despite a divergence around 6 million years ago (Ma) between the ancestral species and differences in their genome composition, we see no evidence of a genome shock: the A. suecica genome is colinear with the ancestral genomes; there is no subgenome dominance in expression; and transposon dynamics appear stable. However, we find changes suggesting gradual adaptation to polyploidy. In particular, the A. thaliana subgenome shows upregulation of meiosis-related genes, possibly to prevent aneuploidy and undesirable homeologous exchanges that are observed in synthetic A. suecica, and the A. arenosa subgenome shows upregulation of cyto-nuclear processes, possibly in response to the new cytoplasmic environment of A. suecica, with plastids maternally inherited from A. thaliana. These changes are not seen in synthetic hybrids, and thus are likely to represent subsequent evolution.
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17

Chéron, Floriane, Valentine Petiot, Christophe Lambing, Charles White, and Heïdi Serra. "Incorrect recombination partner associations contribute to meiotic instability of neo‐allopolyploid Arabidopsis suecica." New Phytologist, December 29, 2023. http://dx.doi.org/10.1111/nph.19487.

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Summary Combining two or more related homoeologous genomes in a single nucleus, newly formed allopolyploids must rapidly adapt meiosis to restore balanced chromosome segregation, production of euploid gametes and fertility. The poor fertility of such neo‐allopolyploids thus strongly selects for the limitation or avoidance of genetic crossover formation between homoeologous chromosomes. In this study, we have reproduced the interspecific hybridization between Arabidopsis thaliana and Arabidopsis arenosa leading to the allotetraploid Arabidopsis suecica and have characterized the first allopolyploid meioses. First‐generation neo‐allopolyploid siblings vary considerably in fertility, meiotic behavior and levels of homoeologous recombination. We show that centromere dynamics at early meiosis is altered in synthetic neo‐allopolyploids compared with evolved A. suecica, with a significant increase in homoeologous centromere interactions at zygotene. At metaphase I, the presence of multivalents involving homoeologous chromosomes confirms that homoeologous recombination occurs in the first‐generation synthetic allopolyploid plants and this is associated with a significant reduction in homologous recombination, compared to evolved A. suecica. Together, these data strongly suggest that the fidelity of recombination partner choice, likely during the DNA invasion step, is strongly impaired during the first meiosis of neo‐allopolyploids and requires subsequent adaptation.
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18

Nibau, Candida, Adrián Gonzalo, Aled Evans, William Sweet‐Jones, Dylan Phillips, and Andrew Lloyd. "Meiosis in allopolyploid Arabidopsis suecica." Plant Journal, June 27, 2022. http://dx.doi.org/10.1111/tpj.15879.

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19

Jiang, Xinyu, Qingxin Song, Wenxue Ye, and Z. Jeffrey Chen. "Concerted genomic and epigenomic changes accompany stabilization of Arabidopsis allopolyploids." Nature Ecology & Evolution, August 19, 2021. http://dx.doi.org/10.1038/s41559-021-01523-y.

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AbstractDuring evolution successful allopolyploids must overcome ‘genome shock’ between hybridizing species but the underlying process remains elusive. Here, we report concerted genomic and epigenomic changes in resynthesized and natural Arabidopsis suecica (TTAA) allotetraploids derived from Arabidopsisthaliana (TT) and Arabidopsisarenosa (AA). A. suecica shows conserved gene synteny and content with more gene family gain and loss in the A and T subgenomes than respective progenitors, although A. arenosa-derived subgenome has more structural variation and transposon distributions than A. thaliana-derived subgenome. These balanced genomic variations are accompanied by pervasive convergent and concerted changes in DNA methylation and gene expression among allotetraploids. The A subgenome is hypomethylated rapidly from F1 to resynthesized allotetraploids and convergently to the T-subgenome level in natural A. suecica, despite many other methylated loci being inherited from F1 to all allotetraploids. These changes in DNA methylation, including small RNAs, in allotetraploids may affect gene expression and phenotypic variation, including flowering, silencing of self-incompatibility and upregulation of meiosis- and mitosis-related genes. In conclusion, concerted genomic and epigenomic changes may improve stability and adaptation during polyploid evolution.
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20

Oruganti, Vidya, Helena Toegelová, Aleš Pečinka, Andreas Madlung, and Korbinian Schneeberger. "Rapid large-scale genomic introgression in Arabidopsis suecica via an autoallohexaploid bridge." Genetics, September 19, 2022. http://dx.doi.org/10.1093/genetics/iyac132.

