Abstract
Cytoplasmic male sterility (CMS) has been widely exploited for hybrid seed production in onions (Allium cepa L.). In contrast to long-day onion cultivars, short-day onion has not yet been investigated for mitochondrial genome structure and DNA rearrangements associated with CMS activity. Here, we report the 3,16,321 bp complete circular mitochondrial genome of tropical onion CMS line (97A). Due to the substantial number of repetitive regions, the assembled mitochondrial genome of maintainer line (97B) remained linear with 15 scaffolds. Additionally, 13 and 20 chloroplast-derived fragments with a size ranging from 143 to 13,984 bp and 153–17,725 bp were identified in the 97A and 97B genomes, respectively. Genome annotation revealed 24 core protein-coding genes along with 24 and 28 tRNA genes in the mitochondrial genomes of 97A and 97B, respectively. Furthermore, comparative genome analysis of the 97A and 97B mitochondrial genomes showed that gene content was almost similar except for the chimeric ORF725 gene which is the extended form of the COX1 gene.
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Data availability
The raw sequencing data are available at Indian Biological Data Centre (IBDC) Accession ID INRP000036 and INSDC Study Accession ID PRJEB57244. The mitochondrial genome assemblies are available at http://45.248.163.59/bic/onion.
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Acknowledgements
The authors are thankful to Science and Engineering Research Board, Department of Science and Technology (DST), India project Grant No. SRG/2019/000632 and Department of Biotechnology, Government of India project Grant No. BT/PR40193/BTIS/137/23/2021 for providing financial assistance.
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RB, RS, and AM optimized the protocol and extracted mitochondrial DNA. OPM and ASD provided the onion samples. DS and RB perform computational analysis of the genome. RB and DS have written the manuscript. ASD and PC gave critical suggestions throughout the study and reviewed the manuscript. The manuscript is seen and approved by all the authors.
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Bishnoi, R., Solanki, R., Singla, D. et al. Comparative mitochondrial genome analysis reveals a candidate ORF for cytoplasmic male sterility in tropical onion. 3 Biotech 14, 6 (2024). https://doi.org/10.1007/s13205-023-03850-2
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DOI: https://doi.org/10.1007/s13205-023-03850-2