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Wang Z, Wang R, Sang Y, Wang T, Su Y, Liao W. Comparative analysis of mitochondrial genomes of invasive weed Mikania micrantha and its indigenous congener Mikania cordata. Int J Biol Macromol 2024; 281:136357. [PMID: 39378918 DOI: 10.1016/j.ijbiomac.2024.136357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 07/21/2024] [Accepted: 10/04/2024] [Indexed: 10/10/2024]
Abstract
Mikania micrantha and Mikania cordata are two distinct species in China. The former is notorious as one of the top 100 worst invasive species, whereas the latter is an indigenous species harmless to native plants or the environment. They form an ideal congener pair for comparative studies aimed at deeply understanding the invasion mechanisms of the exotic weed. In this study, we have assembled and annotated the mitogenomes of both species using Illumina and PacBio sequencing data and compared their characteristic differences. The complete mitogenome of M. micrantha is a double-stranded DNA with a length of 336,564 bp, while the mitogenome of M. cordata exhibits a branching structure, consisting of two small circular molecules and six linear molecules, with a combined length totaling 335,444 bp. Compared to M. cordata, M. micrantha has less SSRs, tandem repeats, dispersed repeats, mitochondrial protein coding genes (PCGs). The two plants show similar codon usage patterns. This comparative study has revealed the structure and function of the mitogenomes of the two species and laid a solid foundation for investigating the effects of gene loss and duplication on the development of invasive traits in M. micrantha.
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Affiliation(s)
- Zhen Wang
- School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, China
| | - Ruonan Wang
- School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, China
| | - Yatong Sang
- School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, China
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, 510642 Guangzhou, China; Research Institute of Sun Yat-sen University in Shenzhen, 518057 Shenzhen, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, China; Research Institute of Sun Yat-sen University in Shenzhen, 518057 Shenzhen, China.
| | - Wenbo Liao
- School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, China.
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Zhang Y, Zhang J, Chen Z, Huang Y, Liu J, Liu Y, Yang Y, Jin X, Yang Y, Chen Y. Comparison of organelle genomes between endangered mangrove plant Dolichandrone spathacea to terrestrial relative provides insights into its origin and adaptative evolution. FRONTIERS IN PLANT SCIENCE 2024; 15:1442178. [PMID: 39376234 PMCID: PMC11457174 DOI: 10.3389/fpls.2024.1442178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 09/02/2024] [Indexed: 10/09/2024]
Abstract
Dolichandrone spathacea is a mangrove associate with high medicinal and ecological values. However, due to the dual-pressure of climate change and human activities, D. spathacea has become endangered in China. Moreover, misidentification between D. spathacea and its terrestrial relative D. cauda-felina poses further challenges to field protection and proper medicinal usage of D. spathacea. Thus, to address these problems, we sequenced and assembled mitochondrial (mt) and chloroplast (cp) genomes for both D. spathacea and D. cauda-felina. Comparative analysis revealed apparently different size and scaffold number between the two mt genomes, but a high similarity between the cp genomes. Eight regions with high sequence divergence were identified between the two cp genomes, which might be used for developing candidate DNA markers for distinguishing the two species. The splitting between D. spathacea and D. cauda-felina was inferred to occur at ~6.8 - 7.7 million years ago (Mya), which may be driven by the environment fluctuations in late Miocene. In the cp genome, 12 genes related to the expression of photosynthesis-associated proteins were detected with signatures of positive selection, which may contribute to the origin and evolutionary adaptation of Dolichandrone mangrove species. These new findings do not only enrich organelle genomic resources of Dolichandrone species, but also provide important genetic clues for improving the conservation and proper usage of endangered mangrove associate D. spathacea.
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Affiliation(s)
- Ying Zhang
- Hainan Academy of Forestry, Hainan Mangrove Research Institute, Haikou, China
- Mangrove Rare and Endangered Species Protection and Utilization Engineering Technology Research Center, Zhanjiang Key Laboratory of Mangrove Ecosystem Protection and Restoration, Lingnan Normal University, Zhanjiang, China
| | - Jingwen Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Zewei Chen
- Mangrove Rare and Endangered Species Protection and Utilization Engineering Technology Research Center, Zhanjiang Key Laboratory of Mangrove Ecosystem Protection and Restoration, Lingnan Normal University, Zhanjiang, China
| | - Yanni Huang
- Mangrove Rare and Endangered Species Protection and Utilization Engineering Technology Research Center, Zhanjiang Key Laboratory of Mangrove Ecosystem Protection and Restoration, Lingnan Normal University, Zhanjiang, China
| | - Jiaxuan Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yuqi Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yong Yang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Xiang Jin
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Yuchen Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yiqing Chen
- Hainan Academy of Forestry, Hainan Mangrove Research Institute, Haikou, China
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Zhang M, Zhang X, Huang Y, Chen Z, Chen B. Comparative mitochondrial genomics of Terniopsis yongtaiensis in Malpighiales: structural, sequential, and phylogenetic perspectives. BMC Genomics 2024; 25:853. [PMID: 39267005 PMCID: PMC11391645 DOI: 10.1186/s12864-024-10765-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 09/03/2024] [Indexed: 09/14/2024] Open
Abstract
BACKGROUND Terniopsis yongtaiensis, a member of the Podostemaceae family, is an aquatic flowering plant displaying remarkable adaptive traits that enable survival in submerged, turbulent habitats. Despite the progressive expansion of chloroplast genomic information within this family, mitochondrial genome sequences have yet to be reported. RESULTS In current study, the mitochondrial genome of the T. yongtaiensis was characterized by a circular genome of 426,928 bp encoding 31 protein-coding genes (PCGs), 18 tRNAs, and 3 rRNA genes. Our comprehensive analysis focused on gene content, repeat sequences, RNA editing processes, intracellular gene transfer, phylogeny, and codon usage bias. Numerous repeat sequences were identified, including 130 simple sequence repeats, 22 tandem repeats, and 220 dispersed repeats. Phylogenetic analysis positioned T. yongtaiensis (Podostemaceae) within the Malpighiales order, showing a close relationship with the Calophyllaceae family, which was consistent with the APG IV classification. A comparative analysis with nine other Malpighiales species revealed both variable and conserved regions, providing insights into the genomic evolution within this order. Notably, the GC content of T. yongtaiensis was distinctively lower compared to other Malpighilales, primarily due to variations in non-coding regions and specific protein-coding genes, particularly the nad genes. Remarkably, the number of RNA editing sites was low (276), distributed unevenly across 27 PCGs. The dN/dS analysis showed only the ccmB gene of T. yongtaiensis was positively selected, which plays a crucial role in cytochrome c biosynthesis. Additionally, there were 13 gene-containing homologous regions between the mitochondrial and chloroplast genomes of T. yongtaiensis, suggesting the gene transfer events between these organellar genomes. CONCLUSIONS This study assembled and annotated the first mitochondrial genome of the Podostemaceae family. The comparison results of mitochondrial gene composition, GC content, and RNA editing sites provided novel insights into the adaptive traits and genetic reprogramming of this aquatic eudicot group and offered a foundation for future research on the genomic evolution and adaptive mechanisms of Podostemaceae and related plant families in the Malpighiales order.
