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Li J, Ni Y, Yang H, Lu Q, Chen H, Liu C. Analysis of the complete mitochondrial genome of Panax quinquefolius reveals shifts from cis-splicing to trans-splicing of intron cox2i373. Gene 2024; 930:148869. [PMID: 39153707 DOI: 10.1016/j.gene.2024.148869] [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: 03/22/2024] [Revised: 07/15/2024] [Accepted: 08/14/2024] [Indexed: 08/19/2024]
Abstract
Panax quinquefolius is a perennial plant with medicinal values. In this study, we assembled the complete mitochondrial genome (mitogenome) of P. quinquefolius using PMAT assembler. The total length of P. quinquefolius mitogenome is 573,154 bp. We annotated a total of 34 protein-coding genes (PCGs), 35 tRNA genes, and 6 rRNA genes in this mitogenome. The analysis of repetitive elements shows that there are 153 SSRs, 24 tandem repeats and 242 pairs of dispersed repeats this mitogenome. Also, we found 24 homologous sequences with a total length of 64,070 bp among its mitogenome and plastome, accounting for 41.05 % of the plastome, and 11.18 % of the mitogenome, showing a remarkable frequent sequence dialogue between plastome and mitogenomes. Besides, a total of 583 C to U RNA editing sites on 34 PCGs of high confidence were predicted by using Deepred-mt. We also inferred the phylogenetic relationships of P. quinquefolius and other angiosperms based on mitochondrial PCGs. Finally, we observed a shift from cis- to trans-splicing in P. quinquefolius for two mitochondrial introns, namely cox2i373 and nad1i728, and a pair of 48 bp short repetitive sequences may be associated with the breaking and rearrangement of the cox2i373 intron. The fragmentation of the cox2i373 intron was further confirmed by our PCR amplification experiments. In summary, our report on the P. quinquefolius mitogenome provides a new perspective on the intron evolution of the mitogenome.
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Affiliation(s)
- Jingling Li
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-Di Herbs, Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Yang Ni
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-Di Herbs, Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Heyu Yang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-Di Herbs, Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Qianqi Lu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-Di Herbs, Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Haimei Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-Di Herbs, Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Chang Liu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-Di Herbs, Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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Veeraragavan S, Johansen M, Johnston IG. Evolution and maintenance of mtDNA gene content across eukaryotes. Biochem J 2024; 481:1015-1042. [PMID: 39101615 PMCID: PMC11346449 DOI: 10.1042/bcj20230415] [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: 04/08/2024] [Revised: 06/26/2024] [Accepted: 07/18/2024] [Indexed: 08/06/2024]
Abstract
Across eukaryotes, most genes required for mitochondrial function have been transferred to, or otherwise acquired by, the nucleus. Encoding genes in the nucleus has many advantages. So why do mitochondria retain any genes at all? Why does the set of mtDNA genes vary so much across different species? And how do species maintain functionality in the mtDNA genes they do retain? In this review, we will discuss some possible answers to these questions, attempting a broad perspective across eukaryotes. We hope to cover some interesting features which may be less familiar from the perspective of particular species, including the ubiquity of recombination outside bilaterian animals, encrypted chainmail-like mtDNA, single genes split over multiple mtDNA chromosomes, triparental inheritance, gene transfer by grafting, gain of mtDNA recombination factors, social networks of mitochondria, and the role of mtDNA dysfunction in feeding the world. We will discuss a unifying picture where organismal ecology and gene-specific features together influence whether organism X retains mtDNA gene Y, and where ecology and development together determine which strategies, importantly including recombination, are used to maintain the mtDNA genes that are retained.
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Affiliation(s)
| | - Maria Johansen
- Department of Mathematics, University of Bergen, Bergen, Norway
| | - Iain G. Johnston
- Department of Mathematics, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
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Yang S, Huang J, Qu Y, Zhang D, Tan Y, Wen S, Song Y. Phylogenetic incongruence in an Asiatic species complex of the genus Caryodaphnopsis (Lauraceae). BMC PLANT BIOLOGY 2024; 24:616. [PMID: 38937691 PMCID: PMC11212351 DOI: 10.1186/s12870-024-05050-3] [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: 12/09/2023] [Accepted: 04/19/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND Caryodaphnopsis, a group of tropical trees (ca. 20 spp.) in the family Lauraceae, has an amphi-Pacific disjunct distribution: ten species are distributed in Southeast Asia, while eight species are restricted to tropical rainforests in South America. Previously, phylogenetic analyses using two nuclear markers resolved the relationships among the five species from Latin America. However, the phylogenetic relationships between the species in Asia remain poorly known. RESULTS Here, we first determined the complete mitochondrial genome (mitogenome), plastome, and the nuclear ribosomal cistron (nrDNA) sequences of C. henryi with lengths of 1,168,029 bp, 154,938 bp, and 6495 bp, respectively. We found 2233 repeats and 368 potential SSRs in the mitogenome of C. henryi and 50 homologous DNA fragments between its mitogenome and plastome. Gene synteny analysis revealed a mass of rearrangements in the mitogenomes of Magnolia biondii, Hernandia nymphaeifolia, and C. henryi and only six conserved clustered genes among them. In order to reconstruct relationships for the ten Caryodaphnopsis species in Asia, we created three datasets: one for the mitogenome (coding genes and ten intergenic regions), another for the plastome (whole genome), and the other for the nuclear ribosomal cistron. All of the 22 Caryodaphnopsis individuals were divided into four, five, and six different clades in the phylogenies based on mitogenome, plastome, and nrDNA datasets, respectively. CONCLUSIONS The study showed phylogenetic conflicts within and between nuclear and organellar genome data of Caryodaphnopsis species. The sympatric Caryodaphnopsis species in Hekou and Malipo SW China may be related to the incomplete lineage sorting, chloroplast capture, and/or hybridization, which mixed the species as a complex in their evolutionary history.
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Affiliation(s)
- Shiting Yang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education) and Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, 541004, Guangxi, China
| | - Jiepeng Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education) and Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, 541004, Guangxi, China
| | - Yaya Qu
- Southwest Forestry University, Kunming, 650224, Yunnan, China
| | - Di Zhang
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences & Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Yunhong Tan
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences & Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Shujun Wen
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guangxi Institute of Botany, Guilin, 541006, China.
| | - Yu Song
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education) and Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, 541004, Guangxi, China.
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Hao Z, Jiang X, Pan L, Guo J, Chen Y, Li J, Liu B, Guo A, Luo L, Jia R. The complete mitochondrial genome of Pontederia crassipes: using HiFi reads to investigate genome recombination and gene transfer from chloroplast genome. FRONTIERS IN PLANT SCIENCE 2024; 15:1407309. [PMID: 39006960 PMCID: PMC11240117 DOI: 10.3389/fpls.2024.1407309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/12/2024] [Indexed: 07/16/2024]
Abstract
Water hyacinth (Pontederia crassipes Mart.) is a monocotyledonous aquatic plant renowned for its rapid growth, extensive proliferation, biological invasiveness, and ecological resilience to variations in pH, nutrients, and temperature. The International Union for Conservation of Nature (IUCN) has listed P. crassipes among the top 100 invasive species. However, comprehensive genomic information, particularly concerning its mitochondrial genome (mitogenome), remains surprisingly limited. In this study, the complete mitogenome of P. crassipes was analyzed using bioinformatics approaches. The mitogenome is 399,263 bp long and contains 38 protein-coding genes (PCGs), 24 tRNA genes, and 3 rRNA genes. Sequence analysis revealed that the complete mitogenome of the species contains 3,289 dispersed repeats, and 765 RNA editing sites in protein-coding genes. The P. crassipes mitogenome possessed un-conserved structures, including extensive sequence transfer between its chloroplasts and mitochondria. Our study on the mitogenome of P. crassipes offers critical insights into its evolutionary patterns and phylogenetic relationships with related taxa. This research enhances our understanding of this invasive species, known for its significant biomass and rapid overgrowth in aquatic environments.
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Affiliation(s)
- Zhigang Hao
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
- Hainan Seed Industry Laboratory, Sanya, Hainan, China
- Department of Plant Pathology, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Xiaoqi Jiang
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Lei Pan
- CAIQ Center for Biosafety in Sanya, Sanya, Hainan, China
| | - Jingyuan Guo
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Yi Chen
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Jianqiang Li
- Department of Plant Pathology, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Biao Liu
- Ministry of Ecology and Environment, Nanjing Institute of Environmental Sciences, Nanjing, China
| | - Anping Guo
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Laixin Luo
- Department of Plant Pathology, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Ruizong Jia
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
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Li Z, Liu J, Liang M, Guo Y, Chen X, Wu H, Jin S. De novo assembly of the complete mitochondrial genome of pepino (Solanum muricatum) using PacBio HiFi sequencing: insights into structure, phylogenetic implications, and RNA editing. BMC PLANT BIOLOGY 2024; 24:361. [PMID: 38702620 PMCID: PMC11069145 DOI: 10.1186/s12870-024-04978-w] [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: 10/29/2023] [Accepted: 04/02/2024] [Indexed: 05/06/2024]
Abstract
BACKGROUND Solanum muricatum is an emerging horticultural fruit crop with rich nutritional and antioxidant properties. Although the chromosome-scale genome of this species has been sequenced, its mitochondrial genome sequence has not been reported to date. RESULTS PacBio HiFi sequencing was used to assemble the circular mitogenome of S. muricatum, which was 433,466 bp in length. In total, 38 protein-coding, 19 tRNA, and 3 rRNA genes were annotated. The reticulate mitochondrial conformations with multiple junctions were verified by polymerase chain reaction, and codon usage, sequence repeats, and gene migration from chloroplast to mitochondrial genome were determined. A collinearity analysis of eight Solanum mitogenomes revealed high structural variability. Overall, 585 RNA editing sites in protein coding genes were identified based on RNA-seq data. Among them, mttB was the most frequently edited (52 times), followed by ccmB (46 times). A phylogenetic analysis based on the S. muricatum mitogenome and those of 39 other taxa (including 25 Solanaceae species) revealed the evolutionary and taxonomic status of S. muricatum. CONCLUSIONS We provide the first report of the assembled and annotated S. muricatum mitogenome. This information will help to lay the groundwork for future research on the evolutionary biology of Solanaceae species. Furthermore, the results will assist the development of molecular breeding strategies for S. muricatum based on the most beneficial agronomic traits of this species.
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Affiliation(s)
- Ziwei Li
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Jiaxun Liu
- Horticultural Research Institute Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Mingtai Liang
- Horticultural Research Institute Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Yanbing Guo
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Xia Chen
- Horticultural Research Institute Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Hongzhi Wu
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
| | - Shoulin Jin
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
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Gong J, Yang J, Lai Y, Pan T, She W. A High-Quality Assembly and Comparative Analysis of the Mitogenome of Actinidia macrosperma. Genes (Basel) 2024; 15:514. [PMID: 38674448 PMCID: PMC11049864 DOI: 10.3390/genes15040514] [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: 01/30/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The mitochondrial genome (mitogenome) of Actinidia macrosperma, a traditional medicinal plant within the Actinidia genus, remains relatively understudied. This study aimed to sequence the mitogenome of A. macrosperma, determining its assembly, informational content, and developmental expression. The results revealed that the mitogenome of A. macrosperma is circular, spanning 752,501 bp with a GC content of 46.16%. It comprises 63 unique genes, including 39 protein-coding genes (PCGs), 23 tRNA genes, and three rRNA genes. Moreover, the mitogenome was found to contain 63 SSRs, predominantly mono-nucleotides, as well as 25 tandem repeats and 650 pairs of dispersed repeats, each with lengths equal to or greater than 60, mainly comprising forward repeats and palindromic repeats. Moreover, 53 homologous fragments were identified between the mitogenome and chloroplast genome (cp-genome), with the longest segment measuring 4296 bp. This study represents the initial report on the mitogenome of the A. macrosperma, providing crucial genetic materials for phylogenetic research within the Actinidia genus and promoting the exploitation of species genetic resources.
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Affiliation(s)
- Jiangmei Gong
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.G.); (Y.L.); (T.P.)
- Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jun Yang
- College of Food and Bioengineering, Bengbu University, Bengbu 233030, China;
| | - Yan Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.G.); (Y.L.); (T.P.)
- Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tengfei Pan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.G.); (Y.L.); (T.P.)
- Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenqin She
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.G.); (Y.L.); (T.P.)
- Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Fukasawa Y, Driguez P, Bougouffa S, Carty K, Putra A, Cheung MS, Ermini L. Plasticity of repetitive sequences demonstrated by the complete mitochondrial genome of Eucalyptus camaldulensis. FRONTIERS IN PLANT SCIENCE 2024; 15:1339594. [PMID: 38601302 PMCID: PMC11005031 DOI: 10.3389/fpls.2024.1339594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/07/2024] [Indexed: 04/12/2024]
Abstract
The tree Eucalyptus camaldulensis is a ubiquitous member of the Eucalyptus genus, which includes several hundred species. Despite the extensive sequencing and assembly of nuclear genomes from various eucalypts, the genus has only one fully annotated and complete mitochondrial genome (mitogenome). Plant mitochondria are characterized by dynamic genomic rearrangements, facilitated by repeat content, a feature that has hindered the assembly of plant mitogenomes. This complexity is evident in the paucity of available mitogenomes. This study, to the best of our knowledge, presents the first E. camaldulensis mitogenome. Our findings suggest the presence of multiple isomeric forms of the E. camaldulensis mitogenome and provide novel insights into minor rearrangements triggered by nested repeat sequences. A comparative sequence analysis of the E. camaldulensis and E. grandis mitogenomes unveils evolutionary changes between the two genomes. A significant divergence is the evolution of a large repeat sequence, which may have contributed to the differences observed between the two genomes. The largest repeat sequences in the E. camaldulensis mitogenome align well with significant yet unexplained structural variations in the E. grandis mitogenome, highlighting the adaptability of repeat sequences in plant mitogenomes.
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Affiliation(s)
- Yoshinori Fukasawa
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Japan
| | - Patrick Driguez
- Core Labs, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Salim Bougouffa
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Karen Carty
- Core Labs, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Alexander Putra
- Core Labs, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ming-Sin Cheung
- Core Labs, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Luca Ermini
- NORLUX NeuroOncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
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Liu J, Feng Y, Chen C, Yan J, Bai X, Li H, Lin C, Xiang Y, Tian W, Qi Z, Yu J, Yan X. Genomic insights into the clonal reproductive Opuntia cochenillifera: mitochondrial and chloroplast genomes of the cochineal cactus for enhanced understanding of structural dynamics and evolutionary implications. FRONTIERS IN PLANT SCIENCE 2024; 15:1347945. [PMID: 38516667 PMCID: PMC10954886 DOI: 10.3389/fpls.2024.1347945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/20/2024] [Indexed: 03/23/2024]
Abstract
Background The cochineal cactus (Opuntia cochenillifera), notable for its substantial agricultural and industrial applications, predominantly undergoes clonal reproduction, which presents significant challenges in breeding and germplasm innovation. Recent developments in mitochondrial genome engineering offer promising avenues for introducing heritable mutations, potentially facilitating selective sexual reproduction through the creation of cytoplasmic male sterile genotypes. However, the lack of comprehensive mitochondrial genome information for Opuntia species hinders these efforts. Here, we intended to sequence and characterize its mitochondrial genome to maximize the potential of its genomes for evolutionary studies, molecular breeding, and molecular marker developments. Results We sequenced the total DNA of the O. cochenillifera using DNBSEQ and Nanopore platforms. The mitochondrial genome was then assembled using a hybrid assembly strategy using Unicycler software. We found that the mitochondrial genome of O. cochenillifera has a length of 1,156,235 bp, a GC content of 43.06%, and contains 54 unique protein-coding genes and 346 simple repeats. Comparative genomic analysis revealed 48 homologous fragments shared between mitochondrial and chloroplast genomes, with a total length of 47,935 bp. Additionally, the comparison of mitochondrial genomes from four Cactaceae species highlighted their dynamic nature and frequent mitogenomic reorganizations. Conclusion Our study provides a new perspective on the evolution of the organelle genome and its potential application in genetic breeding. These findings offer valuable insights into the mitochondrial genetics of Cactaceae, potentially facilitating future research and breeding programs aimed at enhancing the genetic diversity and adaptability of O. cochenillifera by leveraging its unique mitochondrial genome characteristics.
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Affiliation(s)
- Jing Liu
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yuqing Feng
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Cheng Chen
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Jing Yan
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Xinyu Bai
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Huiru Li
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Chen Lin
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Yinan Xiang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Wen Tian
- Animal Plant and Food Inspection Center of Nanjing Customs District, Nanjing, China
| | - Zhechen Qi
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Jing Yu
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Xiaoling Yan
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
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Hao Z, Zhang Z, Zhang J, Cui X, Li J, Luo L, Li Y. The complete mitochondrial genome of Aglaia odorata, insights into its genomic structure and RNA editing sites. FRONTIERS IN PLANT SCIENCE 2024; 15:1362045. [PMID: 38510436 PMCID: PMC10950942 DOI: 10.3389/fpls.2024.1362045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/21/2024] [Indexed: 03/22/2024]
Abstract
Aglaia odorata, native to Guangdong, Guangxi, and Hainan provinces in China, has long been utilized as an herbal remedy in ancient China. In this study, we assembled and annotated the complete mitochondrial genome (mitogenome) of A. odorata, which spans a total length of 537,321 bp. Conformation of the A. odorata recombination was verified through PCR experiments and Sanger sequencing. We identified and annotated 35 protein-coding genes (PCGs), 22 tRNA genes, and 3 rRNA genes within the mitogenome. Analysis of repeated elements revealed the presence of 192 SSRs, 29 pairs of tandem repeats, and 333 pairs of dispersed repeats in the A. odorata mitogenome. Additionally, we analyzed codon usage and mitochondrial plastid DNAs (MTPTs). Twelve MTPTs between the plastome and mitogenome of A. odorata were identified, with a combined length of 2,501 bp, accounting for 0.47% of the mitogenome. Furthermore, 359 high-confidence C to U RNA editing sites were predicted on PCGs, and four selected RNA editing sites were specially examined to verify the creation of start and/or stop codons. Extensive genomic rearrangement was observed between A. odorata and related mitogenomes. Phylogenetic analysis based on mitochondrial PCGs were conducted to elucidate the evolutionary relationships between A. odorata and other angiosperms.
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Affiliation(s)
- Zhigang Hao
- Department of Pesticide Science, State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, China
- Sanya Institute of China Agricultural University, Sanya, Hainan, China
- Hainan Seed Industry Laboratory, Sanya, Hainan, China
| | - Zhiping Zhang
- Department of Pesticide Science, State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Jinan Zhang
- Sanya Institute of China Agricultural University, Sanya, Hainan, China
| | - Xiufen Cui
- Hainan Seed Industry Laboratory, Sanya, Hainan, China
- Department of Plant Pathology, Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, China
| | - Jianqiang Li
- Hainan Seed Industry Laboratory, Sanya, Hainan, China
- Department of Plant Pathology, Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, China
| | - Laixin Luo
- Hainan Seed Industry Laboratory, Sanya, Hainan, China
- MOA Key Lab of Pest Monitoring and Green Management, China Agricultural University, Beijing, China
| | - Yingbin Li
- Department of Pesticide Science, State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, China
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Zwonitzer KD, Tressel LG, Wu Z, Kan S, Broz AK, Mower JP, Ruhlman TA, Jansen RK, Sloan DB, Havird JC. Genome copy number predicts extreme evolutionary rate variation in plant mitochondrial DNA. Proc Natl Acad Sci U S A 2024; 121:e2317240121. [PMID: 38427600 DOI: 10.1073/pnas.2317240121] [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: 10/12/2023] [Accepted: 01/22/2024] [Indexed: 03/03/2024] Open
Abstract
Nuclear and organellar genomes can evolve at vastly different rates despite occupying the same cell. In most bilaterian animals, mitochondrial DNA (mtDNA) evolves faster than nuclear DNA, whereas this trend is generally reversed in plants. However, in some exceptional angiosperm clades, mtDNA substitution rates have increased up to 5,000-fold compared with closely related lineages. The mechanisms responsible for this acceleration are generally unknown. Because plants rely on homologous recombination to repair mtDNA damage, we hypothesized that mtDNA copy numbers may predict evolutionary rates, as lower copy numbers may provide fewer templates for such repair mechanisms. In support of this hypothesis, we found that copy number explains 47% of the variation in synonymous substitution rates of mtDNA across 60 diverse seed plant species representing ~300 million years of evolution. Copy number was also negatively correlated with mitogenome size, which may be a cause or consequence of mutation rate variation. Both relationships were unique to mtDNA and not observed in plastid DNA. These results suggest that homologous recombinational repair plays a role in driving mtDNA substitution rates in plants and may explain variation in mtDNA evolution more broadly across eukaryotes. Our findings also contribute to broader questions about the relationships between mutation rates, genome size, selection efficiency, and the drift-barrier hypothesis.
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Affiliation(s)
- Kendra D Zwonitzer
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - Lydia G Tressel
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
- Marine College, Shandong University, Weihai 264209, China
| | - Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, CO 80523
| | - Jeffrey P Mower
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588
| | - Tracey A Ruhlman
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - Robert K Jansen
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523
| | - Justin C Havird
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
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11
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Feng G, Jiao Y, Ma H, Bian H, Nie G, Huang L, Xie Z, Ran Q, Fan W, He W, Zhang X. The first two whole mitochondrial genomes for the genus Dactylis species: assembly and comparative genomics analysis. BMC Genomics 2024; 25:235. [PMID: 38438835 PMCID: PMC10910808 DOI: 10.1186/s12864-024-10145-0] [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: 09/16/2023] [Accepted: 02/19/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Orchardgrass (Dactylis glomerata L.), a perennial forage, has the advantages of rich leaves, high yield, and good quality and is one of the most significant forage for grassland animal husbandry and ecological management in southwest China. Mitochondrial (mt) genome is one of the major genetic systems in plants. Studying the mt genome of the genus Dactylis could provide more genetic information in addition to the nuclear genome project of the genus. RESULTS In this study, we sequenced and assembled two mitochondrial genomes of Dactylis species of D. glomerata (597, 281 bp) and D. aschersoniana (613, 769 bp), based on a combination of PacBio and Illumina. The gene content in the mitochondrial genome of D. aschersoniana is almost identical to the mitochondrial genome of D. glomerata, which contains 22-23 protein-coding genes (PCGs), 8 ribosomal RNAs (rRNAs) and 30 transfer RNAs (tRNAs), while D. glomerata lacks the gene encoding the Ribosomal protein (rps1) and D. aschersoniana contains one pseudo gene (atp8). Twenty-three introns were found among eight of the 30 protein-coding genes, and introns of three genes (nad 1, nad2, and nad5) were trans-spliced in Dactylis aschersoniana. Further, our mitochondrial genome characteristics investigation of the genus Dactylis included codon usage, sequences repeats, RNA editing and selective pressure. The results showed that a large number of short repetitive sequences existed in the mitochondrial genome of D. aschersoniana, the size variation of two mitochondrial genomes is due largely to the presence of a large number of short repetitive sequences. We also identified 52-53 large fragments that were transferred from the chloroplast genome to the mitochondrial genome, and found that the similarity was more than 70%. ML and BI methods used in phylogenetic analysis revealed that the evolutionary status of the genus Dactylis. CONCLUSIONS Thus, this study reveals the significant rearrangements in the mt genomes of Pooideae species. The sequenced Dactylis mt genome can provide more genetic information and improve our evolutionary understanding of the mt genomes of gramineous plants.
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Affiliation(s)
- Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yongjuan Jiao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huizhen Ma
- Grassland Research Institute, Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Haoyang Bian
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zheni Xie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qifan Ran
- Grassland Research Institute, Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Wenwen Fan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei He
- Grassland Research Institute, Chongqing Academy of Animal Science, Chongqing, 402460, China.
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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12
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He D, Li Y, Yuan C, Pei X, Damaris RN, Yu H, Qian B, Liu Y, Yi B, Huang C, Zeng J. Characterization of the CMS genetic regulation through comparative complete mitochondrial genome sequencing in Nicotiana tabacum. THE PLANT GENOME 2024; 17:e20409. [PMID: 37961811 DOI: 10.1002/tpg2.20409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 10/01/2023] [Accepted: 10/14/2023] [Indexed: 11/15/2023]
Abstract
Mitochondrial genomes (mitogenomes) of flowering plants vary greatly in structure and size, which can lead to frequent gene mutation, rearrangement, or recombination, then result in the cytoplasmic male sterile (CMS) mutants. In tobacco (Nicotiana tabacum), suaCMS lines are widely used in heterosis breeding; however, the related genetic regulations are not very clear. In this study, the cytological observation indicated that the pollen abortion of tobacco suaCMS(HD) occurred at the very early stage of the stamen primordia differentiation. In this study, the complete mitochondrial genomes of suaCMS(HD) and its maintainer HD were sequenced using the PacBio and Illumina Hiseq technology. The total length of the assembled mitogenomes of suaCMS(HD) and HD was 494,317 bp and 430,694 bp, respectively. Comparative analysis indicated that the expanded 64 K bases in suaCMS(HD) were mainly located in noncoding regions, and 23 and 21 big syntenic blocks (>5000 bp) were found in suaCMS(HD) and HD with a series of repeats. Electron transport chain-related genes were highly conserved in two mitogenomes, except five genes (ATP4, ATP6, COX2, CcmFC, and SDH3) with substantial substitutions. Three suaCMS(HD)-specific genes, orf261, orf291, and orf433, were screened. Sequence analysis and RT-PCR verification showed that they were unique to suaCMS(HD). Further gene location analysis and protein property prediction indicated that all the three genes were likely candidates for suaCMS(HD). This study provides new insight into understanding the suaCMS mechanism and is useful for improving tobacco breeding.
