Specifications Table

Subject area	Biology
More specific subject area	Genomics of crop plants
Type of data	Tables and figures, Deoxyribonucleic acid (DNA) sequence
How data was acquired	Illumina MiSeq; Illumina NextSeq 500; Illumina HiSeq 2000
Data format	Raw and analyzed
Experimental factors	De novo assemblies were created using SPAdes Genome Assembler v 3.10.1. Polymorphic sites were called and filtered using SAMtools|BCFtool and manually revised using Integrative Genomics Viewer
Experimental features	Data include chloroplast genomes and the polymorphic sites in the chloroplast genomes of the sunflower isonuclear (alloplasmic) CMS lines with different cytoplasmic backgrounds
Data source location	Southern Federal University, Rostov-on-Don, Russia
Data accessibility	Data are published with this article. The raw reads are available in the FIGSHARE repository at the following linkhttps://doi.org/10.6084/m9.figshare.7520183. Complete chloroplast genome is available in GenBank NCBI under accession numbers: MK341448.1, MK341449.1, MK341450.1, MK341451.1 and MK341452.1
Related research article	M.S. Makarenko, I.V. Kornienko, K.V. Azarin, A.V. Usatov, M.D. Logacheva, N.V. Markin, V.A. Gavrilova, Mitochondrial genomes organization in alloplasmic lines of sunflower (Helianthus annuus L.) with various types of cytoplasmic male sterility, PeerJ. 7 (2018) e5266