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Affiliation(s)
- Miao Zhang
- College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Xiaohui Zhang
- College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
- Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Normal University, Fuzhou, 350117, China
| | - Yinglin Huang
- College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
- Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Normal University, Fuzhou, 350117, China
| | - Zhangxue Chen
- College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
- Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Normal University, Fuzhou, 350117, China
| | - Binghua Chen
- College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.
- Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Normal University, Fuzhou, 350117, China.
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Li L, Li X, Liu Y, Li J, Zhen X, Huang Y, Ye J, Fan L. Comparative analysis of the complete mitogenomes of Camellia sinensis var. sinensis and C. sinensis var. assamica provide insights into evolution and phylogeny relationship. FRONTIERS IN PLANT SCIENCE 2024; 15:1396389. [PMID: 39239196 PMCID: PMC11374768 DOI: 10.3389/fpls.2024.1396389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 07/29/2024] [Indexed: 09/07/2024]
Abstract
Introduction Among cultivated tea plants (Camellia sinensis), only four mitogenomes for C. sinensis var. assamica (CSA) have been reported so far but none for C. sinensis var. sinensis (CSS). Here, two mitogenomes of CSS (CSSDHP and CSSRG) have been sequenced and assembled. Methods Using a combination of Illumina and Nanopore data for the first time. Comparison between CSS and CSA mitogenomes revealed a huge heterogeneity. Results The number of the repetitive sequences was proportional to the mitogenome size and the repetitive sequences dominated the intracellular gene transfer segments (accounting for 88.7%- 92.8% of the total length). Predictive RNA editing analysis revealed that there might be significant editing in NADH dehydrogenase subunit transcripts. Codon preference analysis showed a tendency to favor A/T bases and T was used more frequently at the third base of the codon. ENc plots analysis showed that the natural selection play an important role in shaping the codon usage bias, and Ka/Ks ratios analysis indicated Nad1 and Sdh3 genes may have undergone positive selection. Further, phylogenetic analysis shows that six C. sinensis clustered together, with the CSA and CSS forming two distinct branches, suggesting two different evolutionary pathway. Discussion Altogether, this investigation provided an insight into evolution and phylogeny relationship of C. sinensis mitogenome, thereby enhancing comprehension of the evolutionary patterns within C. sinensis species.
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Affiliation(s)
- Li Li
- College of Tea and Food Science, Wuyi University, Wuyishan, China
| | - Xiangru Li
- College of Tea and Food Science, Wuyi University, Wuyishan, China
| | - Yun Liu
- College of Tea and Food Science, Wuyi University, Wuyishan, China
| | - Junda Li
- College of Tea and Food Science, Wuyi University, Wuyishan, China
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoyun Zhen
- College of Tea and Food Science, Wuyi University, Wuyishan, China
| | - Yu Huang
- College of Tea and Food Science, Wuyi University, Wuyishan, China
| | - Jianghua Ye
- College of Tea and Food Science, Wuyi University, Wuyishan, China
| | - Li Fan
- College of Tea and Food Science, Wuyi University, Wuyishan, China
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Qin N, Yang S, Wang Y, Cheng H, Gao Y, Cheng X, Li S. The de novo assembly and characterization of the complete mitochondrial genome of bottle gourd ( Lagenaria siceraria) reveals the presence of homologous conformations produced by repeat-mediated recombination. FRONTIERS IN PLANT SCIENCE 2024; 15:1416913. [PMID: 39188545 PMCID: PMC11345175 DOI: 10.3389/fpls.2024.1416913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 07/24/2024] [Indexed: 08/28/2024]
Abstract
Introduction Bottle gourd is an annual herbaceous plant that not only has high nutritional value and many medicinal applications but is also used as a rootstock for the grafting of cucurbit crops such as watermelon, cucumber and melon. Organellar genomes provide valuable resources for genetic breeding. Methods A hybrid strategy with Illumina and Oxford Nanopore Technology sequencing data was used to assemble bottle gourd mitochondrial and chloroplast genomes. Results The length of the bottle gourd mitochondrial genome was 357547 bp, and that of the chloroplast genome was 157121 bp. These genomes had 27 homologous fragments, accounting for 6.50% of the total length of the bottle gourd mitochondrial genome. In the mitochondrial genome, 101 simple sequence repeats (SSRs) and 10 tandem repeats were identified. Moreover, 1 pair of repeats was shown to mediate homologous recombination into 1 major conformation and 1 minor conformation. The existence of these conformations was verified via PCR amplification and Sanger sequencing. Evolutionary analysis revealed that the mitochondrial genome sequence of bottle gourd was highly conserved. Furthermore, collinearity analysis revealed many rearrangements between the homologous fragments of Cucurbita and its relatives. The Ka/Ks values for most genes were between 0.3~0.9, which means that most of the genes in the bottle gourd mitochondrial genome are under purifying selection. We also identified a total of 589 potential RNA editing sites on 38 mitochondrial protein-coding genes (PCGs) on the basis of long noncoding RNA (lncRNA)-seq data. The RNA editing sites of nad1-2, nad4L-2, atp6-718, atp9-223 and rps10-391 were successfully verified via PCR amplification and Sanger sequencing. Conclusion In conclusion, we assembled and annotated bottle gourd mitochondrial and chloroplast genomes to provide a theoretical basis for similar organelle genomic studies.
