Massive haplotypes underlie ecotypic differentiation in sunflowers

Todesco, Marco; Owens, Gregory L.; Bercovich, Natalia; Légaré, Jean-Sébastien; Soudi, Shaghayegh; Bürge, Dylan O.; Huang, Kaichi; Ostevik, Katherine L.; Drummond, Emily B. M.; Imerovski, Ivana; Lande, Kathryn; Pascual-Robles, Mariana A.; Nanavati, Mihir; Jahani, Mojtaba; Cheung, Winnie; Staton, S. Evan; Muños, Stéphane; Nielsen, Rasmus; Donovan, Lisa A.; Burke, John M.; Yeaman, Sam; Rieseberg, Loren H.

doi:10.1038/s41586-020-2467-6

Cited by 325 publications

(564 citation statements)

References 83 publications

(41 reference statements)

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“…(B) Inversions become established through a process similar to (A) but by carrying a combination of alleles at two loci that are adapted to different aspects of the local environment (triangles and squares in different colors). For example, in a dune ecotype of the prairie sunflower (Helianthus petiolaris), larger seed size and tolerance to low nutrient soils were found to map to the same inversions (Huang et al, 2019;Todesco et al, 2019). (C) Mixed geographic model proposed by Feder et al (2011).…”

Section: Origin and Establishment Of Inversionsmentioning

confidence: 97%

“…As with the LD method, analyses of genotypic relationships within the predicted inversion can offer further support for the putative inversion. The local population structure approach has been used to detect polymorphic inversions from RAD sequencing data or whole-genome shotgun data within the wild sunflower species, Helianthus annuus, H. argophyllus, and H. petiolaris (Huang et al, 2019;Todesco et al, 2019). While many of the inversions predicted by this method in sunflower have been subsequently confirmed via comparisons of reference sequences, comparative mapping, or Hi-C sequencing, two were not, indicating that these population genomic approaches can offer suggestive evidence of inversions, but are less diagnostic.…”

Section: Population Genomic Approachesmentioning

confidence: 99%

“…The conditions for fixation are relaxed for neutral or weakly underdominant mutations such as inversions. Nonetheless, the fact that inversions are frequent in outcrossing species with large effective population sizes, co-vary with ecological variation, and underlie important adaptive traits (Hoffmann and Rieseberg, 2008;Lowry and Willis, 2010;Todesco et al, 2019), suggests that the establishment and spread of large inversions is most likely driven by natural selection. The jury is still out for the many small inversions that differentiate plant genomes.…”

Section: Origin and Establishment Of Inversionsmentioning

confidence: 99%

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Frequency, Origins, and Evolutionary Role of Chromosomal Inversions in Plants

2020

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Chromosomal inversions have the potential to play an important role in evolution by reducing recombination between favorable combinations of alleles. Until recently, however, most evidence for their likely importance derived from dipteran flies, whose giant larval salivary chromosomes aided early cytogenetic studies. The widespread application of new genomic technologies has revealed that inversions are ubiquitous across much of the plant and animal kingdoms. Here we review the rapidly accumulating literature on inversions in the plant kingdom and discuss what we have learned about their establishment and likely evolutionary role. We show that inversions are prevalent across a wide range of plant groups. We find that inversions are often associated with locally favored traits, as well as with traits that contribute to assortative mating, suggesting that they may be key to adaptation and speciation in the face of gene flow. We also discuss the role of inversions in sex chromosome formation, and explore possible parallels with inversion establishment on autosomes. The identification of inversion origins, as well as the causal variants within them, will advance our understanding of chromosomal evolution in plants.

