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Islam MF, Yamatani H, Takami T, Kusaba M, Sakamoto W. Characterization of organelle DNA degradation mediated by DPD1 exonuclease in the rice genome-edited line. PLANT MOLECULAR BIOLOGY 2024; 114:71. [PMID: 38856917 PMCID: PMC11164812 DOI: 10.1007/s11103-024-01452-x] [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: 03/05/2024] [Accepted: 04/05/2024] [Indexed: 06/11/2024]
Abstract
Mitochondria and plastids, originated as ancestral endosymbiotic bacteria, contain their own DNA sequences. These organelle DNAs (orgDNAs) are, despite the limited genetic information they contain, an indispensable part of the genetic systems but exist as multiple copies, making up a substantial amount of total cellular DNA. Given this abundance, orgDNA is known to undergo tissue-specific degradation in plants. Previous studies have shown that the exonuclease DPD1, conserved among seed plants, degrades orgDNAs during pollen maturation and leaf senescence in Arabidopsis. However, tissue-specific orgDNA degradation was shown to differ among species. To extend our knowledge, we characterized DPD1 in rice in this study. We created a genome-edited (GE) mutant in which OsDPD1 and OsDPD1-like were inactivated. Characterization of this GE plant demonstrated that DPD1 was involved in pollen orgDNA degradation, whereas it had no significant effect on orgDNA degradation during leaf senescence. Comparison of transcriptomes from wild-type and GE plants with different phosphate supply levels indicated that orgDNA had little impact on the phosphate starvation response, but instead had a global impact in plant growth. In fact, the GE plant showed lower fitness with reduced grain filling rate and grain weight in natural light conditions. Taken together, the presented data reinforce the important physiological roles of orgDNA degradation mediated by DPD1.
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Affiliation(s)
- Md Faridul Islam
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Hiroshi Yamatani
- Department of Quantum-Applied Biosciences, Takasaki Institute for Advanced Quantum Science, Foundational Quantum Technology Research Directorate, National Institutes for Quantum Science and Technology (QST), 1233, Watanuki, Takasaki, Gunma, 370-1292, Japan
| | - Tsuneaki Takami
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Makoto Kusaba
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-3 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8528, Japan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan.
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2
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Peñafiel-Ayala A, Peralta-Castro A, Mora-Garduño J, García-Medel P, Zambrano-Pereira AG, Díaz-Quezada C, Abraham-Juárez MJ, Benítez-Cardoza CG, Sloan DB, Brieba LG. Plant Organellar MSH1 Is a Displacement Loop-Specific Endonuclease. PLANT & CELL PHYSIOLOGY 2024; 65:560-575. [PMID: 37756637 DOI: 10.1093/pcp/pcad112] [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: 06/16/2023] [Revised: 09/09/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023]
Abstract
MutS HOMOLOG 1 (MSH1) is an organellar-targeted protein that obstructs ectopic recombination and the accumulation of mutations in plant organellar genomes. MSH1 also modulates the epigenetic status of nuclear DNA, and its absence induces a variety of phenotypic responses. MSH1 is a member of the MutS family of DNA mismatch repair proteins but harbors an additional GIY-YIG nuclease domain that distinguishes it from the rest of this family. How MSH1 hampers recombination and promotes fidelity in organellar DNA inheritance is unknown. Here, we elucidate its enzymatic activities by recombinantly expressing and purifying full-length MSH1 from Arabidopsis thaliana (AtMSH1). AtMSH1 is a metalloenzyme that shows a strong binding affinity for displacement loops (D-loops). The DNA-binding abilities of AtMSH1 reside in its MutS domain and not in its GIY-YIG domain, which is the ancillary nickase of AtMSH1. In the presence of divalent metal ions, AtMSH1 selectively executes multiple incisions at D-loops, but not other DNA structures including Holliday junctions or dsDNA, regardless of the presence or absence of mismatches. The selectivity of AtMSH1 to dismantle D-loops supports the role of this enzyme in preventing recombination between short repeats. Our results suggest that plant organelles have evolved novel DNA repair routes centered around the anti-recombinogenic activity of MSH1.
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Affiliation(s)
- Alejandro Peñafiel-Ayala
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
| | - Antolin Peralta-Castro
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
| | - Josue Mora-Garduño
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
| | - Paola García-Medel
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
| | - Angie G Zambrano-Pereira
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
| | - Corina Díaz-Quezada
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
| | - María Jazmín Abraham-Juárez
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
| | - Claudia G Benítez-Cardoza
- Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-IPN, Guillermo Massieu Helguera No. 239, La Escalera Ticoman 07320 DF, México
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Luis G Brieba
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
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3
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Nishimura Y. Plastid Nucleoids: Insights into Their Shape and Dynamics. PLANT & CELL PHYSIOLOGY 2024; 65:551-559. [PMID: 37542434 DOI: 10.1093/pcp/pcad090] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/26/2023] [Accepted: 08/04/2023] [Indexed: 08/07/2023]
Abstract
Chloroplasts/plastids are unique organelles found in plant cells and some algae and are responsible for performing essential functions such as photosynthesis. The plastid genome, consisting of circular and linear DNA molecules, is packaged and organized into specialized structures called nucleoids. The composition and dynamics of these nucleoids have been the subject of intense research, as they are critical for proper plastid functions and development. In this mini-review, recent advances in understanding the organization and regulation of plastid nucleoids are overviewed, with a focus on the various proteins and factors that regulate the shape and dynamics of nucleoids, including DNA-binding proteins and membrane anchorage proteins. The dynamic nature of nucleoid organization, which is influenced by a variety of developmental cues and the cell cycle, is also examined.
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Affiliation(s)
- Yoshiki Nishimura
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Kita-Shirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
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4
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Ślesak I, Ślesak H. From cyanobacteria and cyanophages to chloroplasts: the fate of the genomes of oxyphototrophs and the genes encoding photosystem II proteins. THE NEW PHYTOLOGIST 2024; 242:1055-1067. [PMID: 38439684 DOI: 10.1111/nph.19633] [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: 11/14/2023] [Accepted: 02/02/2024] [Indexed: 03/06/2024]
Abstract
Chloroplasts are the result of endosymbiosis of cyanobacterial organisms with proto-eukaryotes. The psbA, psbD and psbO genes are present in all oxyphototrophs and encode the D1/D2 proteins of photosystem II (PSII) and PsbO, respectively. PsbO is a peripheral protein that stabilizes the O2-evolving complex in PSII. Of these genes, psbA and psbD remained in the chloroplastic genome, while psbO was transferred to the nucleus. The genomes of selected cyanobacteria, chloroplasts and cyanophages carrying psbA and psbD, respectively, were analysed. The highest density of genes and coding sequences (CDSs) was estimated for the genomes of cyanophages, cyanobacteria and chloroplasts. The synonymous mutation rate (rS) of psbA and psbD in chloroplasts remained almost unchanged and is lower than that of psbO. The results indicate that the decreasing genome size in chloroplasts is more similar to the genome reduction observed in contemporary endosymbiotic organisms than in streamlined genomes of free-living cyanobacteria. The rS of atpA, which encodes the α-subunit of ATP synthase in chloroplasts, suggests that psbA and psbD, and to a lesser extent psbO, are ancient and conservative and arose early in the evolution of oxygenic photosynthesis. The role of cyanophages in the evolution of oxyphototrophs and chloroplastic genomes is discussed.
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Affiliation(s)
- Ireneusz Ślesak
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Kraków, Poland
| | - Halina Ślesak
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland
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5
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Shan Y, Li J, Duan X, Zhang X, Yu J. Elucidating the multichromosomal structure within the Brasenia schreberi mitochondrial genome through assembly and analysis. BMC Genomics 2024; 25:422. [PMID: 38684976 PMCID: PMC11059650 DOI: 10.1186/s12864-024-10331-0] [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: 12/19/2023] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Abstract
Brasenia schreberi, a plant species traditionally utilized in Chinese medicine and cuisine, represents an early evolutionary stage among flowering plants (angiosperms). While the plastid genome of this species has been published, its mitochondrial genome (mitogenome) has not been extensively explored, with a notable absence of thorough comparative analyses of its organellar genomes. In our study, we had assembled the entire mitogenome of B. schreberi utilizing the sequencing data derived from both Illumina platform and Oxford Nanopore. The B. schreberi mitogenome mostly exists as six circular DNA molecules, with the largest being 628,257 base pairs (bp) and the smallest 110,220 bp, amounting to 1.49 megabases (Mb). Then we annotated the mitogenome of B. schreberi. The mitogenome encompasses a total of 71 genes: 40 of these are coding proteins genes (PCGs), 28 are genes for transfer RNA (tRNA), and the remaining 3 are genes for ribosomal RNA (rRNA). In the analysis of codon usage, we noted a unique codon preference specific to each amino acid. The most commonly used codons exhibited an average RSCU of 1.36, indicating a noticeable bias in codon selection. In the repeat sequence analysis, a total of 553 simple sequence repeats (SSRs) were identified, 1,822 dispersed repeats (comprising 1,015 forward and 807 palindromic repeats), and 608 long terminal repeats (LTRs). Additionally, in the analysis of homologous sequences between organelle genomes, we detected 38 homologous sequences derived from the plastid genome, each exceeding 500 bp, within the B. schreberi mitochondrial genome. Notably, ten tRNA genes (trnC-GCA, trnM-CAU, trnI-CAU, trnQ-UUG, trnN-GUU, trnT-GGU, trnW-CCA, trnA-UGC, trnI-GAU, and trnV-GAC) appear to have been completely transferred from the chloroplast to the mitogenome. Utilizing the Deepred-mt to predict the RNA editing sites in the mitogenome, we have identified 675 high-quality RNA editing sites in the 40 mitochondrial PCGs. In the final stage of our study, we performed an analysis of colinearity and inferred the phylogenetic relationship of B. schreberi with other angiosperms, utilizing the mitochondrial PCGs as a basis. The results showed that the non-coding regions of the B. schreberi mitogenome are characterized by an abundance of repetitive sequences and exogenous sequences, and B. schreberi is more closely related with Euryale ferox.
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Affiliation(s)
- 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
| | - Xinmei Duan
- 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.
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing, 400715, China.
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6
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Fragkoulis G, Hangas A, Fekete Z, Michell C, Moraes C, Willcox S, Griffith JD, Goffart S, Pohjoismäki JO. Linear DNA-driven recombination in mammalian mitochondria. Nucleic Acids Res 2024; 52:3088-3105. [PMID: 38300793 PMCID: PMC11014290 DOI: 10.1093/nar/gkae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 01/11/2024] [Indexed: 02/03/2024] Open
Abstract
Mitochondrial DNA (mtDNA) recombination in animals has remained enigmatic due to its uniparental inheritance and subsequent homoplasmic state, which excludes the biological need for genetic recombination, as well as limits tools to study it. However, molecular recombination is an important genome maintenance mechanism for all organisms, most notably being required for double-strand break repair. To demonstrate the existence of mtDNA recombination, we took advantage of a cell model with two different types of mitochondrial genomes and impaired its ability to degrade broken mtDNA. The resulting excess of linear DNA fragments caused increased formation of cruciform mtDNA, appearance of heterodimeric mtDNA complexes and recombinant mtDNA genomes, detectable by Southern blot and by long range PacBio® HiFi sequencing approach. Besides utilizing different electrophoretic methods, we also directly observed molecular complexes between different mtDNA haplotypes and recombination intermediates using transmission electron microscopy. We propose that the known copy-choice recombination by mitochondrial replisome could be sufficient for the needs of the small genome, thus removing the requirement for a specialized mitochondrial recombinase. The error-proneness of this system is likely to contribute to the formation of pathological mtDNA rearrangements.
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Affiliation(s)
- Georgios Fragkoulis
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, 80101 Joensuu, Finland
| | - Anu Hangas
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, 80101 Joensuu, Finland
| | - Zsófia Fekete
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, 80101 Joensuu, Finland
- Department of Genetics and Genomics, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
- Doctoral School of Animal Biotechnology and Animal Science, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Craig Michell
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Carlos T Moraes
- Department of Neurology, University of Miami Miller School of Medicine, Miami,FL, USA
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, USA
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, USA
| | - Steffi Goffart
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, 80101 Joensuu, Finland
| | - Jaakko L O Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, 80101 Joensuu, Finland
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7
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Li C, Liu H, Qin M, Tan YJ, Ou XL, Chen XY, Wei Y, Zhang ZJ, Lei M. RNA editing events and expression profiles of mitochondrial protein-coding genes in the endemic and endangered medicinal plant, Corydalis saxicola. FRONTIERS IN PLANT SCIENCE 2024; 15:1332460. [PMID: 38379941 PMCID: PMC10876856 DOI: 10.3389/fpls.2024.1332460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024]
Abstract
Corydalis saxicola, an endangered medicinal plant endemic to karst habitats, is widely used in Traditional Chinese Medicine to treat hepatitis, abdominal pain, bleeding hemorrhoids and other conditions. However, to date, the mitochondrial (mt) genome of C. saxicola has not been reported, which limits our understanding of the genetic and biological mechanisms of C. saxicola. Here, the mt genome of C. saxicola was assembled by combining the Nanopore and Illumina reads. The mt genome of C. saxicola is represented by a circular chromosome which is 587,939 bp in length, with an overall GC content of 46.50%. 40 unique protein-coding genes (PCGs), 22 tRNA genes and three rRNA genes were identified. Codon usage of the PCGs was investigated and 167 simple sequence repeats were identified. Twelve homologous fragments were identified between the mt and ct genomes of C. saxicola, accounting for 1.04% of the entire mt genome. Phylogenetic examination of the mt genomes of C. saxicola and 30 other taxa provided an understanding of their evolutionary relationships. We also predicted 779 RNA editing sites in 40 C. saxicola mt PCGs and successfully validated 506 (65%) of these using PCR amplification and Sanger sequencing. In addition, we transcriptionally profiled 24 core mt PCGs in C. saxicola roots treated with different concentrations of CaCl2, as well as in other organs. These investigations will be useful for effective utilization and molecular breeding, and will also provide a reference for further studies of the genus Corydalis.
