Evolutionary dynamics of mechanisms that affect genome size in the cotton genus (Gossypium)

Mutation rates vary both within and between bacterial species, and understanding what drives this variation is essential for understanding the evolutionary dynamics of bacterial populations. In this study, we investigate two factors that are predicted to influence the mutation rate: ecology and genome size. We conducted mutation accumulation experiments on eight strains of the emerging zoonotic pathogen Streptococcus suis. Natural variation within this species allows us to compare tonsil carriage and invasive disease isolates, from both more and less pathogenic populations, with a wide range of genome sizes. We find that invasive disease isolates have repeatedly evolved mutation rates that are higher than those of closely related carriage isolates, regardless of variation in genome size. Independent of this variation in overall rate, we also observe a stronger bias towards G/C to A/T mutations in isolates from more pathogenic populations, whose genomes tend to be smaller and more AT-rich. Our results suggest that ecology is a stronger correlate of mutation rate than genome size over these timescales, and that transitions to invasive disease are consistently accompanied by rapid increases in mutation rate. These results shed light on the impact that ecology can have on the adaptive potential of bacterial pathogens.

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Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza

The Plant Journal ◽

10.1111/j.1365-313x.2007.03242.x ◽

2007 ◽

Vol 52 (2) ◽

pp. 342-351 ◽

Cited By ~ 68

Author(s):

Jetty S. S. Ammiraju ◽

Andrea Zuccolo ◽

Yeisoo Yu ◽

Xiang Song ◽

Benoit Piegu ◽

...

Keyword(s):

Genome Size ◽

Evolutionary Dynamics ◽

Retrotransposon Family ◽

Genus Oryza

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Recent Insights into Mechanisms of Genome Size Change in Plants

Journal of Botany ◽

10.1155/2010/382732 ◽

2010 ◽

Vol 2010 ◽

pp. 1-8 ◽

Cited By ~ 63

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.

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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 Size Doubling Arises From the Differential Repetitive DNA Dynamics in the Genus Heloniopsis (Melanthiaceae)

Frontiers in Genetics ◽

10.3389/fgene.2021.726211 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jaume Pellicer ◽

Pol Fernández ◽

Michael F. Fay ◽

Ester Michálková ◽

Ilia J. Leitch

Keyword(s):

Genome Size ◽

Repetitive Dna ◽

High Throughput Sequencing ◽

Evolutionary Dynamics ◽

Dna Dynamics ◽

Closely Related Species ◽

Sequencing Technologies ◽

Genomic Landscape ◽

Evolutionary Changes ◽

Low Coverage

Plant genomes are highly diverse in size and repetitive DNA composition. In the absence of polyploidy, the dynamics of repetitive elements, which make up the bulk of the genome in many species, are the main drivers underpinning changes in genome size and the overall evolution of the genomic landscape. The advent of high-throughput sequencing technologies has enabled investigation of genome evolutionary dynamics beyond model plants to provide exciting new insights in species across the biodiversity of life. Here we analyze the evolution of repetitive DNA in two closely related species of Heloniopsis (Melanthiaceae), which despite having the same chromosome number differ nearly twofold in genome size [i.e., H. umbellata (1C = 4,680 Mb), and H. koreana (1C = 2,480 Mb)]. Low-coverage genome skimming and the RepeatExplorer2 pipeline were used to identify the main repeat families responsible for the significant differences in genome sizes. Patterns of repeat evolution were found to correlate with genome size with the main classes of transposable elements identified being twice as abundant in the larger genome of H. umbellata compared with H. koreana. In addition, among the satellite DNA families recovered, a single shared satellite (HeloSAT) was shown to have contributed significantly to the genome expansion of H. umbellata. Evolutionary changes in repetitive DNA composition and genome size indicate that the differences in genome size between these species have been underpinned by the activity of several distinct repeat lineages.

