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.

Coffea spp. chromosomes are very small and accumulate a variety of repetitive DNA families around centromeres. However, proximal regions of Coffea chromosomes remain poorly understood, especially on the nature and organisation of the sequences. Taking advantage of genome sequences of C. arabica (2n = 44), C. canephora, and C. eugenioides (C. arabica progenitors with 2n = 22) and good coverage genome sequencing of dozens of other wild Coffea spp., repetitive DNA sequences were identified, and the genomes were compared to decipher particularities of pericentromeric structures. The searches revealed a short tandem repeat (82 bp length) typical of Gypsy/TAT LTR retrotransposons, named Coffea_sat11. This repeat organises clusters with fragments of other transposable elements, comprising regions of non-coding RNA production. Cytogenomic analyses showed that Coffea_sat11 extend from pericentromeres towards the middle of the chromosomal arms. This arrangement was observed in the allotetraploid C. arabica chromosomes, as well as in its progenitors. This study improve our understanding of the role of Gypsy/TAT LTR retrotransposon lineage in the organization of Coffea pericentromeres, as well as the conservation of Coffea_sat11 within the genus. The relationships with fragments of other transposable elements and the functional aspects of these sequences on the pericentromere chromatin were also evaluated.

Plant genomes are variable in the accumulation and distribution of repetitive DNA families. Species of Cestrum show large diversity of repetitive DNA families, and B chromosomes have been described in seven species. Different DNA families have been identified in Cestrum, such as AT-rich SSR, 45S and 5S rDNA, C-Giemsa and C-CMA/DAPI bands and retrotransposons. To understand the relationships between B and A chromosomes of Cestrum, the B of C. strigilatum was microdissected, amplified, and fragments were used to produce a small library. Sequences showed the occurrence of stretches of SSR, minisats and LTR-RTs. The probe of B was hybridized in situ against chromosomes of eight Cestrum species. FISH signals were observed in the Bs of C. strigilatum and C. intermedium, besides stretches of A chromosomes of all species tested. Species showed hybridization signals in different positions, such as: i) signals adjacent to C-DAPI bands, ii) lightly dispersed signals throughout the chromosomes, and iii) an intense hybridization signals associated with 5S rDNA sites, in the proximal region of long arm of pair 8. Due to the strong FISH signal associated with 5S rDNA region of A chromosomes of all species, we search for 5S rDNA stretches in the microdissected B chromosome using PCR and Sanger sequencing. Data showed a possible degradation of 5S rDNA in the evolutionary pathways of the Bs. Although A and B chromosomes displayed redundancy in the repetitive DNA families in different species, the Bs of both C. strigilatum and C. intermedium seemed to differ from those of other species by the loss of rDNA fractions. These data indicate a common origin of Bs in Cestrum.

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.

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.