The Use of Long-Read Sequencing to Study the Phylogenetic Diversity of the Potato Varieties Plastome of the Ural Selection

Abstract

Plastid DNA holds a substantial amount of plant genetic information, including maternal ancestry information. It helps to uncover interrelations between a wide variety of tuberous species of the genus Solanum to search for promising sources of high-yielding potato varieties resistant to bio- and abiotic stressors. This paper demonstrated the opportunities of de novo assembly of potato plastid DNA and its phylogenetic and genome type identification based only on Oxford Nanopore Technologies (ONT) long reads. According to our results, of 28 potato varieties developed at the Ural Research Institute of Agriculture, 16 varieties had one of the most primitive W-type plastomes. Ten varieties' plastomes belonged to the T-type of cultivated Solanum tuberosum subsp. tuberosum. The varieties Legenda and 15-27-1 were the closest to the wild species Solanum chacoense plastome. Using long-sequencing reads, we confirmed the presence of two isoforms of the plastid genome differing in the orientation of SSC region. We should note that irrespective of sequencing depth and improvements in software for working with ONT reads, a correct de novo plastome assembly and its annotation using only long-reads is impossible. The most problematic regions are homopolymers longer than 5 bp—they account for all detected indels, leading to a change in the reading frame or the deletion of entire genes.