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Genome-wide features of introns are evolutionary decoupled among themselves and from genome size throughout Eukarya

10.1101/283549 ◽

2018 ◽

Cited By ~ 4

Author(s):

Irma Lozada-Chávez ◽

Peter F. Stadler ◽

Sonja J. Prohaska

Keyword(s):

Genome Size ◽

Evolutionary Dynamics ◽

Protein Coding ◽

Specific Level ◽

Spliceosomal Introns ◽

Major Mechanism ◽

Genome Wide ◽

A Genome ◽

Eukaryotic Gene ◽

The Impact

AbstractThe impact of spliceosomal introns on genome and organismal evolution remains puzzling. Here, we investigated the correlative associations among genome-wide features of introns from protein-coding genes (e.g., size, density, genome-content, repeats), genome size and multicellular complexity on 461 eukaryotes. Thus, we formally distinguished simple from complex multicellular organisms (CMOs), and developed the program GenomeContent to systematically estimate genomic traits. We performed robust phylogenetic controlled analyses, by taking into account significant uncertainties in the tree of eukaryotes and variation in genome size estimates. We found that changes in the variation of some intron features (such as size and repeat composition) are only weakly, while other features measuring intron abundance (within and across genes) are not, scaling with changes in genome size at the broadest phylogenetic scale. Accordingly, the strength of these associations fluctuates at the lineage-specific level, and changes in the length and abundance of introns within a genome are found to be largely evolving independently throughout Eukarya. Thereby, our findings are in disagreement with previous estimations claiming a concerted evolution between genome size and introns across eukaryotes. We also observe that intron features vary homogeneously (with low repetitive composition) within fungi, plants and stramenophiles; but they vary dramatically (with higher repetitive composition) within holozoans, chlorophytes, alveolates and amoebozoans. We also found that CMOs and their closest ancestral relatives are characterized by high intron-richness, regardless their genome size. These patterns contrast the narrow distribution of exon features found across eukaryotes. Collectively, our findings unveil spliceosomal introns as a dynamically evolving non-coding DNA class and strongly argue against both, a particular intron feature as key determinant of eukaryotic gene architecture, as well as a major mechanism (adaptive or non-adaptive) behind the evolutionary dynamics of introns over a large phylogenetic scale. We hypothesize that intron-richness is a pre-condition to evolve complex multicellularity.

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Evolutionary Dynamics of Intron Size, Genome Size, and Physiological Correlates in Archosaurs

The American Naturalist ◽

10.1086/342079 ◽

2002 ◽

Vol 160 (5) ◽

pp. 539-552 ◽

Cited By ~ 67

Author(s):

Eric Waltari ◽

Scott V. Edwards

Keyword(s):

Genome Size ◽

Evolutionary Dynamics ◽

Intron Size

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Evolutionary dynamics of genome size in a radiation of woody plants

American Journal of Botany ◽

10.1002/ajb2.1544 ◽

2020 ◽

Vol 107 (11) ◽

pp. 1527-1541

Author(s):

Morgan K. Moeglein ◽

David S. Chatelet ◽

Michael J. Donoghue ◽

Erika J. Edwards

Keyword(s):

Genome Size ◽

Woody Plants ◽

Evolutionary Dynamics

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Gigantic Genomes Can Provide Empirical Tests of TE Dynamics Models — An Example from Amphibians

10.1101/2020.08.19.257527 ◽

2020 ◽

Author(s):

Jie Wang ◽

Michael W. Itgen ◽

Huiju Wang ◽

Yuzhou Gong ◽

Jianping Jiang ◽

...

Keyword(s):

Genome Size ◽

Evolutionary Dynamics ◽

Diversity Indices ◽

Anatomy And Physiology ◽

A Genome ◽

History Of ◽

Empirical Tests ◽

And Function ◽

Dynamics Models

AbstractTransposable elements (TEs) are a major determinant of eukaryotic genome size. The collective properties of a genomic TE community reveal the history of TE/host evolutionary dynamics and impact present-day host structure and function, from genome to organism levels. In rare cases, TE community/genome size has greatly expanded in animals, associated with increased cell size and altered anatomy and physiology. We characterize the TE landscape of the genome and transcriptome in an amphibian with a giant genome — the caecilian Ichthyophis bannanicus, which we show has a genome size of 12.2 Gb. Amphibians are an important model system because the clade includes independent cases of genomic gigantism. The I. bannanicus genome differs compositionally from other giant amphibian genomes, but shares a low rate of ectopic-recombination-mediated deletion. We examine TE activity using expression and divergence plots; TEs account for 15% of somatic transcription, and most superfamilies appear active. We quantify TE diversity in the caecilian, as well as other vertebrates with a range of genome sizes, using diversity indices commonly applied in community ecology. We synthesize previous models integrating TE abundance, diversity, and activity, and we test whether the caecilian meets model predictions for genomes with high TE abundance. We propose thorough, consistent characterization of TEs to strengthen future comparative analyses. Such analyses will ultimately be required to reveal whether the divergent TE assemblages found across convergent gigantic genomes reflect fundamental shared features of TE/host genome evolutionary dynamics.

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