High‑throughput sequencing of complete genomes of ipomoviruses associated with an epidemic of cassava brown streak disease in the Comoros Archipelago

Scussel, Sarah
Candresse, Thierry
Marais, Armelle
Claverie, Sohini
Hoareau, Murielle
Azali Hamza, Abdou
Verdin, Eric
Tepfer, Mark
Filloux, Denis
Fernandez, Emmanuel
Roumagnac, Philippe
Robene, Isabelle
Lefeuvre, Pierre
Jourda, Cyril
Roux-Cuvelier, Michel
Lett, Jean-Michel

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Publication date

January 2019

DOI

10.1007/s00705-019-04228-7

Publisher

Springer Science and Business Media LLC

Abstract

Using high-throughput sequencing of small interfering RNAs (siRNAs), virion-associated nucleic acid (VANA), and double stranded RNAs (dsRNAs), we have determined the complete genome sequences of Comorian isolates of two ipomoviruses, cassava brown streak virus (CBSV) and a divergent isolate of Ugandan cassava brown streak virus (UCBSV-KM) representing a new strain of this virus. While the large ORF of CBSV shares the highest nucleotide sequence identity (95.9%) with a Tanzanian isolate of CBSV, the large UCBSV-KM ORF shares the highest nucleotide sequence identity (77.5%) with a Malawian isolate of UCBSV. This low value is near the species demarcation threshold for the family Potyviridae (<76%). Phylogenetic analysis confirms that UCBSV-KM ...