Allotetraploid nature of a wild potato species, Solanum stoloniferum Schlechtd. et Bché., as revealed by whole‐genome sequencing

Awie J. Hosaka; Rena Sanetomo; Kazuyoshi Hosaka

doi:10.1111/tpj.17158

journal article Open Access Nov 25, 2024

Allotetraploid nature of a wild potato species, Solanum stoloniferum Schlechtd. et Bché., as revealed by whole‐genome sequencing

Awie J. Hosaka

Rena Sanetomo

Kazuyoshi Hosaka

The Plant Journal Vol. 121 No. 1 · Wiley

View at Publisher Save 10.1111/tpj.17158

Abstract

SUMMARYMexican wild diploid potato species are reproductively isolated from A‐genome species, including cultivated potatoes; thus, their genomic relationships remain unknown. Solanum stoloniferum Schlechtd. et Bché. (2n = 4x = 48, AABB) is a Mexican allotetraploid species frequently used in potato breeding. We constructed a chromosome‐scale assembly of the S. stoloniferum genome using PacBio long‐read sequencing and Hi‐C scaffolding technologies. The final assembly consisted of 1742 Mb, among which 745 Mb and 713 Mb were anchored to the 12 A‐genome and 12 B‐genome chromosomes, respectively. Using the RNA‐seq datasets, we detected 20 994 and 19 450 genes in the A and B genomes, respectively. Among these genes, 5138 and 3594 were specific to the A and B genomes, respectively, and 15 856 were homoeologous, of which 18.6–25.4% were biasedly expressed. Structural variations such as large pericentromeric inversions were frequently found between the A‐ and B‐genome chromosomes. A comparison of the gene sequences from 38 diverse genomes of the related Solanum species revealed that the S. stoloniferum B genome and Mexican diploid species, with the exception of S. verrucosum, were monophyletically distinct from the S. stoloniferum A genome and the other A‐genome species, indicating that the Mexican diploid species share the B genome. The content and divergence of transposable elements (TEs) revealed recent bursts and transpositions of TEs after polyploidization. Thus, the S. stoloniferum genome has undergone dynamic structural differentiation and TE mobilization and reorganization to stabilize the genomic imbalance. This study provides new insights into polyploid evolution and the efficient use of allotetraploid species in potato breeding.

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Published: Nov 25, 2024
Vol/Issue: 121(1)
License: View

Authors

A

Awie J. Hosaka

Nihon BioData Corporation Takatsu Kawasaki Kanagawa 213‐0012 Japan; Kihara Institute for Biological Research Yokohama City University Yokohama 244‐0813 Japan

R

Rena Sanetomo

Potato Germplasm Enhancement Laboratory Obihiro University of Agriculture and Veterinary Medicine Obihiro Hokkaido 080‐8555 Japan

K

Kazuyoshi Hosaka

Potato Germplasm Enhancement Laboratory Obihiro University of Agriculture and Veterinary Medicine Obihiro Hokkaido 080‐8555 Japan

Cite This Article

Awie J. Hosaka, Rena Sanetomo, Kazuyoshi Hosaka (2024). Allotetraploid nature of a wild potato species, Solanum stoloniferum Schlechtd. et Bché., as revealed by whole‐genome sequencing. The Plant Journal, 121(1). https://doi.org/10.1111/tpj.17158

Allotetraploid nature of a wild potato species, Solanum stoloniferum Schlechtd. et Bché., as revealed by whole‐genome sequencing

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