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

Sader, Mariela Analía; Vaio, Magdalena; Cauz-Santos, Luiz Augusto; Dornelas, Marcelo Carnier; Vieira, Maria Lúcia Carneiro; Melo, Natoniel Franklin de; Pedrosa‐Harand, Andrea

doi:10.1007/s00425-021-03598-0

Cited by 27 publications

(28 citation statements)

References 99 publications

(107 reference statements)

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“…The detailed characterisation and identification of repetitive DNA content in the two Heloniopsis species studied highlighted the relative impact of the Ty1/copia-Angela elements in their genomes, with proportions ranging from c. 21 to 26% (Table 2). Among the Ty1/copia lineages that have been identified in plants (Neumann et al, 2019), Angela elements have been reported to be abundant in other genomes, with similar proportions as found here (e.g., Passiflora, Thinopyrum; Divashuk et al, 2020;Sader et al, 2021). Such proportions are, nonetheless, lower than for other LTR-retrotransposon elements reported in some plant genomes of comparable size to those of Heloniopsis.…”

Section: Diversity and Dynamics Of Repetitive Elements In Heloniopsissupporting

confidence: 84%

“…The data provided support to the suggestion that satellite DNAs often evolve rapidly and differ considerably in abundance even in related species with little correlation with genome size ( Macas et al, 2010 ). In addition, recent research in Passiflora (1C range = 207.34–2,621.04 Mb) reported an unusually large number of satellite repeats in the species with the smallest genome, albeit at lower frequencies, leading the authors to propose that, in most species, tandem repeats have only a limited impact on the overall genome size of Passiflora ( Sader et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2021

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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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Section: Diversity and Dynamics Of Repetitive Elements In Heloniopsissupporting

confidence: 84%

Section: Discussionmentioning

confidence: 99%

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

et al. 2021

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“…ml -1 4′,6-diamidino-2-phenylindole (Sigma) in 50% glycerol (Cabral et al, 2006). Four satDNA probes were used for fluorescent in situ hybridization (FISH) experiments (Sader et al, 2021) (PorSat01-161, PorSat04-1800, PorSat07-1004, and PorSat09-1200 and labeled with 5-amino-propargyl-2′deoxyuridine 5′-triphosphate and cyanine red fluorescent dye (GE Healthcare). The FISH procedure applied to mitotic chromosomes was essentially as described in Fonsêca et al (2010).…”

Section: Core Ideasmentioning

confidence: 99%

A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis

et al. 2021

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The genus Passiflora comprises a large group of plants popularly known as passionfruit, much appreciated for their exotic flowers and edible fruits. The species (∼500) are morphologically variable (e.g., growth habit, size, and color of flowers) and are adapted to distinct tropical ecosystems. In this study, we generated the genome of the wild diploid species Passiflora organensis Gardner by adopting a hybrid assembly approach. Passiflora organensis has a small genome of 259 Mbp and a heterozygosity rate of 81%, consistent with its reproductive system. Most of the genome sequences could be integrated into its chromosomes with cytogenomic markers (satellite DNA) as references. The repeated sequences accounted for 58.55% of the total DNA analyzed, and the Tekay lineage was the prevalent retrotransposon. In total, 25,327 coding genes were predicted. Passiflora organensis retains 5,609 singletons and 15,671 gene families. We focused on the genes potentially involved in the locus determining

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“…NGS-related bioinformatics allowed revealing either the complete set of repetitive DNA sequences, the repeatome [8], or the broad collection of satDNAs, the satellitome [9], present in eukaryotic genomes. These approaches showed surprisingly large numbers of satDNAs in eukaryotic genomes, i.e., 62 in the migratory locust Locusta migratoria [9], 129 in the Australian morabine grasshoppers of the genus Vandiemenella [10], 164 in the characiform fish Megaleporinus microcephalus [11] and 37 in the plant Passiflora organensis [12]. Bioinformatic approaches combined with fluorescence Int.…”

Section: Introductionmentioning

confidence: 99%

Satellitome Analysis of the Pacific Oyster Crassostrea gigas Reveals New Pattern of Satellite DNA Organization, Highly Scattered across the Genome

Tunjić-Cvitanić

Pasantes

García-Souto

et al. 2021

IJMS

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Several features already qualified the invasive bivalve species Crassostrea gigas as a valuable non-standard model organism in genome research. C. gigas is characterized by the low contribution of satellite DNAs (satDNAs) vs. mobile elements and has an extremely low amount of heterochromatin, predominantly built of DNA transposons. In this work, we have identified 52 satDNAs composing the satellitome of C. gigas and constituting about 6.33% of the genome. Satellitome analysis reveals unusual, highly scattered organization of relatively short satDNA arrays across the whole genome. However, peculiar chromosomal distribution and densities are specific for each satDNA. The inspection of the organizational forms of the 11 most abundant satDNAs shows association with constitutive parts of Helitron mobile elements. Nine of the inspected satDNAs are dominantly found in mobile element-associated form, two mostly appear standalone, and only one is present exclusively as Helitron-associated sequence. The Helitron-related satDNAs appear in more chromosomes than other satDNAs, indicating that these mobile elements could be leading satDNA propagation in C. gigas. No significant accumulation of satDNAs on certain chromosomal positions was detected in C. gigas, thus establishing a novel pattern of satDNA organization on the genome level.

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

Abstract: doi: bioRxiv preprint MAIN CONCLUSIONSWhile two lineages of retrotransposons were more abundant in larger Passiflora genomes, the satellitome was more diverse and abundant in the smallest genome.

Cited by 27 publications

References 99 publications

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

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

A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis

Satellitome Analysis of the Pacific Oyster Crassostrea gigas Reveals New Pattern of Satellite DNA Organization, Highly Scattered across the Genome

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