A New Catalog of Structural Variants in 1,301 <i>A. thaliana</i> Lines from Africa, Eurasia, and North America Reveals a Signature of Balancing Selection at Defense Response Genes

Göktay, Mehmet; Fulgione, Andrea; Hancock, Angela M.

doi:10.1093/molbev/msaa309

Cited by 31 publications

(33 citation statements)

References 107 publications

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“…Instead, this suggests that this variation has been recreated repeatedly in these species This raises the possibility that there may be a class of loci that are being repeatedly sampled by pangenomic variation across species within a family. To test this possibility would need a deeper phylogenetic sampling within and between species, particularly for understanding the intersection of ecology and evolution ( Göktay et al, 2021 ; Durvasula et al, 2017 ).…”

Section: Discussionmentioning

confidence: 99%

Genetic variation, environment and demography intersect to shape Arabidopsis defense metabolite variation across Europe

Katz

Jaegle

et al. 2021

eLife

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Plants produce diverse metabolites to cope with the challenges presented by complex and ever-changing environments. These challenges drive the diversification of specialized metabolites within and between plant species. However, we are just beginning to understand how frequently new alleles arise controlling specialized metabolite diversity and how the geographic distribution of these alleles may be structured by ecological and demographic pressures. Here, we measure the variation in specialized metabolites across a population of 797 natural Arabidopsis thaliana accessions. We show that a combination of geography, environmental parameters, demography and different genetic processes all combine to influence the specific chemotypes and their distribution. This showed that causal loci in specialized metabolism contain frequent independently generated alleles with patterns suggesting potential within-species convergence. This provides a new perspective about the complexity of the selective forces and mechanisms that shape the generation and distribution of allelic variation that may influence local adaptation.

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Section: Discussionmentioning

confidence: 99%

Genetic variation, environment and demography intersect to shape Arabidopsis defense metabolite variation across Europe

Katz

Jaegle

et al. 2021

eLife

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“…Finally, duplications are just a subset of structural variants, and it is therefore not surprising that other short-read approaches to detect such variants have identified many more using the 1001 Genomes data (Zmienko et al 2020;D.-X. Liu et al 2021;Göktay, Fulgione, and Hancock 2020). Pseudo-SNPs is not the only problem with relying on a reference genome.…”

Section: Discussionmentioning

confidence: 99%

Extensive gene duplication in Arabidopsis revealed by pseudo-heterozygosity

Jaegle

Soto‐Jiménez

Burns

et al. 2021

Preprint

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BackgroundIt is becoming apparent that genomes harbor massive amounts of structural variation, and that this variation has largely gone undetected for technical reasons. In addition to being inherently interesting, structural variation can cause artifacts when short-read sequencing data are mapped to a reference genome. In particular, spurious SNPs (that do not show Mendelian segregation) may result from mapping of reads to duplicated regions. Recalling SNP using the raw reads of the 1001 Arabidopsis Genomes Project we identified 3.3 million heterozygous SNPs (44% of total). Given that Arabidopsis thaliana (A. thaliana) is highly selfing, we hypothesized that these SNPs reflected cryptic copy number variation, and investigated them further.ResultsWhile genuine heterozygosity should occur in tracts within individuals, heterozygosity at a particular locus is instead shared across individuals in a manner that strongly suggests it reflects segregating duplications rather than actual heterozygosity. Focusing on pseudo-heterozygosity in annotated genes, we used GWAS to map the position of the duplicates, identifying 2500 putatively duplicated genes. The results were validated using de novo genome assemblies from six lines. Specific examples included an annotated gene and nearby transposon that, in fact, transpose together.ConclusionsOur study confirms that most heterozygous SNPs calls in A. thaliana are artifacts, and suggest that great caution is needed when analysing SNP data from short-read sequencing. The finding that 10% of annotated genes are copy-number variables, and the realization that neither gene- nor transposon-annotation necessarily tells us what is actually mobile in the genome suggest that future analyses based on independently assembled genomes will be very informative.

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“…Intraspecific differences in DNA content have been reported or are predicted between individuals with: (1) heteromorphic sex chromosomes ( Costich et al , 1991 ; Renner et al , 2017 ), (2) different numbers of B chromosomes ( Leitch et al , 2007 ), dysploidy and aneuploidy, or (3) the presence/absence of specific DNA sequences. Such presence/absence variation may be subdivided into: (a) structural variants including insertion–deletion polymorphisms (indels), (b) copy number variation in protein-coding genes, commonly found in pan-genome studies ( Hirsch et al , 2014 ; W. Wang et al , 2018 ; Gao et al , 2019 ; Hübner et al , 2019 ; Göktay et al , 2021 ), and (c) copy number variation of rDNA copies ( Long et al , 2013 ) or of other genomic repeats ( Chia et al , 2012 ; Haberer et al , 2020 ). Some differences, such as small indels, can be as small as one base pair, while others are large-scale (many megabases), including sequence duplications or loss of a dispensable chromosome.…”

Section: Introductionmentioning

confidence: 99%

The nature of intraspecific and interspecific genome size variation in taxonomically complex eyebrights

Becher

Powell

et al. 2021

Annals of Botany

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Background and aims Genome size varies considerably across the diversity of plant life. Although genome size is, by definition, affected by genetic presence/absence variants, which are ubiquitous in population sequencing studies, genome size is often treated as an intrinsic property of a species. Here, we studied intra- and interspecific genome size variation in taxonomically complex British eyebrights (Euphrasia, Orobanchaceae). Our aim is to document genome size diversity and investigate underlying evolutionary processes shaping variation between individuals, populations and species. Methods We generated genome size data for 192 individuals of diploid and tetraploid Euphrasia and analysed genome size variation in relation to ploidy, taxonomy, population affiliation, and geography. We further compared the genomic repeat content of 30 samples. Key results We found considerable intraspecific genome size variation, and observed isolation-by-distance for genome size in outcrossing diploids. Tetraploid Euphrasia showed contrasting patterns, with genome size increasing with latitude in outcrossing Euphrasia arctica, but with little genome size variation in the highly selfing Euphrasia micrantha. Interspecific differences in genome size and the genomic proportions of repeat sequences were small. Conclusions We show the utility of treating genome size as the outcome of polygenic variation. Like other types of genetic variation, such as single nucleotide polymorphisms, genome size variation may be affected by ongoing hybridisation and the extent of population subdivision. In addition to selection on associated traits, genome size is predicted to be affected indirectly by selection due to pleiotropy of the underlying presence/absence variants.

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A New Catalog of Structural Variants in 1,301 A. thaliana Lines from Africa, Eurasia, and North America Reveals a Signature of Balancing Selection at Defense Response Genes

Cited by 31 publications

References 107 publications

Genetic variation, environment and demography intersect to shape Arabidopsis defense metabolite variation across Europe

Genetic variation, environment and demography intersect to shape Arabidopsis defense metabolite variation across Europe

Extensive gene duplication in Arabidopsis revealed by pseudo-heterozygosity

The nature of intraspecific and interspecific genome size variation in taxonomically complex eyebrights

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