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Comparative genomics reveals insights into anuran genome size evolution.
Zuo B
,
Nneji LM
,
Sun YB
.
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BACKGROUND: Amphibians, particularly anurans, display an enormous variation in genome size. Due to the unavailability of whole genome datasets in the past, the genomic elements and evolutionary causes of anuran genome size variation are poorly understood. To address this, we analyzed whole-genome sequences of 14 anuran species ranging in size from 1.1 to 6.8 Gb. By annotating multiple genomic elements, we investigated the genomic correlates of anuran genome size variation and further examined whether the genome size relates to habitat types.
RESULTS: Our results showed that intron expansions or contraction and Transposable Elements (TEs) diversity do not contribute significantly to genome size variation. However, the recent accumulation of transposable elements (TEs) and the lack of deletion of ancient TEs primarily accounted for the evolution of anuran genome sizes. Our study showed that the abundance and density of simple repeat sequences positively correlate with genome size. Ancestral state reconstruction revealed that genome size exhibits a taxon-specific pattern of evolution, with families Bufonidae and Pipidae experiencing extreme genome expansion and contraction events, respectively. Our result showed no relationship between genome size and habitat types, although large genome-sized species are predominantly found in humid habitats.
CONCLUSIONS: Overall, our study identified the genomic element and their evolutionary dynamics accounting for anuran genome size variation, thus paving a path to a greater understanding of the size evolution of the genome in amphibians.
Fig. 1
Shows the association between genome size and repetitive sequences/transposable elements diversity index in anuran species. (A) Positive correlation between genome size and repetitive elements. The X-axis shows the genome size, the length of the repetitive elements by the Y-axis, and the 95% confidence interval by the gray region. (B) Abundance and Distribution of the Transposable elements across anuran species. (C) Genome size and transposable element diversity index (Simpson diversity index). (D) Genome size and transposable element diversity index (Shannon Diversity Index). Gray shade represents the 95% confidence interval
Fig. 2
Transposable element age distribution landscapes of anuran genome sizes. The Y-axis shows the genomic coverage of different types of TEs, and the X-axis shows the Kimura substitution level as a percentage from 0 to 40. The Y-axis represents TE abundance as a proportion of the genome (e.g., 1.0 = 1% of the genome). The distribution landscape of TE divergence is categorized as follows: L-shaped distribution (TE divergence peak less than or equal to 5%), bimodal distribution (two peaks occur), or multi-peaked distribution (more than two peaks occur)
Fig. 3
Relationship between anuran genome size and exons, introns, intergenic regions and Simple Sequence Repeats, respectively. (Gray shade represents the 95% confidence interval) Figures A, B, C, D, E, F, G, and H represent the relationship between genome size and length of SSRs, number of SSRs, relative abundance of SSRs, relative density of SSRs, intron length, average intron length, average exon length, and intergenic region length for 14 anuran species
Fig. 4
Reconstruction ancestral state of anuran genome size(left) and proportion of Transposable Elements(right) across 14 anuran species. Branching colors represent values reconstructed from phylogenetic relationships. The names and values on the nodes represent ancestral names and ancestral values for the branches, including Pipidae, Ranidae, Bufonidae, Dendrobatidae, Dicroglossidae, Eleutherodactylidae, Leptodactylidae, Myobatrachidae and Pelobatidae. In the figure, the nodes in the size branch of the genome (left) are represented by “node + number” (e.g., node 1), and the nodes in the TE branch are represented by “node + number*” (e.g., node 1*)
Bachmann,
Specific nuclear DNA amounts in toads of the genus Bufo.
1970, Pubmed
Bachmann,
Specific nuclear DNA amounts in toads of the genus Bufo.
1970,
Pubmed
Beauregard,
The take and give between retrotransposable elements and their hosts.
2008,
Pubmed
Benson,
Tandem repeats finder: a program to analyze DNA sequences.
1999,
Pubmed
Canapa,
Transposons, Genome Size, and Evolutionary Insights in Animals.
2015,
Pubmed
Chipman,
The evolution of genome size: what can be learned from anuran development?
2001,
Pubmed
Cong,
Transposons and non-coding regions drive the intrafamily differences of genome size in insects.
