Complete mitochondrial genomes of three Mangifera species, their genomic structure and gene transfer from chloroplast genomes

Abstract

Background Among the Mangifera species, mango (Mangifera indica) is an important commercial fruit crop. However, very few studies have been conducted on the Mangifera mitochondrial genome. This study reports and compares the newly sequenced mitochondrial genomes of three Mangifera species. Results Mangifera mitochondrial genomes showed partial similarities in the overall size, genomic structure, and gene content. Specifically, the genomes are circular and contain about 63–69 predicted functional genes, including five ribosomal RNA (rRNA) genes and 24–27 transfer RNA (tRNA) genes. The GC contents of the Mangifera mitochondrial genomes are similar, ranging from 44.42–44.66%. Leucine (Leu) and serine (Ser) are the most frequently used, while tryptophan (Trp) and cysteine (Cys) are the least used amino acids among the protein-coding genes in Mangifera mitochondrial genomes. We also identified 7–10 large chloroplast genomic fragments in the mitochondrial genome, ranging from 1407 to 6142 bp. Additionally, four intact mitochondrial tRNAs genes (tRNA-Cys, tRNA-Trp, tRNA-Pro, and tRNA-Met) and intergenic spacer regions were identified. Phylogenetic analysis based on the common protein-coding genes of most branches provided a high support value. Conclusions We sequenced and compared the mitochondrial genomes of three Mangifera species. The results showed that the gene content and the codon usage pattern of Mangifera mitochondrial genomes is similar across various species. Gene transfer from the chloroplast genome to the mitochondrial genome were identified. This study provides valuable information for evolutionary and molecular studies of Mangifera and a basis for further studies on genomic breeding of mango.

Multichromosomal Mitochondrial Genome of Paphiopedilum micranthum: Compact and Fragmented Genome, and Rampant Intracellular Gene Transfer

“…These data suggest that the transfer events of ndh genes predated the degradation of ndh in the P. micranthum plastome, or there was more than one donor of their plastome origin sequences. Furthermore, most of the plastome origin genes have been nonfunctional pseudogenes in previous studies [ 3 , 4 , 40 , 42 ], except for a few cases—for instance, psaA , ndhB , and rps7 in H. cannabinus [ 56 ] and petN , psaA , atpI , trnI-CAU , and trnC-GCA in Mangifera [ 63 ]. The mitogenome of P. micranthum contained 44 genes from plastid origin, and 12 of these genes are intact and potentially functional ( ycf4 , cemA , petA , rbcL , rpoA , rpl36 , ndhJ , psbE , psbF , psbJ , psbL , and atpE ), which has been rather rare in previous studies ( Table 2 and Table 3 ).…”

“…Notably, P. micranthum had fewer repeat sequences, both in number and relative percentage compared to other monocot species tested [ 5 ]. Further, the number of repeat sequences (2%) was relatively less than most other species, e.g., Mangifera (3.5% to 4.5%) [ 63 ], Monsonia (3.9% to 6.9%) [ 68 ], Trifolium (6.6% to 8.6%) [ 72 ], and Silene vulgaris (18.8 to 28%) [ 69 ].…”

A Comparative Genomics Approach for Analysis of Complete Mitogenomes of Five Actinidiaceae Plants

“…Dimer repeats were the most abundant SSR type (about 48%) in the Actinidia mitogenome ( Figure 2 C), which is commonly found in Suaeda glauca [ 67 ]. Gene transfer from the chloroplast to the mitogenome frequently occurs during long-term plant evolution [ 68 ]. A total of 9–55 kb of plastid-derived sequences was observed, which occupied 3–6% of the Actinidiaceae mitogenomes ( Figure 3 ).…”

“…The number of RNA editing sites varies in different species [ 72 ]. Previous studies identified approximately 491 RNA editing sites within 34 genes in rice [ 68 ] and 486 RNA editing sites within 31 genes in Primula vulgaris [ 73 ]. In Actinidiaceae, the number of RNA editing sites in most PCGs was extremely conserved in Actinidiaceae, similar to other plant studies [ 74 ].…”

The mitochondrial genome sequence of Abies alba Mill. reveals a high structural and combinatorial variation

“…The mitogenome sequences of angiosperms generally have one or more pairs of large non-tandem repeats that can act as sites for inter- and intramolecular recombination, leading to multiple alternative arrangements within a species (isoforms, including subgenomic forms) [ 16 ]. Although plant mitogenomes are often assembled and displayed as circular maps (e.g., [ 36 ]), plant mtDNA most likely does not exist as one large circular DNA molecule, but mostly as a complex and dynamic collection of linear DNA with combinations of smaller circular and branched DNA molecules [ 3 , 11 , 15 – 17 , 37 – 43 ].…”