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Affiliation(s)
- Nannan Qin
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Department of Development Planning & Cooperation, Shanxi Agricultural University, Taiyuan, China
| | - Shanjie Yang
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
| | - Yunan Wang
- Department of Scientific Research Management, Shanxi Agricultural University, Taiyuan, China
| | - Hui Cheng
- Department of Scientific Research Management, Shanxi Agricultural University, Taiyuan, China
| | - Yang Gao
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
| | - Xiaojing Cheng
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
| | - Sen Li
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
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Luo X, Gu C, Gao S, Li M, Zhang H, Zhu S. Complete mitochondrial genome assembly of Zizania latifolia and comparative genome analysis. FRONTIERS IN PLANT SCIENCE 2024; 15:1381089. [PMID: 39184575 PMCID: PMC11341417 DOI: 10.3389/fpls.2024.1381089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 06/26/2024] [Indexed: 08/27/2024]
Abstract
Zizania latifolia (Griseb.) Turcz. ex Stapf has been cultivated as a popular aquatic vegetable in China due to its important nutritional, medicinal, ecological, and economic values. The complete mitochondrial genome (mitogenome) of Z. latifolia has not been previously studied and reported, which has hindered its molecular systematics and understanding of evolutionary processes. Here, we assembled the complete mitogenome of Z. latifolia and performed a comprehensive analysis including genome organization, repetitive sequences, RNA editing event, intercellular gene transfer, phylogenetic analysis, and comparative mitogenome analysis. The mitogenome of Z. latifolia was estimated to have a circular molecule of 392,219 bp and 58 genes consisting of three rRNA genes, 20 tRNA genes, and 35 protein-coding genes (PCGs). There were 46 and 20 simple sequence repeats (SSRs) with different motifs identified from the mitogenome and chloroplast genome of Z. latifolia, respectively. Furthermore, 49 homologous fragments were observed to transfer from the chloroplast genome to the mitogenome of Z. latifolia, accounting for 47,500 bp, presenting 12.1% of the whole mitogenome. In addition, there were 11 gene-containing homologous regions between the mitogenome and chloroplast genome of Z. latifolia. Also, approximately 85% of fragments from the mitogenome were duplicated in the Z. latifolia nuclear genome. Selection pressure analysis revealed that most of the mitochondrial genes were highly conserved except for ccmFc, ccmFn, matR, rps1, and rps3. A total of 93 RNA editing sites were found in the PCGs of the mitogenome. Z. latifolia and Oryza minuta are the most closely related, as shown by collinear analysis and the phylogenetic analysis. We found that repeat sequences and foreign sequences in the mitogenomes of Oryzoideae plants were associated with genome rearrangements. In general, the availability of the Z. latifolia mitogenome will contribute valuable information to our understanding of the molecular and genomic aspects of Zizania.
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Affiliation(s)
| | | | | | | | | | - Shidong Zhu
- College of Horticulture, Anhui Agricultural University, Hefei, China
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Zeng Z, Zhang Z, Tso N, Zhang S, Chen Y, Shu Q, Li J, Liang Z, Wang R, Wang J, Qiong L. Complete mitochondrial genome of Hippophae tibetana: insights into adaptation to high-altitude environments. FRONTIERS IN PLANT SCIENCE 2024; 15:1449606. [PMID: 39170791 PMCID: PMC11335646 DOI: 10.3389/fpls.2024.1449606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Accepted: 07/17/2024] [Indexed: 08/23/2024]
Abstract
Hippophae tibetana, belonging to the Elaeagnaceae family, is an endemic plant species of the Qinghai-Tibet Plateau, valued for its remarkable ecological restoration capabilities, as well as medicinal and edible properties. Despite being acknowledged as a useful species, its mitochondrial genome data and those of other species of the Elaeagnaceae family are lacking to date. In this study, we, for the first time, successfully assembled the mitochondrial genome of H. tibetana, which is 464,208 bp long and comprises 31 tRNA genes, 3 rRNA genes, 37 protein-coding genes, and 3 pseudogenes. Analysis of the genome revealed a high copy number of the trnM-CAT gene and a high prevalence of repetitive sequences, both of which likely contribute to genome rearrangement and adaptive evolution. Through nucleotide diversity and codon usage bias analyses, we identified specific genes that are crucial for adaptation to high-altitude conditions. Notably, genes such as atp6, ccmB, nad4L, and nad7 exhibited signs of positive selection, indicating the presence of unique adaptive traits for survival in extreme environments. Phylogenetic analysis confirmed the close relationship between the Elaeagnaceae family and other related families, whereas intergenomic sequence transfer analysis revealed a substantial presence of homologous fragments among the mitochondrial, chloroplast, and whole genomes, which may be linked to the high-altitude adaptation mechanisms of H. tibetana. The findings of this study not only enrich our knowledge of H. tibetana molecular biology but also advance our understanding of the adaptive evolution of plants on the Qinghai-Tibet Plateau. This study provides a solid scientific foundation for the molecular breeding, conservation, and utilization of H. tibetana genetic resources.
