Laboratório de Citogenética e Diversidade Vegetal, Universidade Estadual de Londrina, 86057-970, Londrina, Paraná, Brazil.
Departamento de Agronomia, Universidade Estadual de Londrina, 86057-970, Londrina, Paraná, Brazil.
BMC Genomics. 2020 Mar 17;21(1):237. doi: 10.1186/s12864-020-6618-9.
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.
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.
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.
植物基因组富含重复序列，转座元件（TEs）是其中最丰富的。这些移动片段可分为 I 类（逆转座子）和 II 类（转座子）。使用中间 RNA 转座并以“复制粘贴”方式积累的逆转座子在三种辣椒属植物（茄科）的基因组中进行了筛选。本研究旨在通过比较辣椒属核型 TE 谱系的功能、多样性和染色体分布，了解 C. annuum、C. chinense 和 C. baccatum 之间的基因组关系。由于辣椒在自然状态下作为香料或观赏植物具有重要的商业价值，这些基因组已被广泛测序，所有组装都可在 SolGenomics 组中获得。这些序列用于从细胞遗传学角度比较所有重复片段。
LTR-逆转座子（LTR-RT）家族的定性和定量与分子细胞遗传学数据进行了对比，结果表明 C. annuum 和 C. chinense 之间的基因组相似度很强，而与 C. baccatum 相比则较弱。Gypsy 超家族比 Copia 更丰富，特别是 Tekay/Del 谱系成员，在 C. annuum 和 C. chinense 中具有很高的代表性。另一方面，C. baccatum 积累了更多的 Athila/Tat 序列。FISH 结果表明，逆转座子在染色体上呈不同程度的分散，除了 CRM 谱系序列主要与异染色质带相关的近端积累外。
与 C. baccatum 相比，结果证实 C. annuum 和 C. chinense 之间存在密切的基因组关系。着丝粒 GC 丰富带可能与 CRM 元件的积累区域相关，而末端和亚末端的 AT 和 GC 丰富带与三种测试的辣椒属物种中逆转座子的积累无关。