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Affiliation(s)
- Cui Li
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Han Liu
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Mei Qin
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Yao-jing Tan
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Xia-lian Ou
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Xiao-ying Chen
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Ying Wei
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Zhan-jiang Zhang
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Ming Lei
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
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8
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Köhler M, Reginato M, Jin JJ, Majure LC. More than a spiny morphology: plastome variation in the prickly pear cacti (Opuntieae). ANNALS OF BOTANY 2023; 132:771-786. [PMID: 37467174 PMCID: PMC10799996 DOI: 10.1093/aob/mcad098] [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: 03/14/2023] [Revised: 06/30/2023] [Accepted: 07/14/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Plastid genomes (plastomes) have long been recognized as highly conserved in their overall structure, size, gene arrangement and content among land plants. However, recent studies have shown that some lineages present unusual variations in some of these features. Members of the cactus family are one of these lineages, with distinct plastome structures reported across disparate lineages, including gene losses, inversions, boundary movements or loss of the canonical inverted repeat (IR) region. However, only a small fraction of cactus diversity has been analysed so far. METHODS Here, we investigated plastome features of the tribe Opuntieae, the remarkable prickly pear cacti, which represent one of the most diverse and important lineages of Cactaceae. We assembled de novo the plastome of 43 species, representing a comprehensive sampling of the tribe, including all seven genera, and analysed their evolution in a phylogenetic comparative framework. Phylogenomic analyses with different datasets (full plastome sequences and genes only) were performed, followed by congruence analyses to assess signals underlying contentious nodes. KEY RESULTS Plastomes varied considerably in length, from 121 to 162 kbp, with striking differences in the content and size of the IR region (contraction and expansion events), including a lack of the canonical IR in some lineages and the pseudogenization or loss of some genes. Overall, nine different types of plastomes were reported, deviating in the presence of the IR region or the genes contained in the IR. Overall, plastome sequences resolved phylogenetic relationships within major clades of Opuntieae with high bootstrap values but presented some contentious nodes depending on the dataset analysed (e.g. whole plastome vs. genes only). Congruence analyses revealed that most plastidial regions lack phylogenetic resolution, while few markers are supporting the most likely topology. Likewise, alternative topologies are driven by a handful of plastome markers, suggesting recalcitrant nodes in the phylogeny. CONCLUSIONS Our study reveals a dynamic nature of plastome evolution across closely related lineages, shedding light on peculiar features of plastomes. Variation of plastome types across Opuntieae is remarkable in size, structure and content and can be important for the recognition of species in some major clades. Unravelling connections between the causes of plastome variation and the consequences for species biology, physiology, ecology, diversification and adaptation is a promising and ambitious endeavour in cactus research. Although plastome data resolved major phylogenetic relationships, the generation of nuclear genomic data is necessary to confront these hypotheses and assess the recalcitrant nodes further.
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Affiliation(s)
- Matias Köhler
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos, Sorocaba, SP, Brazil
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Marcelo Reginato
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Jian-Jun Jin
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Lucas C Majure
- University of Florida Herbarium (FLAS), Florida Museum of Natural History, Gainesville, FL, USA
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9
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Liu X, Bai Y, Wang Y, Chen Y, Dong W, Zhang Z. Complete Chloroplast Genome of Hypericum perforatum and Dynamic Evolution in Hypericum (Hypericaceae). Int J Mol Sci 2023; 24:16130. [PMID: 38003320 PMCID: PMC10671389 DOI: 10.3390/ijms242216130] [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] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Hypericum perforatum (St. John's Wort) is a medicinal plant from the Hypericaceae family. Here, we sequenced the whole chloroplast genome of H. perforatum and compared the genome variation among five Hypericum species to discover dynamic changes and elucidate the mechanisms that lead to genome rearrangements in the Hypericum chloroplast genomes. The H. perforatum chloroplast genome is 139,725 bp, exhibiting a circular quadripartite structure with two copies of inverted repeats (IRs) separating a large single-copy region and a small single-copy region. The H. perforatum chloroplast genome encodes 106 unique genes, including 73 protein-coding genes, 29 tRNAs, and 4 rRNAs. Hypericum chloroplast genomes exhibit genome rearrangement and significant variations among species. The genome size variation among the five Hypericum species was remarkably associated with the expansion or contraction of IR regions and gene losses. Three genes-trnK-UUU, infA, and rps16-were lost, and three genes-rps7, rpl23, and rpl32-were pseudogenized in Hypericum. All the Hypericum chloroplast genomes lost the two introns in clpP, the intron in rps12, and the second intron in ycf3. Hypericum chloroplast genomes contain many long repeat sequences, suggesting a role in facilitating rearrangements. Most genes, according to molecular evolution assessments, are under purifying selection.
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Affiliation(s)
- Xinyu Liu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (X.L.); (Y.B.); (Y.C.)
| | - Yuran Bai
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (X.L.); (Y.B.); (Y.C.)
| | - Yachao Wang
- School of Life Sciences, Fudan University, Shanghai 200437, China;
| | - Yifeng Chen
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (X.L.); (Y.B.); (Y.C.)
| | - Wenpan Dong
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (X.L.); (Y.B.); (Y.C.)
| | - Zhixiang Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (X.L.); (Y.B.); (Y.C.)
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10
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Guo H, Liu Q, Chen Y, Niu H, Zhao Q, Song H, Pang R, Huang X, Zhang J, Zhao Z, Liu D, Zhu J. Comprehensive assembly and comparative examination of the full mitochondrial genome in Castanea mollissima Blume. Genomics 2023; 115:110740. [PMID: 37923179 DOI: 10.1016/j.ygeno.2023.110740] [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: 09/01/2023] [Revised: 10/23/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
The Chinese chestnut, Castanea mollissima Blume, a nut-bearing tree native to China and North Korea, belongs to the Fagaceae family. As an important genetic resource, C. mollissima is vital in enhancing edible chestnut varieties and offers significant insights into the origin and evolution of chestnut species. While the chloroplast genome of C. mollissima has been sequenced, its mitochondrial genome (mitogenome) remains largely uncharted. In this study, we have characterized the C. mollissima mitogenome, assembling it utilizing reads from both BGI and Nanopore sequencing platforms, and conducted a comparative analysis with the mitochondrial genomes of closely related species. The mitogenome of C. mollissima manifests a polycyclic structure consisting of two circular molecules measuring 363,232 bp and 24,806 bp, respectively. This genome encompasses 35 unique protein-coding genes, 19 tRNA genes, and three rRNA genes. A total of 139 SSRs were identified throughout the entire C. mollissima mitogenome. Furthermore, the combined length of homologous fragments between the chloroplast and mitochondrial genomes was 5766 bp, constituting 1.49% of the mitogenome. We also predicted 484 RNA editing sites in C. mollissima, demonstrating C-to-U RNA editing. Phylogenetic analysis of related species' mitogenomes showed that C. mollissima was closely related to Lithocarpus litseifolius (Hance) Chun and Quercus acutissima Carruth. Interestingly, the mitogenome sequences of C. mollissima, L. litseifolius, Q. acutissima, Fagus sylvatica L., and Juglans mandshurica Maxim did not show conservation in their alignments, indicating frequent genome reorganization. This report marks the inaugural study of the C. mollissima mitogenome, serving as a benchmark genome for economically significant plants within the Castanea genus. Moreover, it supplies invaluable information that can guide future molecular breeding efforts and contribute to the broader understanding of chestnut genomics.
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Affiliation(s)
- Haili Guo
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China
| | - Qiong Liu
- Shandong Refining and Chemical Energy Group Co., Ltd., Jinan 250199, China
| | - Ying Chen
- Shandong Provincial Forestry Protection and Development Service Center, Jinan 250109, China
| | - Hongyun Niu
- Shandong Provincial Center of Aviation Emergency and Rescue, Jinan 250014, China
| | | | - Hui Song
- Shandong Institute of Land Spatial Data and Remote Sensing Technology, Jinan 250002, China
| | - Ruidong Pang
- Shandong Provincial Archives of Natural Resources, Jinan 250013, China
| | - Xiaolu Huang
- Guangxi Forestry Research Institute, Nanning 530002, China
| | - Jingzheng Zhang
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China
| | - Zhiheng Zhao
- Guangxi Forestry Research Institute, Nanning 530002, China; Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China.
| | - Dan Liu
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China.
| | - Jingle Zhu
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China.
