Genome-size evolution in fishes

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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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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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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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 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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Genome size increases in recently diverged hornwort clades

Genome ◽

10.1139/gen-2013-0041 ◽

2013 ◽

Vol 56 (8) ◽

pp. 431-435 ◽

Cited By ~ 19

Author(s):

Jillian D. Bainard ◽

Juan Carlos Villarreal

Keyword(s):

Genome Size ◽

Dna Content ◽

Size Variation ◽

Plant Genome ◽

Ancestral Reconstruction ◽

Genome Size Variation ◽

Important Group ◽

Content Variation ◽

Dna Content Variation ◽

Size Estimates

As our knowledge of plant genome size estimates continues to grow, one group has continually been neglected: the hornworts. Hornworts (Anthocerotophyta) have been traditionally grouped with liverworts and mosses because they share a haploid dominant life cycle; however, recent molecular studies place hornworts as the sister lineage to extant tracheophytes. Given the scarcity of information regarding the DNA content of hornworts, our objective was to estimate the 1C-value for a range of hornwort species within a phylogenetic context. Using flow cytometry, we estimated genome size for 36 samples representing 24 species. This accounts for roughly 10% of known hornwort species. Haploid genome sizes (1C-value) ranged from 160 Mbp or 0.16 pg (Leiosporoceros dussii) to 719 Mbp or 0.73 pg (Nothoceros endiviifolius). The average 1C-value was 261 ± 104 Mbp (0.27 ± 0.11 pg). Ancestral reconstruction of genome size on a hornwort phylogeny suggests a small ancestral genome size and revealed increases in genome size in the most recently divergent clades. Much more work is needed to understand DNA content variation in this phylogenetically important group, but this work has significantly increased our knowledge of genome size variation in hornworts.

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Nuclear DNA content in Sinningia (Gesneriaceae); intraspecific genome size variation and genome characterization in S. speciosa

Genome ◽

10.1139/g10-077 ◽

2010 ◽

Vol 53 (12) ◽

pp. 1066-1082 ◽

Cited By ~ 14

Author(s):

David Zaitlin ◽

Andrew J. Pierce

Keyword(s):

Genome Size ◽

Nuclear Dna ◽

Size Variation ◽

Nuclear Genome ◽

Nuclear Dna Content ◽

Size Estimation ◽

Cell Nuclei ◽

Genome Size Variation ◽

Genome Survey ◽

Size Estimates

The Gesneriaceae (Lamiales) is a family of flowering plants comprising >3000 species of mainly tropical origin, the most familiar of which is the cultivated African violet ( Saintpaulia spp.). Species of Gesneriaceae are poorly represented in the lists of taxa sampled for genome size estimation; measurements are available for three species of Ramonda and one each of Haberlea , Saintpaulia, and Streptocarpus , all species of Old World origin. We report here nuclear genome size estimates for 10 species of Sinningia , a neotropical genus largely restricted to Brazil. Flow cytometry of leaf cell nuclei showed that holoploid genome size in Sinningia is very small (approximately two times the size of the Arabidopsis genome), and is small compared to the other six species of Gesneriaceae with genome size estimates. We also documented intraspecific genome size variation of 21%–26% within a group of wild Sinningia speciosa (Lodd.) Hiern collections. In addition, we analyzed 1210 genome survey sequences from S. speciosa to characterize basic features of the nuclear genome such as guanine–cytosine content, types of repetitive elements, numbers of protein-coding sequences, and sequences unique to S. speciosa. We included several other angiosperm species as genome size standards, one of which was the snapdragon ( Antirrhinum majus L.; Veronicaceae, Lamiales). Multiple measurements on three accessions indicated that the genome size of A. majus is ∼633 × 106 base pairs, which is approximately 40% of the previously published estimate.

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The nucleotypic effects of cellular DNA content in cartilaginous and ray-finned fishes

Genome ◽

10.1139/g03-040 ◽

2003 ◽

Vol 46 (4) ◽

pp. 683-706 ◽

Cited By ~ 92

Author(s):

David C Hardie ◽

Paul D.N Hebert

Keyword(s):

Genome Size ◽

Cell Size ◽

Dna Content ◽

Significant Positive Correlation ◽

Cold Water ◽

Size Variation ◽

Nucleus Size ◽

Genome Size Variation ◽

Cartilaginous Fishes ◽

Cellular Dna

Cytological and organismal characteristics associated with cellular DNA content underpin most adaptionist interpretations of genome size variation. Since fishes are the only group of vertebrate for which relationships between genome size and key cellular parameters are uncertain, the cytological correlates of genome size were examined in this group. The cell and nuclear areas of erythrocytes showed a highly significant positive correlation with each other and with genome size across 22 cartilaginous and 201 ray-finned fishes. Regressions remained significant at all taxonomic levels, as well as among different fish lineages. However, the results revealed that cartilaginous fishes possess higher cytogenomic ratios than ray-finned fishes, as do cold-water fishes relative to their warm-water counterparts. Increases in genome size owing to ploidy shifts were found to influence cell and nucleus size in an immediate and causative manner, an effect that persists in ancient polyploid lineages. These correlations with cytological parameters known to have important influences on organismal phenotypes support an adaptive interpretation for genome size variation in fishes.Key words: evolution, genome size, DNA content, cell size, erythrocyte size, fishes, nucleotypic effect.

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

Annals of Botany ◽

10.1093/aob/mcz183 ◽

2019 ◽

Vol 125 (4) ◽

pp. 611-623 ◽

Cited By ~ 3

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.

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Genome Size and Ploidy Levels of Cercis (Redbud) Species, Cultivars, and Botanical Varieties

HortScience ◽

10.21273/hortsci.51.4.330 ◽

2016 ◽

Vol 51 (4) ◽

pp. 330-333 ◽

Cited By ~ 2

Author(s):

David J. Roberts ◽

Dennis J. Werner

Keyword(s):

Genome Size ◽

Size Variation ◽

Internal Standard ◽

Close Relative ◽

Genome Size Variation ◽

Ploidy Levels ◽

Wide Range ◽

Average Size ◽

Size Estimates ◽

Botanical Varieties

Cercis is an ancient member of Fabaceae, often cultivated as an ornamental tree, and can be found in numerous regions around the world. Previous studies have reported Cercis canadensis as being diploid with 2n = 2x = 14. However, there have been no further investigations into ploidy and genome size variation among Cercis taxa. A study was conducted to evaluate the relative genome size and ploidy levels of numerous species, cultivars, and botanical varieties of Cercis, representing taxa found in North America, Asia, and the Middle East. In addition, the genome size of Bauhinia forficata, a close relative of Cercis, was also determined. Genome size estimates (2C values) were determined by calculating the mean fluorescence of stained nuclei via flow cytometry. Propidium iodide was used as the staining agent and Glycine max was used as an internal standard for each taxon analyzed. Genome size estimates for all Cercis sampled ranged from 0.70 to 0.81 pg with an average size of 0.75 pg. The genome size of B. forficata was found to be smaller than any other Bauhinia sp. currently on record, with an average size of 0.87 pg. This study confirmed an initial estimation of the genome size of Cercis chinensis and found that floral buds of Cercis proved to be an excellent source of plant tissue for obtaining intact nuclei. All species, botanical varieties, and cultivars of Cercis surveyed for this study had remarkably similar genome sizes despite their wide range of distribution. This information can facilitate a better understanding of phylogenetic relationships within Cercideae and Cercis specifically.

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