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Affiliation(s)
- Dongli He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Yifan Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, China
| | - Cheng Yuan
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Xiaoxiong Pei
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, China
| | | | - Haiqin Yu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Bao Qian
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, China
| | - Yong Liu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, China
| | - Changjun Huang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Jianmin Zeng
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
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13
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Bi C, Shen F, Han F, Qu Y, Hou J, Xu K, Xu LA, He W, Wu Z, Yin T. PMAT: an efficient plant mitogenome assembly toolkit using low-coverage HiFi sequencing data. HORTICULTURE RESEARCH 2024; 11:uhae023. [PMID: 38469379 PMCID: PMC10925850 DOI: 10.1093/hr/uhae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 01/14/2024] [Indexed: 03/13/2024]
Abstract
Complete mitochondrial genomes (mitogenomes) of plants are valuable resources for nucleocytoplasmic interactions, plant evolution, and plant cytoplasmic male sterile line breeding. However, the complete assembly of plant mitogenomes is challenging due to frequent recombination events and horizontal gene transfers. Previous studies have adopted Illumina, PacBio, and Nanopore sequencing data to assemble plant mitogenomes, but the poor assembly completeness, low sequencing accuracy, and high cost limit the sampling capacity. Here, we present an efficient assembly toolkit (PMAT) for de novo assembly of plant mitogenomes using low-coverage HiFi sequencing data. PMAT has been applied to the de novo assembly of 13 broadly representative plant mitogenomes, outperforming existing organelle genome assemblers in terms of assembly accuracy and completeness. By evaluating the assembly of plant mitogenomes from different sequencing data, it was confirmed that PMAT only requires 1× HiFi sequencing data to obtain a complete plant mitogenome. The source code for PMAT is available at https://github.com/bichangwei/PMAT. The developed PMAT toolkit will indeed accelerate the understanding of evolutionary variation and breeding application of plant mitogenomes.
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Affiliation(s)
- Changwei Bi
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China
- Department of artificial intelligence, College of Information Science and Technology, College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China
| | - Fei Shen
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Fuchuan Han
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Yanshu Qu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China
| | - Jing Hou
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China
| | - Kewang Xu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China
| | - Li-an Xu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China
| | - Wenchuang He
- 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 518000, China
| | - Zhiqiang 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 518000, China
| | - Tongming Yin
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China
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14
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Ha YH, Chang KS, Gil HY. Characteristics of chloroplast and mitochondrial genomes and intracellular gene transfer in the Korean endemic shrub, Sophora koreensis Nakai (Fabaceae). Gene 2024; 894:147963. [PMID: 37926173 DOI: 10.1016/j.gene.2023.147963] [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: 08/22/2023] [Revised: 10/24/2023] [Accepted: 11/01/2023] [Indexed: 11/07/2023]
Abstract
Sophora koreensis Nakai, an endemic species distributed only in the Korean Peninsula, is of great geographical, economic, and taxonomic importance. Although its complete chloroplast (cp) genome sequence has been reported, its mitochondrial (mt) genome sequence has not yet been studied. Therefore, in this study, we aimed to investigate its mt genome sequence and compare it with those reported for other Fabaceae species. Total genomic DNA was extracted from fresh S. koreensis leaves collected from natural habitats in Gangwon-do Province, South Korea. This was followed by polymerase chain reaction (PCR) amplification of cpDNA insertions in the mt genome and the detection of microsatellites and dispersed repeats in the cp and mt genomes. Finally, the cp and mt genomes of S. koreensis were compared with those reported for other Fabaceae species. The cp sequence of S. koreensis showed identical gene orders and contents as those previously reported. Only six substitutions and one deletion were detected with 99 % homology. Conversely, the complete mt genome sequence, which was 517,845 bp in length and encoded 61 genes, including 43 protein-coding, 15 transfer RNAs, and 3 ribosomal RNA genes, was considerably different from that of S. japonica in terms of gene order and composition. Further, the mt genome of S. koreensis included ca. 7 and 3 kb insertions, representing an intracellular gene transfer (IGT) event, and the regions with these insertions were determined to be originally present in the cp genome. This IGT event was also confirmed via PCR amplification. IGT events can be induced via biological gene expression control or the use of repetitive sequences, and they provide important insights into the evolutionary lineage of S. koreensis. However, further studies are needed to clarify the gene transfer mechanisms between the two organelles.
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Affiliation(s)
- Young-Ho Ha
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon-si, Gyeonggi-do 11186, Republic of Korea
| | - Kae Sun Chang
- DMZ Botanic Garden, Korea National Arboretum, Yanggu-gun, Gangwon-do 24564, Republic of Korea
| | - Hee-Young Gil
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon-si, Gyeonggi-do 11186, Republic of Korea.
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15
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Yang P, Guo K, Yang Y, Lyu M, Liu J, Li X, Feng Y. Phylogeny and genetic variations of the three genome compartments in haptophytes shed light on the rapid evolution of coccolithophores. Gene 2023; 887:147716. [PMID: 37604324 DOI: 10.1016/j.gene.2023.147716] [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: 04/14/2023] [Accepted: 08/15/2023] [Indexed: 08/23/2023]
Abstract
Haptophyte algae, including coccolithophores, play key roles in global carbon cycling and ecosystem. They exhibit exceptional morphological and functional diversity. However, their phylogeny is mostly based on short markers and genome researches are always limited to few species, hindering a better understanding about their evolution and diversification. In this study, by assembling 69 new plastid genomes, 65 new mitochondrial genomes, and 55 nuclear drafts, we systematically analyzed their genome variations and built the most comprehensive phylogenies in haptophytes and Noelaerhabdaceae, with the latter is the family of the model coccolithophore Emiliania huxleyi. The haptophyte genomes vary significantly in size, gene content, and structure. We detected phylogenetic incongruence of Prymnesiales between genome compartments. In Noelaerhabdaceae, by including Reticulofenestra sessilis and a proper outgroup, we found R. sessilis was not the basal taxon of this family. Noelaerhabdaceae strains have very similar genomic features and conserved sequences, but different gene content and dynamic structure. We speculate that was caused by DNA double-strand break repairs. Our results provide valuable genetic resources and new insights into the evolution of haptophytes, especially coccolithophores.
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Affiliation(s)
- Penghao Yang
- Fudan University, Shanghai 200433, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Kangning Guo
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Yuqing Yang
- Fudan University, Shanghai 200433, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Mingjie Lyu
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin 300380, China
| | - Jingwen Liu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Xiaobo Li
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Yanlei Feng
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China.
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16
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Zhu H, Shan Y, Li J, Zhang X, Yu J, Wang H. Assembly and comparative analysis of the complete mitochondrial genome of Viburnum chinshanense. BMC PLANT BIOLOGY 2023; 23:487. [PMID: 37821817 PMCID: PMC10566092 DOI: 10.1186/s12870-023-04493-4] [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: 04/03/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND Viburnum chinshanense is an endemic species found exclusively in the North-Central and South-Central regions of China. This species is a lush garden ornamental tree and is extensively utilized for vegetation restoration in rocky desertification areas. RESULTS In this study, we obtained 13.96 Gb of Oxford Nanopore data for the whole genome, and subsequently, by combining Illumina short-reads, we successfully assembled the complete mitochondrial genome (mitogenome) of the V. chinshanense using a hybrid assembly strategy. The assembled genome can be described as a circular genome. The total length of the V. chinshanense mitogenome measures 643,971 bp, with a GC content of 46.18%. Our annotation efforts have revealed a total of 39 protein-coding genes (PCGs), 28 tRNA genes, and 3 rRNA genes within the V. chinshanense mitogenome. The analysis of repeated elements has identified 212 SSRs, 19 long tandem repeat elements, and 325 pairs of dispersed repeats in the V. chinshanense mitogenome. Additionally, we have investigated mitochondrial plastid DNAs (MTPTs) and identified 21 MTPTs within the mitogenome and plastidial genome. These MTPTs collectively span a length of 9,902 bp, accounting for 1.54% of the mitogenome. Moreover, employing Deepred-mt, we have confidently predicted 623 C to U RNA editing sites across the 39 protein-coding genes. Furthermore, extensive genomic rearrangements have been observed between V. chinshanense and the mitogenomes of related species. Interestingly, we have also identified a bacterial-derived tRNA gene (trnC-GCA) in the V. chinshanense mitogenome. Lastly, we have inferred the phylogenetic relationships of V. chinshanense with other angiosperms based on mitochondrial PCGs. CONCLUSIONS This study marks the first report of a mitogenome from the Viburnum genus, offering a valuable genomic resource for exploring the evolution of mitogenomes within the Dipsacales order.
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Affiliation(s)
- Haoxiang Zhu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing, 400715, China
| | - Yuanyu Shan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Xue Zhang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China.
| | - Haiyang Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China.
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing, 400715, China.
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17
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Xu S, Teng K, Zhang H, Wu J, Duan L, Zhang H, Wen H, Teng W, Yue Y, Fan X. The first complete mitochondrial genome of Carex (C. breviculmis): a significantly expanded genome with highly structural variations. PLANTA 2023; 258:43. [PMID: 37450262 DOI: 10.1007/s00425-023-04169-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/27/2023] [Indexed: 07/18/2023]
Abstract
MAIN CONCLUSION The first complete mitochondrial genome of Carex (C. breviculmis) was sequenced and assembled, and its genomic signature was analyzed and the possible conformations of its mitochondrial genome were validated. Carex breviculmis is a very adaptable grass that is highly resistant to environmental stresses such as drought and low light. It is also admired as a landscape plant with high development prospects and scientific research value. In this study, the mitochondrial genome of C. breviculmis was assembled using Pacbio and Illumina sequencing data. We detected 267 pairs of repeats and found that three pairs of repeats could mediate the recombination of its mitochondrial genome and formed four possible conformations, of which we verified the two conformations mediated by the shortest pair of repeats using PCR amplification and Sanger sequencing. The major conformation of the C. breviculmis mitochondrial genome is a 1,414,795 bp long circular molecule with 33 annotated protein-coding genes, 15 tRNA genes, and three rRNA genes. We detected a total of 25 homologous sequences between the chloroplast and mitochondrial genomes, corresponding to 0.40% of the mitochondrial genome. Combined with the low GC content (41.24%), we conclude that the reduction in RNA editing sites in the C. breviculmis mitochondrial genome may be due to an accumulation of point mutations in C-to-T or retroprocessing events within the genome. The relatively low number of RNA editing sites in its mitochondrial genome could serve as important material for subsequent studies on the selection pressure of RNA editing in angiosperms. A maximum likelihood analysis based on 23 conserved mitochondrial genes from 28 species reflects an accurate evolutionary and taxonomic position of C. breviculmis. This research provided us with a comprehensive understanding of the mitochondrial genome of Carex and also provided important information for its molecular breeding.
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Affiliation(s)
- Shenjian Xu
- Institute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ke Teng
- Institute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Hui Zhang
- Institute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Juying Wu
- Institute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Liusheng Duan
- College of Plants and Technology, Beijing University of Agriculture, Beijing, China
| | - Hongyu Zhang
- Institute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Haifeng Wen
- Institute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Wenjun Teng
- Institute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yuesen Yue
- Institute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
| | - Xifeng Fan
- Institute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
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18
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Zhang X, Shan Y, Li J, Qin Q, Yu J, Deng H. Assembly of the Complete Mitochondrial Genome of Pereskia aculeata Revealed That Two Pairs of Repetitive Elements Mediated the Recombination of the Genome. Int J Mol Sci 2023; 24:ijms24098366. [PMID: 37176072 PMCID: PMC10179450 DOI: 10.3390/ijms24098366] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
Pereskia aculeata is a potential new crop species that has both food and medicinal (antinociceptive activity) properties. However, comprehensive genomic research on P. aculeata is still lacking, particularly concerning its organelle genome. In this study, P. aculeata was studied to sequence the mitochondrial genome (mitogenome) and to ascertain the assembly, informational content, and developmental expression of the mitogenome. The findings revealed that the mitogenome of P. aculeata is circular and measures 515,187 bp in length with a GC content of 44.05%. It contains 52 unique genes, including 33 protein-coding genes, 19 tRNA genes, and three rRNA genes. Additionally, the mitogenome analysis identified 165 SSRs, primarily consisting of tetra-nucleotides, and 421 pairs of dispersed repeats with lengths greater than or equal to 30, which were mainly forward repeats. Based on long reads and PCR experiments, we confirmed that two pairs of long-fragment repetitive elements were highly involved with the mitogenome recombination process. Furthermore, there were 38 homologous fragments detected between the mitogenome and chloroplast genome, and the longest fragment was 3962 bp. This is the first report on the mitogenome in the family Cactaceae. The decoding of the mitogenome of P. aculeata will provide important genetic materials for phylogenetic studies of Cactaceae and promote the utilization of species germplasm resources.