2022,
Pubmed
Ding,
Large-scale analysis reveals that the genome features of simple sequence repeats are generally conserved at the family level in insects.
2017,
Pubmed
Du,
Krait: an ultrafast tool for genome-wide survey of microsatellites and primer design.
2018,
Pubmed
Du,
PSMD: An extensive database for pan-species microsatellite investigation and marker development.
2020,
Pubmed
Du,
MSDB: a user-friendly program for reporting distribution and building databases of microsatellites from genome sequences.
2013,
Pubmed
Edwards,
Draft genome assembly of the invasive cane toad, Rhinella marina.
2018,
Pubmed
Ellinghaus,
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons.
2008,
Pubmed
Elliott,
Do larger genomes contain more diverse transposable elements?
2015,
Pubmed
Emms,
OrthoFinder: phylogenetic orthology inference for comparative genomics.
2019,
Pubmed
Faircloth,
msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design.
2008,
Pubmed
Feschotte,
DNA transposons and the evolution of eukaryotic genomes.
2007,
Pubmed
Finnegan,
Eukaryotic transposable elements and genome evolution.
1989,
Pubmed
Flynn,
RepeatModeler2 for automated genomic discovery of transposable element families.
2020,
Pubmed
Francis,
Similar Ratios of Introns to Intergenic Sequence across Animal Genomes.
2017,
Pubmed
Gall,
Chromosome structure and the C-value paradox.
1981,
Pubmed
Gregory,
Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma.
2001,
Pubmed
Gregory,
Genome size and developmental complexity.
2002,
Pubmed
Griffin,
The influence of DNA content and nuclear volume on the frequency of radiation-induced chromosome aberrations in Bufo species.
1970,
Pubmed
Hahn,
The g-value paradox.
2002,
Pubmed
Haley,
Transposable Element Diversity Remains High in Gigantic Genomes.
2022,
Pubmed
Hammond,
The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA.
2017,
Pubmed
,
Xenbase
Heckenhauer,
Genome size evolution in the diverse insect order Trichoptera.
2022,
Pubmed
Hu,
A chromosomal level genome sequence for Quasipaa spinosa (Dicroglossidae) reveals chromosomal evolution and population diversity.
2022,
Pubmed
,
Xenbase
Hubley,
The Dfam database of repetitive DNA families.
2016,
Pubmed
Ibrahim,
Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus.
2021,
Pubmed
Jurka,
Repbase Update, a database of eukaryotic repetitive elements.
2005,
Pubmed
Kapitonov,
A universal classification of eukaryotic transposable elements implemented in Repbase.
2008,
Pubmed
Kapusta,
Dynamics of genome size evolution in birds and mammals.
2017,
Pubmed
Kofler,
SciRoKo: a new tool for whole genome microsatellite search and investigation.
2007,
Pubmed
Lamichhaney,
A bird-like genome from a frog: Mechanisms of genome size reduction in the ornate burrowing frog, Platyplectrum ornatum.
2021,
Pubmed
Ledenyova,
[Imperfect and Compound Microsatellites in the Genomes of Burkholderia pseudomallei Strains].
2019,
Pubmed
Lertzman-Lepofsky,
Ecological constraints associated with genome size across salamander lineages.
2019,
Pubmed
Letunic,
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation.
2021,
Pubmed
Li,
Microsatellites within genes: structure, function, and evolution.
2004,
Pubmed
Li,
Hiplot: a comprehensive and easy-to-use web service for boosting publication-ready biomedical data visualization.
2022,
Pubmed
Li,
A draft genome assembly of the eastern banjo frog Limnodynastes dumerilii dumerilii (Anura: Limnodynastidae).
2020,
Pubmed
Liedtke,
Macroevolutionary shift in the size of amphibian genomes and the role of life history and climate.
2018,
Pubmed
Liu,
Transposable element expansion and low-level piRNA silencing in grasshoppers may cause genome gigantism.
2022,
Pubmed
Lu,
Profiling of gene duplication patterns of sequenced teleost genomes: evidence for rapid lineage-specific genome expansion mediated by recent tandem duplications.
