New Virus Sequences Found in Bananas Reveal Key Retrovirus Gene in Their DNA

Greg Howard
3rd August, 2024

New Virus Sequences Found in Bananas Reveal Key Retrovirus Gene in Their DNA

Image Source: Natural Science News, 2024

Key Findings

  • The study identified two new banana endogenous virus sequences (BEVs), named GZ5 and GZ13, in different banana varieties
  • BEV GZ5 contains a complete gene for reverse transcriptase (RT) and ribonuclease H (RNase H), suggesting it might retain some functional elements from its viral ancestors
  • BEV GZ5 is integrated into the BB genome of bananas, while BEV GZ13 is specific to the Dajiao variety
Endogenous pararetrovirus sequences (EPRVs) are DNA sequences that have integrated into plant genomes from viruses belonging to the Caulimoviridae family. One group of these viruses, banana streak viruses (BSVs), is known to have left traces in the genomes of various banana species. These traces, termed banana endogenous virus sequences (BEVs), have been a subject of interest due to their potential impact on banana genetics and evolution. However, the detailed genomic characteristics of BEVs have remained largely unexplored. A recent study conducted by South China Agricultural University[1] has shed light on this by identifying two new variants of BEVs, named GZ5 and GZ13. Through sequence analysis, Southern blot, and fluorescent in situ hybridization (FISH), the researchers discovered that BEV GZ5 is integrated into the BB genome of bananas, while BEV GZ13 is specific to the Dajiao variety. One of the most significant findings of this study is that BEV GZ5 contains a complete gene for reverse transcriptase (RT) and ribonuclease H (RNase H) (RT/RNase H). These enzymes are crucial for the replication of retroviruses, suggesting that BEV GZ5 might have retained some functional elements from its viral ancestors. Additionally, the researchers found a 340-base pair inverted repeat sequence overlapping with RNase H both upstream and downstream of BEV GZ5. This structural feature could play a role in the integration and stability of the BEV within the banana genome. Interestingly, BEV GZ5 showed deletions and mutations in its amino acid sequences compared to BSVs. Bioinformatics analyses revealed that the BEV GZ5 protein is composed of 412 amino acids, has a molecular weight of 47.37 kDa, and an isoelectric point of 9.40. The protein is rich in leucine, isoleucine, and lysine, and contains 35 potential phosphorylation sites. It is hydrophilic and lacks both a signal peptide and transmembrane regions, indicating it may function within the cell rather than being secreted or embedded in cellular membranes. The secondary structure consists of 37.26% α-helix and 36.25% random coil, which could influence its functional properties. This study builds on previous research that has explored the integration and evolution of viral sequences within plant genomes. For instance, earlier studies have shown that plant genomes, including those of bananas, are often invaded by badnaviral sequences[2]. These sequences do not require integration for replication, unlike animal retroviruses, but have nonetheless become fixed in the plant genome over evolutionary time[3]. This phenomenon has been particularly well-documented in bananas, where various badnaviral sequences have been identified and characterized[2][3]. The discovery of BEVs with complete RT/RNase H genes, as reported in this study, provides a new perspective on the functional potential of these integrated viral sequences. It raises questions about the role these sequences might play in banana biology and evolution. For example, the presence of functional RT/RNase H genes could suggest that these BEVs are not merely genetic fossils but might have some residual activity or influence on the host genome. Moreover, this study's use of advanced sequencing and mapping technologies highlights the progress made in genomic research. Previous challenges in assembling complex plant genomes, particularly those with high repetitiveness and polyploidy, have been addressed through the use of long-read sequencing and optical mapping[4][5]. These technologies have enabled researchers to achieve more complete and contiguous genome assemblies, facilitating the detailed analysis of integrated viral sequences. In conclusion, the identification and characterization of BEVs GZ5 and GZ13 by South China Agricultural University mark a significant step forward in understanding the genomic landscape of bananas. The presence of a complete RT/RNase H gene in BEV GZ5 opens new avenues for exploring the functional and evolutionary implications of these endogenous viral sequences. This study not only enhances our knowledge of banana genomics but also contributes to the broader field of plant-virus interactions and co-evolution.

GeneticsBiochemPlant Science

References

Main Study

1) Identification of new banana endogenous virus sequences highlights the hallmark gene encoded by retroviruses integrated in banana genomes

Published 2nd August, 2024

https://doi.org/10.1186/s42483-024-00256-7

Related Studies

2) Three infectious viral species lying in wait in the banana genome.

https://doi.org/10.1128/JVI.00899-13

3) Badnaviruses and banana genomes: a long association sheds light on Musa phylogeny and origin.

https://doi.org/10.1111/mpp.13019

4) Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps.

https://doi.org/10.1038/s41477-018-0289-4

5) Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing.

https://doi.org/10.1038/s42003-021-02559-3


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