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Affiliation(s)
- Zhefei Zeng
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
- Yani Observation and Research Station for Wetland Ecosystem of the Tibet (Xizang) Autonomous Region, Tibet University, Lhasa, China
| | - Zhengyan Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Norzin Tso
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Shutong Zhang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Yan Chen
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Qi Shu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Junru Li
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Ziyi Liang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Ruoqiu Wang
- Tech X Academy, Shenzhen Polytechnic University, Shenzhen, China
| | - Junwei Wang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
- Yani Observation and Research Station for Wetland Ecosystem of the Tibet (Xizang) Autonomous Region, Tibet University, Lhasa, China
| | - La Qiong
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
- Yani Observation and Research Station for Wetland Ecosystem of the Tibet (Xizang) Autonomous Region, Tibet University, Lhasa, China
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Wang X, Wang D, Zhang R, Qin X, Shen X, You C. Morphological Structure Identification, Comparative Mitochondrial Genomics and Population Genetic Analysis toward Exploring Interspecific Variations and Phylogenetic Implications of Malus baccata 'ZA' and Other Species. Biomolecules 2024; 14:912. [PMID: 39199300 PMCID: PMC11352593 DOI: 10.3390/biom14080912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 07/19/2024] [Accepted: 07/24/2024] [Indexed: 09/01/2024] Open
Abstract
Malus baccata, a valuable germplasm resource in the genus Malus, is indigenous to China and widely distributed. However, little is known about the lineage composition and genetic basis of 'ZA', a mutant type of M. baccata. In this study, we compared the differences between 'ZA' and wild type from the perspective of morphology and ultrastructure and analyzed their chloroplast pigment content based on biochemical methods. Further, the complete mitogenome of M. baccata 'ZA' was assembled and obtained by next-generation sequencing. Subsequently, its molecular characteristics were analyzed using Geneious, MISA-web, and CodonW toolkits. Furthermore, by examining 106 Malus germplasms and 42 Rosaceae species, we deduced and elucidated the evolutionary position of M. baccata 'ZA', as well as interspecific variations among different individuals. In comparison, the total length of the 'ZA' mitogenome (GC content: 45.4%) is 374,023 bp, which is approximately 2.33 times larger than the size (160,202 bp) of the plastome (GC: 36.5%). The collinear analysis results revealed abundant repeats and genome rearrangements occurring between different Malus species. Additionally, we identified 14 plastid-driven fragment transfer events. A total of 54 genes have been annotated in the 'ZA' mitogenome, including 35 protein-coding genes, 16 tRNAs, and three rRNAs. By calculating nucleotide polymorphisms and selection pressure for 24 shared core mitochondrial CDSs from 42 Rosaceae species (including 'ZA'), we observed that the nad3 gene exhibited minimal variation, while nad4L appeared to be evolving rapidly. Population genetics analysis detected a total of 1578 high-quality variants (1424 SNPs, 60 insertions, and 94 deletions; variation rate: 1/237) among samples from 106 Malus individuals. Furthermore, by constructing phylogenetic trees based on both Malus and Rosaceae taxa datasets, it was preliminarily demonstrated that 'ZA' is closely related to M. baccata, M. sieversii, and other proximate species in terms of evolution. The sequencing data obtained in this study, along with our findings, contribute to expanding the mitogenomic resources available for Rosaceae research. They also hold reference significance for molecular identification studies as well as conservation and breeding efforts focused on excellent germplasms.
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Affiliation(s)
- Xun Wang
- Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, National Key Laboratory of Wheat Improvement, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian 271018, China; (X.W.); (D.W.); (X.Q.)
| | - Daru Wang
- Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, National Key Laboratory of Wheat Improvement, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian 271018, China; (X.W.); (D.W.); (X.Q.)
| | - Ruifen Zhang
- Qingdao Apple Rootstock Research and Development Center, Qingdao Academy of Agricultural Sciences, Qingdao 266100, China;
| | - Xin Qin
- Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, National Key Laboratory of Wheat Improvement, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian 271018, China; (X.W.); (D.W.); (X.Q.)
| | - Xiang Shen
- Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, National Key Laboratory of Wheat Improvement, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian 271018, China; (X.W.); (D.W.); (X.Q.)
| | - Chunxiang You
- Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, National Key Laboratory of Wheat Improvement, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian 271018, China; (X.W.); (D.W.); (X.Q.)
