Structural analysis of the mitochondrial genome of Santalum album reveals a complex branched configuration
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 stru...
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| Published in | Genomics (San Diego, Calif.) Vol. 116; no. 5; p. 110935 |
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| Main Authors | , , , , , , , |
| Format | Journal Article |
| Language | English |
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Elsevier Inc
01.09.2024
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| Abstract | 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. |
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| AbstractList | 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. 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. 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.BACKGROUNDSantalum 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.RESULTSIn 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.CONCLUSIONSWe 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. |
| ArticleNumber | 110935 |
| Author | Zuo, You-Wei Gong, Xin-Yi Chen, Ying Li, Jia-Xi Liao, Xiao-Min Yu, Jie Liu, Guang-Hua Shan, Yuanyu |
| Author_xml | – sequence: 1 givenname: Guang-Hua surname: Liu fullname: Liu, Guang-Hua organization: Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, Huaihua University, 418008 Huaihua, Hunan, China – sequence: 2 givenname: You-Wei surname: Zuo fullname: Zuo, You-Wei email: youweiz@swu.edu.cn organization: Center for Biodiversity Conservation and Utilization, Key Laboratory of Eco-Environment in the Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, 400715 Beibei, Chongqing, China – sequence: 3 givenname: Yuanyu surname: Shan fullname: Shan, Yuanyu organization: College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China – sequence: 4 givenname: Jie surname: Yu fullname: Yu, Jie email: yujie1982@swu.edu.cn organization: College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China – sequence: 5 givenname: Jia-Xi surname: Li fullname: Li, Jia-Xi organization: College of Biological and Food Engineering, Huaihua University, 418008 Huaihua, Hunan, China – sequence: 6 givenname: Ying surname: Chen fullname: Chen, Ying organization: College of Biological and Food Engineering, Huaihua University, 418008 Huaihua, Hunan, China – sequence: 7 givenname: Xin-Yi surname: Gong fullname: Gong, Xin-Yi organization: College of Biological and Food Engineering, Huaihua University, 418008 Huaihua, Hunan, China – sequence: 8 givenname: Xiao-Min surname: Liao fullname: Liao, Xiao-Min email: hunan1262023@126.com organization: Hunan University of Medicine General Hospital, 418008 Huaihua, Hunan, China |
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| Keywords | RNA editing SSR Mitochondrial genome Phylogenetic tree NCBI PCGs Santalum album BLAST MTPT ML |
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| Snippet | 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.... Santalum album L. is an evergreen tree which is mainly distributes throughout tropical and temperate regions. And it has a great medicinal and economic... |
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| SubjectTerms | Mitochondrial genome MTPT Phylogenetic tree RNA editing Santalum album |
| Title | Structural analysis of the mitochondrial genome of Santalum album reveals a complex branched configuration |
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