Next-generation sequencing and comparative analysis of onion mitochondrial genome for the identification of gene(s) conferring cytoplasmic male sterility
Loading...
Date
2022
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
Punjab Agricultural University
Abstract
Cytoplasmic male sterility (CMS) is caused by the gene(s) present in the cytoplasm which has been exploited for the production of F1 hybrid seeds in onion (Allium cepa L.). This phenomenon has been previously reported in long day onion varieties, but is still unexplored in short-day Indian onion varieties. In this study, we have used Illumina Hiseq platform for sequencing mtDNA of 97-A (CMS) and 97-B (maintainer) line that resulted more than 10 million high-quality paired-end reads respectively. These reads were processed for de-novo assembly using Spades software that resulted 7 and 105 contigs for 97-A and 97-B respectively. Finally, we obtained a complete circular genome with the help of primer walking technique for 97-A that comprised of 316321bp whereas the genome of 97-B remained linear with 15 scaffolds. Further, the genome annotation revealed that there were all 24 core protein coding genes along with 24 and 28 tRNA genes present in the 97-A and 97-B mitochondrial genome respectively. Further, comparative genome analysis of both the assemblies revealed that the genomes of both 97-A and 97-B are more or less similar except for the chimeric orf725 gene. Pairwise alignment of 97-A orf725 and 97-B COX-1 gene suggested that in 97-A (CMS) line, complete cox1 sequence was present at 5‘end and further extended by 577bp due to change in stop codon that might be the possible cause of sterility.
Description
Keywords
Citation
Solanki, Ravindra (2022). Next-generation sequencing and comparative analysis of onion mitochondrial genome for the identification of gene(s) conferring cytoplasmic male sterility (Unpublished M.Sc. thesis). Punjab Agricultural University, Ludhiana, Punjab, India.