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

Abstract

Background Ilex metabaptista is a woody tree species with strong waterlogging tolerance and is also admired as a landscape plant with high development prospects and scientific research value. Unfortunately, populations of this species have declined due to habitat loss. Thus, it is a great challenge for us to efficiently protect I. metabaptista resources from extinction. Molecular biology research can provide the scientific basis for the conservation of species. However, the study of I. metabaptista genetics is still in its infancy. To date, no mitochondrial genome (mitogenome) in the genus Ilex has been analysed in detail. Results The mitogenome of I. metabaptista was assembled based on the reads from Illumina and Nanopore sequencing platforms; it was a typical circular DNA molecule of 529,560 bp with a GC content of 45.61% and contained 67 genes, including 42 protein-coding genes, 22 tRNA genes, and 3 rRNA genes. Repeat sequence analysis and prediction of RNA editing sites revealed a total of 286 dispersed repeats, 140 simple repeats, 18 tandem repeats, and 543 RNA editing sites. Analysis of codon usage showed that codons ending in A/T were preferred. Gene migration was observed to occur between the mitogenome and chloroplast genome via the detection of homologous fragments. In addition, Ka/Ks analysis revealed that most of the protein-coding genes in the mitogenome had undergone negative selection, and only the ccmB gene had undergone potential positive selection in most asterids. Nucleotide polymorphism analysis revealed the variation in each gene, with atp9 being the most notable. Furthermore, comparative analysis showed that the GC contents were conserved, but the sizes and structure of mitogenomes varied greatly among asterids. Phylogenetic analysis based on the mitogenomes reflected the exact evolutionary and taxonomic status of I. metabaptista. Conclusion In this study, we sequenced and annotated the mitogenome of I. metabaptista and compared it with the mitogenomes of other asterids, which provided essential background information for further understanding of the genetics of this plant and helped lay the foundation for future studies on molecular breeding of I. metabaptista.

Assembly and comparative analysis of the complete multichromosomal mitochondrial genome of Cymbidium ensifolium, an orchid of high economic and ornamental value

“…All of these values were less than 50%, indicating a bias in the codons of the C. ensifolium mitogenome due to the use of both A and T bases. The effective number of codons (Nc) was 53.48, suggesting a weak codon preference in the C. ensifolium mitogenome [ 30 , 31 ]. As presented in Table 1 , all of the PCGs used ATG as the start codon.…”

“…The mitogenome of C. ensifolium is unique compared to that of most plants, as it is assembled into 19 circular chromosomes, whereas most plants have a single circular chromosome structure [ 31 ]. To further understand its characteristics, the mitogenome of C. ensifolium was compared to those of 47 other plants with multichromosomal mitogenome structures (Table S 9 ) [ 14 – 16 , 21 , 22 , 24 , 27 , 28 , 38 – 67 ].…”

“…Mitochondria are organelles in eukaryotic cells that have their own genetic system and are responsible for energy production through RNA expression and protein synthesis [ 17 ]. In many plant species, mitogenomes are typically visualized as a single circular molecule without any isoforms [ 24 , 31 ]. However, electron micrographs have shown that the mitogenome of Chenopodium album L. contains a subgenome consisting of a circular molecule with a linear tail [ 68 ].…”

“…In our study, we predicted 530 RNA editing sites in the C. ensifolium mitogenome, which is similar to the number reported in previous studies on Hypopitys monotropa Crantz (545) [ 54 ], B. chinense (517) [ 73 ], and Ilex metabaptista Loes. ex Diels (543) [ 31 ]. The number of RNA editing sites in PCGs varied greatly among genes and species.…”

Complete mitochondrial genome of Angelica dahurica and its implications on evolutionary analysis of complex mitochondrial genome architecture in Apiaceae

“…This structural versatility implies a high level of adaptability in mitochondrial genomes, allowing them to respond to different cellular and environmental conditions ( Gualberto et al., 2014 ).Within the Apiaceae family, a remarkable spectrum of genetic diversity is exhibited in the mitochondrial genome structures, underscoring the intricate relationship between genomic architecture and functional dynamics. Predominantly, the mitochondrial genomes of most species within this family, including I. metabaptista and D. carota ( Ronfort et al., 1995 ; Zhou et al., 2023 ), are characterized by a singular, circular chromosomal configuration. Contrasting this norm, A. dahurica, A. biserrate ( Wang et al., 2023 ), and C. sativum ( Wang et al., 2021 ) display multi-chromosomal structures.…”