<i>De Novo</i> Assembly and Comparative Analysis of the Complete Mitochondrial Genome of <i>Chaenomeles speciosa</i> (Sweet) Nakai Revealed the Existence of Two Structural Isomers
As a valuable Chinese traditional medicinal species, <i>Chaenomeles speciosa</i> (Sweet) Nakai (<i>C. speciosa</i>) is a natural resource with significant economic and ornamental value. However, its genetic information is not well understood. In this study, the complete mitoc...
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| Format: | Article |
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MDPI AG
2023-02-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/2/526 |
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| author | Pei Cao Yuan Huang Mei Zong Zilong Xu |
| author_facet | Pei Cao Yuan Huang Mei Zong Zilong Xu |
| author_sort | Pei Cao |
| collection | DOAJ |
| description | As a valuable Chinese traditional medicinal species, <i>Chaenomeles speciosa</i> (Sweet) Nakai (<i>C. speciosa</i>) is a natural resource with significant economic and ornamental value. However, its genetic information is not well understood. In this study, the complete mitochondrial genome of <i>C. speciosa</i> was assembled and characterized to explore the repeat sequences, recombination events, rearrangements, and IGT, to predict RNA editing sites, and to clarify the phylogenetic and evolutionary relationship. The <i>C. speciosa</i> mitochondrial genome was found to have two circular chromosomes as its major conformation, with a total length of 436,464 bp and 45.2% GC content. The mitochondrial genome contained 54 genes, including 33 unique protein-coding genes, 18 tRNAs, and 3 rRNA genes. Seven pairs of repeat sequences involving recombination events were analyzed. Both the repeat pairs, R1 and R2, played significant roles in mediating the major and minor conformations. In total, 18 MTPTs were identified, 6 of which were complete tRNA genes. There were 454 RNA editing sites in the 33 protein-coding sequences predicted by the PREPACT3 program. A phylogenetic analysis based on 22 species of mitochondrial genomes was constructed and indicated highly conserved PCG sequences. Synteny analyses showed extensive genomic rearrangements in the mitochondrial genome of <i>C. speciosa</i> and closely related species. This work is the first to report the <i>C. speciosa</i> mitochondrial genome, which is of great significance for conducting additional genetic studies on this organism. |
| first_indexed | 2024-03-11T08:47:03Z |
| format | Article |
| id | doaj.art-8a579c28166d4ee882dda369f94e0db3 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T08:47:03Z |
| publishDate | 2023-02-01 |
| publisher | MDPI AG |
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| series | Genes |
| spelling | doaj.art-8a579c28166d4ee882dda369f94e0db32023-11-16T20:44:10ZengMDPI AGGenes2073-44252023-02-0114252610.3390/genes14020526<i>De Novo</i> Assembly and Comparative Analysis of the Complete Mitochondrial Genome of <i>Chaenomeles speciosa</i> (Sweet) Nakai Revealed the Existence of Two Structural IsomersPei Cao0Yuan Huang1Mei Zong2Zilong Xu3Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaInstitute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaCollege of Life Sciences, Anqing Normal University, Anqing 246133, ChinaInstitute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaAs a valuable Chinese traditional medicinal species, <i>Chaenomeles speciosa</i> (Sweet) Nakai (<i>C. speciosa</i>) is a natural resource with significant economic and ornamental value. However, its genetic information is not well understood. In this study, the complete mitochondrial genome of <i>C. speciosa</i> was assembled and characterized to explore the repeat sequences, recombination events, rearrangements, and IGT, to predict RNA editing sites, and to clarify the phylogenetic and evolutionary relationship. The <i>C. speciosa</i> mitochondrial genome was found to have two circular chromosomes as its major conformation, with a total length of 436,464 bp and 45.2% GC content. The mitochondrial genome contained 54 genes, including 33 unique protein-coding genes, 18 tRNAs, and 3 rRNA genes. Seven pairs of repeat sequences involving recombination events were analyzed. Both the repeat pairs, R1 and R2, played significant roles in mediating the major and minor conformations. In total, 18 MTPTs were identified, 6 of which were complete tRNA genes. There were 454 RNA editing sites in the 33 protein-coding sequences predicted by the PREPACT3 program. A phylogenetic analysis based on 22 species of mitochondrial genomes was constructed and indicated highly conserved PCG sequences. Synteny analyses showed extensive genomic rearrangements in the mitochondrial genome of <i>C. speciosa</i> and closely related species. This work is the first to report the <i>C. speciosa</i> mitochondrial genome, which is of great significance for conducting additional genetic studies on this organism.https://www.mdpi.com/2073-4425/14/2/526<i>Chaenomeles speciosa</i>mitochondrial genomechloroplastIGTMTPTshomologous recombination |
| spellingShingle | Pei Cao Yuan Huang Mei Zong Zilong Xu <i>De Novo</i> Assembly and Comparative Analysis of the Complete Mitochondrial Genome of <i>Chaenomeles speciosa</i> (Sweet) Nakai Revealed the Existence of Two Structural Isomers Genes <i>Chaenomeles speciosa</i> mitochondrial genome chloroplast IGT MTPTs homologous recombination |
| title | <i>De Novo</i> Assembly and Comparative Analysis of the Complete Mitochondrial Genome of <i>Chaenomeles speciosa</i> (Sweet) Nakai Revealed the Existence of Two Structural Isomers |
| title_full | <i>De Novo</i> Assembly and Comparative Analysis of the Complete Mitochondrial Genome of <i>Chaenomeles speciosa</i> (Sweet) Nakai Revealed the Existence of Two Structural Isomers |
| title_fullStr | <i>De Novo</i> Assembly and Comparative Analysis of the Complete Mitochondrial Genome of <i>Chaenomeles speciosa</i> (Sweet) Nakai Revealed the Existence of Two Structural Isomers |
| title_full_unstemmed | <i>De Novo</i> Assembly and Comparative Analysis of the Complete Mitochondrial Genome of <i>Chaenomeles speciosa</i> (Sweet) Nakai Revealed the Existence of Two Structural Isomers |
| title_short | <i>De Novo</i> Assembly and Comparative Analysis of the Complete Mitochondrial Genome of <i>Chaenomeles speciosa</i> (Sweet) Nakai Revealed the Existence of Two Structural Isomers |
| title_sort | i de novo i assembly and comparative analysis of the complete mitochondrial genome of i chaenomeles speciosa i sweet nakai revealed the existence of two structural isomers |
| topic | <i>Chaenomeles speciosa</i> mitochondrial genome chloroplast IGT MTPTs homologous recombination |
| url | https://www.mdpi.com/2073-4425/14/2/526 |
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