Full-length LTR retroelements in Capsicum annuum revealed a few species-specific family bursts with insertional preferences.

Autor: Yañez-Santos AM; 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., Paz RC; CIGEOBIO (FCEFyN, UNSJ/CONICET), Av. Ignacio de la Roza 590 (Oeste), J5402DCS, Rivadavia, San Juan, Argentina. rosaliapaz@gmail.com., Paz-Sepúlveda PB; Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina (CONICET) - Comisión de Investigaciones Científicas (CIC) - Universidad Nacional de La Plata (UNLP), La Plata, Argentina., Urdampilleta JD; Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad Nacional de Córdoba (UNC), Córdoba, Argentina.
Jazyk: angličtina
Zdroj: Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology [Chromosome Res] 2021 Dec; Vol. 29 (3-4), pp. 261-284. Date of Electronic Publication: 2021 Jun 04.
DOI: 10.1007/s10577-021-09663-4
Abstrakt: 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.
(© 2021. The Author(s), under exclusive licence to Springer Nature B.V.)
Databáze: MEDLINE
Externí odkaz: