Metatranscriptomic analysis of small RNAs present in soybean deep sequencing libraries

Abstract

A large number of small RNAs unrelated to the soybean genome were identified after deep sequencing of soybean small RNA libraries. A metatranscriptomic analysis was carried out to identify the origin of these sequences. Comparative analyses of small interference RNAs (siRNAs) present in samples collected in open areas corresponding to soybean field plantations and samples from soybean cultivated in greenhouses under a controlled environment were made. Different pathogenic, symbiotic and free-living organisms were identified from samples of both growth systems. They included viruses, bacteria and different groups of fungi. This approach can be useful not only to identify potentially unknown pathogens and pests, but also to understand the relations that soybean plants establish with microorganisms that may affect, directly or indirectly, plant health and crop production.

Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench)

“…This indicates that the DNA extraction procedure introduces significant bias, thereby influencing the interpretation of the microbial community observed. PCR-based metagenomic approaches such as DGGE Ramond et al, 2013), t-RFLP (Sessitsch et al, 2012;Ding et al, 2013) and next generation sequencing (Gottel et al, 2011;Lucero et al, 2011;Ìnceoğlu et al, 2011;Molina et al, 2012) are continuously used to elucidate the structure and ecological roles of plant-associated (and other) microbial communities. However, few, if any, of these studies share the same DNA extraction protocol and/or are preceded by an evaluation of DNA extraction procedures to select the most efficient.…”

micro RNA 172 (miR172) signals epidermal infection and is expressed in cells primed for bacterial invasion in Lotus japonicus roots and nodules

“…Apart from affecting core developmental and physiological processes (Chen, 2009;Chuck et al, 2009), sRNA-directed silencing plays an essential role in plant responses to biotic and abiotic stresses Navarro et al, 2006;Ruiz-Ferrer & Voinnet, 2009;Matsui et al, 2013). In recent years, deep sequencing approaches have provided access to sRNA populations of diverse plant species, including symbiotic legumes such as soybean (Subramanian et al, 2008;Joshi et al, 2010;Kulcheski et al, 2011;Li et al, 2012;Molina et al, 2012;Zabala et al, 2012), M. truncatula (Szittya et al, 2008;Jagadeeswaran et al, 2009a;Lelandais-Briere et al, 2009;Devers et al, 2011;Wang et al, 2011;Chen et al, 2012) and L. japonicus (De Luis et al, 2012). Differential sRNA abundances between symbiotic and nonsymbiotic tissues revealed in these studies suggest a role for sRNAs in root symbioses.…”

“Omics” Tools for Better Understanding the Plant–Endophyte Interactions

“…Metatranscriptomic analysis of soybean plant has revealed the presence of a number of small RNA sequences unrelated to soybean genome. Interestingly comparative analysis of the obtained sequences established the presence of various pathogenic, symbiotic and free living microbes in different samples of soybean plant ( Molina et al, 2012 ).…”

“…Transcriptomics has been found as a feasible approach to study the microbial communities associated with different plants ( Molina et al, 2012 ; Sheibani-Tezerji et al, 2015 ). It involves the comparative analysis of transcriptomes of groups of interacting species and helps to understand the response of microbial communities toward changing environments.…”