Heterochromatin distribution and histone modification patterns of H4K5 acetylation and H3S10 phosphorylation in Capsicum L.

Martins, Lívia do Vale; Perón, Ana Paula; Lopes, Ângela Célis de Almeida; Gomes, Regina Lúcia Ferreira; Carvalho, Reginaldo de; Feitoza, Lidiane de Lima

doi:10.1590/1984-70332018v18n2a23

Cited by 7 publications

(19 citation statements)

References 26 publications

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“…annuum and C. chinense, which exhibited just two to four pairs.Moscone et al [20,64], Scaldaferro et al[23] and Martins et al[26] reports have shown wide variability in the presence of terminal, interstitial and proximal heterochromatic bands in Capsicum species, such as the large and minor heterochromatic terminal bands in C. annuum, C. chinense, and C. baccatum observed in the present study. FISH results using different LTR-RT probes showed hybridization signals accumulated from proximal (CRM) to interstitial region (Athila/Tat and Tekay/Del), scattered, or minor dots along chromosomes (Tekay/Del, Oryco and Tork), such as in Brachiaria[14].…”

supporting

confidence: 61%

“…Capsicum species are an excellent model to investigate the dynamics and distribution of LTR-RTs, because of their relatively large genomes, grouped within 2n = 24 and 26 chromosomes, and DNA Cvalues range from 3.16 to 5.77 pg, in which the repetitive DNA families may represent more than 70% of the genomes [19]. Capsicum species present a great diversity of repetitive DNA families, especially regarding the number and distribution of ribosomal sequences and heterochromatin sites [20][21][22][23][24][25][26]. In this context, the present study aims to know and compare the occurrence and distribution of LTR-RTs on the chromosomes, focusing on Gypsy superfamily that has been predominant in the Capsicum genomes, as well as their association with the diversity of other repetitive sequences.…”

mentioning

confidence: 99%

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

Assis

Baba

Cintra

et al. 2020

Preprint

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Background: Plant genomes are rich in repetitive sequences, and transposable elements (TEs) are the most accumulated of them. This mobile fraction can be distinguished as Class I (retrotransposons) and Class II (transposons). Retrotransposons that are transposed using an intermediate RNA and that accumulate in a “copy-and-paste” manner have been screened in three completely sequenced genomes of peppers (Solanaceae family). The goal of this study was to understand the genome relationships among Capsicum annuum , C. chinense and C. baccatum , based on a comparative analysis of the function, diversity and the chromosome distribution of TE lineages in the Capsicum karyotypes. Due to the great commercial importance of pepper in natura , as a spice or as an ornamental plant, these genomes have been widely sequenced, and all of the assemblies are available in the SolGenomics group. These sequences have been used to compare all repetitive fractions from a cytogenomic point of view. Results: The qualification and quantification of LTR-retrotransposons (LTR-RT) families are contrasted with molecular cytogenetics data, and the results show a strong genome similarity between C. annuum and C. chinense as compared to C. baccatum . The Gypsy superfamily is more abundant than Copia , especially for Tekay/Del family members, including a high representation in C. annuum and C. chinense . On the other hand, C. baccatum accumulates more Athila/Tat sequences. The FISH results show retrotransposons differentially scattered along chromosomes, with the exception of CRM family sequences, which mainly have a proximal accumulation associated with heterochromatin bands. Conclusions: The results confirm a close genomic relationship between C. annuum and C. chinense in comparison to C. baccatum . Centromeric GC-rich bands appeared to be associated with the accumulation regions of CRM elements, whereas terminal and subterminal AT- and GC-rich bands do not correspond to the accumulation of the retrotransposons in the three Capsicum species tested here.

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supporting

confidence: 61%

mentioning

confidence: 99%

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

Assis

Baba

Cintra

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Capsicum species are an excellent model to investigate the dynamics and distribution of LTR-RTs, because of their relatively large genomes, grouped within 2n = 24 and 26 chromosomes, and DNA C-values range from 3.16 to 5.77 pg, in which the repetitive DNA families may represent more than 70% of the genomes [20]. Capsicum species present a great diversity of repetitive DNA families, especially regarding number and distribution of ribosomal sequences and heterochromatin sites [21][22][23][24][25][26][27]. In this context, the present study aims to acknowledge and compare the occurrence and distribution of LTR-RTs on the chromosomes, focusing on Gypsy superfamily that has been predominant in Capsicum genomes, as well as their association with the diversity of other repetitive sequences.…”

