Genome relationships and LTR-retrotransposon diversity in three cultivated Capsicum L. (Solanaceae) species
| Autor: | Rosana Rodrigues, Rafael Leandro de Assis, André Luís Laforga Vanzela, Viviane Yumi Baba, Leonardo Adabo Cintra, Leandro Simões Azeredo Gonçalves |
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| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
Transposable element lcsh:QH426-470 Retroelements Heterochromatin lcsh:Biotechnology Lineage (evolution) Retrotransposon Chili peppers Cytogenomics 01 natural sciences Genome Chromosomes Plant 03 medical and health sciences FISH lcsh:TP248.13-248.65 Plant genome Genetics Phylogeny 030304 developmental biology Repetitive Sequences Nucleic Acid 0303 health sciences biology fungi Terminal Repeat Sequences Chromosome food and beverages Genetic Variation Karyotype Genomics biology.organism_classification lcsh:Genetics Transposable elements Capsicum Solanaceae Genome Plant 010606 plant biology & botany Biotechnology Research Article |
| Zdroj: | BMC Genomics BMC Genomics, Vol 21, Iss 1, Pp 1-14 (2020) |
| ISSN: | 1471-2164 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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