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11
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Howe CJ, Nisbet RER, Barbrook AC. Evolution: The plasticity of plastids. Curr Biol 2023; 33:R1058-R1060. [PMID: 37875081 DOI: 10.1016/j.cub.2023.09.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Many chloroplast-bearing plants and algae lost their photosynthetic activity during evolution but retained their chloroplasts for other functions. A group of dinoflagellate algae apparently lost one half of their photosynthetic machinery but retained the other, providing a novel mechanism for light perception.
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Affiliation(s)
- Christopher J Howe
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK.
| | - R Ellen R Nisbet
- School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK.
| | - Adrian C Barbrook
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK.
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12
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Peralta-Castro A, Cordoba-Andrade F, Díaz-Quezada C, Sotelo-Mundo R, Winkler R, Brieba LG. The plant organellar primase-helicase directs template recognition and primosome assembly via its zinc finger domain. BMC PLANT BIOLOGY 2023; 23:467. [PMID: 37803262 PMCID: PMC10557236 DOI: 10.1186/s12870-023-04477-4] [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: 05/22/2023] [Accepted: 09/19/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND The mechanisms and regulation for DNA replication in plant organelles are largely unknown, as few proteins involved in replisome assembly have been biochemically studied. A primase-helicase dubbed Twinkle (T7 gp4-like protein with intramitochondrial nucleoid localization) unwinds double-stranded DNA in metazoan mitochondria and plant organelles. Twinkle in plants is a bifunctional enzyme with an active primase module. This contrast with animal Twinkle in which the primase module is inactive. The organellar primase-helicase of Arabidopsis thaliana (AtTwinkle) harbors a primase module (AtPrimase) that consists of an RNA polymerase domain (RPD) and a Zn + + finger domain (ZFD). RESULTS Herein, we investigate the mechanisms by which AtTwinkle recognizes its templating sequence and how primer synthesis and coupling to the organellar DNA polymerases occurs. Biochemical data show that the ZFD of the AtPrimase module is responsible for template recognition, and this recognition is achieved by residues N163, R166, and K168. The role of the ZFD in template recognition was also corroborated by swapping the RPDs of bacteriophage T7 primase and AtPrimase with their respective ZFDs. A chimeric primase harboring the ZFD of T7 primase and the RPD of AtPrimase synthesizes ribonucleotides from the T7 primase recognition sequence and conversely, a chimeric primase harboring the ZFD of AtPrimase and the RPD of T7 primase synthesizes ribonucleotides from the AtPrimase recognition sequence. A chimera harboring the RPDs of bacteriophage T7 and the ZBD of AtTwinkle efficiently synthesizes primers for the plant organellar DNA polymerase. CONCLUSIONS We conclude that the ZFD is responsible for recognizing a single-stranded sequence and for primer hand-off into the organellar DNA polymerases active site. The primase activity of plant Twinkle is consistent with phylogeny-based reconstructions that concluded that Twinkle´s last eukaryotic common ancestor (LECA) was an enzyme with primase and helicase activities. In plants, the primase domain is active, whereas the primase activity was lost in metazoans. Our data supports the notion that AtTwinkle synthesizes primers at the lagging-strand of the organellar replication fork.
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Affiliation(s)
- Antolin Peralta-Castro
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, 36821, Irapuato Guanajuato, Mexico
| | - Francisco Cordoba-Andrade
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, 36821, Irapuato Guanajuato, Mexico
| | - Corina Díaz-Quezada
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, 36821, Irapuato Guanajuato, Mexico
| | - Rogerio Sotelo-Mundo
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. Carretera Gustavo Enrique Astiazarán Rosas Núm. 46, Ejido a La Victoria, 83304, Hermosillo, Sonora, Mexico
| | - Robert Winkler
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, 36821, Irapuato Guanajuato, Mexico
| | - Luis G Brieba
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, 36821, Irapuato Guanajuato, Mexico.
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13
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Tao H, Zhu P, Xia W, Chu M, Chen K, Wang Q, Gu Y, Lu X, Bai J, Geng D. The Emerging Role of the Mitochondrial Respiratory Chain in Skeletal Aging. Aging Dis 2023:AD.2023.0924. [PMID: 37815897 DOI: 10.14336/ad.2023.0924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/24/2023] [Indexed: 10/12/2023] Open
Abstract
Maintenance of mitochondrial homeostasis is crucial for ensuring healthy mitochondria and normal cellular function. This process is primarily responsible for regulating processes that include mitochondrial OXPHOS, which generates ATP, as well as mitochondrial oxidative stress, apoptosis, calcium homeostasis, and mitophagy. Bone mesenchymal stem cells express factors that aid in bone formation and vascular growth. Positive regulation of hematopoietic stem cells in the bone marrow affects the differentiation of osteoclasts. Furthermore, the metabolic regulation of cells that play fundamental roles in various regions of the bone, as well as interactions within the bone microenvironment, actively participates in regulating bone integrity and aging. The maintenance of cellular homeostasis is dependent on the regulation of intracellular organelles, thus understanding the impact of mitochondrial functional changes on overall bone metabolism is crucially important. Recent studies have revealed that mitochondrial homeostasis can lead to morphological and functional abnormalities in senescent cells, particularly in the context of bone diseases. Mitochondrial dysfunction in skeletal diseases results in abnormal metabolism of bone-associated cells and a secondary dysregulated microenvironment within bone tissue. This imbalance in the oxidative system and immune disruption in the bone microenvironment ultimately leads to bone dysplasia. In this review, we examine the latest developments in mitochondrial respiratory chain regulation and its impacts on maintenance of bone health. Specifically, we explored whether enhancing mitochondrial function can reduce the occurrence of bone cell deterioration and improve bone metabolism. These findings offer prospects for developing bone remodeling biology strategies to treat age-related degenerative diseases.
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Affiliation(s)
- Huaqiang Tao
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Jiangsu, China
| | - Pengfei Zhu
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Jiangsu, China
| | - Wenyu Xia
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Jiangsu, China
| | - Miao Chu
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Jiangsu, China
| | - Kai Chen
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Jiangsu, China
| | - Qiufei Wang
- Department of Orthopedics, Changshu Hospital Affiliated to Soochow University, First People's Hospital of Changshu City, Jiangsu, China
| | - Ye Gu
- Department of Orthopedics, Changshu Hospital Affiliated to Soochow University, First People's Hospital of Changshu City, Jiangsu, China
| | - Xiaomin Lu
- Department of Oncology, Affiliated Haian Hospital of Nantong University, Jiangsu, China
| | - Jiaxiang Bai
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Jiangsu, China
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, China
| | - Dechun Geng
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Jiangsu, China
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14
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Zhou S, Wei N, Jost M, Wanke S, Rees M, Liu Y, Zhou R. The Mitochondrial Genome of the Holoparasitic Plant Thonningia sanguinea Provides Insights into the Evolution of the Multichromosomal Structure. Genome Biol Evol 2023; 15:evad155. [PMID: 37603455 PMCID: PMC10476698 DOI: 10.1093/gbe/evad155] [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: 07/07/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/23/2023] Open
Abstract
Multichromosomal mitochondrial genome (mitogenome) structures have repeatedly evolved in many lineages of angiosperms. However, the underlying mechanism remains unclear. The mitogenomes of three genera of Balanophoraceae, namely Lophophytum, Ombrophytum, and Rhopalocnemis, have already been sequenced and assembled, all showing a highly multichromosomal structure, albeit with different genome and chromosome sizes. It is expected that characterization of additional lineages of this family may expand the knowledge of mitogenome diversity and provide insights into the evolution of the plant mitogenome structure and size. Here, we assembled and characterized the mitogenome of Thonningia sanguinea, which, together with Balanophora, forms a clade sister to the clade comprising Lophophytum, Ombrophytum, and Rhopalocnemis. The mitogenome of T. sanguinea possesses a multichromosomal structure of 18 circular chromosomes of 8.7-19.2 kb, with a total size of 246,247 bp. There are very limited shared regions and poor chromosomal correspondence between T. sanguinea and other Balanophoraceae species, suggesting frequent rearrangements and rapid sequence turnover. Numerous medium- and small-sized repeats were identified in the T. sanguinea mitogenome; however, no repeat-mediated recombination was detected, which was verified by Illumina reads mapping and PCR experiments. Intraspecific mitogenome variations in T. sanguinea are mostly insertions and deletions, some of which can lead to degradation of perfect repeats in one or two accessions. Based on the mitogenome features of T. sanguinea, we propose a mechanism to explain the evolution of a multichromosomal mitogenome from a master circle, which involves mutation in organellar DNA replication, recombination and repair genes, decrease of recombination, and repeat degradation.
