©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 12 (3): 4095-4105 (2013) Molecular characterization of endophytes isolated from Saccharum spp based on esterase and ribosomal DNA (ITS1-5.8S-ITS2) analyses A.C. Leme, M.R.R. Bevilaqua, S.A. Rhoden, C.A. Mangolin, M.F.P.S. Machado and J.A. Pamphile Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, PR, Brasil Corresponding author: J.A. Pamphile E-mail: japamphile@uem.br Genet. Mol. Res. 12 (3): 4095-4105 (2013) Received March 12, 2013 Accepted July 29, 2013 Published September 27, 2013 DOI http://dx.doi.org/10.4238/2013.September.27.11 ABSTRACT. This study used esterases and ribosomal DNA (rDNA) markers to determine endophytic variability in order to better understand endophyte-host interactions. Polyacrylamide gel electrophoresis and esterase isoenzymes (EST; EC 3.1.1.3), with a-naphthyl acetate and β-naphthyl acetate as substrates, were used to assess relationships among endophytes. ITS1-5.8S-ITS2 sequencing data were used as rDNA markers. Thirty-two esterases were obtained from 37 isolates of Saccharum spp, which clustered into fve endophyte groups. Esterase EST-06 was observed with the highest frequency, being present in 22 of the 37 isolates analyzed, followed by esterase EST-11, which was present in 20 isolates. The esterases EST-10 and EST-14 were present in 19 isolates and EST-09 was present in 18 isolates. The esterase EST-01 was unique to isolate 33 and can, therefore, be used as a marker for this isolate. None of the esterases identifed were common to all isolates tested. Similarly, phylogenetic analysis, based on rDNA sequence data, classifed the isolates into 5 genus groups: 1) Curvularia with a 100% bootstrap value (BP), 2) Alternaria with 100% BP, 3) Epicoccum with 60% BP, 4) Phoma with 89% BP, and 5)