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Abstract Gene flow between species in the genus Arabidopsis occurs in significant amounts, but how exactly gene flow is achieved is not well understood. Polyploidization may be one avenue to explain gene flow between species. One problem, however, with polyploidization as a satisfying explanation is the occurrence of lethal genomic instabilities in neopolyploids as a result of genomic exchange, erratic meiotic behavior, and genomic shock. We have created an autoallohexaploid by pollinating naturally co-occurring diploid Arabidopsis thaliana with allotetraploid Arabidopsis suecica (an allotetraploid composed of A. thaliana and Arabidopsis arenosa). Its triploid offspring underwent spontaneous genome duplication and was used to generate a multigenerational pedigree. Using genome resequencing, we show that 2 major mechanisms promote stable genomic exchange in this population. Legitimate meiotic recombination and chromosome segregation between the autopolyploid chromosomes of the 2 A. thaliana genomes occur without any obvious bias for the parental origin and combine the A. thaliana haplotypes from the A. thaliana parent with the A. thaliana haplotypes from A. suecica similar to purely autopolyploid plants. In addition, we repeatedly observed that occasional exchanges between regions of the homoeologous chromosomes are tolerated. The combination of these mechanisms may result in gene flow leading to stable introgression in natural populations. Unlike the previously reported resynthesized neoallotetraploid A. suecica, this population of autoallohexaploids contains mostly vigorous, and genetically, cytotypically, and phenotypically variable individuals. We propose that naturally formed autoallohexaploid populations might serve as an intermediate bridge between diploid and polyploid species, which can facilitate gene flow rapidly and efficiently.
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21

Yu. Novikova, Polina, Takashi Tsuchimatsu, Samson Simon, Viktoria Nizhynska, Viktor Voronin, Robin Burns, Olga M. Fedorenko, et al. "Genome sequencing reveals the origin of the allotetraploid Arabidopsis suecica." Molecular Biology and Evolution, January 12, 2017, msw299. http://dx.doi.org/10.1093/molbev/msw299.

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22

Nibau, Candida, Aled Evans, Holly King, Dylan Wyn Phillips, and Andrew Lloyd. "Homoeologous crossovers are distally biased and underlie genomic instability in first‐generation neo‐allopolyploid Arabidopsis suecica." New Phytologist, September 6, 2024. http://dx.doi.org/10.1111/nph.20095.

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Summary First‐generation polyploids often suffer from more meiotic errors and lower fertility than established wild polyploid populations. One such example is the allopolyploid model species Arabidopsis suecica which originated c. 16 000 generations ago. We present here a comparison of meiosis and its outcomes in naturally evolved and first‐generation ‘synthetic’ A. suecica using a combination of cytological and genomic approaches. We show that while meiosis in natural lines is largely diploid‐like, synthetic lines have high levels of meiotic errors including incomplete synapsis and nonhomologous crossover formation. Whole‐genome re‐sequencing of progeny revealed 20‐fold higher levels of homoeologous exchange and eightfold higher aneuploidy originating from synthetic parents. Homoeologous exchanges showed a strong distal bias and occurred predominantly in genes, regularly generating novel protein variants. We also observed that homoeologous exchanges can generate megabase scale INDELs when occurring in regions of inverted synteny. Finally, we observed evidence of sex‐specific differences in adaptation to polyploidy with higher success in reciprocal crosses to natural lines when synthetic plants were used as the female parent. Our results directly link cytological phenotypes in A. suecica with their genomic outcomes, demonstrating that homoeologous crossovers underlie genomic instability in neo‐allopolyploids and are more distally biased than homologous crossovers.
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23

Karimi-Ashtiyani, Raheleh, Ali Mohammad Banaei-Moghaddam, Takayoshi Ishii, Oda Weiss, Jörg Fuchs, Veit Schubert, and Andreas Houben. "Centromere sequence-independent but biased loading of subgenome-specific CENH3 variants in allopolyploid Arabidopsis suecica." Plant Molecular Biology 114, no. 4 (June 14, 2024). http://dx.doi.org/10.1007/s11103-024-01474-5.

