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Low genetic diversity of Banana bunchy top virus, with a sub-regional pattern of variation, in Democratic Republic of Congo

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Abstract

Banana bunchy top virus (BBTV), belonging to the genus Babuvirus, is the most devastating and widespread banana virus. Banana and plantain are major crops in terms of household income and food security in Democratic Republic of Congo (DRC). Despite the large area under banana and plantain cultivation in the country, before this study, the genetic characterization of BBTV isolates had only been undertaken for two provinces. In the study presented here, genetic variation in BBTV was assessed from 52 BBTV isolates collected in five out of 11 provinces in DRC (Bandundu, Bas-Congo, Katanga, Kinshasa and Kasaï Oriental) and in two provinces using sequences previously described in databases. Full genome sequencing of DNA-R components was performed, revealing low genetic variation (98–100 % nucleotide identity) among the BBTV isolates detected. The phylogenetic analyses showed that all the DRC isolates were clustered in the South Pacific clade of BBTV. Based on the coding region for the replication initiator protein, haplotype diversity was estimated to be 0.944 ± 0.013, with 30 haplotypes from 68 isolates in DRC. Such diversity shows a haplotype distribution mainly at the sub-regional level in DRC. In addition, the sequence determination from the whole genome of selected isolates confirmed low genetic variation among isolates from seven DRC provinces (97–100 % nucleotide identity). This study strengthened the hypothesis of a single BBTV introduction some time ago, followed by the spread of the virus in the country.

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Acknowledgments

The Belgian Agency of Development (CTB/BTC) funded this research work through a scholarship to LM. The authors are very grateful to Wallonie Bruxelles International (WBI), the BeCA-ILRI-Hub, the technicians in the 1/UMR-BGPI team, Campus International de Baillarguet, Cirad-Montpellier/France and Pierre Hellin at ELI/UCL, who contributed to the phylogenetic analysis.

Author’s contribution

CB, LFTM, MLIC and AKM conceived and designed the study. LFTM, VV, SG and NL performed research. GR, AG, CB, MLIC and LFTM analysed data. GR, LFTM, MLIC and C.B wrote the paper.

Author information

Authors and Affiliations

  1. Applied Microbiology – Phytopathology , Earth and Life Institute, Université catholique de Louvain, Croix du Sud 2 Bte L07.05.03, 1348, Louvain-la-Neuve, Belgium

    L. F. T. Mukwa, V. Vanhese, G. Romay & C. Bragard

  2. Clinique des Plantes de Kinshasa, Kinshasa, Democratic Republic of Congo

    L. F. T. Mukwa, A. Kalonji-Mbuyi & C. Bragard

  3. Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, Croix du Sud 2, L7.05.12., 1348, Louvain-la-Neuve, Belgium

    A. Gillis

  4. CIRAD, UMR BGPI, F-34398, Montpellier Cedex 5, France

    S. Galzi, N. Laboureau & M. L. Iskra-Caruana

  5. Faculté des Sciences Agronomiques de l’Université de Kinshasa, Kinshasa, Democratic Republic of Congo

    A. Kalonji-Mbuyi

Authors
  1. L. F. T. Mukwa
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  2. A. Gillis
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  3. V. Vanhese
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  4. G. Romay
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  7. A. Kalonji-Mbuyi
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  8. M. L. Iskra-Caruana
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  9. C. Bragard
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Correspondence to C. Bragard.

Additional information

Edited by Thomas Hohn.

Electronic supplementary material

Below is the link to the electronic supplementary material.

11262_2016_1383_MOESM1_ESM.jpg

Supplementary material 1 (JPEG 2081 kb) Phylogenetic relationships of 98 complete DNA-R sequences of BBTV worldwide. Sequences retrieved from GenBank are identified by geographic origin and accession numbers. The tree was built using the neighbour-joining method. Bootstrap values (1,000 iterations) above 60% are indicated for each node. Abaca bunchy top virus (ABTV) was included as an outgroup. Branches in blue represent isolates from the South Pacific group (SPG) and branches in red represent isolates from the Asian group (AG).

11262_2016_1383_MOESM2_ESM.jpg

Supplementary material 2 (JPEG 1689 kb) Graphical representation of pairwise nucleotide sequence analysis of haplotypes based on the coding region from DNA-R components of African BBTV isolates. The colour scale bar indicates the percentage of nucleotide identity of haplotypes. Geographical origin was added to each haplotype.

Supplementary material 3 (JPEG 1457 kb)

11262_2016_1383_MOESM4_ESM.doc

Supplementary material 4 (DOC 87 kb) Phylogenetic relationships of 51 fully sequenced genomes of BBTV worldwide. Sequences are identified by their geographic origin and isolate names in brackets. The phylogenetic tree was built using the neighbour-joining method. Bootstrap values (1,000 iterations) above 60% are indicated for each node. Abaca bunchy top virus (ABTV) was included as an outgroup. Branches in blue represent isolates from the South Pacific group (SPG) and branches in red represent isolates from the Asian group (AG). Isolates with black circles were sequenced in this study.

Supplementary material 5 (DOC 229 kb)

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Mukwa, L.F.T., Gillis, A., Vanhese, V. et al. Low genetic diversity of Banana bunchy top virus, with a sub-regional pattern of variation, in Democratic Republic of Congo. Virus Genes 52, 900–905 (2016). https://doi.org/10.1007/s11262-016-1383-1

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