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9
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Gong Y, Xie X, Zhou G, Chen M, Chen Z, Li P, Huang H. Assembly and comparative analysis of the complete mitochondrial genome of Brassica rapa var. Purpuraria. BMC Genomics 2024; 25:546. [PMID: 38824587 PMCID: PMC11143693 DOI: 10.1186/s12864-024-10457-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 05/26/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Purple flowering stalk (Brassica rapa var. purpuraria) is a widely cultivated plant with high nutritional and medicinal value and exhibiting strong adaptability during growing. Mitochondrial (mt) play important role in plant cells for energy production, developing with an independent genetic system. Therefore, it is meaningful to assemble and annotate the functions for the mt genome of plants independently. Though there have been several reports referring the mt genome of in Brassica species, the genome of mt in B. rapa var. purpuraria and its functional gene variations when compared to its closely related species has not yet been addressed. RESULTS The mt genome of B. rapa var. purpuraria was assembled through the Illumina and Nanopore sequencing platforms, which revealed a length of 219,775 bp with a typical circular structure. The base composition of the whole B. rapa var. purpuraria mt genome revealed A (27.45%), T (27.31%), C (22.91%), and G (22.32%). 59 functional genes, composing of 33 protein-coding genes (PCGs), 23 tRNA genes, and 3 rRNA genes, were annotated. The sequence repeats, codon usage, RNA editing, nucleotide diversity and gene transfer between the cp genome and mt genome were examined in the B. rapa var. purpuraria mt genome. Phylogenetic analysis show that B. rapa var. Purpuraria was closely related to B. rapa subsp. Oleifera and B. juncea. Ka/Ks analysis reflected that most of the PCGs in the B. rapa var. Purpuraria were negatively selected, illustrating that those mt genes were conserved during evolution. CONCLUSIONS The results of our findings provide valuable information on the B.rapa var. Purpuraria genome, which might facilitate molecular breeding, genetic variation and evolutionary researches for Brassica species in the future.
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Affiliation(s)
- Yihui Gong
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China.
| | - Xin Xie
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Guihua Zhou
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Meiyu Chen
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Zhiyin Chen
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Peng Li
- Xiangtan Agricultural Science Research Institute, Xiangtan, 411100, China
| | - Hua Huang
- Institute of Fruit Tree Research, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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Li C, Liu H, Qin M, Tan YJ, Ou XL, Chen XY, Wei Y, Zhang ZJ, Lei M. RNA editing events and expression profiles of mitochondrial protein-coding genes in the endemic and endangered medicinal plant, Corydalis saxicola. FRONTIERS IN PLANT SCIENCE 2024; 15:1332460. [PMID: 38379941 PMCID: PMC10876856 DOI: 10.3389/fpls.2024.1332460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024]
Abstract
Corydalis saxicola, an endangered medicinal plant endemic to karst habitats, is widely used in Traditional Chinese Medicine to treat hepatitis, abdominal pain, bleeding hemorrhoids and other conditions. However, to date, the mitochondrial (mt) genome of C. saxicola has not been reported, which limits our understanding of the genetic and biological mechanisms of C. saxicola. Here, the mt genome of C. saxicola was assembled by combining the Nanopore and Illumina reads. The mt genome of C. saxicola is represented by a circular chromosome which is 587,939 bp in length, with an overall GC content of 46.50%. 40 unique protein-coding genes (PCGs), 22 tRNA genes and three rRNA genes were identified. Codon usage of the PCGs was investigated and 167 simple sequence repeats were identified. Twelve homologous fragments were identified between the mt and ct genomes of C. saxicola, accounting for 1.04% of the entire mt genome. Phylogenetic examination of the mt genomes of C. saxicola and 30 other taxa provided an understanding of their evolutionary relationships. We also predicted 779 RNA editing sites in 40 C. saxicola mt PCGs and successfully validated 506 (65%) of these using PCR amplification and Sanger sequencing. In addition, we transcriptionally profiled 24 core mt PCGs in C. saxicola roots treated with different concentrations of CaCl2, as well as in other organs. These investigations will be useful for effective utilization and molecular breeding, and will also provide a reference for further studies of the genus Corydalis.
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Affiliation(s)
- Cui Li
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Han Liu
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Mei Qin
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Yao-jing Tan
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Xia-lian Ou
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Xiao-ying Chen
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Ying Wei
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Zhan-jiang Zhang
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Ming Lei
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
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Liu D, Zhang Z, Hao Y, Li M, Yu H, Zhang X, Mi H, Cheng L, Zhao Y. Decoding the complete organelle genomic architecture of Stewartia gemmata: an early-diverging species in Theaceae. BMC Genomics 2024; 25:114. [PMID: 38273225 PMCID: PMC10811901 DOI: 10.1186/s12864-024-10016-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Theaceae, comprising 300 + species, holds significance in biodiversity, economics, and culture, notably including the globally consumed tea plant. Stewartia gemmata, a species of the earliest diverging tribe Stewartieae, is critical to offer insights into Theaceae's origin and evolutionary history. RESULT We sequenced the complete organelle genomes of Stewartia gemmata using short/long reads sequencing technologies. The chloroplast genome (158,406 bp) exhibited a quadripartite structure including the large single-copy region (LSC), a small single-copy region (SSC), and a pair of inverted repeat regions (IRs); 114 genes encoded 80 proteins, 30 tRNAs, and four rRNAs. The mitochondrial genome (681,203 bp) exhibited alternative conformations alongside a monocyclic structure: 61 genes encoding 38 proteins, 20 tRNAs, three rRNAs, and RNA editing-impacting genes, including ATP6, RPL16, COX2, NAD4L, NAD5, NAD7, and RPS1. Comparative analyses revealed frequent recombination events and apparent rRNA gene gains and losses in the mitochondrial genome of Theaceae. In organelle genomes, the protein-coding genes exhibited a strong A/U bias at codon endings; ENC-GC3 analysis implies selection-driven codon bias. Transposable elements might facilitate interorganelle sequence transfer. Phylogenetic analysis confirmed Stewartieae's early divergence within Theaceae, shedding light on organelle genome characteristics and evolution in Theaceae. CONCLUSIONS We studied the detailed characterization of organelle genomes, including genome structure, composition, and repeated sequences, along with the identification of lateral gene transfer (LGT) events and complexities. The discovery of a large number of repetitive sequences and simple sequence repeats (SSRs) has led to new insights into molecular phylogenetic markers. Decoding the Stewartia gemmata organellar genome provides valuable genomic resources for further studies in tea plant phylogenomics and evolutionary biology.
