Chromoanagenesis in plants: triggers, mechanisms, and potential impact

Guo, Weier; Comai, Luca; Henry, Isabelle

doi:10.1016/j.tig.2022.08.003

Cited by 8 publications

(9 citation statements)

References 80 publications

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“…For example, ha04 and ha15 have different arms of ak08, but this structure cannot be the result of a single reciprocal translocation as they are united with arms of ak05 and ak13, respectively, rather than with the arms of a single other chromosome. This extensive remixing of material from multiple chromosomes may suggest that chromosome restructuring or chromoplexy has occurred in both genomes (Guo et al., 2023). In this case, many of the changes in structure observed here would be the result of a single large event within each genome rather than a stepwise accumulation of changes.…”

Section: Resultsmentioning

confidence: 99%

The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed

Laforest,

Martin,

Bisaillon

et al. 2024

The Plant Genome

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Ambrosia artemisiifolia and Ambrosia trifida (Asteraceae) are important pest species and the two greatest sources of aeroallergens globally. Here, we took advantage of a hybrid to simplify genome assembly and present chromosome‐level assemblies for both species. These assemblies show high levels of completeness with Benchmarking Universal Single‐Copy Ortholog (BUSCO) scores of 94.5% for A. artemisiifolia and 96.1% for A. trifida and long terminal repeat (LTR) Assembly Index values of 26.6 and 23.6, respectively. The genomes were annotated using RNA data identifying 41,642 genes in A. artemisiifolia and 50,203 in A. trifida. More than half of the genome is composed of repetitive elements, with 62% in A. artemisiifolia and 69% in A. trifida. Single copies of herbicide resistance‐associated genes PPX2L, HPPD, and ALS were found, while two copies of the EPSPS gene were identified; this latter observation may reveal a possible mechanism of resistance to the herbicide glyphosate. Ten of the 12 main allergenicity genes were also localized, some forming clusters with several copies, especially in A. artemisiifolia. The evolution of genome structure has differed among these two species. The genome of A. trifida has undergone greater rearrangement, possibly the result of chromoplexy. In contrast, the genome of A. artemisiifolia retains a structure that makes the allotetraploidization of the most recent common ancestor of the Heliantheae Alliance the clearest feature of its genome. When compared to other Heliantheae Alliance species, this allowed us to reconstruct the common ancestor's karyotype—a key step for furthering of our understanding of the evolution and diversification of this economically and allergenically important group.

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Section: Resultsmentioning

confidence: 99%

The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed

Laforest,

Martin,

Bisaillon

et al. 2024

The Plant Genome

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“…Genome elimination occurs in early embryonic cell divisions and is associated with chromosome missegregation, formation of micronuclei, and rearranged chromosomes ( Tan et al 2015 , 2023 ; Marimuthu et al 2021 ). This phenomenon is reminiscent of chromothripsis and chromoanagenesis, in which DNA breakage leads to chromosome rearrangements ( Ly and Cleveland 2017 ; Guo et al 2023 ). During haploid induction, centromere dysfunction may lead to inappropriate positioning of chromosomes during cell division and breakage owing to shearing or mechanical stresses.…”

Section: Cenh3 Genome Elimination and Mini-chromosomesmentioning

confidence: 99%

The structure, function, and evolution of plant centromeres

Naish,

Henderson

2024

Genome Res.

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Centromeres are essential regions of eukaryotic chromosomes responsible for the formation of kinetochore complexes, which connect to spindle microtubules during cell division. Notably, although centromeres maintain a conserved function in chromosome segregation, the underlying DNA sequences are diverse both within and between species and are predominantly repetitive in nature. The repeat content of centromeres includes high-copy tandem repeats (satellites), and/or specific families of transposons. The functional region of the centromere is defined by loading of a specific histone 3 variant (CENH3), which nucleates the kinetochore and shows dynamic regulation. In many plants, the centromeres are composed of satellite repeat arrays that are densely DNA methylated and invaded by centrophilic retrotransposons. In some cases, the retrotransposons become the sites of CENH3 loading. We review the structure of plant centromeres, including monocentric, holocentric, and metapolycentric architectures, which vary in the number and distribution of kinetochore attachment sites along chromosomes. We discuss how variation in CENH3 loading can drive genome elimination during early cell divisions of plant embryogenesis. We review how epigenetic state may influence centromere identity and discuss evolutionary models that seek to explain the paradoxically rapid change of centromere sequences observed across species, including the potential roles of recombination. We outline putative modes of selection that could act within the centromeres, as well as the role of repeats in driving cycles of centromere evolution. Although our primary focus is on plant genomes, we draw comparisons with animal and fungal centromeres to derive a eukaryote-wide perspective of centromere structure and function.

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“…We understand chromoanagenesis as the highly localized restructuring (“rebirth”) of chromosomes. Plants are known to be tolerant to genome restructuring, in humans it is associated with cancer (Guo et al, 2023). The specific indel lines in poplar exhibited single chromosome fragmentation and restructuring patterns characterized by a high frequency of clustered CNVs on a single chromosome for each of the two lines (chromosome 1 and chromosome 2, respectively).…”

Section: Induced Svs In Poplarmentioning

confidence: 99%

Structural genomic variations and their effects on phenotypes inPopulus

Porth

Goessen

Heinze

2023

Preprint

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DNA copy numbers have recently emerged as an important new marker system. In the absence of a contiguous reference genome, alternative detection systems such as the comparative hybridization method have been used to detect copy number variations (CNVs). With the advent of chromosome-level resolved reference genomes based on the incorporation of long-read sequencing and powerful bioinformatics pipelines, comprehensive detection of all structural variations (SVs) in the poplar genome is now within reach. Gene CNVs and their inheritance are important because they can cause dosage effects in phenotypic variations. These are potent genetic markers that should be considered in complex trait variation such as growth and adaptation in poplar. SVs such as CNVs could be used in future genomic selection studies for poplar, especially in cases when heterosis increases hybrid performance (hybrid vigor). This Chapter reports recent findings on SVs in natural populations of Populus spp. as well as on artificially induced SVs in poplar to understand their potential importance in generating a considerable amount of phenotypic improvement. The Chapter concludes with an outlook on the future implementation of knowledge on SVs in poplar crop breeding.

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Chromoanagenesis in plants: triggers, mechanisms, and potential impact

Cited by 8 publications

References 80 publications

The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed

The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed

The structure, function, and evolution of plant centromeres

Structural genomic variations and their effects on phenotypes inPopulus

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