Multichromosomal mitochondrial genome of Punica granatum: comparative evolutionary analysis and gene transformation from chloroplast genomes

Abstract

Background Punica granatum is a fundamentally important fruit tree that has important economic, medicinal and ornamental properties. At present, there are few reports on the mitochondrial genome of pomegranate. Hence, in this study the P. granatum mitogenome was sequenced and assembled to further understanding of organization, variation, and evolution of mitogenomes of this tree species. Results The genome structure was multi-chromosomes with seven circular contigs, measuring 382,774 bp in length with a 45.91% GC content. It contained 74 genes, including 46 protein-coding genes, 25 tRNA genes, and three rRNA genes. There were 188 pairs of dispersed repeats with lengths of 30 or greater, primarily consisting of reverse complementary repeats. The mitogenome analysis identified 114SSRs and 466 RNA editing sites. Analyses of codon usage, nucleotide diversity and gene migration from chloroplast to mitochondrial were also conducted. The collinear and comparative analysis of mitochondrial structures between P. granatum and its proximal species indicated that P. granatum ‘Taishanhong’ was closely related to P. granatum ‘Qingpitian’ and Lagerstroemia indica. Phylogenetic examination based on the mitogenome also confirmed the evolutionary relationship. Conclusion The results offered crucial information on the evolutionary biology of pomegranate and highlighted ways to promote the utilization of the species’ germplasm.

Assembly and comparative analysis of the complete mitochondrial and chloroplast genome of Cyperus stoloniferus (Cyperaceae), a coastal plant possessing saline-alkali tolerance

“…Compared to cpDNA, plant mtDNA is generally larger and more complex, with not only single circular DNA, polycyclic DNA [ 38 ], and linear DNA [ 39 ], but also possibly DNA with a complex structure [ 40 , 41 ]. Species such as Camellia sinensis [ 42 ], Coptis deltoidei [ 43 ], Fallopia multiflora [ 44 ], and Prunella vulgaris [ 45 ] possess two circular DNA in their mtDNA, whereas buckwheat possesses 10 [ 46 ] and Amorphophallus albus possesses 19 [ 47 ].…”

“…This study also determined that the mtDNA of C. stoloniferus is 0.927 Mb, and this is 4.98-fold larger than that of cpDNA. Plasmid transfer DNA fragments are randomly dispersed in cpDNA, with a total length of 3.19 kp in C. esculentus [ 38 ], 5.67 kp in C. breviculimis [ 15 ], and 10.19 kp in C. stoloniferus . It is currently the longest known plant plasmid in the family Cyperaceae and transfers plastid DNA to mtDNA.…”