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

Becher, Hannes; Powell, Robyn F.; Mr, Brown; Metherell, Chris; Pellicer, Jaume; Leitch, Ilia J.; Twyford, Alex D.

doi:10.1093/aob/mcab102

Cited by 28 publications

(34 citation statements)

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“…Knowing about the shortcomings of genome assemblies, which tend to be smaller than genomes size estimates obtained by flow cytometry (Bennett et al, 2003), we utilized a k-mer approach in this study. Despite this, we found our bioinformatic genome size estimates were all lower (except for Ro, 1C=0.63 pg) than those we obtained earlier by flow cytometry (Becher et al, 2021), the lowest of which was 1C=0.6 pg. While possible, it seems unlikely that most of our samples truly contained less DNA than all samples analysed in our previous study.…”

Section: Measuring Genome Size Differences With K-merscontrasting

confidence: 98%

“…To associate any genomic copy number differences identified using k-mers with specific repeat types, we used the RepeatExplorer2 output of a previous study (Becher et al, 2021) in which we had carried out an analysis of low-pass sequencing data of several diploid and tetraploid British eyebrights. We selected the first 50 repeat super clusters and concatenated, per super cluster, all contributing reads.…”

Section: Contribution Of Different Repeat Typesmentioning

confidence: 99%

“…While the diploids are largely morphologically distinct from one another (although numerous diploid hybrid combinations are known), they cannot be distinguished reliably by ITS or plastid barcoding (Wang et al, 2018), raising the question whether they are genetically distinct. Adding to this doubt, we have also recently uncovered considerable intra and interspecific genome size variation within Euphrasia ploidy levels and showed that 'population' is a far better predictor of an individual's genome size than 'species' (Becher et al, 2021). As such, our current working hypothesis has been that Euphrasia species may not show genome-wide differentiation, and instead species differences may be maintained by few genomic regions under strong selection while the rest of the genome experiences homogenising gene flow.…”

Section: Genome Comparisons and Our Understanding Of Diploid British Euphrasiamentioning

confidence: 99%

“…So far, only one triploid individual has been confirmed by cytogenetics (Yeo, 1954). In this study, we focus on morphological diploids in which we have previously found 1.2-fold genome size variation (Becher et al, 2021).…”

Section: The Study Systemmentioning

confidence: 99%

“…In this study, we use high-coverage shotgun data to investigate the sequences underlying genome size variation in diploid British eyebrights (Euphrasia L.) in which we had previously uncovered considerable intraspecific genome size variation (Becher et al, 2021). These diploids from a complex of hybridising taxa, which are not distinguishable by DNA barcoding (Wang et al, 2018) albeit there is some genetic structure congruent with morphological difference as evidenced by AFLPs (French et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

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Measuring the invisible – The sequences causal of genome size differences in eyebrights (Euphrasia) revealed by k-mers

Becher

Sampson

Twyford

2021

Preprint

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Genome size variation within plant (and other) taxa may be due to presence/absence variation in low-copy sequences or copy number variation in genomic repeats of various frequency classes. However, identifying the sequences underpinning genome size variation has been challenging because genome assemblies commonly contain collapsed representations of repetitive sequences and because genome skimming studies miss low-copy number sequences.Here, we take a novel approach based on k-mers, short sub-sequences of equal length k, generated from whole genome sequencing data of diploid eyebrights (Euphrasia), a group of plants which have considerable genome size variation within a ploidy level. We compare k-mer inventories within and between closely related species, and quantify the contribution of different copy number classes to genome size differences. We further assign high-copy number k-mers to specific repeat types as retrieved from the RepeatExplorer2 pipeline.We find complex patterns of k-mer differences between samples. While all copy number classes contributed to genome size variation, the largest contribution came from repeats with 1000-10,000 genomic copies including the 45S rDNA satellite DNA and, unexpectedly, a repeat associated with an Angela transposable element. We also find size differences in the low-copy number class, likely indicating differences in gene space between our samples.In this study, we demonstrate that it is possible to pinpoint the sequences causing genome size variation within species without use of a reference genome. Such sequences can serve as targets for future cytogenetic studies. We also show that studies of genome size variation should go beyond repeats and consider the whole genome. To allow future work with other taxonomic groups, we share our analysis pipeline, which is straightforward to run, relying largely on standard GNU command line tools.