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Section: Origin and Establishment Of Inversionsmentioning

confidence: 97%

Section: Population Genomic Approachesmentioning

confidence: 99%

Section: Origin and Establishment Of Inversionsmentioning

confidence: 99%

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Frequency, Origins, and Evolutionary Role of Chromosomal Inversions in Plants

2020

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“…Briefly, raw demultiplexed reads were filtered with cutadapt 1.12 [29], to remove reads containing adapter sequences and > 5% low quality (phred score < 20) or ambiguous bases. Filtered reads were aligned to the HA412-HOv2 genome assembly [30] with BWA-MEM 0.7.17 [31] using default parameters, then sorted and indexed using samtools 1.10 [32]. Indexed reads were merged with BEDtools 2.29 [33], and bases were called for sites with ≥ 6 and ≤ 10,000 reads.…”

Section: Sequence Processing and Variant Callingmentioning

confidence: 99%

Phylogeography and the Evolutionary History of Sunflower (Helianthus annuus L.): Wild Diversity and the Dynamics of Domestication

Park

Burke

2020

Genes

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Patterns of genetic variation in crops are the result of selection and demographic changes that occurred during their domestication and improvement. In many cases, we have an incomplete picture of the origin of crops in the context of their wild progenitors, particularly with regard to the processes producing observed levels of standing genetic variation. Here, we analyzed sequence diversity in cultivated sunflower (Helianthus annuus L.) and its wild progenitor (common sunflower, also H. annuus) to reconstruct phylogeographic relationships and population genetic/demographic patterns across sunflower. In common sunflower, south-north patterns in the distribution of nucleotide diversity and lineage splitting indicate a history of rapid postglacial range expansion from southern refugia. Cultivated sunflower accessions formed a clade, nested among wild populations from the Great Plains, confirming a single domestication event in central North America. Furthermore, cultivated accessions sorted by market type (i.e., oilseed vs. confectionery) rather than breeding pool, recapitulating the secondary development of oil-rich cultivars during its breeding history. Across sunflower, estimates of nucleotide diversity and effective population sizes suggest that cultivated sunflower underwent significant population bottlenecks following its establishment ~5000 years ago. The patterns inferred here corroborate those from previous studies of sunflower domestication, and provide a comprehensive overview of its evolutionary history.

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“…An exceptionally clear example is provided by Helianthus annuus (cultivated sunflower) and Helianthus argophyllus , which generate compatible hybrids. Studying genome sequences, a large 10 Mb chunk containing multiple genes related to early flowering in sunflower has been found in some coastal H. petiolaris populations, where flowering early in the year is advantageous (Todesco et al , ) . With the systematic analysis of many more plant genomes, we will learn about the mosaics of DNA pieces that make up genomes, their evolutionary histories and their relevance for the diversification and adaptability of species.…”

Section: Learning From Plant Genomesmentioning

confidence: 99%

The Earth BioGenome project: opportunities and challenges for plant genomics and conservation

et al. 2020

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Sequencing them all. That is the ambitious goal of the recently launched Earth BioGenome project (Proceedings of the National Academy of Sciences of the United States of America, 115,[4325][4326][4327][4328][4329][4330][4331][4332][4333], which aims to produce reference genomes for all eukaryotic species within the next decade. In this perspective, we discuss the opportunities of this project with a plant focus, but highlight also potential limitations. This includes the question of how to best capture all plant diversity, as the green taxon is one of the most complex clades in the tree of life, with over 300 000 species. For this, we highlight four key points: (i) the unique biological insights that could be gained from studying plants, (ii) their apparent underrepresentation in sequencing efforts given the number of threatened species, (iii) the necessity of phylogenomic methods that are aware of differences in genome complexity and quality, and (iv) the accounting for within-species genetic diversity and the historical aspect of conservation genetics.

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Massive haplotypes underlie ecotypic differentiation in sunflowers

Cited by 325 publications

References 83 publications

Frequency, Origins, and Evolutionary Role of Chromosomal Inversions in Plants

Frequency, Origins, and Evolutionary Role of Chromosomal Inversions in Plants

Phylogeography and the Evolutionary History of Sunflower (Helianthus annuus L.): Wild Diversity and the Dynamics of Domestication

The Earth BioGenome project: opportunities and challenges for plant genomics and conservation

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