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Affiliation(s)
- Shuaixi Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Neng Wei
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Matthias Jost
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Mathew Rees
- School of GeoSciences, University of Edinburgh, Edinburgh, United Kingdom
- Royal Botanic Garden, Edinburgh, United Kingdom
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-Sen University, Guangzhou, Guangdong, China
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15
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Tripathi D, Oldenburg DJ, Bendich AJ. Ribonucleotide and R-Loop Damage in Plastid DNA and Mitochondrial DNA during Maize Development. PLANTS (BASEL, SWITZERLAND) 2023; 12:3161. [PMID: 37687407 PMCID: PMC10489836 DOI: 10.3390/plants12173161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023]
Abstract
Although the temporary presence of ribonucleotides in DNA is normal, their persistence represents a form of DNA damage. Here, we assess such damage and damage defense to DNA in plastids and mitochondria of maize. Shoot development proceeds from meristematic, non-pigmented cells containing proplastids and promitochondria at the leaf base to non-dividing green cells in the leaf blade containing mature organelles. The organellar DNAs (orgDNAs) become fragmented during this transition. Previously, orgDNA damage and damage defense of two types, oxidative and glycation, was described in maize, and now a third type, ribonucleotide damage, is reported. We hypothesized that ribonucleotide damage changes during leaf development and could contribute to the demise of orgDNAs. The levels of ribonucleotides and R-loops in orgDNAs and of RNase H proteins in organelles were measured throughout leaf development and in leaves grown in light and dark conditions. The data reveal that ribonucleotide damage to orgDNAs increased by about 2- to 5-fold during normal maize development from basal meristem to green leaf and when leaves were grown in normal light conditions compared to in the dark. During this developmental transition, the levels of the major agent of defense, RNase H, declined. The decline in organellar genome integrity during maize development may be attributed to oxidative, glycation, and ribonucleotide damages that are not repaired.
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Affiliation(s)
| | | | - Arnold J. Bendich
- Department of Biology, University of Washington, Seattle, WA 98195, USA; (D.T.); (D.J.O.)
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16
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Morton BR. Context and Mutation in Gymnosperm Chloroplast DNA. Genes (Basel) 2023; 14:1492. [PMID: 37510396 PMCID: PMC10378972 DOI: 10.3390/genes14071492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Mutations and subsequent repair processes are known to be strongly context-dependent in the flowering-plant chloroplast genome. At least six flanking bases, three on each side, can have an influence on the relative rates of different types of mutation at any given site. In this analysis, examine context and substitution at noncoding and fourfold degenerate coding sites in gymnosperm DNA. The sequences are analyzed in sets of three, allowing the inference of the substitution direction and the generation of context-dependent rate matrices. The size of the dataset limits the analysis to the tetranucleotide context of the sites, but the evidence shows that there are significant contextual effects, with patterns that are similar to those observed in angiosperms. These effects most likely represent an influence on the underlying mutation/repair dynamics. The data extend the plastome lineages that feature very complex patterns of mutation, which can have significant effects on the evolutionary dynamics of the chloroplast genome.
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Affiliation(s)
- Brian R Morton
- Department of Biology, Barnard College, Columbia University, 3009 Broadway, New York, NY 10027, USA
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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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Lee Y, Cho CH, Noh C, Yang JH, Park SI, Lee YM, West JA, Bhattacharya D, Jo K, Yoon HS. Origin of minicircular mitochondrial genomes in red algae. Nat Commun 2023; 14:3363. [PMID: 37291154 PMCID: PMC10250338 DOI: 10.1038/s41467-023-39084-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
Eukaryotic organelle genomes are generally of conserved size and gene content within phylogenetic groups. However, significant variation in genome structure may occur. Here, we report that the Stylonematophyceae red algae contain multipartite circular mitochondrial genomes (i.e., minicircles) which encode one or two genes bounded by a specific cassette and a conserved constant region. These minicircles are visualized using fluorescence microscope and scanning electron microscope, proving the circularity. Mitochondrial gene sets are reduced in these highly divergent mitogenomes. Newly generated chromosome-level nuclear genome assembly of Rhodosorus marinus reveals that most mitochondrial ribosomal subunit genes are transferred to the nuclear genome. Hetero-concatemers that resulted from recombination between minicircles and unique gene inventory that is responsible for mitochondrial genome stability may explain how the transition from typical mitochondrial genome to minicircles occurs. Our results offer inspiration on minicircular organelle genome formation and highlight an extreme case of mitochondrial gene inventory reduction.
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Affiliation(s)
- Yongsung Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Chanyoung Noh
- Department of Chemistry, Sogang University, Seoul, 04107, Korea
| | - Ji Hyun Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Seung In Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Yu Min Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - John A West
- School of Biosciences 2, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, 08901, USA
| | - Kyubong Jo
- Department of Chemistry, Sogang University, Seoul, 04107, Korea.
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea.
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19
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Tripathi D, Oldenburg DJ, Bendich AJ. Oxidative and Glycation Damage to Mitochondrial DNA and Plastid DNA during Plant Development. Antioxidants (Basel) 2023; 12:antiox12040891. [PMID: 37107266 PMCID: PMC10135910 DOI: 10.3390/antiox12040891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 04/08/2023] Open
Abstract
Oxidative damage to plant proteins, lipids, and DNA caused by reactive oxygen species (ROS) has long been studied. The damaging effects of reactive carbonyl groups (glycation damage) to plant proteins and lipids have also been extensively studied, but only recently has glycation damage to the DNA in plant mitochondria and plastids been reported. Here, we review data on organellar DNA maintenance after damage from ROS and glycation. Our focus is maize, where tissues representing the entire range of leaf development are readily obtained, from slow-growing cells in the basal meristem, containing immature organelles with pristine DNA, to fast-growing leaf cells, containing mature organelles with highly-fragmented DNA. The relative contributions to DNA damage from oxidation and glycation are not known. However, the changing patterns of damage and damage-defense during leaf development indicate tight coordination of responses to oxidation and glycation events. Future efforts should be directed at the mechanism by which this coordination is achieved.