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Affiliation(s)
- Xue Zhang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
| | - Yuanyu Shan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
| | - Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
| | - Qiulin Qin
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Southwest University, Chongqing 400715, China
| | - Hongping Deng
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing 400715, China
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19
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Liu Q, Yuan H, Xu J, Cui D, Xiong G, Schwarzacher T, Heslop-Harrison JS. The mitochondrial genome of the diploid oat Avena longiglumis. BMC PLANT BIOLOGY 2023; 23:218. [PMID: 37098475 PMCID: PMC10131481 DOI: 10.1186/s12870-023-04217-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Avena longiglumis Durieu (2n = 2x = 14) is a wild relative of cultivated oat (Avena sativa, 2n = 6x = 42) with good agronomic and nutritional traits. The plant mitochondrial genome has a complex organization and carries genetic traits of value in exploiting genetic resources, not least male sterility alleles used to generate F1 hybrid seeds. Therefore, we aim to complement the chromosomal-level nuclear and chloroplast genome assemblies of A. longiglumis with the complete assembly of the mitochondrial genome (mitogenome) based on Illumina and ONT long reads, comparing its structure with Poaceae species. RESULTS The complete mitochondrial genome of A. longiglumis can be represented by one master circular genome being 548,445 bp long with a GC content of 44.05%. It can be represented by linear or circular DNA molecules (isoforms or contigs), with multiple alternative configurations mediated by long (4,100-31,235 bp) and medium (144-792 bp) size repeats. Thirty-five unique protein-coding genes, three unique rRNA genes, and 11 unique tRNA genes are identified. The mitogenome is rich in duplications (up to 233 kb long) and multiple tandem or simple sequence repeats, together accounting for more than 42.5% of the total length. We identify homologous sequences between the mitochondrial, plastid and nuclear genomes, including the exchange of eight plastid-derived tRNA genes, and nuclear-derived retroelement fragments. At least 85% of the mitogenome is duplicated in the A. longiglumis nuclear genome. We identify 269 RNA editing sites in mitochondrial protein-coding genes including stop codons truncating ccmFC transcripts. CONCLUSIONS Comparative analysis with Poaceae species reveals the dynamic and ongoing evolutionary changes in mitochondrial genome structure and gene content. The complete mitochondrial genome of A. longiglumis completes the last link of the oat reference genome and lays the foundation for oat breeding and exploiting the biodiversity in the genus.
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Affiliation(s)
- Qing Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
- Center for Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Hongyu Yuan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiaxin Xu
- College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Dongli Cui
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Gui Xiong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Trude Schwarzacher
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, LE1 7RH, UK
| | - John Seymour Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, LE1 7RH, UK.
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20
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Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Photinia serratifolia. Sci Rep 2023; 13:770. [PMID: 36641495 PMCID: PMC9840629 DOI: 10.1038/s41598-022-24327-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 11/14/2022] [Indexed: 01/15/2023] Open
Abstract
Plant mitochondrial genomes (mitogenomes) are a valuable source of genetic information for a better understanding of phylogenetic relationships. However, no mitogenome of any species in the genus of Photinia has been reported. In this study, using NGS sequencing, we reported the mitogenome assembly and annotation of Photinia serratifolia, which is 473,579 bp in length, contains 38 protein-coding genes, 23 tRNAs, and 6 rRNAs, with 61 genes have no introns. The rps2 and rps11 genes are missing in the P. serratifolia mitogenome. Although there are more editing sites (488) in the P. serratifolia mitogenome than in most angiosperms, fewer editing types were found in the P. serratifolia mitogenome, showing a clear bias in RNA-editing. Phylogenetic analysis based on the mitogenomes of P. serratifolia and 8 other taxa of the Rosaceae family reflected the exact evolutionary and taxonomic status of P. serratifolia. However, Ka/Ks analysis revealed that 72.69% of the protein-coding genes in the P. serratifolia mitogenome had undergone negative selections, reflecting the importance of those genes in the P. serratifolia mitogenome. Collectively, these results will provide valuable information for the evolution of P. serratifolia and provide insight into the evolutionary relationships within Photinia and the Rosaceae family.
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21
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Takeda T, Shirai K, Kim YW, Higuchi-Takeuchi M, Shimizu M, Kondo T, Ushijima T, Matsushita T, Shinozaki K, Hanada K. A de novo gene originating from the mitochondria controls floral transition in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2023; 111:189-203. [PMID: 36306001 DOI: 10.1007/s11103-022-01320-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
De novo genes created in the plant mitochondrial genome have frequently been transferred into the nuclear genome via intergenomic gene transfer events. Therefore, plant mitochondria might be a source of de novo genes in the nuclear genome. However, the functions of de novo genes originating from mitochondria and the evolutionary fate remain unclear. Here, we revealed that an Arabidopsis thaliana specific small coding gene derived from the mitochondrial genome regulates floral transition. We previously identified 49 candidate de novo genes that induce abnormal morphological changes on overexpression. We focused on a candidate gene derived from the mitochondrial genome (sORF2146) that encodes 66 amino acids. Comparative genomic analyses indicated that the mitochondrial sORF2146 emerged in the Brassica lineage as a de novo gene. The nuclear sORF2146 emerged following an intergenomic gene transfer event in the A. thaliana after the divergence between Arabidopsis and Capsella. Although the nuclear and mitochondrial sORF2146 sequences are the same in A. thaliana, only the nuclear sORF2146 is transcribed. The nuclear sORF2146 product is localized in mitochondria, which may be associated with the pseudogenization of the mitochondrial sORF2146. To functionally characterize the nuclear sORF2146, we performed a transcriptomic analysis of transgenic plants overexpressing the nuclear sORF2146. Flowering transition-related genes were highly regulated in the transgenic plants. Subsequent phenotypic analyses demonstrated that the overexpression and knockdown of sORF2146 in transgenic plants resulted in delayed and early flowering, respectively. These findings suggest that a lineage-specific de novo gene derived from mitochondria has an important regulatory effect on floral transition.
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Affiliation(s)
- Tomoyuki Takeda
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka-Shi, Fukuoka, 820-8502, Japan
| | - Kazumasa Shirai
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka-Shi, Fukuoka, 820-8502, Japan
| | - You-Wang Kim
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka-Shi, Fukuoka, 820-8502, Japan
| | | | - Minami Shimizu
- RIKEN Center for Sustainable Resource Science, Yokohama-Shi, Kanagawa, 230-0045, Japan
| | - Takayuki Kondo
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka-Shi, Fukuoka, 820-8502, Japan
| | - Tomokazu Ushijima
- Department of Agricultural Science and Technology, Faculty of Agriculture, Setsunan University, Osaka, Japan
| | - Tomonao Matsushita
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Kazuo Shinozaki
- RIKEN Center for Sustainable Resource Science, Yokohama-Shi, Kanagawa, 230-0045, Japan
| | - Kousuke Hanada
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka-Shi, Fukuoka, 820-8502, Japan.
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22
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You C, Cui T, Zhang C, Zang S, Su Y, Que Y. Assembly of the Complete Mitochondrial Genome of Gelsemium elegans Revealed the Existence of Homologous Conformations Generated by a Repeat Mediated Recombination. Int J Mol Sci 2022; 24:ijms24010527. [PMID: 36613970 PMCID: PMC9820418 DOI: 10.3390/ijms24010527] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 12/30/2022] Open
Abstract
Gelsemium elegans (G. elegans) is a Chinese medicinal plant with substantial economic and feeding values. There is a lack of detailed studies on the mitochondrial genome of G. elegans. In this study, the mitochondrial genome of G. elegans was sequenced and assembled, and its substructure was investigated. The mitochondrial genome of G. elegans is represented by two circular chromosomes of 406,009 bp in length with 33 annotated protein-coding genes, 15 tRNA genes, and three rRNA genes. We detected 145 pairs of repeats and found that four pairs of repeats could mediate the homologous recombination into one major conformation and five minor conformations, and the presence of conformations was verified by PCR amplification and Sanger sequencing. A total of 124 SSRs were identified in the G. elegans mitochondrial genome. The homologous segments between the chloroplast and mitochondrial genomes accounted for 5.85% of the mitochondrial genome. We also predicted 477 RNA potential editing sites and found that the nad4 gene was edited 38 times, which was the most frequent occurrence. Taken together, the mitochondrial genome of G. elegans was assembled and annotated. We gained a more comprehensive understanding on the genome of this medicinal plant, which is vital for its effective utilization and genetic improvement, especially for cytoplasmic male sterility breeding and evolution analysis in G. elegans.
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Affiliation(s)
- Chuihuai You
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tianzhen Cui
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chang Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (Y.S.); (Y.Q.); Tel.: +86-591-8385-2547 (Y.S. & Y.Q.)
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (Y.S.); (Y.Q.); Tel.: +86-591-8385-2547 (Y.S. & Y.Q.)
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23
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Szandar K, Jakub S, Paukszto Ł, Krawczyk K, Szczecińska M. Are the Organellar Genomes Useful for Fine Scale Population Structure Analysis of Endangered Plants?-A Case Study of Pulsatilla patens (L.) Mill. Genes (Basel) 2022; 14:genes14010067. [PMID: 36672808 PMCID: PMC9859050 DOI: 10.3390/genes14010067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Pulsatilla patens is a rare and endangered species in Europe and its population resources have significantly decreased over the past decades. Previous genetic studies of this species made it possible to estimate the genetic diversity of the European population and to describe the structure of chloroplast and mitochondrial genomes. The main aim of these studies was to characterize the variability of chloroplast and mitochondrial genomes in more detail at the intra-population and inter-population levels. Our study presents new organelle genome reference sequences that allow the design of novel markers that can be the starting point for testing hypotheses, past and modern biogeography of rare and endangered species P. patens, and adaptive responses of this species to changing environments. The study included sixteen individuals from five populations located in Northeastern Poland. Comparative analysis of 16 P. patens plastomes from 5 populations enabled us to identify 160 point mutations, including 64 substitutions and 96 InDels. The most numerous detected SNPs and Indels (75%) were accumulated in three intergenic spacers: ndhD-ccsA, rps4-rps16, and trnL(UAG)-ndhF. The mitogenome dataset, which was more than twice as large as the plastome (331 kbp vs. 151 kbp), revealed eight times fewer SNPs (8 vs. 64) and six times fewer InDels (16 vs. 96). Both chloroplast and mitochondrial genome identified the same number of haplotypes-11 out of 16 individuals, but both organellar genomes slightly differ in haplotype clustering. Despite the much lower variation, mitogenomic data provide additional resolution in the haplotype detection of P. patens, enabling molecular identification of individuals, which were unrecognizable based on the plastome dataset.
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Affiliation(s)
- Kamil Szandar
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
| | - Sawicki Jakub
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
- Correspondence:
| | - Łukasz Paukszto
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
| | - Katarzyna Krawczyk
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
| | - Monika Szczecińska
- Department of Ecology and Environmental Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 3, 10-727 Olsztyn, Poland
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24
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Kersten B, Rellstab C, Schroeder H, Brodbeck S, Fladung M, Krutovsky KV, Gugerli F. The mitochondrial genome sequence of Abies alba Mill. reveals a high structural and combinatorial variation. BMC Genomics 2022; 23:776. [PMID: 36443651 PMCID: PMC9703787 DOI: 10.1186/s12864-022-08993-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 11/05/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Plant mitogenomes vary widely in size and genomic architecture. Although hundreds of plant mitogenomes of angiosperm species have already been sequence-characterized, only a few mitogenomes are available from gymnosperms. Silver fir (Abies alba) is an economically important gymnosperm species that is widely distributed in Europe and occupies a large range of environmental conditions. Reference sequences of the nuclear and chloroplast genome of A. alba are available, however, the mitogenome has not yet been assembled and studied. RESULTS Here, we used paired-end Illumina short reads generated from a single haploid megagametophyte in combination with PacBio long reads from high molecular weight DNA of needles to assemble the first mitogenome sequence of A. alba. Assembly and scaffolding resulted in 11 mitogenome scaffolds, with the largest scaffold being 0.25 Mbp long. Two of the scaffolds displayed a potential circular structure supported by PCR. The total size of the A. alba mitogenome was estimated at 1.43 Mbp, similar to the size (1.33 Mbp) of a draft assembly of the Abies firma mitogenome. In total, 53 distinct genes of known function were annotated in the A. alba mitogenome, comprising 41 protein-coding genes, nine tRNA, and three rRNA genes. The proportion of highly repetitive elements (REs) was 0.168. The mitogenome seems to have a complex and dynamic structure featured by high combinatorial variation, which was specifically confirmed by PCR for the contig with the highest mapping coverage. Comparative analysis of all sequenced mitogenomes of gymnosperms revealed a moderate, but significant positive correlation between mitogenome size and proportion of REs. CONCLUSIONS The A. alba mitogenome provides a basis for new comparative studies and will allow to answer important structural, phylogenetic and other evolutionary questions. Future long-read sequencing with higher coverage of the A. alba mitogenome will be the key to further resolve its physical structure. The observed positive correlation between mitogenome size and proportion of REs will be further validated once available mitogenomes of gymnosperms would become more numerous. To test whether a higher proportion of REs in a mitogenome leads to an increased recombination and higher structural complexity and variability is a prospective avenue for future research.
