Kingdom Plantae offers some of the most challenging work to be done in genomics. Plant genomes are typically the largest, most repetitive, and most likely to be polyploid when compared to those of other organisms. The combination of repetitive regions and large size makes plant genomes complicated to analyze at both the biochemical and bioinformatics level. Biochemically, short-read technologies cannot bridge the gap of long repetitive regions and all sequencing technologies suffer reduced quality scores from homopolymer (or other highly repetitive) regions of a genome.
From a bioinformatics perspective, the polyploid nature of many plant genomes (including some whose polyploid status varies) combined with their preponderance of repetitive regions can make the production of a reference genome a difficult task. This can be the case even for commercially important (and thus well-studied) crops.
Given these challenges, just about all research-grade genomic services can find an application in the agriculture space. From genotyping individual plants using specific, well-know gene panels to constructing de novo assemblies with the latest long read technology, everything in the sequencing world can find a use in plant research.
Increasingly the study of any given plant biology is not thought of in isolation but rather as part of a larger phytobiome. The field of metagenomics provides a necessary complement to pure plant genomic research in this regard. Metagenomics covers the analysis of microbial and fungal organisms in a plant’s environment.
Beyond our standard services, we are able to customize solutions for any DNA or RNA sequencing-related workflow. Usually it’s best to start with a specific project or list of requirements, especially when dealing with work that must be performed on the newest NGS or third-generation technologies. So if you do not see exactly what you are looking for, please tell us what that is!