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.

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 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 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.

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.

Surprising amount of stasis in repetitive genome content across the Brassicales

2020 ◽  
Author(s):  
Aleksandra Beric ◽  
Makenzie E Mabry ◽  
Alex E Harkess ◽  
M. Eric Schranz ◽  
Gavin C Conant ◽  
...  
Keyword(s):  
Genome Size ◽  
Contributing Factors ◽  
Plant Genomes ◽  
New Methods ◽  
Whole Genome Duplications ◽  
Genome Size Evolution ◽  
Size Evolution ◽  
Genome Duplications ◽  
Genome Content ◽  
Low Coverage

Genome size of plants has long piqued the interest of researchers due to the vast differences among organisms. However, the mechanisms that drive size differences have yet to be fully understood. Two important contributing factors to genome size are expansions of repetitive elements, such as transposable elements (TEs), and whole-genome duplications (WGD). Although studies have found correlations between genome size and both TE abundance and polyploidy, these studies typically test for these patterns within a genus or species. The plant order Brassicales provides an excellent system to test if genome size evolution patterns are consistent across larger time scales, as there are numerous WGDs. This order is also home to one of the smallest plant genomes, Arabidopsis thaliana - chosen as the model plant system for this reason - as well as to species with very large genomes. With new methods that allow for TE characterization from low-coverage genome shotgun data and 71 taxa across the Brassicales, we find no correlation between genome size and TE content, and more surprisingly we identify no significant changes to TE landscape following WGD.

scholarly journals Recent Insights into Mechanisms of Genome Size Change in Plants

2010 ◽  
Vol 2010 ◽  
pp. 1-8 ◽  
Author(s):  
Corrinne E. Grover ◽  
Jonathan F. Wendel
Keyword(s):  
Genome Size ◽  
Related Species ◽  
Evolutionary Dynamics ◽  
Higher Order ◽  
Size Change ◽  
Closely Related Species ◽  
Genome Size Evolution ◽  
Size Evolution ◽  
Recent Developments

Genome sizes vary considerably across all eukaryotes and even among closely related species. The genesis and evolutionary dynamics of that variation have generated considerable interest, as have the patterns of variation themselves. Here we review recent developments in our understanding of genome size evolution in plants, drawing attention to the higher order processes that can influence the mechanisms generating changing genome size.

scholarly journals Comparative phylogenetics of repetitive elements in a diverse order of flowering plants (Brassicales)

2021 ◽  
Author(s):  
Aleksandra Beric ◽  
Makenzie E Mabry ◽  
Alex E Harkess ◽  
Julia Brose ◽  
M Eric Schranz ◽  
...  
Keyword(s):  
Genome Size ◽  
Repetitive Elements ◽  
Contributing Factors ◽  
New Methods ◽  
Whole Genome Duplications ◽  
Genome Size Evolution ◽  
Size Evolution ◽  
Genome Duplications ◽  
Comparative Phylogenetics ◽  
Low Coverage

Abstract Genome sizes of plants have long piqued the interest of researchers due to the vast differences among organisms. However, the mechanisms that drive size differences have yet to be fully understood. Two important contributing factors to genome size are expansions of repetitive elements, such as transposable elements (TEs), and whole-genome duplications (WGD). Although studies have found correlations between genome size and both TE abundance and polyploidy, these studies typically test for these patterns within a genus or species. The plant order Brassicales provides an excellent system to further test if genome size evolution patterns are consistent across larger time scales, as there are numerous WGDs. This order is also home to one of the smallest plant genomes, Arabidopsis thaliana—chosen as the model plant system for this reason—as well as to species with very large genomes. With new methods that allow for TE characterization from low-coverage genome shotgun data and 71 taxa across the Brassicales, we confirm correlation between genome size and TE content, however, we are unable to reconstruct phylogenetic relationships and do not detect any shift in TE abundance associated with WGD.

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