sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms

The NCBI Sequence Read Archive currently hosts microRNA sequencing data for over 800 different species, evidencing the existence of a broad taxonomic distribution in the field of small RNA research. Simultaneously, the number of samples per miRNA-seq study continues to increase resulting in a vast amount of data that requires accurate, fast and user-friendly analysis methods. Since the previous release of sRNAtoolbox in 2019, 55 000 sRNAbench jobs have been submitted which has motivated many improvements in its usability and the scope of the underlying annotation database. With this update, users can upload an unlimited number of samples or import them from Google Drive, Dropbox or URLs. Micro- and small RNA profiling can now be carried out using high-confidence Metazoan and plant specific databases, MirGeneDB and PmiREN respectively, together with genome assemblies and libraries from 441 Ensembl species. The new results page includes straightforward sample annotation to allow downstream differential expression analysis with sRNAde. Unassigned reads can also be explored by means of a new tool that performs mapping to microbial references, which can reveal contamination events or biologically meaningful findings as we describe in the example. sRNAtoolbox is available at: https://arn.ugr.es/srnatoolbox/</a

Composting Spent Mushroom Substrate from Agaricus bisporus and Pleurotus ostreatus Production as a Growing Media Component for Baby Leaf Lettuce Cultivation under Pythium irregulare Biotic Stress

Composts of spent mushrooms substrates can be an alternative for the partial replacement of peat as growing media in horticulture. Three mature composts from Agaricus bisporus (Ag), Pleurotus ostreatus (Pl), and 70% Ag:30% Pl (AgPl) production were used as partial components of peat growing media, used at a 1:4 compost:peat ratio for growing red baby leaf lettuce. They showed higher yields, between 3 and 7 times more than that for peat itself, even under the pressure of the plant pathogen Pythium irregulare. AgPl showed the higher suppressiveness (50%) against Pythium irregulare than Ag- (38%) or Pl- (15%) supplemented media. The combination of these raw materials and a suitable composting process is important for obtaining mature compost for use as a partial component of peat-based growing media.This research was funded by the Spanish Ministry of Economy and Competitiveness (AGL2017-84085-C3-3-R); the Centre for the Development of Industrial Technology (CDTI) funding the project “Biotechnological management of organic waste for obtaining new bioproducts of new generation” code 99193 and the “Fundación Seneca de la Region de Murcia” within the Research Groups of Excellence programme of the Region of Murcia (19896/GERM/15)S

sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms

The NCBI Sequence Read Archive currently hosts microRNA sequencing data for over 800 different species, evidencing the existence of a broad taxonomic distribution in the field of small RNA research. Simultaneously, the number of samples per miRNA-seq study continues to increase resulting in a vast amount of data that requires accurate, fast and user-friendly analysis methods. Since the previous release of sRNAtoolbox in 2019, 55 000 sRNAbench jobs have been submitted which has motivated many improvements in its usability and the scope of the underlying annotation database. With this update, users can upload an unlimited number of samples or import them from Google Drive, Dropbox or URLs. Micro- and small RNA profiling can now be carried out using high-confidence Metazoan and plant specific databases, MirGeneDB and PmiREN respectively, together with genome assemblies and libraries from 441 Ensembl species. The new results page includes straightforward sample annotation to allow downstream differential expression analysis with sRNAde. Unassigned reads can also be explored by means of a new tool that performs mapping to microbial references, which can reveal contamination events or biologically meaningful findings as we describe in the example. sRNAtoolbox is available at: https://arn.ugr.es/srnatoolbox/