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Affiliation(s)
- Diwaker Tripathi
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | | | - Arnold J. Bendich
- Department of Biology, University of Washington, Seattle, WA 98195, USA
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20
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Jin HL, Duan S, Zhang P, Yang Z, Zeng Y, Chen Z, Hong L, Li M, Luo L, Chang Z, Hu J, Wang HB. Dual roles for CND1 in maintenance of nuclear and chloroplast genome stability in plants. Cell Rep 2023; 42:112268. [PMID: 36933214 DOI: 10.1016/j.celrep.2023.112268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 12/19/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023] Open
Abstract
The coordination of chloroplast and nuclear genome status is critical for plant cell function. Here, we report that Arabidopsis CHLOROPLAST AND NUCLEUS DUAL-LOCALIZED PROTEIN 1 (CND1) maintains genome stability in the chloroplast and the nucleus. CND1 localizes to both compartments, and complete loss of CND1 results in embryo lethality. Partial loss of CND1 disturbs nuclear cell-cycle progression and photosynthetic activity. CND1 binds to nuclear pre-replication complexes and DNA replication origins and regulates nuclear genome stability. In chloroplasts, CND1 interacts with and facilitates binding of the regulator of chloroplast genome stability WHY1 to chloroplast DNA. The defects in nuclear cell-cycle progression and photosynthesis of cnd1 mutants are respectively rescued by compartment-restricted CND1 localization. Light promotes the association of CND1 with HSP90 and its import into chloroplasts. This study provides a paradigm of the convergence of genome status across organelles to coordinately regulate cell cycle to control plant growth and development.
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Affiliation(s)
- Hong-Lei Jin
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China; Guangzhou Key Laboratory of Chinese Medicine Research on Prevention and Treatment of Osteoporosis, The Third Affiliated Hospital of Guangzhou University of Chinese Medicine, No. 263, Longxi Avenue, Guangzhou, China.
| | - Sujuan Duan
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Pengxiang Zhang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Ziyue Yang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Yunping Zeng
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Ziqi Chen
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Liu Hong
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Mengshu Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Lujun Luo
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Zhenyi Chang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Jiliang Hu
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Hong-Bin Wang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, China; State Key Laboratory of Dampness Syndrome of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China.
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21
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Su X, Liu Q, Guo H, Hu D, Liu D, Wang Z, Zhang P. Deciphering the mitochondrial genome of Juglans mandshurica (Juglandaceae). Mitochondrial DNA B Resour 2023; 8:249-254. [PMID: 36816062 PMCID: PMC9930755 DOI: 10.1080/23802359.2023.2172974] [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] [Indexed: 02/12/2023] Open
Abstract
Juglans mandshurica Maxim., 1856 is a second-class, protected, rare tree species of high economic and ecological value. We elucidated the complete mitochondrial (mt) genome of J. mandshurica using the Illumina Novaseq 6000 and Nanopore platforms. The complete sequences of 558,032 and 161,386 bp had an overall GC content of 45.0% and 45.3%, respectively, and 61 genes could be annotated, including 38 protein-coding, 20 tRNA, and 3 rRNA genes. The high-quality J. mandshurica mt genomic sequences presented in this study will serve as a useful resource for a range of genetic, functional, evolutionary, and comparative genomic studies on this species of the Juglandaceae family.
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Affiliation(s)
- Xun Su
- School of Life Sciences, Ludong University, Yantai, P.R. China
| | - Qiong Liu
- Shandong Refining and Chemical Energy Group Co., Ltd., Jinan, P.R. China
| | - Haili Guo
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, P.R. China
| | - Dechang Hu
- School of Life Sciences, Ludong University, Yantai, P.R. China,CONTACT Dechang Hu School of Life Sciences, Ludong University, 186# Hongqi Middle Road, Zhifu District, Yantai, Shandong, 264025, P.R. China
| | - Dan Liu
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, P.R. China,Dan Liu Shandong Provincial Center of Forest and Grass Germplasm Resources, No. 2011, Gangjiu Road, Ganggou Street, Jinan, Shandong, 250102, P.R. China
| | - Zihao Wang
- School of Life Sciences, Ludong University, Yantai, P.R. China
| | - Ping Zhang
- School of Life Sciences, Ludong University, Yantai, P.R. China
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22
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Evidence for Strand Asymmetry in Different Plastid Genomes. Genes (Basel) 2023; 14:genes14020320. [PMID: 36833247 PMCID: PMC9956171 DOI: 10.3390/genes14020320] [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: 12/02/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/28/2023] Open
Abstract
A common genome composition pattern in eubacteria is an asymmetry between the leading and lagging strands resulting in opposite skew patterns in the two replichores that lie between the origin and terminus of replication. Although this pattern has been reported for a couple of isolated plastid genomes, it is not clear how widespread it is overall in this chromosome. Using a random walk approach, we examine plastid genomes outside of the land plants, which are excluded since they are known not to initiate replication at a single site, for such a pattern of asymmetry. Although it is not a common feature, we find that it is detectable in the plastid genome of species from several diverse lineages. The euglenozoa in particular show a strong skew pattern as do several rhodophytes. There is a weaker pattern in some chlorophytes but it is not apparent in other lineages. The ramifications of this for analyses of plastid evolution are discussed.
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23
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Comparative analyses of Theobroma cacao and T. grandiflorum mitogenomes reveal conserved gene content embedded within complex and plastic structures. Gene X 2023; 849:146904. [DOI: 10.1016/j.gene.2022.146904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/05/2022] [Accepted: 09/15/2022] [Indexed: 11/20/2022] Open
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24
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Rozov SM, Zagorskaya AA, Konstantinov YM, Deineko EV. Three Parts of the Plant Genome: On the Way to Success in the Production of Recombinant Proteins. PLANTS (BASEL, SWITZERLAND) 2022; 12:38. [PMID: 36616166 PMCID: PMC9824153 DOI: 10.3390/plants12010038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Recombinant proteins are the most important product of current industrial biotechnology. They are indispensable in medicine (for diagnostics and treatment), food and chemical industries, and research. Plant cells combine advantages of the eukaryotic protein production system with simplicity and efficacy of the bacterial one. The use of plants for the production of recombinant proteins is an economically important and promising area that has emerged as an alternative to traditional approaches. This review discusses advantages of plant systems for the expression of recombinant proteins using nuclear, plastid, and mitochondrial genomes. Possibilities, problems, and prospects of modifications of the three parts of the genome in light of obtaining producer plants are examined. Examples of successful use of the nuclear expression platform for production of various biopharmaceuticals, veterinary drugs, and technologically important proteins are described, as are examples of a high yield of recombinant proteins upon modification of the chloroplast genome. Potential utility of plant mitochondria as an expression system for the production of recombinant proteins and its advantages over the nucleus and chloroplasts are substantiated. Although these opportunities have not yet been exploited, potential utility of plant mitochondria as an expression system for the production of recombinant proteins and its advantages over the nucleus and chloroplasts are substantiated.
