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

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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Genome size and intron size in Drosophila

Molecular Biology and Evolution ◽

10.1093/oxfordjournals.molbev.a025980 ◽

1998 ◽

Vol 15 (6) ◽

pp. 770-773 ◽

Cited By ~ 44

Author(s):

E. N. Moriyama ◽

D. A. Petrov ◽

D. L. Hartl

Keyword(s):

Genome Size ◽

Intron Size

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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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Intron Size and Genome Size in Plants

Molecular Biology and Evolution ◽

10.1093/oxfordjournals.molbev.a004062 ◽

2002 ◽

Vol 19 (12) ◽

pp. 2346-2352 ◽

Cited By ~ 42

Author(s):

Jonathan F. Wendel ◽

Richard C. Cronn ◽

Ines Alvarez ◽

Bao Liu ◽

Randall L. Small ◽

...

Keyword(s):

Genome Size ◽

Intron Size

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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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Two Classes of Genes in Plants

Genetics ◽

10.1093/genetics/154.4.1819 ◽

2000 ◽

Vol 154 (4) ◽

pp. 1819-1825 ◽

Cited By ~ 1

Author(s):

Nicolas Carels ◽

Giorgio Bernardi

Keyword(s):

Genome Size ◽

Base Composition ◽

Relative Size ◽

Intron Size ◽

Dna Base Composition ◽

Homologous Genes ◽

Dna Base ◽

Functional Relevance ◽

Poor Class

Abstract Two classes of genes were identified in three Gramineae (maize, rice, barley) and six dicots (Arabidopsis, soybean, pea, tobacco, tomato, potato). One class, the GC-rich class, contained genes with no, or few, short introns. In contrast, the GC-poor class contained genes with numerous, long introns. The similarity of the properties of each class, as present in the genomes of maize and Arabidopsis, is particularly remarkable in view of the fact that these plants exhibit large differences in genome size, average intron size, and DNA base composition. The functional relevance of the two classes of genes is stressed by (1) the conservation in homologous genes from maize and Arabidopsis not only of the number of introns and of their positions, but also of the relative size of concatenated introns; and (2) the existence of two similar classes of genes in vertebrates; interestingly, the differences in intron sizes and numbers in genes from the GC-poor and GC-rich classes are much more striking in plants than in vertebrates.

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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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