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Endophytic fungi are microfungi that live for all, or at least a part of, their lives inter- or intracellularly in plant parts without causing apparent symptoms of infection. Rice is a natural resource pool containing abundant endophytic fungi which play important roles in promoting plant growth and providing adaptation toward the abiotic and biotic stresses. Barnyard grass (Echinochloa crus-galli) is a major weed in paddy fields. Despite the negative impact to rice production, barnyard grass had been reported to harbor beneficial organisms like endophytic fungi which can serve as biocontrol agents against a variety of pathogens responsible for numerous plant diseases of rice. This study was conducted to characterize the diversity, composition and phylogeny of endophytic fungi from aerial parts of rice and barnyard grass in Mazandaran and Gilan provinces of Iran. In total 121 samples of rice and 53 samples of barnyard grass were examined from which 1650 and 194 isolates were recovered, respectively. Selected strains by morphological studies were studied molecularly based on sequences of ITS rDNA and, in some cases, other regions including LSU rDNA and TEF-1α. Our results, based on morphological and phylogenetic studies, shows that the composition of endophytic fungi differs between plant species, and, to some degree, among different tissues within an individual plant. Ascomycota was found to be the dominant phylum of endophytic fungi in both rice and barnyard grass with a relative abundance of 91.5% and 95.8%, respectively, followed by unidentified sterile fungi with a relative abundance of 4.24 and 3.09%, respectively. However, the ascomycetous endophytic fungi of rice were predominantly classified in the Sordariomycetes and Dothideomycetes with the identical relative abundance of 45%, and those of barnyard grass in the Dothideomycetes (77.29%). In addition, endophytic fungi of rice and barnyard grass were classified in 30 and 12 families, respectively. The Nectriaceae was the dominant family in rice (30.42%), and the Pleosporaceae was the dominant family in barnyard grass (54.1%). At the genus level, endophytic fungi of rice and barnyard grass were identified in 44 genera and 16 genera, respectively. Among these, 13 were shared endophytic fungal genera in rice and barnyard grass. Members of Fusarium (30.42%), Epicoccum (16.6%) and Alternaria (15.09%) were the most predominant fungi of rice, respectively. However, among the endophytic fungi of barnyard grass, members of Drechslera (28.35%), Epicoccum (23.19%) and Alternaria and Fusarium (11.85%) were the most frequent fungi, respectively. The endophytic fungi of rice and barnyard grass in this study were identified as 39 and nine known species, respectively, from which six were shared species from these host plants. The genera Achroiostachys and Cladorrhinum, and 11 species, i.e. Apiospora guangdongensis, Didymella myriophyllana, Epicoccum oryzae, Fusarium commune, F. liriodendri, F. nanum, F. planum, F. sulawesiense, Nigrospora saccharicola, Phaeosphaeria lunariae and Plectosphaerella pauciseptata are new records for the mycobita of Iran. Twelve genera identified from rice and seven genera identified from barnyard grass are here reported as endophytic fungi of these host plants for the first time. Endophytic fungal diversity evaluated by Shannon, Simpson and Chao1 indices revealed the highest diversity in rice sheaths and barnyard grass seeds, and the highest richness in seeds of both host plants. In addition, diversity analysis of endophytic fungi in rice varieties showed that leaves, stems and sheaths of high-yielding and local varieties had nearly the same fungal diversity, however, seeds of local varieties had higher fungal diversity than high-yielding varieties. Nevertheless, all plant tissues of local varieties had higher fungal richness than high-yielding varieties.
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