Genome size variation at constant chromosome number is not correlated with repetitive DNA dynamism in Anacyclus (Asteraceae)

Abstract Background and Aims Changes in the amount of repetitive DNA (dispersed and tandem repeats) are considered the main contributors to genome size variation across plant species in the absence of polyploidy. However, the study of repeatome dynamism in groups showing contrasting genomic features and complex evolutionary histories is needed to determine whether other processes underlying genome size variation may have been overlooked. The main aim here was to elucidate which mechanism best explains genome size evolution in Anacyclus (Asteraceae). Methods Using data from Illumina sequencing, we analysed the repetitive DNA in all species of Anacyclus, a genus with a reticulate evolutionary history, which displays significant genome size and karyotype diversity albeit presenting a stable chromosome number. Key Results By reconstructing ancestral genome size values, we inferred independent episodes of genome size expansions and contractions during the evolution of the genus. However, analysis of the repeatome revealed a similar DNA repeat composition across species, both qualitative and quantitative. Using comparative methods to study repeatome dynamics in the genus, we found no evidence for repeat activity causing genome size variation among species. Conclusions Our results, combined with previous cytogenetic data, suggest that genome size differences in Anacyclus are probably related to chromosome rearrangements involving losses or gains of chromosome fragments, possibly associated with homoploid hybridization. These could represent balanced rearrangements that do not disrupt gene dosage in merged genomes, for example via chromosome segment exchanges.

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Impact of parasitic lifestyle and different types of centromere organization on chromosome and genome evolution in the plant genus Cuscuta

10.1101/2020.07.03.186437 ◽

2020 ◽

Cited By ~ 1

Author(s):

Pavel Neumann ◽

Ludmila Oliveira ◽

Jana Čížková ◽

Tae-Soo Jang ◽

Sonja Klemme ◽

...

Keyword(s):

Chromosome Number ◽

Genome Size ◽

Repetitive Dna ◽

Repetitive Sequences ◽

Size Variation ◽

Basic Chromosome Number ◽

Holocentric Chromosomes ◽

List Type ◽

Genome Size Variation ◽

Sequence Composition

SummaryThe parasitic genus Cuscuta (Convolvulaceae) is exceptional among plants with respect to centromere organization, including both monocentric and holocentric chromosomes, and substantial variation in genome size and chromosome number. We investigated 12 species representing the diversity of the genus in a phylogenetic context to reveal the molecular and evolutionary processes leading to diversification of their genomes.We measured genome sizes and investigated karyotypes and centromere organization using molecular cytogenetic techniques. We also performed low-pass whole genome sequencing and comparative analysis of repetitive DNA composition.A remarkable 102-fold variation in genome sizes (342–34,734 Mbp/1C) was detected for monocentric Cuscuta species, while genomes of holocentric species were of moderate sizes (533–1,545 Mbp/1C). The genome size variation was primarily driven by the differential accumulation of repetitive sequences. The transition to holocentric chromosomes in the subgenus Cuscuta was associated with loss of histone H2A phosphorylation and elimination of centromeric retrotransposons. In addition, the basic chromosome number (x) decreased from 15 to 7, presumably due to chromosome fusions.We demonstrated that the transition to holocentricity in Cuscuta was accompanied by significant changes in epigenetic marks, chromosome number and the repetitive DNA sequence composition.

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Comparative analysis reveals within-population genome size variation in a rotifer is driven by large genomic elements with highly abundant satellite DNA repeat elements

BMC Biology ◽

10.1186/s12915-021-01134-w ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

C. P. Stelzer ◽

J. Blommaert ◽

A. M. Waldvogel ◽

M. Pichler ◽

B. Hecox-Lea ◽

...

