Molecular Microbiology Research 2024, Vol.14, No.2, 99-108 http://microbescipublisher.com/index.php/mmr 102 Figure 1 Distribution of cultivated endophytes according to sample type and plant species (Adopted from Ofek-Lalzar et al., 2016) Image caption: Venn diagrams of the cOTUs were produced based on the cOTUs presence/absence data. (a) Shared and unique fungal endophytic cOTUs across sample types for each plant species. (b) Shared and unique fungal endophytic cOTUs across plant species for each sample type. The numbers of core cOTUs in each comparison are indicated in brackets (Adopted from Ofek-Lalzar et al., 2016) 4.2 Phylogenetic analysis Phylogenetic analysis is a crucial step in understanding the evolutionary relationships and diversity of endophytic communities (Comby et al., 2016). By constructing phylogenetic trees, researchers can infer the genetic relatedness of endophytes and identify novel taxa. In the study of fungal root endophytes in wild barley (Hordeum murinum), phylogenetic analysis based on ITS sequence similarity revealed representatives from 8 orders, 12 families, and 18 genera. Notably, 21% of the isolates had no significant match in GenBank, indicating a high proportion of novel fungi (Murphy et al., 2015). This underscores the potential of wild relatives of crops as reservoirs of unexplored genetic diversity. Similarly, phylogenetic analysis of endophytic bacteria in various agricultural crops, including coffee, sugar cane, beans, corn, soybean, tomatoes, and grapes, identified common orders such as Bacillales, Enterobacteriales, and Actinomycetales. The most frequently observed genera were Bacillus, Pseudomonas, and Microbacterium. This analysis demonstrated the reliability of 16S rRNA gene sequencing in accurately grouping endophytic bacteria (Bredow et al., 2015). In another study, the phylogenetic diversity of endophytic bacteria in wheat was analyzed using 16S rRNA variability. This metagenomic approach revealed changes in bacterial endophytes associated with drought stress, highlighting the dynamic nature of endophytic communities in response to environmental conditions (Žiarovská et al., 2020).
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