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Affiliation(s)
- Daliang Liu
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High-Value Utilization, College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
- Key Laboratory of Functional Agriculture in Higher Education of Guizhou Province, College of Agriculture, Guizhou University, Guiyang, 550025, China
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang, 550025, China
| | - Zhihan Zhang
- Key Laboratory of Functional Agriculture in Higher Education of Guizhou Province, College of Agriculture, Guizhou University, Guiyang, 550025, China
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang, 550025, China
- College of Engineering and Technology, Northeast Forestry University, Harbin, 150040, China
| | - Yanlin Hao
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High-Value Utilization, College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Mengge Li
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High-Value Utilization, College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Houlin Yu
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA
- Present address: Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Xingruo Zhang
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Haoyang Mi
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Lin Cheng
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High-Value Utilization, College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China.
| | - Yiyong Zhao
- Key Laboratory of Functional Agriculture in Higher Education of Guizhou Province, College of Agriculture, Guizhou University, Guiyang, 550025, China.
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang, 550025, China.
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Han Y, Feng YL, Wang J, Zhu SS, Jin XJ, Wu ZQ, Zhang YH. Comprehensive Analysis of the Complete Mitochondrial Genome of Rehmannia chingii: An Autotrophic Species in the Orobanchaceae Family. Genes (Basel) 2024; 15:98. [PMID: 38254987 PMCID: PMC10815111 DOI: 10.3390/genes15010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Rehmannia chingii is an important medicinal plant with immense value in scientific research. However, its mitochondrial genome (mitogenome) has not yet been characterized. Herein, based on whole-genome Illumina short reads and PacBio HiFi reads, we obtained the complete mitogenome of R. chingii through a de novo assembly strategy. We carried out comparative genomic analyses and found that, in comparison with the plastid genome (plastome) showing a high degree of structural conservation, the R. chingii mitogenome structure is relatively complex, showing an intricate ring structure with 16 connections, owing to five repetitive sequences. The R. chingii mitogenome was 783,161 bp with a GC content of 44.8% and contained 77 genes, comprising 47 protein-coding genes (CDS), 27 tRNA genes, and 3 rRNA genes. We counted 579 RNA editing events in 47 CDS and 12,828 codons in all CDSs of the R. chingii mitogenome. Furthermore, 24 unique sequence transfer fragments were found between the mitogenome and plastome, comprising 8 mitogenome CDS genes and 16 plastome CDS genes, corresponding to 2.39% of the R. chingii mitogenome. Mitogenomes had shorter but more collinear regions, evidenced by a comparison of the organelles of non-parasitic R. chingii, hemiparasitic Pedicularis chinensis, and holoparasitic Aeginetia indica in the Orobanchaceae family. Moreover, from non-parasitic to holoparasitic species, the genome size in the mitogenomes of Orobanchaceae species did not decrease gradually. Instead, the smallest mitogenome was found in the hemiparasitic species P. chinensis, with a size of 225,612 bp. The findings fill the gap in the mitogenome research of the medicinal plant R. chingii, promote the progress of the organelle genome research of the Orobanchaceae family, and provide clues for molecular breeding.
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Affiliation(s)
- Ying Han
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Y.H.); (X.-J.J.)
| | - Yan-Lei Feng
- College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China;
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China;
| | - Shan-Shan Zhu
- School of Marine Sciences, Ningbo University, Ningbo 315211, China;
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
| | - Xin-Jie Jin
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Y.H.); (X.-J.J.)
- Institute for Eco-Environmental Research of Sanyang Wetland, Wenzhou University, Wenzhou 325035, China
| | - Zhi-Qiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China;
| | - Yong-Hua Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Y.H.); (X.-J.J.)
- Institute for Eco-Environmental Research of Sanyang Wetland, Wenzhou University, Wenzhou 325035, China
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Zhang F, Kang H, Gao L. Complete Mitochondrial Genome Assembly of an Upland Wild Rice Species, Oryza granulata and Comparative Mitochondrial Genomic Analyses of the Genus Oryza. Life (Basel) 2023; 13:2114. [PMID: 38004254 PMCID: PMC10672236 DOI: 10.3390/life13112114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 10/15/2023] [Accepted: 10/18/2023] [Indexed: 11/26/2023] Open
Abstract
Wild upland rice species, including Oryza granulata, possess unique characteristics that distinguish them from other Oryza species. For instance, O. granulata characteristically has a GG genome and is accordingly classified as a basal lineage of the genus Oryza. Here, we deployed a versatile hybrid approach by integrating Illumina and PacBio sequencing data to generate a high-quality mitochondrial genome (mitogenome) assembly for O. granulata. The mitogenome of O. granulata was 509,311 base pairs (bp) with sixty-seven genes comprising two circular chromosomes, five ribosomal RNA (rRNA) coding genes, twenty-five transfer RNA (tRNA) coding genes, and thirty-seven genes coding for proteins. We identified a total of 378 simple sequence repeats (SSRs). The genome also contained 643 pairs of dispersed repeats comprising 340 palindromic and 303 forward. In the O. granulata mitogenome, the length of 57 homologous fragments in the chloroplast genome occupied 5.96% of the mitogenome length. Collinearity analysis of three Oryza mitogenomes revealed high structural variability and frequent rearrangements. Phylogenetic analysis showed that, compared to other related genera, O. granulata had the closest genetic relationship with mitogenomes reported for all members of Oryza, and occupies a position at the base of the Oryza phylogeny. Comparative analysis of complete mitochondrial genome assemblies for Oryza species revealed high levels of mitogenomic diversity, providing a foundation for future conservation and utilization of wild rice biodiversity.
