Do plants have a segregated germline?

Lanfear, Robert

doi:10.1371/journal.pbio.2005439

Cited by 108 publications

(95 citation statements)

References 73 publications

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“…DNA methylation in plants is a relatively stable and transgenerationally heritable epigenetic mark, yet it also is known to be dynamic in its genomic distribution, undergoing spontaneous epimutations and being subject to intrinsic and extrinsic perturbations (Zhang et al ., ; Schmitz et al ., ; Kawakatsu et al ., ; Niederhuth et al ., ; Quadrana & Colot, ; Takuno et al ., ). Because plants do not set aside an early, clearly defined germline (Grossniklaus, ; but see Lanfear, ), somatically acquired DNA methylation modifications can be transgenerationally inherited, potentially contributing to adaptation and evolution. Among the intrinsic causative factors that may drive the evolution of DNA methylation, interspecific hybridization and WGD are perhaps the most pervasive.…”

Section: Introductionmentioning

confidence: 99%

DNA methylation repatterning accompanying hybridization, whole genome doubling and homoeolog exchange in nascent segmental rice allotetraploids

Zhang

et al. 2019

New Phytologist

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Summary Allopolyploidization, which entails interspecific hybridization and whole genome duplication (WGD), is associated with emergent genetic and epigenetic instabilities that are thought to contribute to adaptation and evolution. One frequent genomic consequence of nascent allopolyploidization is homoeologous exchange (HE), which arises from compromised meiotic fidelity and generates genetically and phenotypically variable progenies. Here, we used a genetically tractable synthetic rice segmental allotetraploid system to interrogate genome‐wide DNA methylation and gene expression responses and outcomes to the separate and combined effects of hybridization, WGD and HEs. Progenies of the tetraploid rice were genomically diverse due to genome‐wide HEs that affected all chromosomes, yet they exhibited overall methylome stability. Nonetheless, regional variation of cytosine methylation states was widespread in the tetraploids. Transcriptome profiling revealed genome‐wide alteration of gene expression, which at least in part associates with changes in DNA methylation. Intriguingly, changes of DNA methylation and gene expression could be decoupled from hybridity and sustained and amplified by HEs. Our results suggest that HEs, a prominent genetic consequence of nascent allopolyploidy, can exacerbate, diversify and perpetuate the effects of allopolyploidization on epigenetic and gene expression variation, and hence may contribute to allopolyploid evolution.

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Section: Introductionmentioning

confidence: 99%

DNA methylation repatterning accompanying hybridization, whole genome doubling and homoeolog exchange in nascent segmental rice allotetraploids

Zhang

et al. 2019

New Phytologist

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“…With some additional assumptions it is also possible to estimate the mutation rate per generation, and to compare this to estimates from other plants. The average height of an adult E. melliodora individual is between 15 m and 30 m 24 , so if we assume that all somatic mutations are potentially heritable (about which there is limited evidence 1 and ongoing discussion 25 ) we can estimate that the per-generation mutation rate is between 4.13×10 −8 and 8.25×10 −8 mutations per base per generation. For comparison the roughly 20 cm tall Arabidopsis thaliana has a per-generation mutation rate of 7.1×10 −9 mutations per base 26 .…”

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confidence: 99%

A phylogenomic approach reveals a low somatic mutation rate in a long-lived plant

Orr

Padovan

Kainer

et al. 2019

Preprint

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evolution of plants, but the rate at which they accumulate is poorly understood, and has 21 been very difficult to measure directly. Here, we demonstrate a novel method to measure 22 somatic mutations in individual plants and use this approach to estimate the somatic 23 mutation rate in a large, long-lived, phenotypically mosaic Eucalyptus melliodora tree. 24Despite being 100 times larger than Arabidopsis, this tree has a per-generation mutation 25

