Genome relationships and LTR-retrotransposon diversity in three cultivated Capsicum L. (Solanaceae) species

Assis, Rafael de; Baba, Viviane Yumi; Cintra, Leonardo Adabo; Gonçalves, Leandro Simões Azeredo; Rodrigues, Rosana; Vanzela, André Luís Laforga

doi:10.1186/s12864-020-6618-9

Cited by 26 publications

(26 citation statements)

References 80 publications

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“…At the lineage level, for the Copia superfamily, Ale elements were the most frequent, similar to other species, such as Erythrostemon hughesii [ 43 ]. For the Gypsy superfamily, the Chromovirus lineage (in particular, the Tekay sublineage) showed the highest abundance as already reported in other species, like pepper and Hieracium [ 37 , 44 ].…”

Section: Discussionsupporting

confidence: 64%

LTR-retrotransposon dynamics in common fig (Ficus carica L.) genome

et al. 2021

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Background Long Terminal Repeat retrotransposons (LTR-REs) are repetitive DNA sequences that constitute a large part of the genome. The improvement of sequencing technologies and sequence assembling strategies has achieved genome sequences with much greater reliability than those of the past, especially in relation to repetitive DNA sequences. Results In this study, we analysed the genome of Ficus carica L., obtained using third generation sequencing technologies and recently released, to characterise the complete complement of full-length LTR-REs to study their dynamics during fig genome evolution. A total of 1867 full-length elements were identified. Those belonging to the Gypsy superfamily were the most abundant; among these, the Chromovirus/Tekay lineage was the most represented. For the Copia superfamily, Ale was the most abundant lineage. Measuring the estimated insertion time of each element showed that, on average, Ivana and Chromovirus/Tekay were the youngest lineages of Copia and Gypsy superfamilies, respectively. Most elements were inactive in transcription, both constitutively and in leaves of plants exposed to an abiotic stress, except for some elements, mostly belonging to the Copia/Ale lineage. A relationship between the inactivity of an element and inactivity of genes lying in close proximity to it was established. Conclusions The data reported in this study provide one of the first sets of information on the genomic dynamics related to LTR-REs in a plant species with highly reliable genome sequence. Fig LTR-REs are highly heterogeneous in abundance and estimated insertion time, and only a few elements are transcriptionally active. In general, the data suggested a direct relationship between estimated insertion time and abundance of an element and an inverse relationship between insertion time (or abundance) and transcription, at least for Copia LTR-REs.

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Section: Discussionsupporting

confidence: 64%

LTR-retrotransposon dynamics in common fig (Ficus carica L.) genome

et al. 2021

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“…Such proportions are, nonetheless, lower than for other LTR-retrotransposon elements reported in some plant genomes of comparable size to those of Heloniopsis . For example, Tekay/Del elements which belong to the Ty3/gypsy lineage were reported to account for c. 67 and 97% of the repetitive landscape in Capsicum anuum and C. chinense , respectively ( de Assis et al, 2020 ), although they only accounted for 15% of the repetitive genome of the closely related C. baccatum (of similar genome size), illustrating that even within a genus, contrasting evolutionary dynamics can give rise to distinctive repeat profiles. Overall, the analyses indicate that it is often the combined activity of a diverse array of repeat lineages which contribute to differences in genome size observed between species rather than the differential rates of amplification/deletion of just one or few transposable element families.…”

Section: Discussionmentioning

confidence: 99%

“…A non-denaturing and formamide-free fluorescent in situ hybridisation (FISH) protocol based on Cuadrado et al (2009) and Mian (2019) was applied. A 26 bp oligo probe of HeloSAT was synthesized and labeled with FITC based on the output RE cluster monomers obtained (Supplementary Online Resource 1).…”

Section: Chromosome Preparations and Mapping Of Dna Satellite Helosat By Fluorescence In Situ Hybridisation (Fish)mentioning

confidence: 99%

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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“…This result once again confirms the correctness of the idea of the independent fate of TE during genome differentiation, which was, for example, shown in the analysis of the evolution of the genomes of Nicotiana or Capsicum spp. [53][54][55]. Finally, this theory can explain finding of the fourth and fifth groups of the Cannabaceae LTRs, which were C. sativa-(Bianca and Tork) and H. lupulus-specific (Ale), respectively.…”

Section: Discussionmentioning

confidence: 75%

The Comparative Analysis of the DNA Repeat Composition among Cannabis Sativa L., Humulus Lupulus L. And Humulus Japonicus Siebold & Zucc. With Heteromorphic Sex Chromosomes

Bocharkina¹,

Alexandrov²,

Razumova³

et al. 2021

Preprint

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Heteromorphic sex chromosomes are rarely found in plants. They were observed only in 47 species from phylogenetically distant families, suggesting that the evolution of sex chromosomes was independent in these species. It was shown that DNA repeat sequences are one of the major factors driving sex chromosomes evolution, and an accumulation or elimination of the repetitive DNA elements are closely linked with the formation of differences in the sex chromosomes. The goal of this study was to characterize the transposon composition in male and female plants of Cannabis sativa L., Humulus lupulus L. and Humulus japonicus Siebold &amp; Zucc. For the first time, the male and female genomes of H. japonicus as well as male genomes of H. lupulus and C. sativa have been sequenced (there were no open data about them). The analysis of genome-wide sequencing data with using Repeatexplorer2 and author’s scripts was carried out. It was shown that accumulation of Ty3-gypsy may be associated with speciation in Cannabaceae family which is the opposite of the theory of speciation throw whole-genome duplication. Moreover, the sex-specific DNA repeat clusters in C. sativa and H. japonicus were found. The analysis also revealed that the concentration of Tekay, Retand and Ikeros repeats in the Y chromosome of C. sativa is lower than in the X chromosome and the Angela concentration is higher in the Y chromosome.

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Genome relationships and LTR-retrotransposon diversity in three cultivated Capsicum L. (Solanaceae) species

Cited by 26 publications

References 80 publications

LTR-retrotransposon dynamics in common fig (Ficus carica L.) genome

LTR-retrotransposon dynamics in common fig (Ficus carica L.) genome

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

The Comparative Analysis of the DNA Repeat Composition among <em>Cannabis Sativa</em> L., <em>Humulus Lupulus</em> L. And <em>Humulus Japonicus</em> Siebold & Zucc. With Heteromorphic Sex Chromosomes

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