Genetic diversity of Sugarcane bacilliform virus isolates infecting Saccharum spp. in India
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Genetic diversity of Sugarcane bacilliform virus isolates infecting Saccharum spp. in India R. Karuppaiah • R. Viswanathan • V. Ganesh Kumar
Received: 31 October 2012 / Accepted: 5 February 2013 / Published online: 22 February 2013 Ó Springer Science+Business Media New York 2013
Abstract Sugarcane bacilliform virus (SCBV), which causes leaf freckle in sugarcane, is a member of the genus Badnavirus. Studies were conducted to characterize SCBV in Saccharum officinarum germplasm and cultivated varieties in India by sequencing the complete genomes of five isolates. Genome lengths ranged from 7,553 to 7,884 nucleotides. Duplications in ORF3 and insertions in the RNase H-domain in some of the isolates were found to contribute to the large size of their genomes. The Indian SCBV isolates share identities of 69–85 % for the complete genomic sequence, indicating wide genetic diversity among them, and share 70–82 % identity with Sugarcane bacilliform Ireng Maleng virus (SCBIMV) and Sugarcane bacilliform Morocco virus (SCBMV), as well as 43–46 % identity with Banana streak virus (BSV) and BSV-related SCBV species from Guadeloupe, indicating that the Indian SCBV isolates are distinct from SCBV isolates reported to date. Irrespective of the region compared, SCBV isolates from India, Australia, and Morocco clustered together. BSV and BSV-related SCBV isolates from Guadeloupe formed another cluster. A phylogenetic analysis based on the partial RT/RNase H-sequence separated SCBV and BSV-related SCBV sequences into 11 SCBV groups viz.
Electronic supplementary material The online version of this article (doi:10.1007/s11262-013-0890-6) contains supplementary material, which is available to authorized users. R. Karuppaiah R. Viswanathan V. G. Kumar Plant Pathology Section, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore 641007, India R. Viswanathan (&) Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore 641007, India e-mail: [email protected]; [email protected]
SCBV-A to -K. Among the 11 groups, the SCBV sequences separated under H, I, J, and K are newly identified in this study, representing three new species and are tentatively named as SCBBBV, SCBBOV, and SCBBRV. Thus, the PASC and phylogenetic analyses evidenced that the symptoms associated with badnaviruses in sugarcane in India are caused by at least three new species, SCBBBV, SCBBOV, and SCBBRV, besides SCBIMV and SCBMV represented by SCBV-BT and SCBV-Iscam, respectively. Keywords Sugarcane Sugarcane bacilliform virus Badnavirus Leaf freckle Genome variation India
Introduction Sugarcane bacilliform virus (SCBV) was first reported in Cuba, infecting cultivar B34104, in 1985 and subsequently in Morocco [1]. The SCBV presence in India was suspected in Saccharum officinarum L. genotypes Black Tanna, Listada and D1135 during 1992, and was later confirmed by electron microscopy and ELISA [2]. So far the occurrence of SCBV has been reported in more than 20 cou
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