Keyword(s):

Genome Size ◽

Satellite Dna ◽

Gc Content ◽

Size Variation ◽

Isolated Populations ◽

Genome Size Variation ◽

Variable Regions ◽

Geographic Population ◽

Genome Size Evolution ◽

Size Evolution

Abstract Background Eukaryotic genomes are known to display an enormous variation in size, but the evolutionary causes of this phenomenon are still poorly understood. To obtain mechanistic insights into such variation, previous studies have often employed comparative genomics approaches involving closely related species or geographically isolated populations within a species. Genome comparisons among individuals of the same population remained so far understudied—despite their great potential in providing a microevolutionary perspective to genome size evolution. The rotifer Brachionus asplanchnoidis represents one of the most extreme cases of within-population genome size variation among eukaryotes, displaying almost twofold variation within a geographic population. Results Here, we used a whole-genome sequencing approach to identify the underlying DNA sequence differences by assembling a high-quality reference genome draft for one individual of the population and aligning short reads of 15 individuals from the same geographic population including the reference individual. We identified several large, contiguous copy number variable regions (CNVs), up to megabases in size, which exhibited striking coverage differences among individuals, and whose coverage overall scaled with genome size. CNVs were of remarkably low complexity, being mainly composed of tandemly repeated satellite DNA with only a few interspersed genes or other sequences, and were characterized by a significantly elevated GC-content. CNV patterns in offspring of two parents with divergent genome size and CNV patterns in several individuals from an inbred line differing in genome size demonstrated inheritance and accumulation of CNVs across generations. Conclusions By identifying the exact genomic elements that cause within-population genome size variation, our study paves the way for studying genome size evolution in contemporary populations rather than inferring patterns and processes a posteriori from species comparisons.

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Genome size variation in the North American sunfish genus Lepomis (Pisces: Centrarchidae)

Genetics Research ◽

10.1017/s0016672300028135 ◽

1989 ◽

Vol 53 (3) ◽

pp. 173-182 ◽

Cited By ~ 16

Author(s):

Chara J. Ragland ◽

John R. Gold

Keyword(s):

Genome Size ◽

North American ◽

Size Variation ◽

Hierarchical Level ◽

Size Difference ◽

Similar Data ◽

Genome Size Variation ◽

The North ◽

Essentially Normal ◽

Genome Size Evolution

SummaryGenome sizes (nuclear DNA contents) were documented spectrophotometrically from individuals of each of nine species of the North American centrarchid (sunfish) genus Lepomis. The distributions of DNA values within and among the nine species were essentially normal and continuous, suggesting that changes in DNA quantity in Lepomis are small in amount, involve both gains and losses of DNA, and are cumulative and independent in effect. Significant differences in mean genome size were found between individuals within populations in all nine species and between species. Nested analysis of variance and comparisons of average genome size difference or distance between individuals drawn from different levels of taxonomic organization revealed that the majority of genome size divergence in Lepomis occurs above the hierarchical level of individuals within populations. The Lepomis data when compared to similar data from North American cyprinid fishes appear to suggest that: (i) genome size evolution in these fishes at least follows a continuous rather than a discontinuous mode; (ii) the general predictions of hypothetical models relating genome size variation as a function of organismal position along adaptive continua may be oversimplified, or not applicable to complex, higher eukaryotes; and (iii) changes in genome size in these fishes may be concentrated in speciation episodes.

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In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae

PLoS ONE ◽

10.1371/journal.pone.0143424 ◽

2015 ◽

Vol 10 (11) ◽

pp. e0143424 ◽

Cited By ~ 75

Author(s):

Jiří Macas ◽

Petr Novák ◽

Jaume Pellicer ◽

Jana Čížková ◽

Andrea Koblížková ◽

...

Keyword(s):

Genome Size ◽

Repetitive Dna ◽

Size Variation ◽

Genome Size Variation ◽

Plant Genomes

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On the Tempo of Genome Size Evolution in Angiosperms

Journal of Botany ◽

10.1155/2010/989152 ◽

2010 ◽

Vol 2010 ◽

pp. 1-8 ◽

Cited By ~ 16

Author(s):

Jeremy M. Beaulieu ◽

Stephen A. Smith ◽

Ilia J. Leitch

Keyword(s):

