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

2020 ◽  
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.

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

2019 ◽  
Vol 125 (4) ◽  
pp. 611-623 ◽  
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.

scholarly journals Large vs small genomes in Passiflora: the influence of the mobilome and the satellitome

2020 ◽  
Author(s):  
Mariela Sader ◽  
Magdalena Vaio ◽  
Luiz Augusto Cauz-Santos ◽  
Marcelo Carnier Dornelas ◽  
Maria Lucia Carneiro Vieira ◽  
...  
Keyword(s):  
Genome Size ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Large Scale ◽  
Repetitive Sequences ◽  
Size Variation ◽  
Repetitive Dna Sequences ◽  
Ltr Retrotransposons ◽  
Genome Size Variation ◽  
Satellite Dnas

ABSTRACTRepetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. Within Passiflora genus, a ten-fold variation in genome size, not attributed to polyploidy, is known. Here, we applied a combined in silico and cytological approach to study the organization and diversification of repetitive elements in three species of these genera representing its known range in genome size variation. Sequences were classified in terms of type and repetitiveness and the most abundant were mapped to chromosomes. We identified Long Terminal Repeat (LTR) retrotransposons as the most abundant elements in the three genomes, showing a considerable variation among species. Satellite DNAs (satDNAs) were less representative, but highly diverse between subgenera. Our results clearly confirm that the largest genome species (Passiflora quadrangularis) presents a higher accumulation of repetitive DNA sequences, specially Angela and Tekay elements, making up most of its genome. Passiflora cincinnata, with intermediate genome and from the same subgenus, showed similarity with P. quadrangularis regarding the families of repetitive DNA sequences, but in different proportions. On the other hand, Passiflora organensis, the smallest genome, from a different subgenus, presented greater diversity and the highest proportion of satDNA. Altogether, our data indicate that while large genome evolve by an accumulation of retrotransponsons, small genomes most evolved by diversification of different repeat types, particularly satDNAs.MAIN CONCLUSIONSWhile two lineages of retrotransposons were more abundant in larger Passiflora genomes, the satellitome was more diverse and abundant in the smallest genome.

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

PLoS ONE ◽  
2015 ◽  
Vol 10 (11) ◽  
pp. e0143424 ◽  
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

Chromosome number and genome size variation in Colocasia (Araceae) from China

2017 ◽  
Vol 130 (6) ◽  
pp. 989-997 ◽  
Author(s):  
Guang-Yan Wang ◽  
Xiao-Ming Zhang ◽  
Min Qian ◽  
Xiang-Yang Hu ◽  
Yong-Ping Yang
Keyword(s):  
Chromosome Number ◽  
Genome Size ◽  
Size Variation ◽  
Genome Size Variation

Genome size variation in Begonia

Genome ◽  
2009 ◽  
Vol 52 (10) ◽  
pp. 829-838 ◽  
Author(s):  
Angelo Dewitte ◽  
Leen Leus ◽  
Tom Eeckhaut ◽  
Ives Vanstechelman ◽  
Johan Van Huylenbroeck ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Chromosome Number ◽  
Genome Size ◽  
Size Variation ◽  
South American ◽  
Chromosome Size ◽  
Genome Size Variation ◽  
Length Width ◽  
South American Origin ◽  
Secondary Constrictions

The genome sizes of a Begonia collection comprising 37 species and 23 hybrids of African, Asiatic, Middle American, and South American origin were screened using flow cytometry. Within the collection, 1C values varied between 0.23 and 1.46 pg DNA. Genome sizes were, in most cases, not positively correlated with chromosome number, but with pollen size. A 12-fold difference in mean chromosome size was found between the genotypes with the largest and smallest chromosomes. In general, chromosomes from South American genotypes were smaller than chromosomes of African, Asian, or Middle American genotypes, except for B. boliviensis and B. pearcei. Cytological chromosome studies in different genotypes showed variable chromosome numbers, length, width, and total chromosome volume, which confirmed the diversity in genome size. Large secondary constrictions were present in several investigated genotypes. These data show that chromosome number and structure exhibit a great deal of variation within the genus Begonia, and likely help to explain the large number of taxa found within the genus.

scholarly journals The nature of intraspecific genome size variation in taxonomically complex eyebrights

2021 ◽  
Author(s):  
Hannes Becher ◽  
Robyn F. Powell ◽  
Max R. Brown ◽  
Chris Metherell ◽  
Jaume Pellicer ◽  
...  
Keyword(s):  
Genome Size ◽  
Isolation By Distance ◽  
Size Variation ◽  
Intrinsic Property ◽  
Population Subdivision ◽  
List Type ◽  
Nucleotide Polymorphisms ◽  
Genome Size Variation ◽  
Repeat Content ◽  
Genomic Repeat

