Parental transposable element loads influence their dynamics in young <i>Nicotiana</i> hybrids and allotetraploids

Mhiri, Corinne; Parisod, Christian; Daniel, Julien; Petit, Maud; Lim, K. Yoong; Borne, François Dorlhac de; Kovařı́k, Aleš; Leitch, Andrew R.; Grandbastien, Marie–Angèle

doi:10.1111/nph.15484

Cited by 27 publications

(34 citation statements)

References 65 publications

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“…When hybridization and polyploidy are combined, this can lead to TE bursts in the genome. As originally proposed by Barbara McClintock, allopolyploidization produces a "genomic shock", a genome instability associated with the relaxation of the TE silencing mechanisms and the reactivation of ancient TEs (McClintock 1984;Mhiri et al 2019). Hybridization, polyploidy and asexual reproduction are combined in M. incognita with relative effects on the TE load extremely challenging, if not impossible, to disentangle.…”

Section: Fig 5: Categories Of Polymorphic Te Locimentioning

confidence: 99%

Transposable Elements are an evolutionary force shaping genomic plasticity in the parthenogenetic root-knot nematode Meloidogyne incognita

Kozlowski

Hassanaly-Goulamhoussen

Rocha

et al. 2020

Preprint

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AbstractDespite reproducing without sexual recombination, the root-knot nematode Meloidogyne incognita is adaptive and versatile. Indeed, this species displays a global distribution, is able to parasitize a large range of plants and can overcome plant resistance in a few generations. The mechanisms underlying this adaptability without sex remain poorly known and only low variation at the single nucleotide polymorphism level have been observed so far across different geographical isolates with distinct ranges of compatible hosts. Hence, other mechanisms than the accumulation of point mutations are probably involved in the genomic dynamics and plasticity necessary for adaptability. Transposable elements (TEs), by their repetitive nature and mobility, can passively and actively impact the genome dynamics. This is particularly expected in polyploid hybrid genomes such as the one of M. incognita. Here, we have annotated the TE content of M. incognita, analyzed the statistical properties of this TE content, and used population genomics approach to estimate the mobility of these TEs across 12 geographical isolates, presenting phenotypic variations. The TE content is more abundant in DNA transposons and the distribution of TE copies identity to their consensuses sequence suggests they have been at least recently active. We have identified loci in the genome where the frequencies of presence of a TE showed variations across the different isolates. Compared to the M. incognita reference genome, we detected the insertion of some TEs either within genic regions or in the upstream regulatory regions. These predicted TEs insertions might thus have a functional impact. We validated by PCR the insertion of some of these TEs, confirming TE movements probably play a role in the genome plasticity with possible functional impacts.

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Section: Fig 5: Categories Of Polymorphic Te Locimentioning

confidence: 99%

Transposable Elements are an evolutionary force shaping genomic plasticity in the parthenogenetic root-knot nematode Meloidogyne incognita

Kozlowski

Hassanaly-Goulamhoussen

Rocha

et al. 2020

Preprint

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“…The merger of two distinct genomes in one allopolyploid nucleus may result in ‘genomic shock’ [7], which yields changes in gene expression [8–12], chromosomal rearrangements [13, 14], increase of transposable element activity [15, 16], alterations of physiological processes [17, 18], changes in morphology [19, 20], and niche shifts [21]. These processes and their results can isolate newly formed allopolyploids from their diploid progenitors and may facilitate their establishment as a new species.…”