Life History ◽

Genome Size ◽

Large Scale ◽

Growth Form ◽

Size Variation ◽

Threshold Effect ◽

Phenotypic Traits ◽

Genome Size Variation ◽

Genome Size Evolution ◽

Size Evolution

Broadly sampled phylogenies have uncovered extreme deviations from a molecular clock with the rates of molecular substitution varying dramatically within/among lineages. While growth form, a proxy for life history, is strongly correlated with molecular rate heterogeneity, its influence on trait evolution has yet to be examined. Here, we explore genome size evolution in relation to growth form by combining recent advances in large-scale phylogeny construction with model-based phylogenetic comparative methods. We construct phylogenies for Monocotyledonae (monocots) and Fabaceae (legumes), including all species with genome size information, and assess whether rates of genome size evolution depend on growth form. We found that the rates of genome size evolution for woody lineages were consistently an order of magnitude slower than those of herbaceous lineages. Our findings also suggest that growth form constrains genome size evolution, not through consequences associated with the phenotype, but instead through the influence of life history attributes on the tempo of evolution. Consequences associated with life history now extend to genomic evolution and may shed light on the frequently observed threshold effect of genome size variation on higher phenotypic traits.

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Chromosome number and genome size variation in Colocasia (Araceae) from China

Journal of Plant Research ◽

10.1007/s10265-017-0959-8 ◽

2017 ◽

Vol 130 (6) ◽

pp. 989-997 ◽

Cited By ~ 2

Author(s):

Guang-Yan Wang ◽

Xiao-Ming Zhang ◽

Min Qian ◽

Xiang-Yang Hu ◽

Yong-Ping Yang

Keyword(s):

Chromosome Number ◽

Genome Size ◽

Size Variation ◽

Genome Size Variation

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Genome size variation in Begonia

Genome ◽

10.1139/g09-056 ◽

2009 ◽

Vol 52 (10) ◽

pp. 829-838 ◽

Cited By ~ 10

Author(s):

Angelo Dewitte ◽

Leen Leus ◽

Tom Eeckhaut ◽

Ives Vanstechelman ◽

Johan Van Huylenbroeck ◽

...

Keyword(s):

Flow Cytometry ◽

Chromosome Number ◽

Genome Size ◽

Size Variation ◽

South American ◽

Chromosome Size ◽

Genome Size Variation ◽

Length Width ◽

South American Origin ◽

Secondary Constrictions

The genome sizes of a Begonia collection comprising 37 species and 23 hybrids of African, Asiatic, Middle American, and South American origin were screened using flow cytometry. Within the collection, 1C values varied between 0.23 and 1.46 pg DNA. Genome sizes were, in most cases, not positively correlated with chromosome number, but with pollen size. A 12-fold difference in mean chromosome size was found between the genotypes with the largest and smallest chromosomes. In general, chromosomes from South American genotypes were smaller than chromosomes of African, Asian, or Middle American genotypes, except for B. boliviensis and B. pearcei. Cytological chromosome studies in different genotypes showed variable chromosome numbers, length, width, and total chromosome volume, which confirmed the diversity in genome size. Large secondary constrictions were present in several investigated genotypes. These data show that chromosome number and structure exhibit a great deal of variation within the genus Begonia, and likely help to explain the large number of taxa found within the genus.

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Comparative Analysis of Transposable Elements in Genus Calliptamus Grasshoppers Revealed That Satellite DNA Contributes to Genome Size Variation

Insects ◽

10.3390/insects12090837 ◽

2021 ◽

Vol 12 (9) ◽

pp. 837

Author(s):

Muhammad Majid ◽

Huang Yuan

Keyword(s):

