Mitochondrial genome characterization and comparative study in shallots (Allium cepa L. var. aggregatum)

The research was conducted for Mitochondrial genome characterization and a comparative study in shallots (Allium cepa L. var. aggregatum). Mitochondrial DNA was extracted from the shallot leaves of Bima and Sumenep cultivars. A Percoll-based differential density gradient technique was used to separate intact mitochondria from the leaves. In the MGI sequencing process, Bima and Sumenep yielded 101.234436 million paired-end reads in Bima and 101.792714 million in Sumenep, with a read length of 300 bp. The quality of raw data was assessed using FastQC. Trimmomatic v0.39 was used to filter low-quality data. The quality and quantity of the library samples were assessed using a TapeStation and a Qubit Fluorometer. The de novo assembly of the mitochondrial genome was conducted using high-quality data with a K-mer value. We used automatic coverage-cutoff settings to reduce the number of mismatches, short insertions, and deletions. To assess assembly quality, we used the Quality Assessment Tool (QUAST) and MUMmer. To find the position of the gene and assess its function, we annotated the assembled genome. Genome annotation was done using Plant Mitochondrial Genome Annotator (PMGA).