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Affiliation(s)
- Fen Zhang
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China;
| | - Haiqi Kang
- Tropical Biodiversity and Genomics Research Center, Engineering Research Center for Selecting and Breeding New Tropical Crop Varieties, Ministry of Education, Hainan University, Haikou 570228, China;
| | - Lizhi Gao
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China;
- Tropical Biodiversity and Genomics Research Center, Engineering Research Center for Selecting and Breeding New Tropical Crop Varieties, Ministry of Education, Hainan University, Haikou 570228, China;
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Feng L, Wang Z, Wang C, Yang X, An M, Yin Y. Multichromosomal mitochondrial genome of Punica granatum: comparative evolutionary analysis and gene transformation from chloroplast genomes. BMC PLANT BIOLOGY 2023; 23:512. [PMID: 37880586 PMCID: PMC10598957 DOI: 10.1186/s12870-023-04538-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/18/2023] [Indexed: 10/27/2023]
Abstract
BACKGROUND Punica granatum is a fundamentally important fruit tree that has important economic, medicinal and ornamental properties. At present, there are few reports on the mitochondrial genome of pomegranate. Hence, in this study the P. granatum mitogenome was sequenced and assembled to further understanding of organization, variation, and evolution of mitogenomes of this tree species. RESULTS The genome structure was multi-chromosomes with seven circular contigs, measuring 382,774 bp in length with a 45.91% GC content. It contained 74 genes, including 46 protein-coding genes, 25 tRNA genes, and three rRNA genes. There were 188 pairs of dispersed repeats with lengths of 30 or greater, primarily consisting of reverse complementary repeats. The mitogenome analysis identified 114SSRs and 466 RNA editing sites. Analyses of codon usage, nucleotide diversity and gene migration from chloroplast to mitochondrial were also conducted. The collinear and comparative analysis of mitochondrial structures between P. granatum and its proximal species indicated that P. granatum 'Taishanhong' was closely related to P. granatum 'Qingpitian' and Lagerstroemia indica. Phylogenetic examination based on the mitogenome also confirmed the evolutionary relationship. CONCLUSION The results offered crucial information on the evolutionary biology of pomegranate and highlighted ways to promote the utilization of the species' germplasm.
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Affiliation(s)
- Lijuan Feng
- Shandong Institute of Pomology, Taian, 271000, Shandong, China
| | - Zenghui Wang
- Shandong Institute of Pomology, Taian, 271000, Shandong, China
| | - Chuanzeng Wang
- Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Xuemei Yang
- Shandong Institute of Pomology, Taian, 271000, Shandong, China
| | - Mengmeng An
- Zibo Academy of Agricultural Sciences, Zibo, 255000, Shandong, China
| | - Yanlei Yin
- Shandong Institute of Pomology, Taian, 271000, Shandong, China.
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Li X, Li M, Li W, Zhou J, Han Q, Lu W, Luo Q, Zhu S, Xiong A, Tan G, Zheng Y. Comparative Analysis of the Complete Mitochondrial Genomes of Apium graveolens and Apium leptophyllum Provide Insights into Evolution and Phylogeny Relationships. Int J Mol Sci 2023; 24:14615. [PMID: 37834070 PMCID: PMC10572446 DOI: 10.3390/ijms241914615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/14/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
The genus Apium, belonging to the family Apiaceae, comprises roughly 20 species. Only two species, Apium graveolens and Apium leptophyllum, are available in China and are both rich in nutrients and have favorable medicinal properties. However, the lack of genomic data has severely constrained the study of genetics and evolution in Apium plants. In this study, Illumina NovaSeq 6000 and Nanopore sequencing platforms were employed to identify the mitochondrial genomes of A. graveolens and A. leptophyllum. The complete lengths of the mitochondrial genomes of A. graveolens and A. leptophyllum were 263,017 bp and 260,164 bp, respectively, and contained 39 and 36 protein-coding genes, five and six rRNA genes, and 19 and 20 tRNA genes. Consistent with most angiosperms, both A. graveolens and A. leptophyllum showed a preference for codons encoding leucine (Leu). In the mitochondrial genome of A. graveolens, 335 SSRs were detected, which is higher than the 196 SSRs found in the mitochondrial genome of A. leptophyllum. Studies have shown that the most common RNA editing type is C-to-U, but, in our study, both A. graveolens and A. leptophyllum exhibited the U-C editing type. Furthermore, the transfer of the mitochondrial genomes of A. graveolens and A. leptophyllum into the chloroplast genomes revealed homologous sequences, accounting for 8.14% and 4.89% of the mitochondrial genome, respectively. Lastly, in comparing the mitochondrial genomes of 29 species, it was found that A. graveolens, A. leptophyllum, and Daucus carota form a sister group with a support rate of 100%. Overall, this investigation furnishes extensive insights into the mitochondrial genomes of A. graveolens and A. leptophyllum, thereby enhancing comprehension of the traits and evolutionary patterns within the Apium genus. Additionally, it offers supplementary data for evolutionary and comparative genomic analyses of other species within the Apiaceae family.
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Affiliation(s)
- Xiaoyan Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (X.L.); (M.L.); (W.L.); (J.Z.); (Q.H.); (W.L.)
| | - Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (X.L.); (M.L.); (W.L.); (J.Z.); (Q.H.); (W.L.)
| | - Weilong Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (X.L.); (M.L.); (W.L.); (J.Z.); (Q.H.); (W.L.)
| | - Jin Zhou
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (X.L.); (M.L.); (W.L.); (J.Z.); (Q.H.); (W.L.)
| | - Qiuju Han
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (X.L.); (M.L.); (W.L.); (J.Z.); (Q.H.); (W.L.)
| | - Wei Lu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (X.L.); (M.L.); (W.L.); (J.Z.); (Q.H.); (W.L.)
| | - Qin Luo
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China; (Q.L.); (S.Z.)
| | - Shunhua Zhu
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China; (Q.L.); (S.Z.)
| | - Aisheng Xiong
- College of Horticulture, Nanjing Agricultural University, Nanjing 611130, China;
| | - Guofei Tan
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China; (Q.L.); (S.Z.)
| | - Yangxia Zheng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (X.L.); (M.L.); (W.L.); (J.Z.); (Q.H.); (W.L.)