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Affiliation(s)
- Birgit Kersten
- Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927 Grosshansdorf, Germany
| | - Christian Rellstab
- grid.419754.a0000 0001 2259 5533Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Hilke Schroeder
- Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927 Grosshansdorf, Germany
| | - Sabine Brodbeck
- grid.419754.a0000 0001 2259 5533Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Matthias Fladung
- Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927 Grosshansdorf, Germany
| | - Konstantin V. Krutovsky
- grid.7450.60000 0001 2364 4210Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Felix Gugerli
- grid.419754.a0000 0001 2259 5533Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
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25
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Wei L, Liu TJ, Hao G, Ge XJ, Yan HF. Comparative analyses of three complete Primula mitogenomes with insights into mitogenome size variation in Ericales. BMC Genomics 2022; 23:770. [PMID: 36424546 PMCID: PMC9686101 DOI: 10.1186/s12864-022-08983-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 11/01/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Although knowledge of the sizes, contents, and forms of plant mitochondrial genomes (mitogenomes) is increasing, little is known about the mechanisms underlying their structural diversity. Evolutionary information on the mitogenomes of Primula, an important ornamental taxon, is more limited than the information on their nuclear and plastid counterparts, which has hindered the comprehensive understanding of Primula mitogenomic diversity and evolution. The present study reported and compared three Primula mitogenomes and discussed the size expansion of mitogenomes in Ericales. RESULTS Mitogenome master circles were sequenced and successfully assembled for three Primula taxa and were compared with publicly available Ericales mitogenomes. The three mitogenomes contained similar gene contents and varied primarily in their structures. The Primula mitogenomes possessed relatively high nucleotide diversity among all examined plant lineages. In addition, high nucleotide diversity was found among Primula species between the Mediterranean and Himalaya-Hengduan Mountains. Most predicted RNA editing sites appeared in the second amino acid codon, increasing the hydrophobic character of the protein. An early stop in atp6 caused by RNA editing was conserved across all examined Ericales species. The interfamilial relationships within Ericales and interspecific relationships within Primula could be well resolved based on mitochondrial data. Transfer of the two longest mitochondrial plastid sequences (MTPTs) occurred before the divergence of Primula and its close relatives, and multiple independent transfers could also occur in a single MTPT sequence. Foreign sequence [MTPTs and mitochondrial nuclear DNA sequences (NUMTs)] uptake and repeats were to some extent associated with changes in Ericales mitogenome size, although none of these relationships were significant overall. CONCLUSIONS The present study revealed relatively conserved gene contents, gene clusters, RNA editing, and MTPTs but considerable structural variation in Primula mitogenomes. Relatively high nucleotide diversity was found in the Primula mitogenomes. In addition, mitogenomic genes, collinear gene clusters, and locally collinear blocks (LCBs) all showed phylogenetic signals. The evolutionary history of MTPTs in Primula was complicated, even in a single MTPT sequence. Various reasons for the size variation observed in Ericales mitogenomes were found.
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Affiliation(s)
- Lei Wei
- grid.458495.10000 0001 1014 7864Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Tong-Jian Liu
- grid.458495.10000 0001 1014 7864Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Gang Hao
- grid.20561.300000 0000 9546 5767College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xue-Jun Ge
- grid.458495.10000 0001 1014 7864Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Hai-Fei Yan
- grid.458495.10000 0001 1014 7864Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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26
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Zou Y, Zhu W, Sloan DB, Wu Z. Long-read sequencing characterizes mitochondrial and plastid genome variants in Arabidopsis msh1 mutants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:738-755. [PMID: 36097957 PMCID: PMC9617793 DOI: 10.1111/tpj.15976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 09/01/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
The abundant repeats in plant mitochondrial genomes can cause rapid genome rearrangements and are also a major obstacle in short-read sequencing studies. Nuclear-encoded proteins such as MSH1 are known to suppress the generation of repeat-associated mitochondrial genome variants, but our understanding of these mechanisms has been constrained by the limitations of short-read technologies. Here, we used highly accurate long-read sequencing (PacBio HiFi) to characterize mitochondrial and plastid genome variants in Arabidopsis thaliana msh1 mutant individuals. The HiFi reads provided a global view of recombination dynamics with detailed quantification of parental and crossover recombination products for both large and small repeats. We found that recombination breakpoints were distributed relatively evenly across the length of repeated sequences and detected widespread internal exchanges of sequence variants between pairs of imperfect repeats in the mitochondrial genome of msh1 mutants. Long-read assemblies of mitochondrial genomes from seven other A. thaliana wild-type accessions differed by repeat-mediated structural rearrangements similar to those observed in msh1 mutants, but they were all in a simple low-heteroplasmy state. The Arabidopsis plastid genome generally lacks small repeats and exhibited a very different pattern of variant accumulation in msh1 mutants compared with the mitochondrial genome. Our data illustrate the power of HiFi technology in studying repeat-mediated recombination in plant organellar genomes and improved the sequence resolution for recombinational processes suppressed by MSH1. Plant organellar genomes can undergo rapid rearrangements. Long-read sequencing provides a detailed and quantitative view of mitochondrial and plastid genome variants normally suppressed by MSH1, advancing our understanding of plant organellar genome dynamics.
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Affiliation(s)
- Yi Zou
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Weidong Zhu
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523
| | - Zhiqiang Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
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27
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Fan W, Liu F, Jia Q, Du H, Chen W, Ruan J, Lei J, Li DZ, Mower JP, Zhu A. Fragaria mitogenomes evolve rapidly in structure but slowly in sequence and incur frequent multinucleotide mutations mediated by microinversions. THE NEW PHYTOLOGIST 2022; 236:745-759. [PMID: 35731093 DOI: 10.1111/nph.18334] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Plant mitochondrial DNA has been described as evolving rapidly in structure but slowly in sequence. However, many of the noncoding portions of plant mitogenomes are not homologous among species, raising questions about the rate and spectrum of mutations in noncoding regions. Recent studies have suggested that the lack of homology in noncoding regions could be due to increased sequence divergence. We compared 30 kb of coding and 200 kb of noncoding DNA from 13 sequenced Fragaria mitogenomes, followed by analysis of the rate of sequence divergence, microinversion events and structural variations. Substitution rates in synonymous sites and nongenic sites are nearly identical, suggesting that the genome-wide point mutation rate is generally consistent. A surprisingly high number of large multinucleotide substitutions were detected in Fragaria mitogenomes, which may have resulted from microinversion events and could affect phylogenetic signal and local rate estimates. Fragaria mitogenomes preferentially accumulate deletions relative to insertions and substantial genomic arrangements, whereas mutation rates could positively associate with these sequence and structural changes among species. Together, these observations suggest that plant mitogenomes exhibit low point mutations genome-wide but exceptionally high structural variations, and our results favour a gain-and-loss model for the rapid loss of homology among plant mitogenomes.
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Affiliation(s)
- Weishu Fan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Fang Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiaoya Jia
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, China
| | - Haiyuan Du
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wu Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiwei Ruan
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Jiajun Lei
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Andan Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
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Sun M, Zhang M, Chen X, Liu Y, Liu B, Li J, Wang R, Zhao K, Wu J. Rearrangement and domestication as drivers of Rosaceae mitogenome plasticity. BMC Biol 2022; 20:181. [PMID: 35986276 PMCID: PMC9392253 DOI: 10.1186/s12915-022-01383-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/04/2022] [Indexed: 11/10/2022] Open
Abstract
Background The mitochondrion is an important cellular component in plants and that functions in producing vital energy for the cell. However, the evolution and structure of mitochondrial genomes (mitogenomes) remain unclear in the Rosaceae family. In this study, we assembled 34 Rosaceae mitogenomes and characterized genome variation, rearrangement rate, and selection signal variation within these mitogenomes. Results Comparative analysis of six genera from the Amygdaloideae and five from the Rosoideae subfamilies of Rosaceae revealed that three protein-coding genes were absent from the mitogenomes of five Rosoideae genera. Positive correlations between genome size and repeat content were identified in 38 Rosaceae mitogenomes. Twenty repeats with high recombination frequency (> 50%) provided evidence for predominant substoichiometric conformation of the mitogenomes. Variations in rearrangement rates were identified between eleven genera, and within the Pyrus, Malus, Prunus, and Fragaria genera. Based on population data, phylogenetic inferences from Pyrus mitogenomes supported two distinct maternal lineages of Asian cultivated pears. A Pyrus-specific deletion (DEL-D) in selective sweeps was identified based on the assembled genomes and population data. After the DEL-D sequence fragments originally arose, they may have experienced a subsequent doubling event via homologous recombination and sequence transfer in the Amygdaloideae; afterwards, this variant sequence may have significantly expanded to cultivated groups, thereby improving adaptation during the domestication process. Conclusions This study characterizes the variations in gene content, genome size, rearrangement rate, and the impact of domestication in Rosaceae mitogenomes and provides insights into their structural variation patterns and phylogenetic relationships. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01383-3.
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Xiang QP, Tang JY, Yu JG, Smith DR, Zhu YM, Wang YR, Kang JS, Yang J, Zhang XC. The evolution of extremely diverged plastomes in Selaginellaceae (lycophyte) is driven by repeat patterns and the underlying DNA maintenance machinery. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:768-784. [PMID: 35648423 DOI: 10.1111/tpj.15851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/25/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Two factors are proposed to account for the unusual features of organellar genomes: the disruptions of organelle-targeted DNA replication, repair, and recombination (DNA-RRR) systems in the nuclear genome and repetitive elements in organellar genomes. Little is known about how these factors affect organellar genome evolution. The deep-branching vascular plant family Selaginellaceae is known to have a deficient DNA-RRR system and convergently evolved organellar genomes. However, we found that the plastid genome (plastome) of Selaginella sinensis has extremely accelerated substitution rates, a low GC content, pervasive repeat elements, a dynamic network structure, and it lacks direct or inverted repeats. Unexpectedly, its organelle DNA-RRR system is short of a plastid-targeted Recombinase A1 (RecA1) and a mitochondrion-targeted RecA3, in line with other explored Selaginella species. The plastome contains a large collection of short- and medium-sized repeats. Given the absence of RecA1 surveillance, we propose that these repeats trigger illegitimate recombination, accelerated mutation rates, and structural instability. The correlations between repeat quantity and architectural complexity in the Selaginella plastomes support these conclusions. We, therefore, hypothesize that the interplay of the deficient DNA-RRR system and the high repeat content has led to the extraordinary divergence of the S. sinensis plastome. Our study not only sheds new light on the mechanism of plastome divergence by emphasizing the power of cytonuclear integration, but it also reconciles the longstanding contradiction on the effects of DNA-RRR system disruption on genome structure evolution.
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Affiliation(s)
- Qiao-Ping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Jun-Yong Tang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ji-Gao Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - David Roy Smith
- Department of Biology, University of Western Ontario, London, N6A 5B7, Ontario, Canada
| | - Yan-Mei Zhu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Ya-Rong Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Jong-Soo Kang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Jie Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
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Xu Y, Dong Y, Cheng W, Wu K, Gao H, Liu L, Xu L, Gong B. Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Diospyros oleifera, the first representative from the family Ebenaceae. Heliyon 2022; 8:e09870. [PMID: 35847622 PMCID: PMC9283892 DOI: 10.1016/j.heliyon.2022.e09870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/18/2022] [Accepted: 06/30/2022] [Indexed: 01/30/2023] Open
Abstract
Plant mitochondrial genomes are a valuable source of genetic information for a better understanding of phylogenetic relationships. However, no mitochondrial genome of any species in Ebenaceae has been reported. In this study, we reported the first mitochondrial genome of an Ebenaceae model plant Diospyros oleifera. The mitogenome was 493,958 bp in length, contained 39 protein-coding genes, 27 transfer RNA genes, and 3 ribosomal RNA genes. The rps2 and rps11 genes were missing in the D. oleifera mt genome, while the rps10 gene was identified. The length of the repetitive sequence in the D. oleifera mt genome was 31 kb, accounting for 6.33%. A clear bias in RNA-editing sites were found in the D. oleifera mt genome. We also detected 28 chloroplast-derived fragments significantly associated with D. oleifera mt genes, indicating intracellular tRNA genes transferred frequently from chloroplasts to mitochondria in D. oleifera. Phylogenetic analysis based on the mt genomes of D. oleifera and 27 other taxa reflected the exact evolutionary and taxonomic status of D. oleifera. Ka/Ks analysis revealed that 95.16% of the protein-coding genes in the D. oleifera mt genome had undergone negative selections. But, the rearrangement of mitochondrial genes has been widely occur among D. oleifera and these observed species. These results will lay the foundation for identifying further evolutionary relationships within Ebenaceae.
