TY - JOUR

T1 - Assembly and Analysis of Plastomes for 15 Potato Cultivars Grown in Russia

AU - Karetnikov, Dmitry I.

AU - Salina, Elena A.

AU - Kochetov, Alex V.

AU - Afonnikov, Dmitry A.

N1 - This work was funded by the Kurchatov Genome Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, in agreement with the Ministry of Education and Science of the Russian Federation, no. 075-15-2019-1662.

PY - 2023/6

Y1 - 2023/6

N2 - Chloroplasts are important organelles in a plant cell, having their own DNA (cpDNA), transmitted only through the female line, and performing the function of photosynthesis. The determination of chloroplast DNA is of interest in the study of the genetic diversity and phylogeny of potatoes, and of cytoplasmic sterility, as well as for applications in biotechnology and genetic engineering. Here, we reconstructed the complete plastomes of 15 S. tuberosum potato cultivars grown in Russia. Our analysis allowed us to determine the composition and location of genes for these plastid DNAs. It was shown that the plastid genome contains both highly and low-variable regions. The region at position 63,001–68,000 nt has the highest variability. We determined the types of cpDNA based on in silico approaches: 10 cultivars have cpDNA of the W-type and 5 cultivars have cpDNA of the T-type. The genetic diversity of the plastid DNA for these potato cultivars was analyzed alongside the previously reconstructed plastomes of South American accessions, European/North American commercial cultivars and potato cultivars bred in the Ural region. The results show that plastid DNAs of the same type form clusters by sequence similarity, in agreement with previous studies.

AB - Chloroplasts are important organelles in a plant cell, having their own DNA (cpDNA), transmitted only through the female line, and performing the function of photosynthesis. The determination of chloroplast DNA is of interest in the study of the genetic diversity and phylogeny of potatoes, and of cytoplasmic sterility, as well as for applications in biotechnology and genetic engineering. Here, we reconstructed the complete plastomes of 15 S. tuberosum potato cultivars grown in Russia. Our analysis allowed us to determine the composition and location of genes for these plastid DNAs. It was shown that the plastid genome contains both highly and low-variable regions. The region at position 63,001–68,000 nt has the highest variability. We determined the types of cpDNA based on in silico approaches: 10 cultivars have cpDNA of the W-type and 5 cultivars have cpDNA of the T-type. The genetic diversity of the plastid DNA for these potato cultivars was analyzed alongside the previously reconstructed plastomes of South American accessions, European/North American commercial cultivars and potato cultivars bred in the Ural region. The results show that plastid DNAs of the same type form clusters by sequence similarity, in agreement with previous studies.

KW - InDels

KW - SNP

KW - Solanum tuberosumL

KW - chloroplast DNA

KW - cytoplasmic DNA type

KW - genetic diversity

KW - potato

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85163956222&origin=inward&txGid=ee06b4e297ff72a6e9e999233e830dde

UR - https://www.mendeley.com/catalogue/056cc17c-fc48-3d05-98be-f1a7a6e37c90/

U2 - 10.3390/agronomy13061454

DO - 10.3390/agronomy13061454

M3 - Article

VL - 13

JO - Agronomy

JF - Agronomy

SN - 2073-4395

IS - 6

M1 - 1454

ER -