Section: Introductionmentioning

confidence: 99%

Early consequences of allopolyploidy alter floral evolution in Nicotiana (Solanaceae)

et al. 2019

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Background Polyploidy has played a major role in angiosperm evolution. Previous studies have examined polyploid phenotypes in comparison to their extant progenitors, but not in context of predicted progenitor phenotypes at allopolyploid origin. In addition, differences in the trends of polyploid versus diploid evolution have not been investigated. We use ancestral character-state reconstructions to estimate progenitor phenotype at allopolyploid origin to determine patterns of polyploid evolution leading to morphology of the extant species. We also compare trends in diploid versus allopolyploid evolution to determine if polyploidy modifies floral evolutionary patterns. Results Predicting the ancestral phenotype of a nascent allopolyploid from reconstructions of diploid phenotypes at the time of polyploid formation generates different phenotype predictions than when extant diploid phenotypes are used, the outcome of which can alter conclusions about polyploid evolution; however, most analyses yield the same results. Using ancestral reconstructions of diploid floral phenotypes indicate that young polyploids evolve shorter, wider corolla tubes, but older polyploids and diploids do not show any detectable evolutionary trends. Lability of the traits examined (floral shape, corolla tube length, and corolla tube width) differs across young and older polyploids and diploids. Corolla length is more evolutionarily labile in older polyploids and diploids. Polyploids do not display unique suites of floral characters based on both morphological and color traits, but some suites of characters may be evolving together and seem to have arisen multiple times within Nicotiana , perhaps due to the influence of pollinators. Conclusions Young polyploids display different trends in floral evolution (shorter, wider corolla tubes, which may result in more generalist pollination) than older polyploids and diploids, suggesting that patterns of divergence are impacted by the early consequences of allopolyploidy, perhaps arising from genomic shock and/or subsequent genome stabilization associated with diploidization. Convergent evolution in floral morphology and color in Nicotiana can be consistent with pollinator preferences, suggesting that pollinators may have shaped floral evolution in Nicotiana . Electronic supplementary material The online version of this article (10.1186/s12870-019-1771-5) contains supplementary material, which is available to authorized users.

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“…Lim et al (2004) suggested that greater imbalance is leading to stronger genome shock intensity. Recently, Mhiri et al (2019) found that the proportion of new loci correlates with the extent of each TE load imbalance in different Nicotiana accessions and thus supported the influence of the genome shock intensity on TE activation. Genome dominance at the genomic level may be achieved by different regulation and composition of dominant TEs in the parental lineages (Freeling et al, 2012).…”

Section: Genomic Changes and Te Dynamics In Allopolyploidsmentioning

confidence: 77%

Competition of Parental Genomes in Plant Hybrids

et al. 2020

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Interspecific hybridization represents one of the main mechanisms of plant speciation. Merging of two genomes from different subspecies, species, or even genera is frequently accompanied by whole-genome duplication (WGD). Besides its evolutionary role, interspecific hybridization has also been successfully implemented in multiple breeding programs. Interspecific hybrids combine agronomic traits of two crop species or can be used to introgress specific loci of interests, such as those for resistance against abiotic or biotic stresses. The genomes of newly established interspecific hybrids (both allopolyploids and homoploids) undergo dramatic changes, including chromosome rearrangements, amplifications of tandem repeats, activation of mobile repetitive elements, and gene expression modifications. To ensure genome stability and proper transmission of chromosomes from both parental genomes into subsequent generations, allopolyploids often evolve mechanisms regulating chromosome pairing. Such regulatory systems allow only pairing of homologous chromosomes and hamper pairing of homoeologs. Despite such regulatory systems, several hybrid examples with frequent homoeologous chromosome pairing have been reported. These reports open a way for the replacement of one parental genome by the other. In this review, we provide an overview of the current knowledge of genomic changes in interspecific homoploid and allopolyploid hybrids, with strictly homologous pairing and with relaxed pairing of homoeologs.

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Parental transposable element loads influence their dynamics in young Nicotiana hybrids and allotetraploids

Cited by 27 publications

References 65 publications

Transposable Elements are an evolutionary force shaping genomic plasticity in the parthenogenetic root-knot nematode Meloidogyne incognita

Transposable Elements are an evolutionary force shaping genomic plasticity in the parthenogenetic root-knot nematode Meloidogyne incognita

Early consequences of allopolyploidy alter floral evolution in Nicotiana (Solanaceae)

Competition of Parental Genomes in Plant Hybrids

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