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Affiliation(s)
- Yang Xu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
| | - Yi Dong
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
| | - Wenqiang Cheng
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
| | - Kaiyun Wu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
| | - Haidong Gao
- Genepioneer Biotechnologies Co. Ltd, Nanjing, 210023, China
| | - Lei Liu
- Genepioneer Biotechnologies Co. Ltd, Nanjing, 210023, China
| | - Lei Xu
- Genepioneer Biotechnologies Co. Ltd, Nanjing, 210023, China
| | - Bangchu Gong
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
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Li J, Li J, Ma Y, Kou L, Wei J, Wang W. The complete mitochondrial genome of okra (Abelmoschus esculentus): using nanopore long reads to investigate gene transfer from chloroplast genomes and rearrangements of mitochondrial DNA molecules. BMC Genomics 2022; 23:481. [PMID: 35768783 PMCID: PMC9245263 DOI: 10.1186/s12864-022-08706-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/13/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Okra (Abelmoschus esculentus L. Moench) is an economically important crop and is known for its slimy juice, which has significant scientific research value. The A. esculentus chloroplast genome has been reported; however, the sequence of its mitochondrial genome is still lacking. RESULTS We sequenced the plastid and mitochondrial genomes of okra based on Illumina short reads and Nanopore long reads and conducted a comparative study between the two organelle genomes. The plastid genome of okra is highly structurally conserved, but the mitochondrial genome of okra has been confirmed to have abundant subgenomic configurations. The assembly results showed that okra's mitochondrial genome existed mainly in the form of two independent molecules, which could be divided into four independent molecules through two pairs of long repeats. In addition, we found that four pairs of short repeats could mediate the integration of the two independent molecules into one complete molecule at a low frequency. Subsequently, we also found extensive sequence transfer between the two organelles of okra, where three plastid-derived genes (psaA, rps7 and psbJ) remained intact in the mitochondrial genome. Furthermore, psbJ, psbF, psbE and psbL were integrated into the mitochondrial genome as a conserved gene cluster and underwent pseudogenization as nonfunctional genes. Only psbJ retained a relatively complete sequence, but its expression was not detected in the transcriptome data, and we speculate that it is still nonfunctional. Finally, we characterized the RNA editing events of protein-coding genes located in the organelle genomes of okra. CONCLUSIONS In the current study, our results not only provide high-quality organelle genomes for okra but also advance our understanding of the gene dialogue between organelle genomes and provide information to breed okra cultivars efficiently.
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Affiliation(s)
- Jihan Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
| | - Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
| | - Yubo Ma
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
| | - Lu Kou
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
| | - Juanjuan Wei
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, No.2 Tiansheng Road, Beibei District, Chongqing, 400716 China
| | - Weixing Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, No.2 Tiansheng Road, Beibei District, Chongqing, 400716 China
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Yang Z, Ni Y, Lin Z, Yang L, Chen G, Nijiati N, Hu Y, Chen X. De novo assembly of the complete mitochondrial genome of sweet potato (Ipomoea batatas [L.] Lam) revealed the existence of homologous conformations generated by the repeat-mediated recombination. BMC PLANT BIOLOGY 2022; 22:285. [PMID: 35681138 PMCID: PMC9185937 DOI: 10.1186/s12870-022-03665-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/30/2022] [Indexed: 05/27/2023]
Abstract
Sweet potato (Ipomoea batatas [L.] Lam) is an important food crop, an excellent fodder crop, and a new type of industrial raw material crop. The lack of genomic resources could affect the process of industrialization of sweet potato. Few detailed reports have been completed on the mitochondrial genome of sweet potato. In this research, we sequenced and assembled the mitochondrial genome of sweet potato and investigated its substructure. The mitochondrial genome of sweet potato is 270,304 bp with 23 unique core genes and 12 variable genes. We detected 279 pairs of repeat sequences and found that three pairs of direct repeats could mediate the homologous recombination into four independent circular molecules. We identified 70 SSRs in the whole mitochondrial genome of sweet potato. The longest dispersed repeat in mitochondrial genome was a palindromic repeat with a length of 915 bp. The homologous fragments between the chloroplast and mitochondrial genome account for 7.35% of the mitochondrial genome. We also predicted 597 RNA editing sites and found that the rps3 gene was edited 54 times, which occurred most frequently. This study further demonstrates the existence of multiple conformations in sweet potato mitochondrial genomes and provides a theoretical basis for the evolution of higher plants and cytoplasmic male sterility breeding.
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Affiliation(s)
- Zhijian Yang
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yang Ni
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zebin Lin
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
| | - Liubin Yang
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
| | - Guotai Chen
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
| | - Nuerla Nijiati
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
| | - Yunzhuo Hu
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
| | - Xuanyang Chen
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fuzhou, Fujian China
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The Roles of Mutation and Selection Acting on Mitochondrial Genomes Inferred from Intraspecific Variation in Seed Plants. Genes (Basel) 2022; 13:genes13061036. [PMID: 35741799 PMCID: PMC9222611 DOI: 10.3390/genes13061036] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/20/2022] [Accepted: 06/07/2022] [Indexed: 12/03/2022] Open
Abstract
There is a paradox in the plant mitochondrial genome, that is, the genic region evolves slowly while the intergenic region evolves rapidly. Thus, the intergenic regions of the plant mitochondrial genome are difficult to align across different species, even in closely related species. Here, to character the mechanism of this paradox, we identified interspecific variations in the Ginkgo biloba, Oryza sativa, and Arabidopsis thaliana mitochondrial and plastid genome at a genome-wide level. The substitution rate of synonymous sites in genic regions was similar to the substitution rate of intergenic regions, while the substitution rate of nonsynonymous sites in genic regions was lower than that in intergenic regions, suggesting the mutation inputs were the same among different categories within the organelle genome, but the selection pressure varied. The substitution rate of single-copy regions was higher than that of IR (inverted repeats) in the plastid genome at an intraspecific level. The substitution rate of single-copy regions was higher than that of repeats in the G. biloba and A. thaliana mitochondrial genomes, but lower in that of O. sativa. This difference may be related to the length and distribution of repeats. Copy number variations that existed in the G. biloba and O. sativa mitochondrial genomes were confirmed. This study reveals the intraspecific variation pattern of organelle genomes at a genome-wide level, and that copy number variations were common in plant mitochondrial genomes.
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34
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Tarasenko TA, Koulintchenko MV. Heterogeneity of the Mitochondrial Population in Cells of Plants and Other Organisms. Mol Biol 2022. [DOI: 10.1134/s0026893322020157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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35
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Chevigny N, Weber-Lotfi F, Le Blevenec A, Nadiras C, Fertet A, Bichara M, Erhardt M, Dietrich A, Raynaud C, Gualberto JM. RADA-dependent branch migration has a predominant role in plant mitochondria and its defect leads to mtDNA instability and cell cycle arrest. PLoS Genet 2022; 18:e1010202. [PMID: 35550632 PMCID: PMC9129000 DOI: 10.1371/journal.pgen.1010202] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/24/2022] [Accepted: 04/14/2022] [Indexed: 12/21/2022] Open
Abstract
Mitochondria of flowering plants have large genomes whose structure and segregation are modulated by recombination activities. The post-synaptic late steps of mitochondrial DNA (mtDNA) recombination are still poorly characterized. Here we show that RADA, a plant ortholog of bacterial RadA/Sms, is an organellar protein that drives the major branch-migration pathway of plant mitochondria. While RadA/Sms is dispensable in bacteria, RADA-deficient Arabidopsis plants are severely impacted in their development and fertility, correlating with increased mtDNA recombination across intermediate-size repeats and accumulation of recombination-generated mitochondrial subgenomes. The radA mutation is epistatic to recG1 that affects the additional branch migration activity. In contrast, the double mutation radA recA3 is lethal, underlining the importance of an alternative RECA3-dependent pathway. The physical interaction of RADA with RECA2 but not with RECA3 further indicated that RADA is required for the processing of recombination intermediates in the RECA2-depedent recombination pathway of plant mitochondria. Although RADA is dually targeted to mitochondria and chloroplasts we found little to no effects of the radA mutation on the stability of the plastidial genome. Finally, we found that the deficient maintenance of the mtDNA in radA apparently triggers a retrograde signal that activates nuclear genes repressing cell cycle progression. In flowering plants, the mitochondrial genome is very large and dynamic, and its stability influences plant fitness and development. Rearrangements by recombination drive its very rapid evolution and can lead to valuable agronomic traits such as cytoplasmic sterility, used by breeders for the production of hybrid seeds. Here we describe RADA, a DNA helicase essential for the stability of the mitochondrial DNA in Arabidopsis. We demonstrate that RADA has branch migrating activity, accelerating the processing of recombination intermediates. radA mutants are severely affected in development and fertility. They display mitochondrial genome instability that results in uncoordinated replication of subgenomes created by recombination. Furthermore, we found that an important component of the growth defects of radA mutants is apparently a cellular response triggered by the sensing of damages to the mitochondrial genome, resulting in the activation of genes that suppress the progression of the cell cycle. Our results underline the importance of better understanding the plant mitochondrial recombination pathways and their cross-talk with nuclear gene expression.
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Affiliation(s)
- Nicolas Chevigny
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Frédérique Weber-Lotfi
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Anaïs Le Blevenec
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Cédric Nadiras
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Arnaud Fertet
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Marc Bichara
- Biotechnologie et Signalisation Cellulaire, CNRS, Université de Strasbourg, Illkirch-Graffenstaden, France
| | - Mathieu Erhardt
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - André Dietrich
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Cécile Raynaud
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - José M. Gualberto
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
- * E-mail:
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Hao W. From Genome Variation to Molecular Mechanisms: What we Have Learned From Yeast Mitochondrial Genomes? Front Microbiol 2022; 13:806575. [PMID: 35126340 PMCID: PMC8811140 DOI: 10.3389/fmicb.2022.806575] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/03/2022] [Indexed: 11/26/2022] Open
Abstract
Analysis of genome variation provides insights into mechanisms in genome evolution. This is increasingly appreciated with the rapid growth of genomic data. Mitochondrial genomes (mitogenomes) are well known to vary substantially in many genomic aspects, such as genome size, sequence context, nucleotide base composition and substitution rate. Such substantial variation makes mitogenomes an excellent model system to study the mechanisms dictating mitogenome variation. Recent sequencing efforts have not only covered a rich number of yeast species but also generated genomes from abundant strains within the same species. The rich yeast genomic data have enabled detailed investigation from genome variation into molecular mechanisms in genome evolution. This mini-review highlights some recent progresses in yeast mitogenome studies.
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Fang B, Li J, Zhao Q, Liang Y, Yu J. Assembly of the Complete Mitochondrial Genome of Chinese Plum ( Prunus salicina): Characterization of Genome Recombination and RNA Editing Sites. Genes (Basel) 2021; 12:genes12121970. [PMID: 34946920 PMCID: PMC8701122 DOI: 10.3390/genes12121970] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 12/28/2022] Open
Abstract
Despite the significant progress that has been made in the genome sequencing of Prunus, this area of research has been lacking a systematic description of the mitochondrial genome of this genus for a long time. In this study, we assembled the mitochondrial genome of the Chinese plum (Prunus salicina) using Illumina and Oxford Nanopore sequencing data. The mitochondrial genome size of P. salicina was found to be 508,035 base pair (bp), which is the largest reported in the Rosaceae family to date, and P. salicina was shown to be 63,453 bp longer than sweet cherry (P. avium). The P. salicina mitochondrial genome contained 37 protein-coding genes (PCGs), 3 ribosomal RNA (rRNA) genes, and 16 transfer RNA (tRNA) genes. Two plastid-derived tRNA were identified. We also found two short repeats that captured the nad3 and nad6 genes and resulted in two copies. In addition, nine pairs of repeat sequences were identified as being involved in the mediation of genome recombination. This is crucial for the formation of subgenomic configurations. To characterize RNA editing sites, transcriptome data were used, and we identified 480 RNA editing sites in protein-coding sequences. Among them, the initiation codon of the nad1 gene confirmed that an RNA editing event occurred, and the genomic encoded ACG was edited as AUG in the transcript. Combined with previous reports on the chloroplast genome, our data complemented our understanding of the last part of the organelle genome of plum, which will facilitate our understanding of the evolution of organelle genomes.
