The importance and prevalence of allopolyploidy in Aotearoa New Zealand

Behling, Anna H; Shepherd, Lara D.; Cox, Murray P.

doi:10.1080/03036758.2019.1676797

Cited by 8 publications

(5 citation statements)

References 170 publications

(173 reference statements)

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“…Allopolyploidization is the coupling of whole genome duplication and interspecific hybridization, resulting in organisms possessing two or more diverged genomes. This intriguing evolutionary transition is widespread in nature ( Albertin and Marullo, 2012 ; Barker et al, 2016 ) and is of agricultural importance ( Behling et al, 2020 ). Allopolyploidization is expected to have both short-term and long-term consequences: not only can the merging of divergent genomes itself be seen as a macromutation but also it triggers subsequent genomic changes over distinct time scales.…”

Section: Introductionmentioning

confidence: 99%

Separating phases of allopolyploid evolution with resynthesized and natural Capsella bursa-pastoris

Duan

Glémin

Lascoux

2024

eLife

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Allopolyploidization is a frequent evolutionary transition in plants that combines whole-genome duplication (WGD) and interspecific hybridization. The genome of an allopolyploid species results from initial interactions between parental genomes and long-term evolution. Telling apart the contributions of these two phases is essential to understand the evolutionary trajectory of allopolyploid species. Here, we compared phenotypic and transcriptomic changes in natural and resynthesized Capsella allotetraploids with their diploid parental species. We focused on phenotypic traits associated with the selfing syndrome and on transcription-level phenomena such as expression level dominance (ELD), transgressive expression (TRE), and homoeolog expression bias (HEB). We found that selfing syndrome, high pollen and seed quality in natural allotetraploids likely resulted from long-term evolution. Similarly, TRE and most down-regulated ELDs were only found in natural allopolyploids. Natural allotetraploids also had more ELDs toward the self-fertilizing parental species than resynthesized allotetraploids, mirroring the establishment of the selfing syndrome. However, short-term changes mattered, and 40% of ELDs in natural allotetraploids were already observed in resynthesized allotetraploids. Resynthesized allotetraploids showed striking HEB variation among chromosomes and individuals. Homoeologous synapsis was its primary source and may still be a source of genetic variation in natural allotetraploids. In conclusion, both short- and long-term mechanisms contributed to transcriptomic and phenotypic changes in natural allotetraploids. However, the initial gene expression changes were largely reshaped during long-term evolution leading to further morphological changes.

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Section: Introductionmentioning

confidence: 99%

Separating phases of allopolyploid evolution with resynthesized and natural Capsella bursa-pastoris

Duan

Glémin

Lascoux

2024

eLife

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“…Allopolyploidization is the coupling of whole genome duplication and interspecific hybridization, resulting in organisms possessing two or more diverged genomes. This intriguing evolutionary transition is widespread in nature (Albertin & Marullo, 2012; Barker et al ., 2016), and is of agricultural importance (Behling et al ., 2019). Allopolyploidization is expected to have both short-term and long-term consequences: not only can the merging of divergent genomes itself be seen as a macromutation, but it also triggers subsequent genomic changes over distinct time scales.…”

Section: Introductionmentioning

confidence: 99%

Separating phases of allopolyploid evolution with resynthesized and naturalCapsella bursa-pastoris

Duan

Glémin

Lascoux

2023

Preprint

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Allopolyploidization is a frequent evolutionary transition in plants that combines whole-genome duplication (WGD) and interspecific hybridization. The genome of an allopolyploid species results from initial interactions between parental genomes and long-term evolution. Telling apart the contributions of these two phases is essential to understand the evolutionary trajectory of allopolyploid species. Here, we compared phenotypic and transcriptomic changes in natural and resynthesizedCapsellaallotetraploids with their diploid parental species. We focused on phenotypic traits associated with the selfing syndrome and on transcription-level phenomena such as expression level dominance (ELD), transgressive expression (TRE), and homoeolog expression bias (HEB). We found that selfing syndrome, high pollen and seed quality in natural allotetraploids likely resulted from long-term evolution. Similarly, TRE and most down-regulated ELDs were only found in natural allopolyploids. Natural allotetraploids also had more ELDs toward the self-fertilizing parental species than resynthesized allotetraploids, mirroring the establishment of the selfing syndrome. However, short-term changes mattered, and 40% of ELDs in natural allotetraploids were already observed in resynthesized allotetraploids. Resynthesized allotetraploids showed striking HEB variation among chromosomes and individuals. Homoeologous synapsis was its primary source and may still be a source of genetic variation in natural allotetraploids. In conclusion, both short- and long-term mechanisms contributed to transcriptomic and phenotypic changes in natural allotetraploids. However, the initial gene expression changes were largely reshaped during long-term evolution leading to further morphological changes.

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“…In allopolyploids with their chromosome sets originating from different taxa, a synergy between the chromosome duplication and the hybrid vigor or heterosis effect may occur, associated with increased growth rates, a diverging morphology as well as an improved ability to adapt to new environmental conditions (Comai, 2005;Sattler et al, 2016). Therefore, allopolyploidization is an attractive strategy for the optimization of crop plants in agriculture (Matsuoka, 2011;Behling et al, 2020), and allows them to take over new niches (Cheng et al, 2018). For example, there is molecular evidence for allopolyploidy in some mosses of the genus Physcomitrium representing important land pioneers (Beike et al, 2014, Medina et al, 2018.…”

Section: Introductionmentioning

confidence: 99%

Autopolyploidization affects transcript patterns and gene targeting frequencies in Physcomitrella

Rempfer

Wiedemann

Schween

et al. 2021

Preprint

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Qualitative changes in gene expression after an autopolyploidization event, a pure duplication of the whole genome, might be relevant for a different regulation of molecular mechanisms between angiosperms growing in a life cycle with a dominant diploid sporophytic stage and the haploid-dominant bryophytes. Whereas angiosperms repair DNA double strand breaks (DSB) preferentially via non-homologous end joining (NHEJ), in bryophytes homologous recombination (HR) is the main DNA-DSB repair pathway facilitating the precise integration of foreign DNA into the genome via gene targeting (GT). Here, we studied the influence of ploidy on gene expression patterns and GT efficiency in the moss Physcomitrella using haploid plants and autodiploid plants, generated via an artificial duplication of the whole genome. Single cells (protoplasts) were transfected with a GT construct and material from different time-points after transfection was analysed by microarrays and SuperSAGE sequencing. In the SuperSAGE data, we detected 3.7% of the Physcomitrella genes as differentially expressed in response to the whole genome duplication event. Among the differentially expressed genes involved in DNA-DSB repair was an upregulated gene encoding the X-ray repair cross-complementing protein 4 (XRCC4), a key player in NHEJ. Analysing the GT efficiency, we observed that autodiploid plants were significantly GT suppressed (p<0.001) attaining only one third of the expected GT rates. Hence, an alteration of global transcript patterns, including genes related to DNA repair, in autodiploid Physcomitrella plants correlated with a drastic suppression of HR.

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The importance and prevalence of allopolyploidy in Aotearoa New Zealand

Cited by 8 publications

References 170 publications

Separating phases of allopolyploid evolution with resynthesized and natural Capsella bursa-pastoris

Separating phases of allopolyploid evolution with resynthesized and natural Capsella bursa-pastoris

Separating phases of allopolyploid evolution with resynthesized and naturalCapsella bursa-pastoris

Autopolyploidization affects transcript patterns and gene targeting frequencies in Physcomitrella

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