2012,
Pubmed
Lu,
A large genome with chromosome-scale assembly sheds light on the evolutionary success of a true toad (Bufo gargarizans).
2021,
Pubmed
Lyu,
Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes.
2018,
Pubmed
Ma,
Rapid recent growth and divergence of rice nuclear genomes.
2004,
Pubmed
Malmstrøm,
The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes.
2018,
Pubmed
Mitros,
A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis.
2019,
Pubmed
,
Xenbase
Morgante,
Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes.
2002,
Pubmed
Neafsey,
Genome size evolution in pufferfish: a comparative analysis of diodontid and tetraodontid pufferfish genomes.
2003,
Pubmed
Olmo,
Evolution of the genome and cell sizes in salamanders.
1975,
Pubmed
Olmo,
Genome size evolution in vertebrates: trends and constraints.
1989,
Pubmed
Ou,
LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons.
2018,
Pubmed
Pagel,
Variation across species in the size of the nuclear genome supports the junk-DNA explanation for the C-value paradox.
1992,
Pubmed
Petrov,
Evolution of genome size: new approaches to an old problem.
2001,
Pubmed
Petrov,
Evidence for DNA loss as a determinant of genome size.
2000,
Pubmed
Petrov,
Mutational equilibrium model of genome size evolution.
2002,
Pubmed
Piégu,
A survey of transposable element classification systems--a call for a fundamental update to meet the challenge of their diversity and complexity.
2015,
Pubmed
Seidl,
Genome of Spea multiplicata, a Rapidly Developing, Phenotypically Plastic, and Desert-Adapted Spadefoot Toad.
2019,
Pubmed
Session,
Genome evolution in the allotetraploid frog Xenopus laevis.
2016,
Pubmed
,
Xenbase
Simão,
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
2015,
Pubmed
Smit,
Interspersed repeats and other mementos of transposable elements in mammalian genomes.
1999,
Pubmed
Song,
Comparison of the Microsatellite Distribution Patterns in the Genomes of Euarchontoglires at the Taxonomic Level.
2021,
Pubmed
Song,
Comparison of microsatellite distribution patterns in twenty-nine beetle genomes.
2020,
Pubmed
Sotero-Caio,
Evolution and Diversity of Transposable Elements in Vertebrate Genomes.
2017,
Pubmed
Streicher,
The genome sequence of the common frog, Rana temporaria Linnaeus 1758.
2021,
Pubmed
Stuckert,
The genomics of mimicry: Gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system.
2021,
Pubmed
Sun,
LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders.
2012,
Pubmed
Sun,
Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes.
2015,
Pubmed
,
Xenbase
Sun,
Perspectives on studying molecular adaptations of amphibians in the genomic era.
2020,
Pubmed
Tarailo-Graovac,
Using RepeatMasker to identify repetitive elements in genomic sequences.
2009,
Pubmed
Thiel,
Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.).
2003,
Pubmed
Van de Peer,
The evolutionary significance of polyploidy.
2017,
Pubmed
Vinogradov,
Genome size and GC-percent in vertebrates as determined by flow cytometry: the triangular relationship.
1998,
Pubmed
Vitte,
LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss.
2007,
Pubmed
Waltari,
Evolutionary dynamics of intron size, genome size, and physiological correlates in archosaurs.
2002,
Pubmed
Wang,
Gigantic Genomes Provide Empirical Tests of Transposable Element Dynamics Models.
2021,
Pubmed
Wang,
GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and Viewing.
2016,
Pubmed
Weber,
The whale shark genome reveals how genomic and physiological properties scale with body size.
2020,
Pubmed
White,
Copepod development rates in relation to genome size and 18S rDNA copy number.
2000,
Pubmed
Wicker,
A unified classification system for eukaryotic transposable elements.
2007,
Pubmed
Wright,
Metabolic 'engines' of flight drive genome size reduction in birds.
2014,
Pubmed
Yuan,
Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp.
2021,
Pubmed
Zhang,
Penaeid shrimp genome provides insights into benthic adaptation and frequent molting.
2019,
Pubmed
de Vienne,
Lifemap: Exploring the Entire Tree of Life.
2016,
Pubmed