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Affiliation(s)
- Bo Fang
- Fruit Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China; (B.F.); (Q.Z.)
| | - Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China;
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, Chongqing 400716, China
| | - Qian Zhao
- Fruit Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China; (B.F.); (Q.Z.)
| | - Yuping Liang
- College of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China;
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China;
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, Chongqing 400716, China
- Correspondence:
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Fang J, Chen Y, Liu G, Verbruggen H, Zhu H. Chloroplast Genome Traits Correlate With Organismal Complexity and Ecological Traits in Chlorophyta. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.791166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A positive relationship between cell size and chloroplast genome size within chloroplast-bearing protists has been hypothesized in the past and shown in some case studies, but other factors influencing chloroplast genome size during the evolution of chlorophyte algae have been less studied. We study chloroplast genome size and GC content as a function of habitats and cell size of chlorophyte algae. The chloroplast genome size of green algae in freshwater, marine and terrestrial habitats was differed significantly, with terrestrial algae having larger chloroplast genome sizes in general. The most important contributor to these enlarged genomes in terrestrial species was the length of intergenic regions. There was no clear difference in the GC content of chloroplast genomes from the three habitats categories. Functional morphological categories also showed differences in chloroplast genome size, with filamentous algae having substantially larger genomes than other forms of algae, and foliose algae had lower GC content than other groups. Chloroplast genome size showed no significant differences among the classes Ulvophyceae, Trebouxiophyceae, and Chlorophyceae, but the GC content of Chlorophyceae chloroplast genomes was significantly lower than that of Ulvophyceae and Trebouxiophyceae. There was a certain positive relationship between chloroplast genome size and cell size for the Chlorophyta as a whole and within each of three major classes. Our data also confirmed previous reports that ancestral quadripartite architecture had been lost many times independently in Chlorophyta. Finally, the comparison of the phenotype of chlorophytes algae harboring plastids uncovered that most of the investigated Chlorophyta algae housed a single plastid per cell.
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Liu H, Yu J, Yu X, Zhang D, Chang H, Li W, Song H, Cui Z, Wang P, Luo Y, Wang F, Wang D, Li Z, Huang Z, Fu A, Xu M. Structural variation of mitochondrial genomes sheds light on evolutionary history of soybeans. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1456-1472. [PMID: 34587339 DOI: 10.1111/tpj.15522] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 08/27/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
The architecture and genetic diversity of mitogenome (mtDNA) are largely unknown in cultivated soybean (Glycine max), which is domesticated from the wild progenitor, Glycine soja, 5000 years ago. Here, we de novo assembled the mitogenome of the cultivar 'Williams 82' (Wm82_mtDNA) with Illumina PE300 deep sequencing data, and verified it with polymerase chain reaction (PCR) and Southern blot analyses. Wm82_mtDNA maps as two autonomous circular chromosomes (370 871-bp Chr-m1 and 62 661-bp Chr-m2). Its structure is extensively divergent from that of the mono-chromosomal mitogenome reported in the landrace 'Aiganhuang' (AGH_mtDNA). Synteny analysis showed that the structural variations (SVs) between two genomes are mainly attributed to ectopic and illegitimate recombination. Moreover, Wm82_mtDNA and AGH_mtDNA each possess six and four specific regions, which are absent in their counterparts and likely result from differential sequence-loss events. Mitogenome SV was further studied in 39 wild and 182 cultivated soybean accessions distributed world-widely with PCR/Southern analyses or a comparable in silico analysis. The results classified both wild and cultivated soybeans into five cytoplasmic groups, named as GSa-GSe and G1-G5; 'Williams 82' and 'Aiganhuang' belong to G1 and G5, respectively. Notably, except for members in GSe and G5, all accessions carry a bi-chromosomal mitogenome with a common Chr-m2. Phylogenetic analyses based on mtDNA structures and chloroplast gene sequences both inferred that G1-G3, representing >90% of cultigens, likely inherited cytoplasm from the ancestor of domestic soybean, while G4 and G5 likely inherited cytoplasm from wild soybeans carrying GSa- and GSe-like cytoplasm through interspecific hybridization, offering new insights into soybean cultivation history.
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Affiliation(s)
- Hao Liu
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Junping Yu
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Xiaoxia Yu
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Dan Zhang
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Han Chang
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Wei Li
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Haifeng Song
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Zheng Cui
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Peng Wang
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Yixin Luo
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Fei Wang
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Dagang Wang
- Key Laboratory of Crop Quality Improvement of Anhui Province, Anhui Academy of Agricultural Sciences, Crop Research Institute, Hefei, Anhui, 230031, China
| | - Zhi Li
- Fuyang Academy of Agricultural Sciences, Fuyang, Anhui, 236000, China
| | - Zhiping Huang
- Key Laboratory of Crop Quality Improvement of Anhui Province, Anhui Academy of Agricultural Sciences, Crop Research Institute, Hefei, Anhui, 230031, China
| | - Aigen Fu
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Min Xu
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
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García-Medel PL, Peralta-Castro A, Baruch-Torres N, Fuentes-Pascacio A, Pedroza-García JA, Cruz-Ramirez A, Brieba LG. Arabidopsis thaliana PrimPol is a primase and lesion bypass DNA polymerase with the biochemical characteristics to cope with DNA damage in the nucleus, mitochondria, and chloroplast. Sci Rep 2021; 11:20582. [PMID: 34663822 PMCID: PMC8523556 DOI: 10.1038/s41598-021-00151-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/07/2021] [Indexed: 11/09/2022] Open
Abstract
PrimPol is a novel Primase–Polymerase that synthesizes RNA and DNA primers de novo and extents from these primers as a DNA polymerase. Animal PrimPol is involved in nuclear and mitochondrial DNA replication by virtue of its translesion DNA synthesis (TLS) and repriming activities. Here we report that the plant model Arabidopsis thaliana encodes a functional PrimPol (AtPrimPol). AtPrimPol is a low fidelity and a TLS polymerase capable to bypass DNA lesions, like thymine glycol and abasic sites, by incorporating directly across these lesions or by skipping them. AtPrimPol is also an efficient primase that preferentially recognizes the single-stranded 3′-GTCG-5′ DNA sequence, where the 3′-G is cryptic. AtPrimPol is the first DNA polymerase that localizes in three cellular compartments: nucleus, mitochondria, and chloroplast. In vitro, AtPrimPol synthesizes primers that are extended by the plant organellar DNA polymerases and this reaction is regulated by organellar single-stranded binding proteins. Given the constant exposure of plants to endogenous and exogenous DNA-damaging agents and the enzymatic capabilities of lesion bypass and re-priming of AtPrimPol, we postulate a predominant role of this enzyme in avoiding replication fork collapse in all three plant genomes, both as a primase and as a TLS polymerase.
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Affiliation(s)
- Paola L García-Medel
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, CP 36821, Irapuato, Guanajuato, Mexico
| | - Antolín Peralta-Castro
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, CP 36821, Irapuato, Guanajuato, Mexico
| | - Noe Baruch-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, CP 36821, Irapuato, Guanajuato, Mexico.,Department of Pharmacology and Toxicology, The University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA
| | - Alma Fuentes-Pascacio
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, CP 36821, Irapuato, Guanajuato, Mexico
| | - José A Pedroza-García
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 510-3, 62250, Cuernavaca, Morelos, Mexico
| | - Alfredo Cruz-Ramirez
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, CP 36821, Irapuato, Guanajuato, Mexico
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, CP 36821, Irapuato, Guanajuato, Mexico.
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Kim H, Yang JH, Bustamante DE, Calderon MS, Mansilla A, Maggs CA, Hansen GI, Yoon HS. Organelle Genome Variation in the Red Algal Genus Ahnfeltia (Florideophyceae). Front Genet 2021; 12:724734. [PMID: 34646303 PMCID: PMC8503264 DOI: 10.3389/fgene.2021.724734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/09/2021] [Indexed: 11/13/2022] Open
Abstract
The agarophyte Ahnfeltia (Ahnfeltiales, Rhodophyta) is a globally widespread genus with 11 accepted species names. Two of the most widespread species in this genus, A. plicata and A. fastigiata, may have diverged genetically due to past geographic changes and subsequent geographic isolation. To investigate this genomic and genetic diversity, we generated new plastid (ptDNAs) and mitochondrial genomes (mtDNAs) of these Ahnfeltia species from four different regions (A. plicata - Chile and UK and A. fastigiata - Korea and Oregon). Two architecture variations were found in the Ahnfeltia genomes: in ptDNA of A. fastigiata Oregon, the hypothetical pseudogene region was translocated, likely due to recombination with palindromic repeats or a gene transfer from a red algal plasmid. In mtDNA of A. fastigiata Korea, the composition of the group II intronic ORFs was distinct from others suggesting different scenarios of gain and loss of group II intronic ORFs. These features resulted in genome size differences between the two species. Overall gene contents of organelle genomes of Ahnfeltia were conserved. Phylogenetic analysis using concatenated genes from ptDNAs and mtDNAs supported the monophyly of the Ahnfeltiophycidae. The most probable individual gene trees showed that the Ahnfeltia populations were genetically diversified. These trees, the cox1 haplotype network, and a dN/dS analysis all supported the theory that these Ahnfeltia populations have diversified genetically in accordance with geographic distribution.
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Affiliation(s)
- Hocheol Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Ji Hyun Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Danilo E Bustamante
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Peru
| | - Martha S Calderon
- Laboratorio de Macroalgas Antárticas y Subantárticas, Universidad de Magallanes, Punta Arenas, Chile
| | - Andres Mansilla
- Laboratorio de Macroalgas Antárticas y Subantárticas, Universidad de Magallanes, Punta Arenas, Chile
| | - Christine A Maggs
- School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Gayle I Hansen
- Marine Algal Biodiversity Research, Newport, OR, United States
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
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Xia H, Zhao W, Shi Y, Wang XR, Wang B. Microhomologies Are Associated with Tandem Duplications and Structural Variation in Plant Mitochondrial Genomes. Genome Biol Evol 2021; 12:1965-1974. [PMID: 32790831 PMCID: PMC7643612 DOI: 10.1093/gbe/evaa172] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2020] [Indexed: 12/15/2022] Open
Abstract
Short tandem repeats (STRs) contribute to structural variation in plant mitochondrial genomes, but the mechanisms underlying their formation and expansion are unclear. In this study, we detected high polymorphism in the nad7-1 region of the Pinus tabuliformis mitogenome caused by the rapid accumulation of STRs and rearrangements over a few million years ago. The STRs in nad7-1 have a 7-bp microhomology (TAG7) flanking the repeat array. We then scanned the mitogenomes of 136 seed plants to understand the role of microhomology in the formation of STR and mitogenome evolution. A total of 13,170 STRs were identified, and almost half of them were associated with microhomologies. A substantial amount (1,197) of microhomologies was long enough to mediate structural variation, and the length of microhomology is positively correlated with the length of tandem repeat unit. These results suggest that microhomology may be involved in the formation of tandem repeat via microhomology-mediated pathway, and the formation of longer duplicates required greater length of microhomology. We examined the abundance of these 1,197 microhomologies, and found 75% of them were enriched in the plant mitogenomes. Further analyses of the 400 prevalent microhomologies revealed that 175 of them showed differential enrichment between angiosperms and gymnosperms and 186 differed between angiosperms and conifers, indicating lineage-specific usage and expansion of microhomologies. Our study sheds light on the sources of structural variation in plant mitochondrial genomes and highlights the importance of microhomology in mitochondrial genome evolution.
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Affiliation(s)
- Hanhan Xia
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wei Zhao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Department of Ecology and Environmental Science, UPSC, Umeå University, Umeå, Sweden
| | - Yong Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xiao-Ru Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Department of Ecology and Environmental Science, UPSC, Umeå University, Umeå, Sweden
| | - Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Corresponding author: E-mail:
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Li J, Xu Y, Shan Y, Pei X, Yong S, Liu C, Yu J. Assembly of the complete mitochondrial genome of an endemic plant, Scutellaria tsinyunensis, revealed the existence of two conformations generated by a repeat-mediated recombination. PLANTA 2021; 254:36. [PMID: 34302538 DOI: 10.1007/s00425-021-03684-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
We assembled the complete mitochondrial genome of Scutellaria tsinyunensis in this study. Repeat-mediated recombination resulted in the formation of two conformations of the mitochondrial genome in S. tsinyunensis. Scutellaria tsinyunensis belongs to the family Lamiaceae, distributed only in the Jinyun Mountain, Chongqing, China. As a valuable endemic and small population species, it is regarded as a natural resource potentially with significant economic and ecological importance. In this study, we assembled a complete and gap-free mitochondrial genome of S. tsinyunensis. This genome had a length of 354,073 bp and the base composition of the genome was A (27.44%), T (27.30%), C (22.58%), and G (22.68%). This genome encodes 59 genes, including 32 protein-coding genes, 24 tRNA genes, and 3 rRNA genes. The Sanger sequencing and Oxford Nanopore sequencing confirmed a pair of direct repeats had mediated genome recombination, resulting in the formation of two conformations. The gene conversation between plastome and mitochondrial genome was also observed in S. tsinyunensis by detecting gene migration, including six tRNA genes (namely, trnW-CCA, trnI-CAU, trnH-UUU, trnD-GUC, trnN-GUU, and trnM-CAU), five protein-coding gene fragments, and the fragments from 2 rRNA genes. Moreover, the dN/dS analysis revealed the atp9 gene had undergone strong negative selection, and four genes (atp4, mttB, ccmFc, and ccmB) probably had undergone positive selection during evolution in Lamiales. This work reported the first mitochondrial genome of S. tsinyunensis, which could be used as a reference genome for the important medicinal plants of the genus Scutellaria, and also provide much-desired information for molecular breeding.
