Diversity of the repetitive DNA fraction in Cestrum, the genus with the largest genomes within Solanaceae

Chili peppers (Solanaceae family) have great commercial value. They are commercialized in natura and used as spices and for ornamental and medicinal purposes. Although three whole genomes have been published, limited information about satellite DNA sequences, their composition and genomic distribution were provided. Here, we exploited the non-coding repetitive fraction, represented by satellite sequences, that tends to accumulate in blocks along chromosomes, especially near the chromosome ends of peppers. Two satellite DNA sequences were identified (CDR-1 and CDR-2), characterized and mapped in silico in three Capsicum genomes (C. annuum, C. chinense, and C. baccatum) using data from the published high-coverage sequencing and repeats finding bioinformatic tools. Localization using FISH in the chromosomes of these species and in two others (C. frutescens and C. chacoense) totaling five species, showed signals adjacent to the rDNA sites. Sequence comparison with existing Solanaceae repeats, showed that CDR-1 and CDR-2 have different origins, but without homology to rDNA sequences. Satellites occupied sub-terminal chromosomal regions, sometimes collocated or adjacent to 35S rDNA sequences. Our results expand knowledge about the diversity of sub-terminal regions of Capsicum chromosomes, showing different amounts and distributions within and between karyotypes. In addition, these sequences may be useful for future phylogeny studies.

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Distinct patterns of satDNA distribution in spike-sedges (Eleocharis, Cyperaceae): evidence of repeat-based holocentromeres

Souza,

Parteka,

Kuo

et al. 2024

Preprint

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Eleocharis R. Br. (Cyperaceae) species are known for having holocentric chromosomes, which enable rapid karyotype differentiation. Indeed, high intra- and interspecific variations in chromosome numbers and genome sizes are documented for different Eleocharis species, frequently accompanied by fluctuations in the repetitive DNA fraction. However, a lack of detailed analysis has hampered a better understanding of the interplay between holocentricity and repetitive DNA evolution in the genus. In this study, we confirmed the holocentricity of Eleocharis chromosomes by immunostaining against KNL1, histone H2AThr121ph and H3S10ph. We further studied the composition and chromosomal distribution of the main satellite DNA repeats found in five newly sequenced species. Five of the six satellites discovered were arranged in clusters, while EmaSAT14 was dispersed irregularly along the chromatid length in a line-like manner. This satDNA was accumulated exclusively by species belonging to the series Maculosae of the subgenus Eleocharis. The chromosomal distribution and genomic organization of EmaSAT14 suggest that it is a potential holocentromeric repeat. Our findings suggest that repeat-based holocentromeres are likely to evolve in a similar way across holocentric plants.

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Diversity of the repetitive DNA fraction in Cestrum, the genus with the largest genomes within Solanaceae

Cited by 4 publications

References 51 publications

Poisoning in ruminants caused by species of the genus Cestrum L. (Solanaceae) in Brazil: A review of toxicological and phytochemical evidence

Poisoning in ruminants caused by species of the genus Cestrum L. (Solanaceae) in Brazil: A review of toxicological and phytochemical evidence

Abundance of distal repetitive DNA sequences in Capsicum L. (Solanaceae) chromosomes

Distinct patterns of satDNA distribution in spike-sedges (Eleocharis, Cyperaceae): evidence of repeat-based holocentromeres

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