| Summary: | The release of mitochondrial genome sequences provides the basis for characterizing interspecific and intraspecific variation in Brassica mitochondrial genomes. However, few B. juncea (mustard) mitochondrial genomes have been published. We assembled the mitochondrial genomes of three B. juncea subspecies and compared them with previously published genomes. The genomes were phylogenetically classified into A, B, C, and Bna clades. Two variant sites, a transversion (C → A) at nt 79,573 and a 31-bp copy-number variation between nts 65,564 and 65,596, were identified. Based on these variant sites, mitotype-specific sequence markers were developed to characterize the variation among worldwide 558 B. juncea accessions. Three mitochondrial genome types (mitotypes MT1–MT3) were identified. In terms of geographical distribution, MT1 and MT2 accessions were distributed mainly to the north and MT3 to the south of 34°N. Root mustards carried only MT1, leaf and stem mustards carried mainly MT3, and seed mustards carried all three mitotypes, implying that the mitotypes underwent selection during B. juncea domestication. A new form of oil mustard evolved by hybridization between two gene pools in southwest China.
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