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Affiliation(s)
- Jingling Li
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400716, China
| | - Yicen Xu
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400716, China
| | - Yuanyu Shan
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400716, China
| | - Xiaoying Pei
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400716, China
| | - Shunyuan Yong
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400716, China
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing, 100093, People's Republic of China.
| | - Jie Yu
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400716, China.
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Tarasenko TA, Klimenko ES, Tarasenko VI, Koulintchenko MV, Dietrich A, Weber-Lotfi F, Konstantinov YM. Plant mitochondria import DNA via alternative membrane complexes involving various VDAC isoforms. Mitochondrion 2021; 60:43-58. [PMID: 34303006 DOI: 10.1016/j.mito.2021.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/17/2021] [Accepted: 07/19/2021] [Indexed: 12/23/2022]
Abstract
Mitochondria possess transport mechanisms for import of RNA and DNA. Based on import into isolated Solanum tuberosum mitochondria in the presence of competitors, inhibitors or effectors, we show that DNA fragments of different size classes are taken up into plant organelles through distinct channels. Alternative channels can also be activated according to the amount of DNA substrate of a given size class. Analyses of Arabidopsis thaliana knockout lines pointed out a differential involvement of individual voltage-dependent anion channel (VDAC) isoforms in the formation of alternative channels. We propose several outer and inner membrane proteins as VDAC partners in these pathways.
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Affiliation(s)
- Tatiana A Tarasenko
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk 664033, Russia
| | - Ekaterina S Klimenko
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk 664033, Russia
| | - Vladislav I Tarasenko
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk 664033, Russia
| | - Milana V Koulintchenko
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk 664033, Russia.
| | - André Dietrich
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 Rue du Général Zimmer, 67084 Strasbourg, France
| | - Frédérique Weber-Lotfi
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 Rue du Général Zimmer, 67084 Strasbourg, France
| | - Yuri M Konstantinov
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk 664033, Russia; Irkutsk State University, 1 Karl Marx St, Irkutsk 664003, Russia
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Insights into molecular structure, genome evolution and phylogenetic implication through mitochondrial genome sequence of Gleditsia sinensis. Sci Rep 2021; 11:14850. [PMID: 34290263 PMCID: PMC8295344 DOI: 10.1038/s41598-021-93480-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/23/2021] [Indexed: 11/14/2022] Open
Abstract
Gleditsia sinensis is an endemic species widely distributed in China with high economic and medicinal value. To explore the genomic evolution and phylogenetic relationships of G. sinensis, the complete mitochondrial (mt) genome of G. sinensis was sequenced and assembled, which was firstly reported in Gleditsia. The mt genome was circular and 594,121 bp in length, including 37 protein-coding genes (PCGs), 19 transfer RNA (tRNA) genes and 3 ribosomal RNA (rRNA) genes. The overall base composition of the G. sinensis mt genome was 27.4% for A, 27.4% for T, 22.6% for G, 22.7% for C. The comparative analysis of PCGs in Fabaceae species showed that most of the ribosomal protein genes and succinate dehydrogenase genes were lost. In addition, we found that the rps4 gene was only lost in G. sinensis, whereas it was retained in other Fabaceae species. The phylogenetic analysis based on shared PCGs of 24 species (22 Fabaceae and 2 Solanaceae) showed that G. sinensis is evolutionarily closer to Senna species. In general, this research will provide valuable information for the evolution of G. sinensis and provide insight into the phylogenetic relationships within the family Fabaceae.
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Choi IS, Wojciechowski MF, Ruhlman TA, Jansen RK. In and out: Evolution of viral sequences in the mitochondrial genomes of legumes (Fabaceae). Mol Phylogenet Evol 2021; 163:107236. [PMID: 34147655 DOI: 10.1016/j.ympev.2021.107236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 10/21/2022]
Abstract
Plant specific mitoviruses in the 'genus' Mitovirus (Narnaviridae) and their integrated sequences (non-retroviral endogenous RNA viral elements or NERVEs) have been recently identified in various plant lineages. However, the sparse phylogenetic coverage of complete plant mitochondrial genome (mitogenome) sequences and the non-conserved nature of mitochondrial intergenic regions have hindered comparative studies on mitovirus NERVEs in plants. In this study, 10 new mitogenomes were sequenced from legumes (Fabaceae). Based on comparative genomic analysis of 27 total mitogenomes, we identified mitovirus NERVEs and transposable elements across the family. All legume mitogenomes included NERVEs and total NERVE length varied from ca. 2 kb in the papilionoid Trifolium to 35 kb in the mimosoid Acacia. Most of the NERVE integration sites were in highly variable intergenic regions, however, some were positioned in six cis-spliced mitochondrial introns. In the Acacia mitogenome, there were L1-like transposon sequences including an almost full-length copy with target site duplications (TSDs). The integration sites of NERVEs in four introns showed evidence of L1-like retrotransposition events. Phylogenetic analysis revealed that there were multiple instances of precise deletion of NERVEs between TSDs. This study provides clear evidence that a L1-like retrotransposition mechanism has a long history of contributing to the integration of viral RNA into plant mitogenomes while microhomology-mediated deletion can restore the integration site.
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Affiliation(s)
- In-Su Choi
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | | | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA; Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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Ren Q, Wang YC, Lin Y, Zhen Z, Cui Y, Qin S. The extremely large chloroplast genome of the green alga Haematococcus pluvialis: Genome structure, and comparative analysis. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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48
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Singh S, Bhatia R, Kumar R, Behera TK, Kumari K, Pramanik A, Ghemeray H, Sharma K, Bhattacharya RC, Dey SS. Elucidating Mitochondrial DNA Markers of Ogura-Based CMS Lines in Indian Cauliflowers ( Brassica oleracea var. botrytis L.) and Their Floral Abnormalities Due to Diversity in Cytonuclear Interactions. FRONTIERS IN PLANT SCIENCE 2021; 12:631489. [PMID: 33995434 PMCID: PMC8120243 DOI: 10.3389/fpls.2021.631489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Mitochondrial markers can be used to differentiate diverse mitotypes as well as cytoplasms in angiosperms. In cauliflower, cultivation of hybrids is pivotal in remunerative agriculture and cytoplasmic male sterile lines constitute an important component of the hybrid breeding. In diversifying the source of male sterility, it is essential to appropriately differentiate among the available male sterile cytoplasms in cauliflower. PCR polymorphism at the key mitochondrial genes associated with male sterility will be instrumental in analyzing, molecular characterization, and development of mitotype-specific markers for differentiation of different cytoplasmic sources. Presence of auto- and alloplasmic cytonuclear combinations result in complex floral abnormalities. In this context, the present investigation highlighted the utility of organelle genome-based markers in distinguishing cytoplasm types in Indian cauliflowers and unveils the epistatic effects of the cytonuclear interactions influencing floral phenotypes. In PCR-based analysis using a set of primers targeted to orf-138, 76 Indian cauliflower lines depicted the presence of Ogura cytoplasm albeit the amplicons generated exhibited polymorphism within the ofr-138 sequence. The polymorphic fragments were found to be spanning over 200-280 bp and 410-470 bp genomic regions of BnTR4 and orf125, respectively. Sequence analysis revealed that such cytoplasmic genetic variations could be attributed to single nucleotide polymorphisms and insertion or deletions of 31/51 nucleotides. The cytoplasmic effects on varying nuclear-genetic backgrounds rendered an array of floral abnormalities like reduction in flower size, fused flowers, splitted style with the exposed ovule, absence of nonfunctional stamens, and petaloid stamens. These floral malformations caused dysplasia of flower structure affecting female fertility with inefficient nectar production. The finding provides an important reference to ameliorate understanding of mechanism of cytonuclear interactions in floral organ development in Brassicas. The study paves the way for unraveling developmental biology of CMS phenotypes in eukaryotic organisms and intergenomic conflict in plant speciation.
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Affiliation(s)
- Saurabh Singh
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Reeta Bhatia
- Division of Floriculture and Landscaping, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Raj Kumar
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Tusar K. Behera
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Khushboo Kumari
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Achintya Pramanik
- ICAR-Indian Agricultural Research Institute, Regional Station, Kullu Valley, India
| | - Hemant Ghemeray
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Kanika Sharma
- ICAR-Indian Agricultural Research Institute, Regional Station, Kullu Valley, India
| | | | - Shyam S. Dey
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Plant Mitochondria are a Riddle Wrapped in a Mystery Inside an Enigma. J Mol Evol 2021; 89:151-156. [PMID: 33486550 DOI: 10.1007/s00239-020-09980-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 12/03/2020] [Indexed: 12/23/2022]
Abstract
A fundamental paradox motivates the study of plant mitochondrial genomics: the mutation rate is very low (lower than in the nucleus) but the rearrangement rate is high. A landmark paper published in Journal of Molecular Evolution in 1988 established these facts and revealed the paradox. Jeffrey Palmer and Laura Herbon did a prodigious amount of work in the pre-genome sequencing era to identify both the high frequency of rearrangements between closely related species, and the low frequency of mutations, observations that have now been confirmed many times by sequencing. This paper was also the first to use molecular data on rearrangements as a phylogenetic trait to build a parsimonious tree. The work was a technical tour-de-force, its findings are still at the heart of plant mitochondrial genomics, and the underlying molecular mechanisms that produce this paradox are still not completely understood.
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Yang GL, Feng D, Liu YT, Lv SM, Zheng MM, Tan AJ. Research Progress of a Potential Bioreactor: Duckweed. Biomolecules 2021; 11:biom11010093. [PMID: 33450858 PMCID: PMC7828363 DOI: 10.3390/biom11010093] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/09/2021] [Accepted: 01/11/2021] [Indexed: 02/01/2023] Open
Abstract
Recently, plant bioreactors have flourished into an exciting area of synthetic biology because of their product safety, inexpensive production cost, and easy scale-up. Duckweed is the smallest and fastest-growing aquatic plant, and has advantages including simple processing and the ability to grow high biomass in smaller areas. Therefore, duckweed could be used as a new potential bioreactor for biological products such as vaccines, antibodies, pharmaceutical proteins, and industrial enzymes. Duckweed has made a breakthrough in biosynthesis as a chassis plant and is being utilized for the production of plenty of biological products or bio-derivatives with multiple uses and high values. This review summarizes the latest progress on genetic background, genetic transformation system, and bioreactor development of duckweed, and provides insights for further exploration and application of duckweed.
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Affiliation(s)
- Gui-Li Yang
- College of Life Sciences, Guizhou University, Guiyang 550025, China; (G.-L.Y.); (D.F.); (Y.-T.L.); (M.-M.Z.)
- Key Laboratory of Conservation and Germplasm Innovation of Mountain Plant Resources, Ministry of Education, Guiyang 550025, China
| | - Dan Feng
- College of Life Sciences, Guizhou University, Guiyang 550025, China; (G.-L.Y.); (D.F.); (Y.-T.L.); (M.-M.Z.)
- Key Laboratory of Conservation and Germplasm Innovation of Mountain Plant Resources, Ministry of Education, Guiyang 550025, China
| | - Yu-Ting Liu
- College of Life Sciences, Guizhou University, Guiyang 550025, China; (G.-L.Y.); (D.F.); (Y.-T.L.); (M.-M.Z.)
- Key Laboratory of Conservation and Germplasm Innovation of Mountain Plant Resources, Ministry of Education, Guiyang 550025, China
| | - Shi-Ming Lv
- College of Animal Science, Guizhou University, Guiyang 550025, China;
| | - Meng-Meng Zheng
- College of Life Sciences, Guizhou University, Guiyang 550025, China; (G.-L.Y.); (D.F.); (Y.-T.L.); (M.-M.Z.)
- Key Laboratory of Conservation and Germplasm Innovation of Mountain Plant Resources, Ministry of Education, Guiyang 550025, China
| | - Ai-Juan Tan
- College of Life Sciences, Guizhou University, Guiyang 550025, China; (G.-L.Y.); (D.F.); (Y.-T.L.); (M.-M.Z.)
- Key Laboratory of Conservation and Germplasm Innovation of Mountain Plant Resources, Ministry of Education, Guiyang 550025, China
- Correspondence: ; Tel.: +86-1376-513-6919
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