Next-generation sequencing has triggered an explosion of available genomic and
transcriptomic resources in the plant sciences. Although genome and transcriptome …

Motivation: Comparative transcriptomics is a common approach in functional gene discovery
efforts. It allows for finding conserved co-expression patterns between orthologous genes in …

Crops face increased risk from heat stress due to climate change. Potato (Solanum
tuberosum L.) tubers grown in hot summers often have defects including pre-harvest …

Neonicotinoids are effective insecticides used on many important arable and horticultural
crops. They are nicotinic acetylcholine receptor agonists which disrupt the function of insect …

Nitrogen (N) is the most important nutrient for the growth of potato (Solanum tuberosum L.).
Foliar gene expression in potato plants with and without N supplementation at 180 kg N ha …

Annotating gene structures and functions to genome assemblies is necessary to make
assembly resources useful for biological inference. Gene Ontology (GO) term assignment is …

Tuberization is an important developmental process in potatoes, but it is highly affected by
environmental conditions. Temperature is a major environmental factor affecting …

Short interspersed nuclear elements (SINEs) are highly abundant non‐autonomous
retrotransposons that are widespread in plants. They are short in size, non‐coding, show …

Comparative transcriptomics between species can provide valuable understanding of plant-
pathogen interactions. Here, we focus on wild Solanum species and potato clones with …

Orthology is a cornerstone of comparative genomics and has numerous applications in
current biology. In this chapter, we first introduce the concepts of orthology and paralogy. We …