Pepo aphid-borne yellows virus: a new species in the genus Polerovirus Jacques D. Ibaba 1 • Mark D. Laing 1 • Augustine Gubba 1 Received: 12 May 2016 / Accepted: 2 September 2016 / Published online: 13 September 2016 Ó Springer Science+Business Media New York 2016 Abstract Pepo aphid-borne yellows virus (PABYV) has been proposed as a putative representative of a new species in the genus Polerovirus in the family Luteoviridae. The genomes of two South African (SA) isolates of cucurbit- infecting PABYV were described in this record. Total RNA, extracted from a pattypan (Cucurbita pepo L.) and a baby marrow (C. pepo L.) leaf samples, was subjected to next-generation sequencing (NGS) on the HiSeq Illumina platform. Sanger sequencing was subsequently used to authenticate the integrity of PABYV’s genome generated from de novo assembly of the NGS data. PABYV genome of SA isolates consists of 5813 nucleotides and displays an organisation typical of poleroviruses. Genome sequence comparisons of the SA PABYV isolates to other pole- roviruses support the classification of PABYV as a new species in the genus Polerovirus. Recombination analyses showed that PABYV and Cucurbit aphid-borne yellows virus (CABYV) shared the same ancestor for the genome part situated between breaking points. Phylogenetic anal- yses of the RNA-dependent RNA polymerase and the coat protein genes showed that SA PABYV isolates shared distant relationship with CABYV and Suakwa aphid-borne yellows virus. Based on our results, we propose that PABYV is a distinct species in the genus Polerovirus. Keywords Luteoviridae Á Emerging plant-infecting viruses Á Cucurbit Á Southern Africa Á Yellowing Á Next- generation sequencing The genus Polerovirus, one of the three that composes the family Luteoviridae [1], is an important genus of emerging plant-infecting viruses. The use of degenerate primers that hybridize to the conserved regions of the polerovirus gen- ome in diagnosis of plant-infecting viruses has resulted in the number of cucurbit-infecting poleroviruses increasing from one, Cucurbit aphid-borne yellows virus (CABYV), to three, with the addition of the Melon aphid-borne yellows virus (MABYV) and Suakwa aphid-borne yellows virus (SABYV) [2, 3]. Two additional cucurbit-infecting viruses, provisionally named Luffa aphid-borne yellows virus (LABYV) and Pepo aphid-borne yellows virus (PABYV), have been proposed as representatives of new species in the same genus [3]. PABYV was reported for the first time in Mali [3]. Then, the virus was identified from baby marrow (Cucurbita pepo L.), pattypan (C. pepo L.), butternut (C. moschata Duch.) and pumpkin (C. maxima Duch.) in the Republic of South Africa (RSA) [4], from zucchini (C. Pepo L.) in Cote d’Ivoire [5], from watermelon (Citrullus lanatus (Thunb.) Matsum. and Nakai) in Greece [6], and more recently from watermelon (C. lanatus (Thunb.) Matsum. and Nakai) in Tanzania and from melon (C. lanatus (Thunb.) Matsum. and Nakai) in Mayotte [7]. The portion of the genome spanning from the 3 0 end of the RNA-dependent RNA polymerase (RdRp) to the coat protein (CP) has been the only available section of the PABYV’s genome [3–7]. In this report, the genome sequences of two South African (SA) isolates of cucurbit-infecting PABYV are analysed. The virus isolates consisted of two PABYV-infected leaf samples from a pattypan and a baby marrow kept in Edited by Seung-Kook Choi. Electronic supplementary material The online version of this article (doi:10.1007/s11262-016-1390-2) contains supplementary material, which is available to authorized users. & Augustine Gubba gubbaa@ukzn.ac.za 1 Department of Plant Pathology, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa 123 Virus Genes (2017) 53:134–136 DOI 10.1007/s11262-016-1390-2