scholarly journals 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 ◽  
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.

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

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.

scholarly journals On the Tempo of Genome Size Evolution in Angiosperms

2010 ◽  
Vol 2010 ◽  
pp. 1-8 ◽  
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.

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

Insects ◽  
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.

Genome-size evolution in fishes

2004 ◽  
Vol 61 (9) ◽  
pp. 1636-1646 ◽  
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.

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

1989 ◽  
Vol 53 (3) ◽  
pp. 173-182 ◽  
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.

scholarly journals Substantial intraspecific genome size variation in golden-brown algae and its phenotypic consequences

2020 ◽  
Vol 126 (6) ◽  
pp. 1077-1087
Author(s):  
Dora Čertnerová ◽  
Pavel Škaloud
Keyword(s):  
Growth Rate ◽  
Genome Size ◽  
Cell Size ◽  
Nuclear Dna ◽  
Gc Content ◽  
Size Variation ◽  
Nuclear Dna Content ◽  
Genome Size Variation ◽  
Adaptive Consequences ◽  
Genomic Gc Content

Abstract Background and Aims While nuclear DNA content variation and its phenotypic consequences have been well described for animals, vascular plants and macroalgae, much less about this topic is known regarding unicellular algae and protists in general. The dearth of data is especially pronounced when it comes to intraspecific genome size variation. This study attempts to investigate the extent of intraspecific variability in genome size and its adaptive consequences in a microalgal species. Methods Propidium iodide flow cytometry was used to estimate the absolute genome size of 131 strains (isolates) of the golden-brown alga Synura petersenii (Chrysophyceae, Stramenopiles), identified by identical internal transcribed spacer (ITS) rDNA barcodes. Cell size, growth rate and genomic GC content were further assessed on a sub-set of strains. Geographic location of 67 sampling sites across the Northern hemisphere was used to extract climatic database data and to evaluate the ecogeographical distribution of genome size diversity. Key Results Genome size ranged continuously from 0.97 to 2.02 pg of DNA across the investigated strains. The genome size was positively associated with cell size and negatively associated with growth rate. Bioclim variables were not correlated with genome size variation. No clear trends in the geographical distribution of strains of a particular genome size were detected, and strains of different genome size occasionally coexisted at the same locality. Genomic GC content was significantly associated only with genome size via a quadratic relationship. Conclusions Genome size variability in S. petersenii was probably triggered by an evolutionary mechanism operating via gradual changes in genome size accompanied by changes in genomic GC content, such as, for example, proliferation of transposable elements. The variation was reflected in cell size and relative growth rate, possibly with adaptive consequences.

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

2019 ◽  
Vol 125 (4) ◽  
pp. 611-623 ◽  
Author(s):  
Daniel Vitales ◽  
Inés Álvarez ◽  
Sònia Garcia ◽  
Oriane Hidalgo ◽  
Gonzalo Nieto Feliner ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Genome Size ◽  
Repetitive Dna ◽  
Tandem Repeats ◽  
Gene Dosage ◽  
Size Variation ◽  
Genome Size Variation ◽  
Dna Repeat ◽  
Genome Size Evolution ◽  
Chromosome Fragments

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.

Genome size evolution and chromosome numbers of species of the cryptanthoid complex (Bromelioideae, Bromeliaceae) in a phylogenetic framework

2019 ◽  
Vol 192 (4) ◽  
pp. 887-899 ◽  
Author(s):  
Geyner Alves Dos Santos Cruz ◽  
José Roseno De Mendonça Filho ◽  
Santelmo Vasconcelos ◽  
Jaílson Gitaí ◽  
José Marcello Salabert De Campos ◽  
...  
Keyword(s):  
Genome Size ◽  
Chromosome Numbers ◽  
Habitat Preferences ◽  
Size Variation ◽  
Campos Rupestres ◽  
Genome Size Variation ◽  
Complex Species ◽  
Genome Size Evolution ◽  
Significant Difference ◽  
Phylogenetic Framework

Abstract We describe the chromosome numbers and genome sizes of species of the cryptanthoid complex of Bromeliaceae in a phylogenetic framework and their relationship with habitat preferences. The 2C DNA contents varied 2.13-fold among species, ranging from 0.76 to 1.66 pg. A significant difference in DNA content was found among Cryptanthus, Hoplocryptanthus and Rokautskyia. Moreover, species from campos rupestres and the Atlantic Forest had lower and higher genome size values, respectively. The smaller genome sizes of Hoplocryptanthus spp. from campos rupestres may be related with the large genome constraint. The species show a highly conserved ploidy (with 2n = 32 and 34), although the genome sizes varied considerably. The observed variation in chromosome numbers seems to be influenced by dysploidy, but additional investigations are needed. Our study demonstrates that the genome size variation in the cryptanthoid complex species is not strictly related to the phylogenetic relationships and has probably been influenced by different evolutionary processes.

scholarly journals Genome Size Dynamics and Evolution in Monocots

2010 ◽  
Vol 2010 ◽  
pp. 1-18 ◽  
Author(s):  
Ilia J. Leitch ◽  
Jeremy M. Beaulieu ◽  
Mark W. Chase ◽  
Andrew R. Leitch ◽  
Michael F. Fay
Keyword(s):  
Genome Size ◽  
Chromosome Evolution ◽  
Gc Content ◽  
Statistical Modelling ◽  
Genomic Diversity ◽  
Ancestral Genome ◽  
Ploidy Levels ◽  
Genome Size Evolution ◽  
Size Evolution ◽  
Wide Range

Monocot genomic diversity includes striking variation at many levels. This paper compares various genomic characters (e.g., range of chromosome numbers and ploidy levels, occurrence of endopolyploidy, GC content, chromosome packaging and organization, genome size) between monocots and the remaining angiosperms to discern just how distinctive monocot genomes are. One of the most notable features of monocots is their wide range and diversity of genome sizes, including the species with the largest genome so far reported in plants. This genomic character is analysed in greater detail, within a phylogenetic context. By surveying available genome size and chromosome data it is apparent that different monocot orders follow distinctive modes of genome size and chromosome evolution. Further insights into genome size-evolution and dynamics were obtained using statistical modelling approaches to reconstruct the ancestral genome size at key nodes across the monocot phylogenetic tree. Such approaches reveal that while the ancestral genome size of all monocots was small ( pg), there have been several major increases and decreases during monocot evolution. In addition, notable increases in the rates of genome size-evolution were found in Asparagales and Poales compared with other monocot lineages.

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