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

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TitleBadnaviruses and banana genomes: a long association sheds light on Musa phylogeny and origin
Publication TypeJournal Article
Year of Publication2020
AuthorsChabannes M, Gabriel M, Aksa A, Galzi S, Dufayard J-F, Iskra-Caruana M-L, Muller E
JournalMolecular Plant Pathology
KeywordsBadnavirus, banana streak virus, endogenous pararetrovirus, host and virus coevolution, Musa phylogeny

Abstract Badnaviruses are double-stranded DNA pararetroviruses of the family Caulimoviridae. Badnaviral sequences found in banana are distributed over three main clades of the genus Badnavirus and exhibit wide genetic diversity. Interestingly, the nuclear genome of many plants, including banana, is invaded by numerous badnaviral sequences although badnaviruses do not require an integration step to replicate, unlike animal retroviruses. Here, we confirm that banana streak viruses (BSVs) are restricted to clades 1 and 3. We also show that only BSVs from clade 3 encompassing East African viral species are not integrated into Musa genomes, unlike BSVs from clade 1. Finally, we demonstrate that sequences from clade 2 are definitively integrated into Musa genomes with no evidence of episomal counterparts; all are phylogenetically distant from BSVs known to date. Using different molecular approaches, we dissected the coevolution between badnaviral sequences of clade 2 and banana by comparing badnavirus integration patterns across a banana sampling representing major Musa speciation events. Our data suggest that primary viral integrations occurred millions of years ago in banana genomes under different possible scenarios. Endogenous badnaviral sequences can be used as powerful markers to better characterize the Musa phylogeny, narrowing down the likely geographical origin of the Musa ancestor.

Showing 21 of 21 accessions
Accession Name Pictures Accession number Species / Group SubSpecies / SubGroup Origin Collection Available for distribution
THA018 ITC1067 acuminata Unknown Thailand ITC
Agutay ITC1028 acuminata Unknown Unknown ITC
Butuhan, intermediate apex ITC0565 balbisiana Unknown Philippines ITC
Balbisiana ITC0626 balbisiana Unknown Papua New Guinea ITC
Calcutta 4 ITC0249 acuminata subsp. burmannicoides Unknown ITC
Pahang ITC0609 acuminata subsp. malaccensis Unknown ITC
Musa textilis ITC1072 textilis subsp. textilis Unknown ITC
Zebrina ITC1177 acuminata subsp. zebrina Unknown ITC
Khae (Phrae) ITC0660 acuminata subsp. siamea Thailand ITC
Malaccensis ITC0250 acuminata subsp. malaccensis Unknown ITC
Pa (Songkhla) ITC0408 acuminata Unknown Unknown ITC
Malaccensis ITC0399 acuminata subsp. malaccensis Unknown ITC
Cameroun ITC0246 balbisiana Unknown Unknown ITC
Borneo ITC0253 acuminata subsp. microcarpa Unknown ITC
Wikago ITC0888 AA Unknown Papua New Guinea ITC
Long Tavoy ITC0283 acuminata subsp. burmannica Unknown ITC
Musa coccinea ITC0287 coccinea subsp. coccinea Unknown ITC
Honduras ITC0247 balbisiana Unknown Unknown ITC
Pa (Rayong) ITC0672 acuminata subsp. siamea Thailand ITC
ITC0254 acuminata subsp. malaccensis Unknown ITC
ITC0856 schizocarpa Unknown Papua New Guinea ITC