Population-Specific Selection on Standing Variation Generated by Lateral Gene Transfers in a Grass

Olofsson, Jill K.; Dunning, Luke T.; Lundgren, Marjorie R.; Barton, Henry J; Thompson, James T.; Cuff, Nicholas; Ariyarathne, Menaka; Yakandawala, Deepthi; Sotelo, Graciela; Zeng, Kai; Osborne, Colin P.; Nosil, Patrik; Christin, Pascal‐Antoine

doi:10.1016/j.cub.2019.09.023

Cited by 29 publications

(45 citation statements)

References 54 publications

(69 reference statements)

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“…The organelle phylogenetic trees recovered the seven major lineages reported in previous studies, as well as a clear incongruence between the two organelles (figure 1 and electronic supplementary material, figure S2 [10][11][12]). Indeed, six individuals, including one hexaploid and one dodecaploid, from Cameroon, Democratic Republic of Congo (DRC) and Zambia form a monophyletic group within plastid lineage DE, but form a paraphyletic group within mitochondrial lineage FG (electronic supplementary material, figure S2).…”

Section: (B) Time-calibrated Organelle Phylogeniessupporting

confidence: 64%

“…The different photosynthetic types of A. semialata are associated with distinct ploidy levels in South Africa, but both C 4 and non-C 4 diploids exist in other parts of Africa [4,10], and nuclear genome analyses have found evidence of genetic exchanges between lineages with different photosynthetic types [11]. In addition, previously reported discrepancies between mitochondrial and plastid genomes [12] might reflect the footprint of intraspecific allopolyploidization, as previously suggested based on cytological analyses [13]. However, the history of nuclear exchanges and their effect on the spread of different photosynthetic types through ecological and geographical spaces remain to be formally established.…”

Section: Introductionmentioning

confidence: 99%

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Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species

et al. 2020

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C 4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C 4 and non-C 4 populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during and after photosynthetic divergence in A. semialata . We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C 4 lineage after dispersal to warmer areas of lower elevation. Nuclear genome analyses highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C 4 phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple intraspecific allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C 4 physiology away from its region of origin.

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Section: (B) Time-calibrated Organelle Phylogeniessupporting

confidence: 64%

Section: Introductionmentioning

confidence: 99%

Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species

et al. 2020

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“…This underlines the 272 importance of HGT in diatoms and indicates that fixation of a laterally transferred gene takes place 273 quickly after the initial uptake. Indeed, in grasses it was recently shown that several plant-to-plant LGT 274 fragments were rapidly integrated and spread across the population, after which erosion occurred on 275 neutrally selected genes within those fragments 67 . 276…”

Section: Discussion 255mentioning

confidence: 99%

Systematic and functional analysis of horizontal gene transfer events in diatoms

Vancaester

Osuna-Cruz

Depuydt

et al. 2020

Preprint

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1.AbstractDiatoms are a diverse group of mainly photosynthetic algae, responsible for 20% of worldwide oxygen production, which can rapidly respond to favourable conditions and often outcompete other phytoplankton. We investigated the contribution of horizontal gene transfer (HGT) to its ecological success. A systematic phylogeny-based bacterial HGT detection procedure across nine sequenced diatoms showed that 3-5% of their proteome has a horizontal origin and a large influx occurred at the ancestor of diatoms. More than 90% of HGT genes are expressed, and species-specific HGT genes in Phaeodactylum tricornutum undergo strong purifying selection. They are implicated in several processes including environmental sensing, and expand the metabolic toolbox. Cobalamin (vitamin B12) is an essential cofactor for roughly half of the diatoms and is only produced by bacteria. Genes involved in its final synthesis were detected as HGT, including five consecutive enzymes in Fragilariopsis cylindrus. This might give diatoms originating from the Southern Ocean, a region typically depleted in cobalamin, a competitive advantage. Overall, we show that HGT is a prevalent mechanism that is actively used in diatoms to expand its adaptive capabilities.

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“…Such beneficial LGTs include those transferring functional genes that have undergone substantial modification through prolonged periods of positive selection in the donor genomes before being transferred (Christin et al., ). A gene that is selected for may also be accompanied by hitchhikers on the same fragment of foreign DNA, which can act as standing genetic variation for secondary selection (Olofsson et al., ). Lateral gene transfer thus provides a mechanism by which plants can effectively “steal” the genetic blueprints for molecular adaptation, thereby recycling the product of natural selection and altering the evolutionary trajectory of a species.…”

Section: Lateral Gene Transfers Represent Novel Mutations Of Major Fumentioning

confidence: 99%

Reticulate evolution, lateral gene transfer, and innovation in plants

Dunning

Christin

2020

American J of Botany

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Population-Specific Selection on Standing Variation Generated by Lateral Gene Transfers in a Grass

Cited by 29 publications

References 54 publications

Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species

Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species

Systematic and functional analysis of horizontal gene transfer events in diatoms

Reticulate evolution, lateral gene transfer, and innovation in plants

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