Abstract
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.
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Abbreviations
- C:
-
centromeric chromosome portion
- CTAB:
-
cetyl trimethyl ammonium bromide
- FISH:
-
fluorescent in situ hybridization
- IP:
-
interstitial-proximal chromosome portion
- IT:
-
interstitial-terminal chromosome portion
- LTR:
-
long terminal repeats
- Mya:
-
millions of years ago
- P:
-
proximal chromosome portion
- PCR:
-
polymerase chain reaction
- RH:
-
RNase-H
- RT:
-
retrotranscriptase
- T:
-
terminal chromosome portion
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Acknowledgements
The authors acknowledge Dr. Maria Virginia Sanchez-Puerta for her valuable help with phylogenetic tree construction, Dr. Carlos Llorens for his support in retroelements classification, Dr. Thomas Wicker for providing retroelement reference sequences, and to Dr. Alejandra Trenchi for sharing her experience during experiments FISH. We also appreciate the valuable language assistance of Lic. Vanesa Heredia and Dr. Hernan G. Rosli. The authors are also grateful for anonymous reviewers' and the editor Dr. Jiming Jiang's comments which improved substantially this work. This work was part of the PhD thesis of YSA, which benefited from AGENCIA and CONICET fellowship.
Funding
This work was funded by Agencia Nacional de Promoción Científica y Tecnológica, Argentina (AGENCIA), D-TEC 0008/13; PROJOVI 2015 and 2018 (Universidad Nacional de San Juan); and FONCyT, PICT-2018-01691 (AGENCIA).
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Yañez-Santos, A.M., Paz, R.C., Paz-Sepúlveda, P.B. et al. Full-length LTR retroelements in Capsicum annuum revealed a few species-specific family bursts with insertional preferences. Chromosome Res 29, 261–284 (2021). https://doi.org/10.1007/s10577-021-09663-4
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DOI: https://doi.org/10.1007/s10577-021-09663-4