RNAi-mediated down-regulation of MsWOX13-2 leads to enhanced waterlogging tolerance in alfalfa

The files listed here contain the differentially expressed genes obtained via RNA-Sequencing conducted on alfalfa genotypes (MsWOX13-2 RNAi and N4.4.2) under waterlogging as well as normally-watered conditions. RNA integrity was assessed using the RNA Nano 6000 Assay Kit and an Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA), and stranded mRNA library preparation was carried out using 1000 ng total RNA and the NEBNext Ultra RNA Library Prep kit (New England Biolabs, Whitby, ON). Subsequently, sequencing was carried out on an Illumina Novaseq platform (Illumina Inc., San Diego, CA), generating 150-bp paired-end reads. Raw data were cleaned and trimmed using in-house perl scripts (Novogene, Sacramento, California, USA), and the resulting data were then mapped to the Medicago truncatula (v. 4.01.4) reference genome, which is a close diploid relative of alfalfa with a very well-annotated genome, using Hisat2 v2.0.5 (Kim et al., 2015).