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

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.

Download Full-text

In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae

PLoS ONE ◽

10.1371/journal.pone.0143424 ◽

2015 ◽

Vol 10 (11) ◽

pp. e0143424 ◽

Cited By ~ 75

Author(s):

Jiří Macas ◽

Petr Novák ◽

Jaume Pellicer ◽

Jana Čížková ◽

Andrea Koblížková ◽

...

Keyword(s):

Genome Size ◽

Repetitive Dna ◽

Size Variation ◽

Genome Size Variation ◽

Plant Genomes

Download Full-text

Clustered and interspersed repetitive DNA sequences in four amphibian species with different genome size

Biochimica et Biophysica Acta (BBA) - Nucleic Acids and Protein Synthesis ◽

10.1016/0005-2787(78)90224-1 ◽

1978 ◽

Vol 520 (2) ◽

pp. 245-252 ◽

Cited By ~ 7

Author(s):

Irene Bozzoni ◽

Elena Beccari

Keyword(s):

Genome Size ◽

Repetitive Dna ◽

Dna Sequences ◽

Repetitive Dna Sequences ◽

Amphibian Species ◽

Interspersed Repetitive Dna

Download Full-text

Variability and evolutionary implications of repetitive DNA dynamics in genome of Astyanax scabripinnis (Teleostei, Characidae)

Comparative Cytogenetics ◽

10.3897/compcytogen.v11i1.11149 ◽

2017 ◽

Vol 11 (1) ◽

pp. 143-162 ◽

Cited By ~ 5

Author(s):

Patrícia Barbosa ◽

Eliza Viola Leal ◽

Maelin da Silva ◽

Mara Cristina de Almeida ◽

Orlando Moreira-Filho ◽

...

Keyword(s):

Repetitive Dna ◽

Dna Dynamics ◽

Astyanax Scabripinnis

Download Full-text

Evolution of Genome Size in Conifers

Silvae Genetica ◽

10.1515/sg-2005-0020 ◽

2005 ◽

Vol 54 (1-6) ◽

pp. 126-137 ◽

Cited By ~ 73

Author(s):

M. Raj Ahuja ◽

David B. Neale

Keyword(s):

Genome Size ◽

Repetitive Dna ◽

Gene Families ◽

Gene Duplications ◽

Large Genome ◽

Repeat Units ◽

Conifer Genome ◽

Large Genome Size ◽

Highly Repetitive Dna ◽

Open Question

AbstractConifers are the most widely distributed group of gymnosperms in the world. They have large genome size (1C-value) compared with most animal and plant species. The genome size ranges from ~6,500 Mb to ~37,000 Mb in conifers. How and why conifers have evolved such large genomes is not understood. The conifer genome contains ~75% highly repetitive DNA. Most of the repetitive DNA is composed of non-coding DNA, including ubiquitous transposable elements. Conifers have relatively larger rDNA repeat units, larger gene families generated by gene duplications, larger nuclear volume, and perhaps larger genes, as compared to angiosperm plants. These genomic components may partially account for the large genome size, as well as variation in genome size, in conifers. One of the major mechanisms for genome size expansion and evolution of species is polyploidy, which is widespread in angiosperms, but it is rare in conifers. There are only a few natural polyploids in one family of conifers, Cupressaceae. Other conifers, including well-studied pines, are nearly all diploids. Whether ancient polyploidy has played a role in the evolution of genome size in conifers still remains an open question. The mechanisms that account for the variation and evolution of genome size in conifers are addressed in this review.

Download Full-text

Impact of parasitic lifestyle and different types of centromere organization on chromosome and genome evolution in the plant genus Cuscuta

10.1101/2020.07.03.186437 ◽

2020 ◽

Cited By ~ 1

Author(s):

Pavel Neumann ◽

Ludmila Oliveira ◽

Jana Čížková ◽

Tae-Soo Jang ◽

Sonja Klemme ◽

...

Keyword(s):

Chromosome Number ◽

Genome Size ◽

Repetitive Dna ◽

Repetitive Sequences ◽

Size Variation ◽

Basic Chromosome Number ◽

Holocentric Chromosomes ◽

List Type ◽

Genome Size Variation ◽

Sequence Composition

SummaryThe parasitic genus Cuscuta (Convolvulaceae) is exceptional among plants with respect to centromere organization, including both monocentric and holocentric chromosomes, and substantial variation in genome size and chromosome number. We investigated 12 species representing the diversity of the genus in a phylogenetic context to reveal the molecular and evolutionary processes leading to diversification of their genomes.We measured genome sizes and investigated karyotypes and centromere organization using molecular cytogenetic techniques. We also performed low-pass whole genome sequencing and comparative analysis of repetitive DNA composition.A remarkable 102-fold variation in genome sizes (342–34,734 Mbp/1C) was detected for monocentric Cuscuta species, while genomes of holocentric species were of moderate sizes (533–1,545 Mbp/1C). The genome size variation was primarily driven by the differential accumulation of repetitive sequences. The transition to holocentric chromosomes in the subgenus Cuscuta was associated with loss of histone H2A phosphorylation and elimination of centromeric retrotransposons. In addition, the basic chromosome number (x) decreased from 15 to 7, presumably due to chromosome fusions.We demonstrated that the transition to holocentricity in Cuscuta was accompanied by significant changes in epigenetic marks, chromosome number and the repetitive DNA sequence composition.

Download Full-text

Sustained retrotransposition is mediated by nucleotide deletions and interelement recombinations

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0805694105 ◽

2008 ◽

Vol 105 (40) ◽

pp. 15470-15474 ◽

Cited By ~ 31

Author(s):

Anupma Sharma ◽

Kevin L. Schneider ◽

Gernot G. Presting

Keyword(s):

Transposable Elements ◽

Genome Size ◽

Repetitive Dna ◽

Sympatric Species ◽

Illegitimate Recombination ◽

Crop Plant ◽

Morphological Complexity ◽

C Value ◽

Unique Mechanism

The term “C-value paradox” was coined by C. A. Thomas, Jr. in 1971 [Thomas CA (1971)Ann Rev Genetics5:237–256] to describe the initially puzzling lack of correlation between an organism's genome size and its morphological complexity. Polyploidy and the expansion of repetitive DNA, primarily transposable elements, are two mechanisms that have since been found to account for this differential. While the inactivation of retrotransposons by methylation and their removal from the genome by illegitimate recombination have been well documented, the cause of the apparently periodic bursts of retrotranposon expansion is as yet unknown. We show that the expansion of the CRM1 retrotransposon subfamily in the ancient allotetraploid crop plant corn is linked to the repeated formation of novel recombinant elements derived from two parental retrotransposon genotypes, which may have been brought together during the hybridization of two sympatric species that make up the present day corn genome, thus revealing a unique mechanism linking polyploidy and retrotransposition.

Download Full-text

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.

Download Full-text