Genome assembly of six polyploid potato genomes

Maria Kyriakidou,Helen H Tai,David Ellis,Noelle L Anglin,Martina V Strömvik

doi:10.1038/s41597-020-0428-4

Maria Kyriakidou, Helen H Tai + Show 3 more

Open Access

https://doi.org/10.1038/s41597-020-0428-4

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Abstract

Genome assembly of polyploid plant genomes is a laborious task as they contain more than two copies of the genome, are often highly heterozygous with a high level of repetitive DNA. Next Generation genome sequencing data representing one Chilean and five Peruvian polyploid potato (Solanum spp.) landrace genomes was used to construct genome assemblies comprising five taxa. Third Generation sequencing data (Linked and Long-read data) was used to improve the assembly for one of the genomes. Native landraces are valuable genetic resources for traits such as disease and pest resistance, environmental tolerance and other qualities of interest such as nutrition and fiber for breeding programs. The need for conservation and enhanced understanding of genetic diversity of cultivated potato from South America is also crucial to North American and European cultivars. Here, we report draft genomes from six polyploid potato landraces representing five taxa, illustrating how Third Generation Sequencing can aid in assembling polyploid genomes.

Highlights

Background & SummaryNative potato species are distributed from the southwestern United States to Argentina1
Cultivated potato landraces can range from diploids (2n = 2x = 24) to pentaploids (2n = 5x = 60)2 and wild potato species from the United States, Mexico and central America include hexaploid species3
A single reference genome cannot capture the great diversity found across different potato genomes, especially in the case of polyploids since they are more heterozygous than the diploids9,10

Summary

Introduction

Background & SummaryNative potato species are distributed from the southwestern United States to Argentina1. We have focused on assembling the reads for the six polyploid genomes from the previously sequenced cultivated potato landraces covering five taxa (based on)10,15: Solanum chaucha (3x: CHA), S. juzepczukii (3x: JUZ), two genomes of S. tuberosum subsp. Genome Illumina PE sequence data was generated for the six polyploid genomes: Solanum chaucha (3x: CHA – CIP 707129 doi:10.18730/CS5*), S. juzepczukii (3x: JUZ – CIP 706050 doi:10.18730/ C09D), two genomes of S. tuberosum subsp.

Results

Conclusion