Bioinformatic, genetic and molecular analysis of several badnavirus sequences integrated in the genomes of diverse cocoa (Theobroma cacao L.) germplasm

Ullah, I. ORCID: https://orcid.org/0000-0002-9367-6741 and Dunwell, J. M. ORCID: https://orcid.org/0000-0003-2147-665X (2023) Bioinformatic, genetic and molecular analysis of several badnavirus sequences integrated in the genomes of diverse cocoa (Theobroma cacao L.) germplasm. Saudi Journal of Biological Sciences, 30 (5). 103648. ISSN 1319-562X doi: 10.1016/j.sjbs.2023.103648

Abstract/Summary

Endogenous viral elements (EVEs) are integrations of whole or partial viral genomes into the host genome, where they act as host alleles. They exist in a wide range of plant species including Theobroma cacao, the source of chocolate. Because of the international transfer of cacao germplasm, it is important to discriminate between the presence of these inserts and any episomal viruses that may be present in the material. This study was designed to survey a wide range of cacao germplasm, to assess the number, length, orientation, and precise location of the inserts and to identify any effect on the transcription of the gene into which they are inserted. Using a combination of bioinformatic, genetic and molecular approaches, we cloned and sequenced a series of different inserts, including one full-length virus sequence. We also identified, for the first time, an inhibitory effect of the insert on the expression of host genes. Such information is of practical importance in determining the regulation of germplasm transfer and of fundamental relevance to aiding an understanding of the role that such inserts may have on the performance of the host plant.

Item Type	Article
URI	https://reading-pure-test.eprints-hosting.org/id/eprint/111684
Identification Number/DOI	10.1016/j.sjbs.2023.103648
Refereed	Yes
Divisions	Life Sciences > School of Agriculture, Policy and Development > Department of Crop Science Central Services Life Sciences > School of Agriculture, Policy and Development > Department of Sustainable Land Management
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