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“…Proliferation throughout the population could then occur as other polymorphisms, probably predominately through stochastic demographic forces but possibly also through natural selection (Shedge et al 2010). Several aspects of this process are unknown, including how mitogenomes are replicated (Gualberto & Newton 2017), the timing of germline segregation (Lanfear 2018), and when, where, and under what circumstances AGCs arise. For these reasons, the relationship between recombination within individuals summarized in Table 4 and re-arrangement rates among species is unclear.…”

Section: Resultsmentioning

confidence: 99%

The mitogenome of Norway spruce and a reappraisal of mitochondrial recombination in plants

Sullivan

Eldfjell

Schiffthaler

et al. 2019

Preprint

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27Plant mitogenomes can be difficult to assemble because they are structurally dynamic and prone 28 to intergenomic DNA transfers, leading to the unusual situation where an organelle genome is far 29 outnumbered by its nuclear counterparts. As a result, comparative mitogenome studies are in 30 their infancy and some key aspects of genome evolution are still known mainly from pre-31 genome, qualitative methods. To help address these limitations, we combined machine learning 32 and in silico enrichment of mitochondrial-like long reads to assemble the bacterial-sized 33 mitogenome of Norway spruce (Pinaceae: Picea abies). We conducted comparative analyses of 34 repeat abundance, intergenomic transfers, substitution and rearrangement rates, and estimated 35 repeat-by-repeat homologous recombination rates. Prompted by our discovery of highly 36 recombinogenic small repeats in P. abies, we assessed the genomic support for the prevailing 37 hypothesis that intramolecular recombination is predominantly driven by repeat length, with 38 larger repeats facilitating DNA exchange more readily. Overall, we found mixed support for this 39 view: recombination dynamics were heterogeneous across vascular plants and highly active 40 small repeats (ca. 200 bp) were present in about a third of studied mitogenomes. As in previous 41 studies, we did not observe any robust relationships among commonly-studied genome 42 attributes, but we identify variation in recombination rates as a underinvestigated source of plant 43 mitogenome diversity. 44 45 forest tree, Norway spruce (Pinaceae: Picea abies), from whole-genome shotgun sequencing 77 reads. The P. abies mitogenome helps to fill a phylogenetic gap in comparative analyses, and to 78 that end we analyzed gene repertoires; sources of genome size heterogeneity; intraspecific 79 variation; and mutation, recombination, and rearrangement rates in gymnosperms. Prompted by 80 the detection of highly recombinogenic small repeats in P. abies, we reevaluated published 81 recombination rates in seed plants. Despite early recognition of recombination as a factor in 82 generating the diversity of eukaryotic mitogenomes (Palmer & Herbon 1988; Gray et al. 1999), 83 surprisingly little attention has been given to recombinational dynamics as a source of 84 mitogenomic diversity within plants. As in previous studies, we found no clear relationship 85 between mitogenome traits and potential mechanisms infor example, genome size and the 86 proportion of intergenomically transferred DNAbut the role of recombination as a driver of 87 mitogenomic diversity within plants merits further scrutiny. 88 Results and Discussion 89Mitogenome assembly 90 We combined machine learning, in silico enrichment of long sequencing reads, and assembly 91 reconciliation to produce a highly contiguous P. abies draft mitogenome (Fig. 1). First, we 92 developed a support vector machine (SVM) to identify mitochondrial-like scaffolds from the P. 93 abies v. 1.0 genome assembly (Nystedt et al. 2013). Training the SVM classifier...

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Do plants have a segregated germline?

Cited by 108 publications

References 73 publications

DNA methylation repatterning accompanying hybridization, whole genome doubling and homoeolog exchange in nascent segmental rice allotetraploids

DNA methylation repatterning accompanying hybridization, whole genome doubling and homoeolog exchange in nascent segmental rice allotetraploids

A phylogenomic approach reveals a low somatic mutation rate in a long-lived plant

The mitogenome of Norway spruce and a reappraisal of mitochondrial recombination in plants

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