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Zhou P, Zhang Q, Li F, Huang J, Zhang M. Assembly and comparative analysis of the complete mitochondrial genome of Ilex metabaptista (Aquifoliaceae), a Chinese endemic species with a narrow distribution. BMC PLANT BIOLOGY 2023; 23:393. [PMID: 37580695 PMCID: PMC10424370 DOI: 10.1186/s12870-023-04377-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 07/12/2023] [Indexed: 08/16/2023]
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.
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Affiliation(s)
- Peng Zhou
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing, 211153, China
| | - Qiang Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, 210037, Nanjing, China.
| | - Fei Li
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing, 211153, China
| | - Jing Huang
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing, 211153, China
| | - Min Zhang
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing, 211153, China.
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Zhong F, Ke W, Li Y, Chen X, Zhou T, Xu B, Qi L, Yan Z, Ma Y. Comprehensive analysis of the complete mitochondrial genomes of three Coptis species ( C. chinensis, C. deltoidea and C. omeiensis): the important medicinal plants in China. FRONTIERS IN PLANT SCIENCE 2023; 14:1166420. [PMID: 37313257 PMCID: PMC10258346 DOI: 10.3389/fpls.2023.1166420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/11/2023] [Indexed: 06/15/2023]
Abstract
Coptis plants (Ranunculaceae) contain high levels of isoquinoline alkaloids and have a long history of medicinal use. Coptis species are of great value in pharmaceutical industries and scientific research. Mitochondria are considered as one of the central units for receiving stress signals and arranging immediate responses. Comprehensive characterizations of plant mitogenomes are imperative for revealing the relationship between mitochondria, elucidating biological functions of mitochondria and understanding the environmental adaptation mechanisms of plants. Here, the mitochondrial genomes of C. chinensis, C. deltoidea and C. omeiensis were assembled through the Nanopore and Illumina sequencing platform for the first time. The genome organization, gene number, RNA editing sites, repeat sequences, gene migration from chloroplast to mitochondria were compared. The mitogenomes of C. chinensis, C. deltoidea and C. omeiensis have six, two, two circular-mapping molecules with the total length of 1,425,403 bp, 1,520,338 bp and 1,152,812 bp, respectively. The complete mitogenomes harbors 68-86 predicted functional genes including 39-51 PCGs, 26-35 tRNAs and 2-5 rRNAs. C. deltoidea mitogenome host the most abundant repeat sequences, while C. chinensis mitogenome has the largest number of transferred fragments from its chloroplasts. The large repeat sequences and foreign sequences in the mitochondrial genomes of Coptis species were related to substantial rearrangements, changes in relative position of genes and multiple copy genes. Further comparative analysis illustrated that the PCGs under selected pressure in mitochondrial genomes of the three Coptis species mainly belong to the mitochondrial complex I (NADH dehydrogenase). Heat stress adversely affected the mitochondrial complex I and V, antioxidant enzyme system, ROS accumulation and ATP production of the three Coptis species. The activation of antioxidant enzymes, increase of T-AOC and maintenance of low ROS accumulation in C. chinensis under heat stress were suggested as the factors for its thermal acclimation and normal growth at lower altitudes. This study provides comprehensive information on the Coptis mitogenomes and is of great importance to elucidate the mitochondrial functions, understand the different thermal acclimation mechanisms of Coptis plants, and breed heat-tolerant varieties.
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Affiliation(s)
- Furong Zhong
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Wenjia Ke
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yirou Li
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaoyan Chen
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Tao Zhou
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Binjie Xu
- Innovative institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Luming Qi
- School of Health Preservation and Rehabilitation, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- Key Laboratory of Traditional Chinese Medicine Regimen and Health, State Administration of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Zhuyun Yan
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yuntong Ma
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Wu Z, Yang T, Qin R, Liu H. Complete Mitogenome and Phylogenetic Analysis of the Carthamus tinctorius L. Genes (Basel) 2023; 14:genes14050979. [PMID: 37239339 DOI: 10.3390/genes14050979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/16/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Carthamus tinctorius L. 1753 (Asteraceae), also called safflower, is a cash crop with both edible and medical properties. We analyzed and reported the safflower mitogenome based on combined short and long reads obtained from Illumina and Pacbio platforms, respectively. This safflower mitogenome mainly contained two circular chromosomes, with a total length of 321,872 bp, and encoded 55 unique genes, including 34 protein-coding genes (PCGs), 3 rRNA genes, and 18 tRNA genes. The total length of repeat sequences greater than 30 bp was 24,953 bp, accounting for 7.75% of the whole mitogenome. Furthermore, we characterized the RNA editing sites of protein-coding genes located in the safflower mitogenome, and the total number of RNA editing sites was 504. Then, we revealed partial sequence transfer events between plastid and mitochondria, in which one plastid-derived gene (psaB) remained intact in the mitogenome. Despite extensive arrangement events among the three mitogenomes of C. tinctorius, Arctium lappa, and Saussurea costus, the constructed phylogenetic tree based on mitogenome PCGs showed that C. tinctorius has a closer relationship with three Cardueae species, A. lappa, A. tomentosum, and S. costus, which is similar to the phylogeny constructed from the PCGs of plastid genomes. This mitogenome not only enriches the genetic information of safflower but also will be useful in the phylogeny and evolution study of the Asteraceae.
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Affiliation(s)
- Zhihua Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Tiange Yang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
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