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Introduction Driven by advances in long-read sequencing technologies, high-quality phased (haplotype-resolved) reference genomes are becoming increasingly available for complex polyploid organisms, including agronomically important crops. In this blog post, we will explain what phased reference genomes are and how they can be combined with long-read RNA-seq to unlock the secrets of allele- and haplotype-specific gene expression in complex polyploid organisms.

Introduction Differential gene expression analysis is a fundamental step in the interpretation of RNA-seq data. It aims to identify genes whose expression levels change significantly between experimental conditions, such as treated versus control samples or different biological states. These changes provide insight into the molecular mechanisms underlying phenotypic differences, enabling the discovery of biomarkers, regulatory pathways, and functional responses to

Establishing a high-quality de novo transcriptome is the first step for quantifying transcript abundance and mapping the biological pathways active in non-model species. For researchers working with non-model plants like Rorippa indica, a wild mustard known for its tolerance to the mustard aphid (Lipaphis erysimi), the challenge lies in turning millions of raw Illumina short reads into a biological insight

Introduction Differential Expression vs Gene Co-Expression Analyses In transcriptomics, differential expression analysis (DEA) is a standard step to identify genes whose expression levels significantly differ between conditions. This approach highlights candidate genes associated with a phenotype but focuses only on changes in expression magnitude and typically evaluates a limited number of factors or pairwise comparisons. As a result, it does