Comparative Analysis ◽

Transposable Elements ◽

Genome Size ◽

Structural Changes ◽

Evolutionary Dynamics ◽

Size Variation ◽

Genome Size Variation ◽

Genome Size Evolution ◽

Size Evolution ◽

Low Coverage

Transposable elements (TEs) play a significant role in both eukaryotes and prokaryotes genome size evolution, structural changes, duplication, and functional variabilities. However, the large number of different repetitive DNA has hindered the process of assembling reference genomes, and the genus level TEs diversification of the grasshopper massive genomes is still under investigation. The genus Calliptamus diverged from Peripolus around 17 mya and its species divergence dated back about 8.5 mya, but their genome size shows rather large differences. Here, we used low-coverage Illumina unassembled short reads to investigate the effects of evolutionary dynamics of satDNAs and TEs on genome size variations. The Repeatexplorer2 analysis with 0.5X data resulted in 52%, 56%, and 55% as repetitive elements in the genomes of Calliptamus barbarus, Calliptamus italicus, and Calliptamus abbreviatus, respectively. The LINE and Ty3-gypsy LTR retrotransposons and TcMar-Tc1 dominated the repeatomes of all genomes, accounting for 16–35% of the total genomes of these species. Comparative analysis unveiled that most of the transposable elements (TEs) except satDNAs were highly conserved across three genomes in the genus Calliptamus grasshoppers. Out of a total of 20 satDNA families, 17 satDNA families were commonly shared with minor variations in abundance and divergence between three genomes, and 3 were Calliptamus barbarus specific. Our findings suggest that there is a significant amplification or contraction of satDNAs at genus phylogeny which is the main cause that made genome size different.

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Genome structure of Brachionus asplanchnoidis, a Eukaryote with intrapopulation variation in genome size

10.1101/2021.03.09.434534 ◽

2021 ◽

Author(s):

C.P. Stelzer ◽

J. Blommaert ◽

A.M. Waldvogel ◽

M. Pichler ◽

B. Hecox-Lea ◽

...

Keyword(s):

Genome Size ◽

Genome Structure ◽

Gc Content ◽

Size Variation ◽

Genome Size Variation ◽

Variable Regions ◽

Geographic Population ◽

Intrapopulation Variation ◽

Genome Size Evolution ◽

Size Evolution

AbstractEukaryotic genomes vary greatly in size due to variation in the proportion of non-coding DNA, a pattern that emerges both in comparisons at a larger taxonomic scale and at the level of individuals within a species. The rotifer Brachionus asplanchnoidis represents one of the most extreme cases of intraspecific genome size variation among Eukaryotes, displaying almost 2-fold variation within a geographic population. Here we used a whole-genome sequencing approach to identify the underlying DNA sequence differences by assembling a high-quality reference genome draft for one individual of the population and aligning short-reads of 15 individuals from the same geographic population. We identified large, contiguous copy number variable regions (CNVs), which exhibited significant coverage differences among individuals, and whose coverage overall scaled with genome size. CNVs were mainly composed of tandemly repeated satellite DNA, with only few interspersed genes or other sequences, and were characterized by an elevated GC-content. Judging from their distributions across contigs, some CNVs are fragments of accessory (B-)chromosomes while others resemble large insertions to normal chromosomes. CNV patterns in offspring of two parents with divergent genome size, and CNV patterns in several individuals from an inbred line differing in genome size demonstrated inheritance and accumulation of CNVs across generations. Our study provides unprecedented insights into genome size evolution at microevolutionary time scales and thus paves the way for studying genome size evolution in contemporary populations rather than inferring patterns and processes a posteriori from species comparisons.

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Genome-size evolution in fishes

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f04-106 ◽

2004 ◽

Vol 61 (9) ◽

pp. 1636-1646 ◽

Cited By ~ 91

Author(s):

David C Hardie ◽

Paul DN Hebert

Keyword(s):

Genome Size ◽

Size Variation ◽

Evolutionary Significance ◽

Genome Size Variation ◽

Genome Size Evolution ◽

Size Evolution ◽

Size Diversity ◽

Cartilaginous Fishes ◽

Egg Diameter ◽

Size Estimates

Fishes possess both the largest and smallest vertebrate genomes, but the evolutionary significance of this variation is unresolved. The present study provides new genome-size estimates for more than 500 species, with a focus on the cartilaginous and ray-finned fishes. These results confirm that genomes are smaller in ray-finned than in cartilaginous fishes, with the exception of polyploids, which account for much genome-size variation in both groups. Genome-size diversity in ray-finned fishes is not related to metabolic rate, but is positively correlated with egg diameter, suggesting linkages to the evolution of parental care. Freshwater and other eurybiotic fishes have larger genomes than their marine and stenobiotic counterparts. Although genome-size diversity among the fishes appears less clearly linked to any single biological correlate than in the birds, mammals, or amphibians, this study highlights several particularly variable taxa that are suitable for further study.

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