Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

Vanneste, Kevin; Baele, Guy; Maere, Steven; Peer, Yves Van de

doi:10.1101/gr.168997.113

Cited by 405 publications

(463 citation statements)

References 149 publications

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“…3a). Estimating the timing of the Dc-β WGD to around the CretaceousPaleogene (K-Pg) boundary further supports the hypothesis that a WGD burst occurred around that time, perhaps reflecting a selective polyploid advantage in comparison to diploid progenitors 30 . These results may also suggest a co-occurrence of the Dc-β WGD with Apiales-Asterales divergence.…”

Section: Genome Evolutionmentioning

confidence: 54%

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A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

et al. 2016

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5 7Carrot (Daucus carota subsp. carota L.; 2n = 2x = 18) is a globally important root crop whose production has quadrupled between 1976 and 2013 (FAO Statistics; see URLs), outpacing the overall rate of increase in vegetable production and world population growth (FAO Statistics; see URLs) through development of high-value products for fresh consumption, juices, and natural pigments and cultivars adapted to warmer production regions 1 .The first documented colors for domesticated carrot root were yellow and purple in Central Asia approximately 1,100 years ago 2,3 , with orange carrots not reliably reported until the sixteenth century in Europe 4,5 . The popularity of orange carrots is fortuitous for modern consumers because the orange pigmentation results from high quantities of alpha-and beta-carotene, making carrots the richest source of provitamin A in the US diet 6 . Carrot breeding has substantially increased nutritional value, with a 50% average increase in carotene content in the United States as compared to 40 years ago 6 . Lycopene and lutein in red and yellow carrots, respectively, are also nutritionally important carotenoids, making carrot a model system to study storage root development and carotenoid accumulation.Carrot is the most important crop in the Apiaceae family, which includes numerous other vegetables, herbs, spices, and medicinal plants that enhance the epicurean experience 7 , including celery, parsnip, arracacha, parsley, fennel, coriander, and cumin. The Apiaceae family belongs to the euasterid II clade, which includes important crops such as lettuce and sunflower 8 . Genome sequences of euasterid I species have been reported, but only two genomes 9,10 have been published among the other euasterid II species.Here we report a high-quality genome assembly of a doubledhaploid orange carrot, characterization of the mechanism controlling carotenoid accumulation in storage roots, and the resequencing of 35 accessions spanning the genetic diversity of the Daucus genus. Our comprehensive genomic analyses provide insights into the evolution of the asterids and several gene families. These results will facilitate biological discovery and crop improvement in carrot and other crops.A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution We report a high-quality chromosome-scale assembly and analysis of the carrot (Daucus carota) genome, the first sequenced genome to include a comparative evolutionary analysis among members of the euasterid II clade. We characterized two new polyploidization events, both occurring after the divergence of carrot from members of the Asterales order, clarifying the evolutionary scenario before and after radiation of the two main asterid clades. Large- and small-scale lineage-specific duplications have contributed to the expansion of gene families, including those with roles in flowering time, defense response, flavor, and pigment accumulation. We identified a candidate gene, DCAR_032551, that conditions caro...

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Section: Genome Evolutionmentioning

confidence: 54%

“…Divergence and WGD time points in the carrot and tomato genomes were estimated using a method described by Vanneste et al 30 Table 64). …”

Section: (Ref 105) (Supplementary Tables 19 and 62)mentioning

confidence: 99%

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

et al. 2016

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“…Absolute dating of the identified WGD event was performed as described previously 13,29 . In brief, paralogueous gene pairs located in duplicated segments (anchors) and duplicated pairs lying under the WGD peak (peak-based duplicates) were collected for phylogenetic dating.…”

Section: )mentioning

confidence: 99%

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

Olsen

Rouzé

Verhelst

et al. 2016

Nature

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458

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Seagrasses colonized the sea 1 on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet 2 . Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes 3 , genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae 4 and that is important for ion homoeostasis, nutrient uptake and O 2 /CO 2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming 5,6 , to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants 7

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“…Both lineages were inherited by dicot species, except for S. indicum, which lost the NRG1 lineage, similar to all monocot genomes. Several whole-genome duplications (WGDs) occurred throughout angiosperm evolution, causing gene duplications and functional divergence (Jiao et al, 2011;Vanneste et al, 2014). The separation of the ADR1 and NRG1 lineages prior to the divergence of angiosperms prompted us to investigate the involvement of an ancient WGD event.…”

Section: The Three Nbs Classes Show Distinct Evolutionary Patterns Inmentioning

confidence: 99%

Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns

et al. 2016

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Nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes make up the largest plant disease resistance gene family (R genes), with hundreds of copies occurring in individual angiosperm genomes. However, the expansion history of NBS-LRR genes during angiosperm evolution is largely unknown. By identifying more than 6,000 NBS-LRR genes in 22 representative angiosperms and reconstructing their phylogenies, we present a potential framework of NBS-LRR gene evolution in the angiosperm. Three anciently diverged NBS-LRR classes (TNLs, CNLs, and RNLs) were distinguished with unique exon-intron structures and DNA motif sequences. A total of seven ancient TNL, 14 CNL, and two RNL lineages were discovered in the ancestral angiosperm, from which all current NBS-LRR gene repertoires were evolved. A pattern of gradual expansion during the first 100 million years of evolution of the angiosperm clade was observed for CNLs. TNL numbers remained stable during this period but were eventually deleted in three divergent angiosperm lineages. We inferred that an intense expansion of both TNL and CNL genes started from the Cretaceous-Paleogene boundary. Because dramatic environmental changes and an explosion in fungal diversity occurred during this period, the observed expansions of R genes probably reflect convergent adaptive responses of various angiosperm families. An ancient whole-genome duplication event that occurred in an angiosperm ancestor resulted in two RNL lineages, which were conservatively evolved and acted as scaffold proteins for defense signal transduction. Overall, the reconstructed framework of angiosperm NBS-LRR gene evolution in this study may serve as a fundamental reference for better understanding angiosperm NBS-LRR genes.

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Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

Cited by 405 publications

References 149 publications

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns

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