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AbstractCentromeric nucleosomes are determined by the replacement of the canonical histone H3 with the centromere-specific histone H3 (CENH3) variant. Little is known about the centromere organization in allopolyploid species where different subgenome-specific CENH3s and subgenome-specific centromeric sequences coexist. Here, we analyzed the transcription and centromeric localization of subgenome-specific CENH3 variants in the allopolyploid species Arabidopsis suecica. Synthetic A. thaliana x A. arenosa hybrids were generated and analyzed to mimic the early evolution of A. suecica. Our expression analyses indicated that CENH3 has generally higher expression levels in A. arenosa compared to A. thaliana, and this pattern persists in the hybrids. We also demonstrated that despite a different centromere DNA composition, the centromeres of both subgenomes incorporate CENH3 encoded by both subgenomes, but with a positive bias towards the A. arenosa-type CENH3. The intermingled arrangement of both CENH3 variants demonstrates centromere plasticity and may be an evolutionary adaption to handle more than one CENH3 variant in the process of allopolyploidization.
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24

Carlson, Keisha D., Noe Fernandez-Pozo, Aureliano Bombarely, Rahul Pisupati, Lukas A. Mueller, and Andreas Madlung. "Natural variation in stress response gene activity in the allopolyploid Arabidopsis suecica." BMC Genomics 18, no. 1 (August 23, 2017). http://dx.doi.org/10.1186/s12864-017-4067-x.

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25

Novikova, Polina Yu, Uliana K. Kolesnikova, and Alison Dawn Scott. "Ancestral self-compatibility facilitates the establishment of allopolyploids in Brassicaceae." Plant Reproduction, October 25, 2022. http://dx.doi.org/10.1007/s00497-022-00451-6.

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AbstractSelf-incompatibility systems based on self-recognition evolved in hermaphroditic plants to maintain genetic variation of offspring and mitigate inbreeding depression. Despite these benefits in diploid plants, for polyploids who often face a scarcity of mating partners, self-incompatibility can thwart reproduction. In contrast, self-compatibility provides an immediate advantage: a route to reproductive viability. Thus, diploid selfing lineages may facilitate the formation of new allopolyploid species. Here, we describe the mechanism of establishment of at least four allopolyploid species in Brassicaceae (Arabidopsis suecica, Arabidopsis kamchatica, Capsella bursa-pastoris, and Brassica napus), in a manner dependent on the prior loss of the self-incompatibility mechanism in one of the ancestors. In each case, the degraded S-locus from one parental lineage was dominant over the functional S-locus of the outcrossing parental lineage. Such dominant loss-of-function mutations promote an immediate transition to selfing in allopolyploids and may facilitate their establishment.
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26

Gabriel, Kristina E. "Investigating the role of the ERF104 gene in stress tolerance in model plant Arabidopsis suecica using CRISPR." FASEB Journal 36, S1 (May 2022). http://dx.doi.org/10.1096/fasebj.2022.36.s1.r6026.

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27

Zhang, Zhibin, Xiaowan Gou, Hongwei Xun, Yao Bian, Xintong Ma, Juzuo Li, Ning Li, et al. "Homoeologous exchanges occur through intragenic recombination generating novel transcripts and proteins in wheat and other polyploids." Proceedings of the National Academy of Sciences, June 9, 2020, 202003505. http://dx.doi.org/10.1073/pnas.2003505117.