mentioning

confidence: 99%

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

et al. 2020

View full text Add to dashboard Cite

Background: Plant genomes are rich in repetitive sequences, and transposable elements (TEs) are the most accumulated of them. This mobile fraction can be distinguished as Class I (retrotransposons) and Class II (transposons). Retrotransposons that are transposed using an intermediate RNA and that accumulate in a "copy-and-paste" manner were screened in three genomes of peppers (Solanaceae). The present study aimed to understand the genome relationships among Capsicum annuum, C. chinense, and C. baccatum, based on a comparative analysis of the function, diversity and chromosome distribution of TE lineages in the Capsicum karyotypes. Due to the great commercial importance of pepper in natura, as a spice or as an ornamental plant, these genomes have been widely sequenced, and all of the assemblies are available in the SolGenomics group. These sequences were used to compare all repetitive fractions from a cytogenomic point of view. Results: The qualification and quantification of LTR-retrotransposons (LTR-RT) families were contrasted with molecular cytogenetic data, and the results showed a strong genome similarity between C. annuum and C. chinense as compared to C. baccatum. The Gypsy superfamily is more abundant than Copia, especially for Tekay/Del lineage members, including a high representation in C. annuum and C. chinense. On the other hand, C. baccatum accumulates more Athila/Tat sequences. The FISH results showed retrotransposons differentially scattered along chromosomes, except for CRM lineage sequences, which mainly have a proximal accumulation associated with heterochromatin bands. Conclusions: The results confirm a close genomic relationship between C. annuum and C. chinense in comparison to C. baccatum. Centromeric GC-rich bands may be associated with the accumulation regions of CRM elements, whereas terminal and subterminal AT-and GC-rich bands do not correspond to the accumulation of the retrotransposons in the three Capsicum species tested.

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“…have been restricted to rDNA probes [25], which demonstrated that C. baccatum accumulates more in terminal 35S rDNA sites compared to C. annuum and C. chinense, which exhibited just two to four pairs. This is interesting because the reports of Moscone et al [21,65], Scaldaferro et al [24] and Martins et al [27] The FISH using the Athila/Tat probe was strongly hybridized at proximal to interstitial regions in almost all the chromosomes, and in this case, there was also no evident co-location with heterochromatic regions, although there were small AT-and GC-rich minor bands in very few chromosomes, i.e., without evident correlation with heterochromatin hotspots. In this case as well, the scattered signals (or dots) observed after FISH with Tekay/Del and Oryco probes are in agreement with the concept of dispersed localization of retroelements within plant genomes but without a dependence on co-localization with heterochromatin blocks.…”

Section: Not All Ltr-rt Rich Regions In Capsicum Chromosomes Are Hetementioning

confidence: 61%

“…Capsicum species are an excellent model to investigate LTR-RTs' dynamics and distribution, because they have relatively large genomes, with 2n = 24 and 26 chromosomes. Representatives of Capsicum present a large diversity of repetitive DNA families, especially in relation to number and distribution of ribosomal sequences and heterochromatin sites [21][22][23][24][25][26][27]. In this context, we aim to know and compare the occurrence and distribution of LTR-RTs, and their association with other repetitive sequences' diversity and location on the chromosomes.…”

Section: The Presence Of Tes Within Genomes Can Have An Influence On mentioning

confidence: 99%

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

Assis

Baba

Cintra

et al. 2019

Preprint

View full text Add to dashboard Cite

Background: Plant genomes are rich in repetitive sequences, and Transposable Elements (TE, mobile fraction) are the most accumulated of them. This mobile fraction can be divided into Class I (retrotransposons) and Class II (transposons). Retrotransposons that are transposed using an intermediated RNA and accumulate in a “copy-and-paste” way have been screened in three completely sequenced genomes of peppers (Solanaceae family). The goal of this study was to understand the genome relationships among Capsicum annuum , C. chinense and C. baccatum , based on a comparative analysis of function, diversity and the chromosome distribution of TE lineages in the Capsicum karyotypes. Due to the great commercial importance of pepper in natura , as a spice or as an ornamental plant, these genomes have been widely sequenced, and all the assemblies are available in the SolGenomics group. These sequences have been used to compare all repetitive fractions from a cytogenomic point of view. Results: The qualification and quantification of LTR-RT families are contrasted with molecular cytogenetics data, and the results show a strong genome similarity between C. annuum and C. chinense , compared to C. baccatum . The Gypsy superfamily is more abundant than Copia , especially for Tekay/Del family members, including a high representation in C. annuum and C. chinense . On the other hand, C. baccatum accumulates more Athila/Tat sequences. The FISH results show retrotransposons differentially scattered along chromosomes, with the exception of CRM family sequences, which mainly have a proximal accumulation associated with heterochromatin bands. Conclusions: The results confirm a close genomic relationship between C. annuum and C. chinense in comparison to C. baccatum, displaying only centromeric GC-rich bands associated with the accumulation of CRM elements, whereas terminal and subterminal AT- and GC-rich bands do not correspond to the accumulation of the retrotransposons in the three Capsicum species tested here.

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Heterochromatin distribution and histone modification patterns of H4K5 acetylation and H3S10 phosphorylation in Capsicum L.

Abstract: Heterochromatin distribution and histone modification patterns of H4K5 acetylation and H3S10 phosphorylation in Capsicum L.

Cited by 7 publications

References 26 publications

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

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

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

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

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