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Affiliation(s)
- Sergey M. Rozov
- Federal Research Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, pr. Akad. Lavrentieva 10, Novosibirsk 630090, Russia
| | - Alla A. Zagorskaya
- Federal Research Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, pr. Akad. Lavrentieva 10, Novosibirsk 630090, Russia
| | - Yuri M. Konstantinov
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch of Russian Academy of Sciences, Lermontova Str. 132, Irkutsk 664033, Russia
| | - Elena V. Deineko
- Federal Research Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, pr. Akad. Lavrentieva 10, Novosibirsk 630090, Russia
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25
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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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26
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Xiao S, Xing J, Nie T, Su A, Zhang R, Zhao Y, Song W, Zhao J. Comparative analysis of mitochondrial genomes of maize CMS-S subtypes provides new insights into male sterility stability. BMC PLANT BIOLOGY 2022; 22:469. [PMID: 36180833 PMCID: PMC9526321 DOI: 10.1186/s12870-022-03849-6] [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: 05/11/2022] [Accepted: 09/06/2022] [Indexed: 05/11/2023]
Abstract
BACKGROUND Cytoplasmic male sterility (CMS) is a trait of economic importance in the production of hybrid seeds. In CMS-S maize, exerted anthers appear frequently in florets of field-grown female populations where only complete male-sterile plants were expected. It has been reported that these reversions are associated with the loss of sterility-conferring regions or other rearrangements in the mitochondrial genome. However, the relationship between mitochondrial function and sterility stability is largely unknown. RESULTS In this study, we determined the ratio of plants carrying exerted anthers in the population of two CMS-S subtypes. The subtype with a high ratio of exerted anthers was designated as CMS-Sa, and the other with low ratio was designated as CMS-Sb. Through next-generation sequencing, we assembled and compared mitochondrial genomes of two CMS-S subtypes. Phylogenetic analyses revealed strong similarities between the two mitochondrial genomes. The sterility-associated regions, S plasmids, and terminal inverted repeats (TIRs) were intact in both genomes. The two subtypes maintained high transcript levels of the sterility gene orf355 in anther tissue. Most of the functional genes/proteins were identical at the nucleotide sequence and amino acid sequence levels in the two subtypes, except for NADH dehydrogenase subunit 1 (nad1). In the mitochondrial genome of CMS-Sb, a 3.3-kilobase sequence containing nad1-exon1 was absent from the second copy of the 17-kb repeat region. Consequently, we detected two copies of nad1-exon1 in CMS-Sa, but only one copy in CMS-Sb. During pollen development, nad1 transcription and mitochondrial biogenesis were induced in anthers of CMS-Sa, but not in those of CMS-Sb. We suggest that the impaired mitochondrial function in the anthers of CMS-Sb is associated with its more stable sterility. CONCLUSIONS Comprehensive analyses revealed diversity in terms of the copy number of the mitochondrial gene nad1-exon1 between two subtypes of CMS-S maize. This difference in copy number affected the transcript levels of nad1 and mitochondrial biogenesis in anther tissue, and affected the reversion rate of CMS-S maize. The results of this study suggest the involvement of mitochondrial robustness in modulation of sterility stability in CMS-S maize.
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Affiliation(s)
- Senlin Xiao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jingfeng Xing
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Tiange Nie
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Aiguo Su
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Ruyang Zhang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yanxin Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Wei Song
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Jiuran Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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27
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Niehaus M, Straube H, Specht A, Baccolini C, Witte CP, Herde M. The nucleotide metabolome of germinating Arabidopsis thaliana seeds reveals a central role for thymidine phosphorylation in chloroplast development. THE PLANT CELL 2022; 34:3790-3813. [PMID: 35861422 PMCID: PMC9516053 DOI: 10.1093/plcell/koac207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/13/2022] [Indexed: 05/29/2023]
Abstract
Thymidylates are generated by several partially overlapping metabolic pathways in different subcellular locations. This interconnectedness complicates an understanding of how thymidylates are formed in vivo. Analyzing a comprehensive collection of mutants and double mutants on the phenotypic and metabolic level, we report the effect of de novo thymidylate synthesis, salvage of thymidine, and conversion of cytidylates to thymidylates on thymidylate homeostasis during seed germination and seedling establishment in Arabidopsis (Arabidopsis thaliana). During germination, the salvage of thymidine in organelles contributes predominantly to the thymidylate pools and a mutant lacking organellar (mitochondrial and plastidic) thymidine kinase has severely altered deoxyribonucleotide levels, less chloroplast DNA, and chlorotic cotyledons. This phenotype is aggravated when mitochondrial thymidylate de novo synthesis is additionally compromised. We also discovered an organellar deoxyuridine-triphosphate pyrophosphatase and show that its main function is not thymidylate synthesis but probably the removal of noncanonical nucleotide triphosphates. Interestingly, cytosolic thymidylate synthesis can only compensate defective organellar thymidine salvage in seedlings but not during germination. This study provides a comprehensive insight into the nucleotide metabolome of germinating seeds and demonstrates the unique role of enzymes that seem redundant at first glance.
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Affiliation(s)
- Markus Niehaus
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Henryk Straube
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - André Specht
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | | | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
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28
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Santana I, Jeon SJ, Kim HI, Islam MR, Castillo C, Garcia GFH, Newkirk GM, Giraldo JP. Targeted Carbon Nanostructures for Chemical and Gene Delivery to Plant Chloroplasts. ACS NANO 2022; 16:12156-12173. [PMID: 35943045 DOI: 10.1021/acsnano.2c02714] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Nanotechnology approaches for improving the delivery efficiency of chemicals and molecular cargoes in plants through plant biorecognition mechanisms remain relatively unexplored. We developed targeted carbon-based nanomaterials as tools for precise chemical delivery (carbon dots, CDs) and gene delivery platforms (single-walled carbon nanotubes, SWCNTs) to chloroplasts, key organelles involved in efforts to improve plant photosynthesis, assimilation of nutrients, and delivery of agrochemicals. A biorecognition approach of coating the nanomaterials with a rationally designed chloroplast targeting peptide improved the delivery of CDs with molecular baskets (TP-β-CD) for delivery of agrochemicals and of plasmid DNA coated SWCNT (TP-pATV1-SWCNT) from 47% to 70% and from 39% to 57% of chloroplasts in leaves, respectively. Plants treated with TP-β-CD (20 mg/L) and TP-pATV1-SWCNT (2 mg/L) had a low percentage of dead cells, 6% and 8%, respectively, similar to controls without nanoparticles, and no permanent cell and chloroplast membrane damage after 5 days of exposure. However, targeted nanomaterials transiently increased leaf H2O2 (0.3225 μmol gFW-1) above control plant levels (0.03441 μmol gFW-1) but within the normal range reported in land plants. The increase in leaf H2O2 levels was associated with oxidative damage in whole plant cell DNA, a transient effect on chloroplast DNA, and a decrease in leaf chlorophyll content (-17%) and carbon assimilation rates at saturation light levels (-32%) with no impact on photosystem II quantum yield. This work provides targeted delivery approaches for carbon-based nanomaterials mediated by biorecognition and a comprehensive understanding of their impact on plant cell and molecular biology for engineering safer and efficient agrochemical and biomolecule delivery tools.
