Assembly and comparative analysis of the complete mitochondrial genome of the Maclura tricuspidata

TL;DR

This study reports the complete mitochondrial genome of Maclura tricuspidata, revealing its structure, gene content, and evolutionary relationships with other plants.

Contribution

The first complete mitochondrial genome assembly and comparative analysis of Maclura tricuspidata is presented.

Findings

The mitogenome has a multi-chromosomal structure with 28 protein-coding genes and 154 SSRs.

Phylogenetic analysis places M. tricuspidata within the Moraceae family, closely related to Ficus carica and Morus notabilis.

Most protein-coding genes show negative selection, while ccmB and sdh4 show potential positive selection.

Abstract

Maclura tricuspidata is an important medicinal and horticultural plant. However, the complete mitochondrial genome (mitogenome) of M. tricuspidata has not been reported, hindering molecular phylogenetic studies, species identification, and evolutionary research.

We present the first comprehensive analysis of the M. tricuspidata mitogenome. It features a multi-chromosomal structure comprising three circular-mapping chromosomes, with a total length of 416,801 bp and a GC content of 44.94%. Annotation identified 28 unique protein-coding genes (PCGs), 18 tRNA genes, and 3 rRNA genes. Codon usage analysis revealed GCU and CAA as the predominant codons for alanine and glutamine, respectively, while methionine and tryptophan, as single-codon amino acids, showed no bias. A total of 154 simple sequence repeats (SSRs) were detected: 84 on chromosome 1, 48 on chromosome 2, and 22 on chromosome 3. Analysis identified 19 homologous fragments transferred from the chloroplast genome (cpDNA), accounting for 4.31% of the mitogenome length. Using the Deepred-mt suite, 409 C-to-U RNA editing sites were predicted from the complete set of 28 mitochondrial PCGs, with the highest number in nad4 and the lowest in sdh4. Phylogenetic analysis confirmed the placement of M. tricuspidata within the Moraceae family, showing closest relationships to Ficus carica and Morus notabilis, consistent with the APG IV system. Comparative analysis revealed extensive syntenic blocks between the M. tricuspidata mitogenome and those of related species, alongside regions lacking homology. In addition, dN/dS analysis revealed that most of the protein-coding genes in the mitogenome had undergone negative selection, and only the ccmB and sdh4 gene had undergone potential positive selection in M. tricuspidata.

The unique structural features and complexities of the M. tricuspidata mitogenome, along with its similarities and differences compared to related species, provide valuable insights into plant mitochondrial evolution, energy metabolism, and environmental adaptation. These findings contribute significantly to the understanding of plant mitogenome diversity and biology.

The online version contains supplementary material available at 10.1186/s12864-025-12491-z.

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