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Section: Measuring Genome Size Differences With K-merscontrasting

confidence: 98%

Section: Contribution Of Different Repeat Typesmentioning

confidence: 99%

Section: Genome Comparisons and Our Understanding Of Diploid British Euphrasiamentioning

confidence: 99%

Section: The Study Systemmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Measuring the invisible – The sequences causal of genome size differences in eyebrights (Euphrasia) revealed by k-mers

Becher

Sampson

Twyford

2021

Preprint

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Is there hybridization between diploid and tetraploid Euphrasia in a secondary contact zone?

Becher

Williams

et al. 2022

American J of Botany

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Premise: Strong postzygotic reproductive isolating barriers are usually expected to limit the extent of natural hybridization between species with contrasting ploidy. However, genomic sequencing has revealed previously overlooked examples of natural cross-ploidy hybridization in some flowering plant genera, suggesting that the phenomenon may be more common than once thought. We investigated potential cross-ploidy hybridization in British eyebrights (Euphrasia, Orobanchaceae), a group from which 13 putative cross-ploidy hybrid combinations have been reported based on morphology. Methods: We analyzed a contact zone between diploid Euphrasia rostkoviana and tetraploid E. arctica in Wales. We sequenced part of the internal transcribed spacer (ITS) of nuclear ribosomal DNA and used genotyping by sequencing (GBS) to look for evidence of cross-ploidy hybridization and introgression. Results: Common variant sites in the ITS region were fixed between diploids and tetraploids, indicating a strong barrier to hybridization. Clustering analyses of 356 single-nucleotide polymorphisms (SNPs) generated using GBS clearly separated samples by ploidy and revealed strong genetic structure (F ST = 0.44). However, the F ST distribution across all SNPs was bimodal, indicating potential differential selection on loci between diploids and tetraploids. Demographic inference suggested potential gene flow, limited to around one or fewer migrants per generation. Conclusions: Our results suggest that recent cross-ploidy hybridization is rare or absent in a site of secondary contact in Euphrasia. While a strong ploidy barrier prevents hybridization over ecological timescales, such hybrids may form in stable populations over evolutionary timescales, potentially allowing cross-ploidy introgression to take place.

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Comparative microscopic investigations of leaf epidermis in four Ajuga species from Korea

Choi,

Hwang,

McAdam

et al. 2023

Microscopy Res & Technique

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The genus Ajuga is widely distributed in temperate to subtropical regions, and four species are currently recognized in Korea (A. decumbens, A. multiflora, A. nipponensis, and A. spectabilis), but epidermal anatomical differences across these species have never been described. A comparative study of the leaf micromorphological characteristics of Korean Ajuga species was performed using light microscopy (LM) and scanning electron microscopy (SEM) to elucidate their taxonomic usefulness and to assess leaf micromorphological diversity. Considerable diversity in epidermal and stomatal anatomy was observed across Korean Ajuga species. Species had both hypostomatic or amphistomatic leaves, with anomocytic, anisocytic, diactyic, or actinocytic stomatal complexes. Guard cell length across species ranged from 17.66 ± 0.57 μm to 32.50 ± 2.38 μm and correlated with genome size. Abnormal stomata were frequently observed in three species (A. decumbens, A. multiflora, and A. nipponensis) but not in A. spectabilis. Three types of glandular trichomes were found: peltate in all species, short‐stalked in all species, and long‐stalked glandular trichomes in A. multiflora. Among the investigated leaf micromophological characters, trichome type, epidermal cell shape, and stomatal morphology were all taxonomically informative traits at a species level.Research Highlights A comprehensive micromorphological description of the leaf surface is provided for Korean Ajuga species using scanning electron microscopic (SEM) and light microscopic (LM) analyses. The diverse range of stomatal development and the occurrence of polymorphic stomatal types are documented for the first time in Korean Ajuga species. The great diversity in stomatal and trichome morphology in Korean Ajuga species are taxonomically useful traits for species identification.

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

Cited by 28 publications

References 105 publications

Measuring the invisible – The sequences causal of genome size differences in eyebrights (Euphrasia) revealed by k-mers

Measuring the invisible – The sequences causal of genome size differences in eyebrights (Euphrasia) revealed by k-mers

Is there hybridization between diploid and tetraploid Euphrasia in a secondary contact zone?

Comparative microscopic investigations of leaf epidermis in four Ajuga species from Korea

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