SummaryGenome size (GS) is a key trait related to morphology, life history, and evolvability. Although GS is, by definition, affected by presence/absence variants (PAVs), which are ubiquitous in population sequencing studies, GS is often treated as an intrinsic property of a species. Here, we studied intra- and interspecific GS variation in taxonomically complex British eyebrights (Euphrasia).We generated GS data for 192 individuals of diploid and tetraploid Euphrasia and analysed GS variation in relation to ploidy, taxonomy, population affiliation, and geography. We further compared the genomic repeat content of 30 samples.We found considerable genuine intraspecific GS variation, and observed isolation-by-distance for GS in outcrossing diploids. Tetraploid Euphrasia showed contrasting patterns, with GS increasing with latitude in outcrossing Euphrasia arctica, but little GS variation in the highly selfing Euphrasia micrantha. Interspecific differences in GS genomic repeat percentages were small.We show the utility of treating GS as the outcome of polygenic variation. Like other types of genetic variation, such as single nucleotide polymorphisms, GS variation may be increased through hybridisation and population subdivision. In addition to selection on associated traits, GS is predicted to be affected indirectly by selection due to pleiotropy of the underlying PAVs.

scholarly journals Chromosome and genome size variation inLuzula(Juncaceae), a genus with holocentric chromosomes

2012 ◽  
Vol 170 (4) ◽  
pp. 529-541 ◽  
Author(s):  
Monika Bozek ◽  
Andrew R. Leitch ◽  
Ilia J. Leitch ◽  
Lenka Záveská Drábková ◽  
Elżbieta Kuta
Keyword(s):  
Genome Size ◽  
Size Variation ◽  
Holocentric Chromosomes ◽  
Genome Size Variation

scholarly journals Genome Size and Chromosome Number Evolution in Korean Iris L. Species (Iridaceae Juss.)

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1284 ◽  
Author(s):  
Bokyung Choi ◽  
Hanna Weiss-Schneeweiss ◽  
Eva M. Temsch ◽  
Soonku So ◽  
Hyeon-Ho Myeong ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Genome Size ◽  
Chromosome Numbers ◽  
Size Variation ◽  
Chromosomal Evolution ◽  
Genome Size Variation ◽  
Molecular Cytogenetic ◽  
Chromosome Number Evolution ◽  
Phylogenetic Framework ◽  
Phylogenomic Analyses

Chromosome numbers, karyotypes, and genome sizes of 14 Iris L. (Iridaceae Juss.) species in Korea and their closely related taxon, Sisyrinchium rosulatum, are presented and analyzed in a phylogenetic framework. To date, understanding the chromosomal evolution of Korean irises has been hampered by their high chromosome numbers. Here, we report analyses of chromosome numbers and karyotypes obtained via classic Feulgen staining and genome sizes measured using flow cytometry in Korean irises. More than a two-fold variation in chromosome numbers (2n = 22 to 2n = 50) and over a three-fold genome size variation (2.39 pg to 7.86 pg/1 C) suggest the putative polyploid and/or dysploid origin of some taxa. Our study demonstrates that the patterns of genome size variation and chromosome number changes in Korean irises do not correlate with the phylogenetic relationships and could have been affected by different evolutionary processes involving polyploidy or dysploidy. This study presents the first comprehensive chromosomal and genome size data for Korean Iris species. Further studies involving molecular cytogenetic and phylogenomic analyses are needed to interpret the mechanisms involved in the origin of chromosomal variation in the Iris.

scholarly journals Molecular Karyotypes of Pathogeic Strains of Fusarium oxysporum

1995 ◽  
Author(s):  
Harold Corby Kistler ◽  
Talma Katan ◽  
Dani Zamir
Keyword(s):  
Genetic Diversity ◽  
Chromosome Number ◽  
Fusarium Oxysporum ◽  
Genome Size ◽  
Size Variation ◽  
Electrophoretic Karyotype ◽  
Genome Size Variation ◽  
Dna Variation ◽  
Forma Specialis ◽  
Compatibility Group

Genetic diversity of pathogenic strains of the fungus Fusarium oxysporum was determied by analysis of electrophoretic karyotype, as well as by DNA variation detected by Restriction Fragment Length Polymorphisms (RFLPs) and Random Amplified Polymorphic DNAs (RAPDs). The electrophoretic karyotypes for 130 isolates of the fungus pathogenic to tomato, melon, and banana were analyzed. Electrophoretic karyotype variation, reflected in differences in apparent chromosome number and genome size, was observed even among isolates from the same host and sub specific category. Sub specific categories studied were forma specialis, vegetative compatibility group (VCG) and race. Chromosome number and genome size variation was less for isolates within the same VCG than for the collection of isolates as a whole. RFLP and RAPD analysis were performed on 62 isolates of F. oxysporum from tomato and melon. Polygenetic trees were constructed from genetic diversity data. The results support the hypothesis that isolates belonging to the same VCG originate from a single ancestor compared to other isolates. The results do not support the hypothesis that all isolates belonging to the same forma specialis originate from a common ancestor. These conclusions have profound implication for breeding resistance to diseases caused by particular formae speciales of F. oxysporum.

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