Nanopore sequencing for the analysis of genomes and transcriptomes in the tripartite symbiotic associations of Pisum sativum

Alexey Afonin

Alexey Afonin, All-Russia Research Institute for Agricultural Microbiology


The legume Pisum sativum was the first model organism for genetics and remains the focus of modern research concerning plant-microbe interactions. The genome of the plant was assembled using only nanopore reads to high contiguity N50 = 2.5 Mbp., genome length ~4Gbp. Using the newly assembled plant genome, we investigated the transcriptional profiles of the root nodules and of the mycorrhizal roots of the plant using cDNA sequencing with nanopore. We were able to perform genome annotation and discern transcripts and isoforms, unique for the respective symbioses, improving the overall quality of genome annotation. Nanopore sequencing proved to be a potent method for rapid assembly of large, repeat-rich plant genomes and can also be used to perform transcriptome and isoform annotation.


Alexey Afonin received his Bachelor's degree in biology and Master's degree in microbiology from the Saint-Petersburg State University in Russia. He is currently a PhD student in the All-Russia Research Institute for Agricultural Microbiology studying the specificity of interactions between the nodule bacteria and pea. His work interests lie in leveraging omics data to investigate the mechanisms of plant-microbe interactions.