Genetic diversity in the coat protein coding region of eighty-six sugarcane mosaic virus isolates from eight countries, particularly from Cameroon and Congo

Abstract

Fifty-eight sugarcane virus isolates were obtained from leaves showing mosaic symptoms, and collected in Cameroon (26 isolates), Congo (20 isolates), Egypt (1 isolate), South Africa (3 isolates) and the U.S.A. (8 isolates). All these isolates belonged to Sugarcane mosaic virus (SCMV) based on the amplification product obtained by RT-PCR with SCMV-specific primers. The amplicons (0.9 kb) from the coat protein (CP) coding region were cloned, sequenced and compared to each other as well as to the sequences (GenBank accessions) of 16 SCMV isolates from sugarcane (Australia, South Africa and U.S.A.) and 12 SCMV isolates from maize (Australia, Germany and China). Maximum likelihood and maximum parsimony analyses robustly supported two major monophyletic groups that were correlated with the host of origin: the SCE or sugarcane group that included all isolates from sugarcane and the MZ or maize group that contained all isolates from maize. The 86 virus isolates were distributed in 13 minor phylogenetic groups, four (I-IV) restricted to maize and nine (V-XIII) to sugarcane. A strong correlation was observed between the sugarcane groups and the geographical origin of the SCMV isolates. Each SCMV type strain from sugarcane (A, B, D, E and SC) was distributed in a different phylogenetic group or subgroup. The 26 isolates from Cameroon constituted a relatively homogeneous group (group V) whereas the 20 isolates from Congo belonged to two other groups (VI and VII). All the isolates from Cameroon and Congo were different from the SCMV type strains and other strains or isolates studied so far. It appears, therefore, that the population of SCMV from sugarcane in Africa contains virus genotypes that have not yet been described.

Genetic diversity of viruses associated with sugarcane mosaic disease of sugarcane inter-specific hybrids in China

“…Table 1 summarizes all the virus coat protein (CP) gene specific primers developed in this work to detect SrMV, SCMV, and SCSMV. Other utilized primers include SCMV-CP2, SCMV-F3-R3, SCMV-F4-R3 (Alegria et al 2003;Xu et al 2008), SrMV-CP1 and SrMV-CP2 (Zhang et al 2015), and the universal primer pair M13-47/RV-M. PCR reactions contained 1 μl of cDNA, 0.5 μl of each specific primer (10 μM), 2 μl of 10×PCR buffer, 1 μl of 2.5 mM dNTPs, 0.25 units of Ex-Taq DNA polymerase (Takara, China) with ddH 2 O added to a final volume of 20 μl. The amplification cycle was performed as follows: 94°C for 3 min, and 35 cycles at 94°C for 30 s, 50°C for 30 s, and 72°C for 1 min and with a final elongation at 72°C for 10 min.…”

“…The molecular variations in the CP genes showed that SCMV, SrMV, and SCSMV are genetically diverse depending on the different geographical distributions (Alegria et al 2003). In this study, we surveyed 78 samples from Saccharum hybrids and S. officinarum, and examined them for the presence of SMD related viruses.…”

Variabilidade genética de Sugarcane mosaic virus, causando mosaico em milho no Brasil

“…As reações de transcrição reversa (RT) foram realizadas com o kit cMaster Rtplus (EppendorfNetheler, Hamburg, Alemanha), tendo-se aplicado 2 µg de RNA total extraído das plantas infectadas, em combinação com 5 µ mol L -1 do oligonucleotídeo dT 17 V, previamente incubados a 70 o C por 10 min. Os oligonucleotídeos senso, SCMVF4 (Alegria et al, 2003) e SrMVF3 (Yang & Mirkov, 1997), e os oligonucleotídeos anti-senso, SCMVR3 e SrMVF3 (Yang & Mirkov, 1997), foram usados para amplificar regiões do genoma correspondentes à capa proteica (CP) das espécies SCMV e SrMV, respectivamente. O oligonucleotídeo senso GARGCATGGGGATA (SCMVNI2), localizado na região C-terminal da proteína de inclusão NIb, desenvolvido no presente trabalho a partir do alinhamento de sequências de nucleotídeos correspondentes de diversas espécies e estirpes do subgrupo do SCMV, também foi utilizado nas reações.…”

Caracterização de um isolado do Sugarcane mosaic virus que quebra a resistência de variedades comerciais de cana-de-açúcar

“…As reações de transcrição reversa (RT) foram realizadas com o kit cMaster Rtplus (Eppendorf -Netheler, Hamburg, Germany) aplicando-se 2 µg de RNA total extraído das plantas infectadas, em combinação com 5 µM do oligonucleotídeo dT 17 V, previamente incubados a 70 o C por 10 minutos. Os oligonucleotídeos senso SCMVF4 (Alegria et al, 2003) e SrMVF3 (Yang & Mirkov, 1999) e os oligonucleotídeos anti-senso SCMVR3 e SrMVF3 (Yang & Mirkov, 1997) foram usados para amplificar regiões do genoma correspondentes à capa protéica (CP) das espécies SCMV e SrMV, respectivamente. O cDNA proveniente da reação de RT foi amplificado com 2 combinações de oligonucleotídeos: (i) 5 µM do oligonucleotídeo degenerado SCMVF4 e 1 µM do oligonucleotídeo SCMVF3; (ii) 1 µM dos oligonucleotídeos SrMVF3 e SrMVR3.…”