Assembly and comparative analysis of the complete mitochondrial genome of three Macadamia species (M. integrifolia, M. ternifolia and M. tetraphylla)

Abstract

Background Macadamia is a true dicotyledonous plant that thrives in a mild, humid, low wind environment. It is cultivated and traded internationally due to its high-quality nuts thus, has significant development prospects and scientific research value. However, information on the genetic resources of Macadamia spp. remains scanty. Results The mitochondria (mt) genomes of three economically important Macadamia species, Macadamia integrifolia, M. ternifolia and M. tetraphylla, were assembled through the Illumina sequencing platform. The results showed that each species has 71 genes, including 42 protein-coding genes, 26 tRNAs, and 3 rRNAs. Repeated sequence analysis, RNA editing site prediction, and analysis of genes migrating from chloroplast (cp) to mt were performed in the mt genomes of the three Macadamia species. Phylogenetic analysis based on the mt genome of the three Macadamia species and 35 other species was conducted to reveal the evolution and taxonomic status of Macadamia. Furthermore, the characteristics of the plant mt genome, including genome size and GC content, were studied through comparison with 36 other plant species. The final non-synonymous (Ka) and synonymous (Ks) substitution analysis showed that most of the protein-coding genes in the mt genome underwent negative selections, indicating their importance in the mt genome. Conclusion The findings of this study provide a better understanding of the Macadamia genome and will inform future research on the genus.

Assembly and comparative analysis of the complete mitochondrial genome of Ilex metabaptista (Aquifoliaceae), a Chinese endemic species with a narrow distribution

“…Therefore, the I. metabaptista mitogenome has more RNA-editing sites but fewer editing types. Consistent with previous studies, the most abundant transfer type in I. metabaptista was TCA = > TTA [ 7 , 21 ], and the selection of editing sites showed a strong bias, with all editing sites being C-T editing, which is the most common editing type in plant mitogenomes [ 22 ]. Additionally, the second position base of the triplet codon was most prone to RNA editing events, and a leucine tendency after RNA editing was found in the amino acids of predicted editing codons [ 28 ].…”

“…Mitochondria and chloroplasts are organelles with a semiautonomous genetic system in higher plant cells, and they carry relevant genetic information [ 6 , 7 ]. The nuclear genomes carry the overwhelming majority of information, but the chloroplast and mitochondrial genomes are nonetheless also indispensable in eukaryotes [ 8 ].…”

Complete mitochondrial genome assembly and comparative analysis of Colocasia esculenta

“…Mitochondrial DNA is a naked double-stranded DNA molecule that primarily forms a closed circular structure [15]. In nongreen plants or dark environments, the energy produced by plant cells mainly occurs in mitochondria.…”

“…The mitochondrial genomes of plants are complex, surpassing those of animals [16]. In most seed plants, mitochondrial genes are maternally inherited [15]. The genome is highly conserved and can serve as a basis for species classification, solving the problem of identifying closely related species.…”

Macadamia germplasm and genomic database (MacadamiaGGD): A comprehensive platform for germplasm innovation and functional genomics in Macadamia

“…A chromosome-scale genome assembly of M. tetraphylla has also been constructed from long-read Oxford Nanopore Technologies (ONT) sequencing data (1059 scaffolds, N50 = 51 Mb, 751 Mb) ( Niu et al., 2022a ). Moreover, in recent years, the chloroplast and mitochondrion genomes of M. integrifolia , M. tetraphylla , and M. ternifolia have been assembled and thoroughly annotated ( Niu et al., 2022b ).…”