CIGEOBIO (FCEFyN, UNSJ/CONICET), Av. Ignacio de la Roza 590 (Oeste), J5402DCS, Rivadavia, San Juan, Argentina.
Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad Nacional de Córdoba (UNC), Córdoba, Argentina.
Chromosome Res. 2021 Dec;29(3-4):261-284. doi: 10.1007/s10577-021-09663-4. Epub 2021 Jun 4.
Capsicum annuum is a species that has undergone an expansion of the size of its genome caused mainly by the amplification of repetitive DNA sequences, including mobile genetic elements. Based on information obtained from sequencing the genome of pepper, the estimated fraction of retroelements is approximately 81%, and previous results revealed an important contribution of lineages derived from Gypsy superfamily. However, the dynamics of the retroelements in the C. annuum genome is poorly understood. In this way, the present work seeks to investigate the phylogenetic diversity and genomic abundance of the families of autonomous (complete and intact) LTR retroelements from C. annuum and inspect their distribution along its chromosomes. In total, we identified 1151 structurally full-length retroelements (340 Copia; 811 Gypsy) grouped in 124 phylogenetic families in the base of their retrotranscriptase. All the evolutive lineages of LTR retroelements identified in plants were present in pepper; however, three of them comprise 83% of the entire LTR retroelements population, the lineages Athila, Del/Tekay, and Ale/Retrofit. From them, only three families represent 70.8% of the total number of the identified retroelements. A massive family-specific wave of amplification of two of them occurred in the last 0.5 Mya (GypsyCa_16; CopiaCa_01), whereas the third is more ancient and occurred 3.0 Mya (GypsyCa_13). Fluorescent in situ hybridization performed with family and lineage-specific probes revealed contrasting patterns of chromosomal affinity. Our results provide a database of the populations LTR retroelements specific to C. annuum genome. The most abundant families were analyzed according to chromosome insertional preferences, suppling useful tools to the design of retroelement-based markers specific to the species.
甜椒是一个基因组发生扩张的物种，主要是由于重复 DNA 序列（包括移动遗传元件）的扩增所致。基于测序辣椒基因组获得的信息，逆转录转座子的估计分数约为 81%，之前的结果表明 Gypsy 超家族衍生的谱系有重要贡献。然而，C. annuum 基因组中逆转录转座子的动态仍知之甚少。因此，本工作旨在研究 C. annuum 中自主（完整）LTR 逆转座子家族的系统发育多样性和基因组丰度，并检查它们在其染色体上的分布。总共，我们在其逆转录酶的基础上，鉴定了 1151 个结构完整的全长逆转座子（340 个 Copia；811 个 Gypsy），它们分为 124 个系统发育家族。在植物中发现的所有 LTR 逆转座子的进化谱系都存在于甜椒中；然而，其中三个谱系占整个 LTR 逆转座子群体的 83%，即 Athila、Del/Tekay 和 Ale/Retrofit。其中，只有三个家族代表了所鉴定的逆转座子总数的 70.8%。其中两个家族（GypsyCa_16；CopiaCa_01）在最近的 0.5 Mya 发生了大规模的家族特异性扩增，而第三个家族则更为古老，发生在 3.0 Mya（GypsyCa_13）。用家族和谱系特异性探针进行荧光原位杂交显示出染色体亲和力的对比模式。我们的结果提供了一个特定于 C. annuum 基因组的 LTR 逆转座子群体数据库。根据染色体插入偏好分析了最丰富的家族，为设计特定于该物种的基于逆转座子的标记提供了有用的工具。
