Structural analysis of the mitochondrial genome of Santalum album reveals a complex branched configuration

• Published in: Genomics (San Diego, Calif.) Vol. 116; no. 5; p. 110935
• Main Authors: Liu, Guang-Hua, Zuo, You-Wei, Shan, Yuanyu, Yu, Jie, Li, Jia-Xi, Chen, Ying, Gong, Xin-Yi, Liao, Xiao-Min
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.09.2024
• Subjects: Mitochondrial genome; MTPT; Phylogenetic tree; RNA editing; Santalum album; RNA editing; SSR; Mitochondrial genome; Phylogenetic tree; NCBI; PCGs; Santalum album; BLAST; MTPT; ML
• ISSN: 0888-7543; 1089-8646; 1089-8646
• DOI: 10.1016/j.ygeno.2024.110935

Santalum album L. is an evergreen tree which is mainly distributes throughout tropical and temperate regions. And it has a great medicinal and economic value. In this study, the complete mitochondrial genome of S. album were assembled and annotated, which could be descried by a complex branched structure consisting of three contigs. The lengths of these three contigs are 165,122 bp, 93,430 bp and 92,491 bp. We annotated 34 genes coding for proteins (PCGs), 26 tRNA genes, and 4 rRNA genes. The analysis of repeated elements shows that there are 89 SSRs and 242 pairs of dispersed repeats in S. album mitochondrial genome. Also we found 20 MTPTs among the chloroplast and mitochondria. The 20 MTPTs sequences span a combined length of 22,353 bp, making up 15.52 % of the plastome, 6.37 % of the mitochondrial genome. Additionally, by using the Deepred-mt tool, we found 628 RNA editing sites in 34 PCGs. Moreover, significant genomic rearrangement is observed between S. album and its associated mitochondrial genomes. Finally, based on mitochondrial genome PCGs, we deduced the phylogenetic ties between S. album and other angiosperms. We reported the mitochondrial genome from Santalales for the first time, which provides a crucial genetic resource for our study of the evolution of mitochondrial genome. •In this study, the complete mitochondrial genome of S. album were assembled and annotated, which could be described by a complex branched structure consisting of three contigs.•The lengths of these three contigs are 165,122 bp, 93,430 bp and 92,491 bp.•We annotated 34 genes coding for proteins (PCGs), 26 tRNA genes, and 4 rRNA genes.•The analysis of repeated elements shows that there are 89 SSRs and 242 pairs of dispersed repeats in S. album mitochondrial genome.•Also we found 20 MTPTs among the chloroplast and mitochondria.•The 20 MTPTs sequences span a combined length of 22,353 bp, making up 15.52 % of the plastome, 6.37 % of the mitochondrial genome.•Additionally, by using the Deepred-mt tool, we found 628 RNA editing sites in 34 PCGs.•Moreover, significant genomic rearrangement is observed between S. album and its associated mitochondrial genomes.•Finally, based on mitochondrial genome PCGs, we deduced the phylogenetic ties between S. album and other angiosperms.