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Recombination between homeologous chromosomes, also known as homeologous exchange (HE), plays a significant role in shaping genome structure and gene expression in interspecific hybrids and allopolyploids of several plant species. However, the molecular mechanisms that govern HEs are not well understood. Here, we studied HE events in the progeny of a nascent allotetraploid (genome AADD) derived from two diploid progenitors of hexaploid bread wheat using cytological and whole-genome sequence analyses. In total, 37 HEs were identified and HE junctions were mapped precisely. HEs exhibit typical patterns of homologous recombination hotspots, being biased toward low-copy, subtelomeric regions of chromosome arms and showing association with known recombination hotspot motifs. But, strikingly, while homologous recombination preferentially takes place upstream and downstream of coding regions, HEs are highly enriched within gene bodies, giving rise to novel recombinant transcripts, which in turn are predicted to generate new protein fusion variants. To test whether this is a widespread phenomenon, a dataset of high-resolution HE junctions was analyzed for allopolyploid Brassica, rice, Arabidopsis suecica, banana, and peanut. Intragenic recombination and formation of chimeric genes was detected in HEs of all species and was prominent in most of them. HE thus provides a mechanism for evolutionary novelty in transcript and protein sequences in nascent allopolyploids.
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28

Kornstad, Torbjørn, Mikael Ohlson, and Siri Fjellheim. "Phenotypic responses to light, water, and nutrient conditions in the allopolyploid Arabidopsis suecica and its parent species A. thaliana and A. arenosa : Does the allopolyploid outrange its parents?" Ecology and Evolution 12, no. 5 (May 2022). http://dx.doi.org/10.1002/ece3.8915.

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29

Leal, J. L., Pascal Milesi, Jarkko Salojärvi, and Martin Lascoux. "Phylogenetic Analysis of Allotetraploid Species Using Polarized Genomic Sequences." Systematic Biology, March 18, 2023. http://dx.doi.org/10.1093/sysbio/syad009.

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Abstract Phylogenetic analysis of polyploid hybrid species has long posed a formidable challenge as it requires the ability to distinguish between alleles of different ancestral origins in order to disentangle their individual evolutionary history. This problem has been previously addressed by conceiving phylogenies as reticulate networks, using a two-step phasing strategy that first identifies and segregates homoeologous loci and then, during a second phasing step, assigns each gene copy to one of the subgenomes of an allopolyploid species. Here, we propose an alternative approach, one that preserves the core idea behind phasing – to produce separate nucleotide sequences that capture the reticulate evolutionary history of a polyploid – while vastly simplifying its implementation by reducing a complex multi-stage procedure to a single phasing step. While most current methods used for phylogenetic reconstruction of polyploid species require sequencing reads to be pre-phased using experimental or computational methods – usually an expensive, complex, and/or time-consuming endeavor – phasing executed using our algorithm is performed directly on the multiple-sequence alignment (MSA), a key change that allows for the simultaneous segregation and sorting of gene copies. We introduce the concept of genomic polarization which, when applied to an allopolyploid species, produces nucleotide sequences that capture the fraction of a polyploid genome that deviates from that of a reference sequence, usually one of the other species present in the MSA. We show that if the reference sequence is one of the parental species, the polarized polyploid sequence has a close resemblance (high pairwise sequence identity) to the second parental species. This knowledge is harnessed to build a new heuristic algorithm where, by replacing the allopolyploid genomic sequence in the MSA by its polarized version, it is possible to identify the phylogenetic position of the polyploid's ancestral parents in an iterative process. The proposed methodology can be used with long-read as well as short-read high-throughput sequencing (HTS) data, and requires only one representative individual for each species to be included in the phylogenetic analysis. In its current form, it can be used in the analysis of phylogenies containing tetraploid and diploid species. We test the newly developed method extensively using simulated data in order to evaluate its accuracy. We show empirically that the use of polarized genomic sequences allows for the correct identification of both parental species of an allotetraploid with up to 97% certainty in phylogenies with moderate levels of incomplete lineage sorting (ILS), and 87% in phylogenies containing high levels of ILS. We then apply the polarization protocol to reconstruct the reticulate histories of Arabidopsis kamchatica and A. suecica, two allopolyploids whose ancestry has been well documented.
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