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Affiliation(s)
- Israel Santana
- Department of Botany and Plant Sciences, University of California-Riverside, Riverside, California 92521, United States
| | - Su-Ji Jeon
- Department of Botany and Plant Sciences, University of California-Riverside, Riverside, California 92521, United States
| | - Hye-In Kim
- Department of Botany and Plant Sciences, University of California-Riverside, Riverside, California 92521, United States
| | - Md Reyazul Islam
- Department of Botany and Plant Sciences, University of California-Riverside, Riverside, California 92521, United States
| | - Christopher Castillo
- Department of Botany and Plant Sciences, University of California-Riverside, Riverside, California 92521, United States
| | - Gail F H Garcia
- Department of Botany and Plant Sciences, University of California-Riverside, Riverside, California 92521, United States
| | - Gregory M Newkirk
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, California 92521, United States
| | - Juan Pablo Giraldo
- Department of Botany and Plant Sciences, University of California-Riverside, Riverside, California 92521, United States
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29
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Pandey A, Chaudhary S, Bhat B. The Potential Role of Plastome Copy Number as a Quality Biomarker for Plant Products using Real-time Quantitative Polymerase Chain Reaction. Curr Genomics 2022; 23:289-298. [PMID: 36777877 PMCID: PMC9875542 DOI: 10.2174/1389202923666220513111643] [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: 01/21/2022] [Revised: 02/28/2022] [Accepted: 03/18/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Plastids are plant-specific semi-autonomous self-replicating organelles, containing circular DNA molecules called plastomes. Plastids perform crucial functions, including photosynthesis, stress perception and response, synthesis of metabolites, and storage. The plastome and plastid numbers have been shown to be modulated by developmental stage and environmental stimuli and have been used as a biomarker (identification of plant species) and biosensor (an indicator of abiotic and biotic stresses). However, the determination of plastome sequence and plastid number is a laborious process requiring sophisticated equipment. Methods: This study proposes using plastome copy number (PCN), which can be determined rapidly by real-time quantitative polymerase chain reaction (RT-qPCR) as a plant product quality biomarker. This study shows that the PCN log10 and range PCN log10 values calculated from RT-qPCR data, which was obtained for two years from leaves and lint samples of cotton and seed samples of cotton, rice, soybean, maize, and sesame can be used for assessing the quality of the samples. Results: Observation of lower range PCN log10 values for CS (0.31) and CR (0.58) indicated that the PCN showed little variance from the mean PCN log10 values for CS (3.81) and CR (3.85), suggesting that these samples might have encountered ambient environmental conditions during growth and/ or post-harvest storage and processing. This conclusion was further supported by observation of higher range PCN log10 values for RS (3.09) versus RP (0.05), where rice seeds in the RP group had protective hull covering compared to broken hull-less seeds in the RS group. To further support that PCN is affected by external factors, rice seeds treated with high temperatures and pathogens exhibited lower PCN values when compared to untreated seeds. Furthermore, the range PCN log10 values were found to be high for cotton leaf (CL) and lint (Clt) sample groups, 4.11 and 3.63, respectively, where leaf and lint samples were of different sizes, indicating that leaf samples might be of different developmental stage and lint samples might have been processed differently, supporting that the PCN is affected by both internal and external factors, respectively. Moreover, PCN log10 values were found to be plant specific, with oil containing seeds such as SeS (6.49) and MS (5.05) exhibiting high PCN log10 values compared to non-oil seeds such as SS (1.96). Conclusion: In conclusion, it was observed that PCN log10 values calculated from RT-qPCR assays were specific to plant species and the range of PCN log10 values can be directly correlated to the internal and external factors and, therefore might be used as a potential biomarker for assessing the quality of plant products.
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Affiliation(s)
- Amita Pandey
- 19 University Road, Shriram Institute for Industrial Research, Analytical Science Division - Biology, Molecular Biology Laboratory, New Delhi, India
| | - Shifa Chaudhary
- 19 University Road, Shriram Institute for Industrial Research, Analytical Science Division - Biology, Molecular Biology Laboratory, New Delhi, India
| | - Binu Bhat
- 19 University Road, Shriram Institute for Industrial Research, Analytical Science Division - Biology, Molecular Biology Laboratory, New Delhi, India
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30
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Ceriotti LF, Gatica-Soria L, Sanchez-Puerta MV. Cytonuclear coevolution in a holoparasitic plant with highly disparate organellar genomes. PLANT MOLECULAR BIOLOGY 2022; 109:673-688. [PMID: 35359176 DOI: 10.1007/s11103-022-01266-9] [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: 11/25/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Contrasting substitution rates in the organellar genomes of Lophophytum agree with the DNA repair, replication, and recombination gene content. Plastid and nuclear genes whose products form multisubunit complexes co-evolve. The organellar genomes of the holoparasitic plant Lophophytum (Balanophoraceae) show disparate evolution. In the plastid, the genome has been severely reduced and presents a > 85% AT content, while in the mitochondria most protein-coding genes have been replaced by homologs acquired by horizontal gene transfer (HGT) from their hosts (Fabaceae). Both genomes carry genes whose products form multisubunit complexes with those of nuclear genes, creating a possible hotspot of cytonuclear coevolution. In this study, we assessed the evolutionary rates of plastid, mitochondrial and nuclear genes, and their impact on cytonuclear evolution of genes involved in multisubunit complexes related to lipid biosynthesis and proteolysis in the plastid and those in charge of the oxidative phosphorylation in the mitochondria. Genes from the plastid and the mitochondria (both native and foreign) of Lophophytum showed extremely high and ordinary substitution rates, respectively. These results agree with the biased loss of plastid-targeted proteins involved in angiosperm organellar repair, replication, and recombination machinery. Consistent with the high rate of evolution of plastid genes, nuclear-encoded subunits of plastid complexes showed disproportionate increases in non-synonymous substitution rates, while those of the mitochondrial complexes did not show different rates than the control (i.e. non-organellar nuclear genes). Moreover, the increases in the nuclear-encoded subunits of plastid complexes were positively correlated with the level of physical interaction they possess with the plastid-encoded ones. Overall, these results suggest that a structurally-mediated compensatory factor may be driving plastid-nuclear coevolution in Lophophytum, and that mito-nuclear coevolution was not altered by HGT.
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Affiliation(s)
- Luis F Ceriotti
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina
| | - Leonardo Gatica-Soria
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina
| | - M Virginia Sanchez-Puerta
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina.
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina.
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31
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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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Complex Physical Structure of Complete Mitochondrial Genome of Quercus acutissima (Fagaceae): A Significant Energy Plant. Genes (Basel) 2022; 13:genes13081321. [PMID: 35893058 PMCID: PMC9331829 DOI: 10.3390/genes13081321] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 02/06/2023] Open
Abstract
Quercus acutissima Carruth. is a Chinese important energy plant with high ecological and economic values. While the species chloroplast genome has been reported, its mitochondrial genome (mitogenome) is still unexplored. Here, we assembled and annotated the Q. acutissima mitogenome, and we compared its characteristic differences with several closely related species. The Q. acutissima mitogenome’s main structure is branched with three distinguished contigs (linear molecule 1, circular molecule 2, and circular molecule 3) with 448,982 bp total length and 45.72% GC content. The mitogenome contained 51 genes, including 32 protein-coding, 16 tRNA and 3 rRNA genes. We examined codon usage, repeated sequences, genome recombination, chloroplast to mitochondrion DNA transformation, RNA editing, and synteny in the Q. acutissima mitogenome. Phylogenetic trees based on 29 species mitogenomes clarified the species classification. Our results provided comprehensive information of Q. acutissima mitogenome, and they are expected to provide valuable information for Fagaceae evolutionary biology and to promote the species germplasm utilization.
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Fischer A, Dotzek J, Walther D, Greiner S. Graph-based models of the Oenothera mitochondrial genome capture the enormous complexity of higher plant mitochondrial DNA organization. NAR Genom Bioinform 2022; 4:lqac027. [PMID: 35372837 PMCID: PMC8969700 DOI: 10.1093/nargab/lqac027] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 03/02/2022] [Accepted: 03/09/2022] [Indexed: 12/26/2022] Open
Abstract
Plant mitochondrial genomes display an enormous structural complexity, as recombining repeat-pairs lead to the generation of various sub-genomic molecules, rendering these genomes extremely challenging to assemble. We present a novel bioinformatic data-processing pipeline called SAGBAC (Semi-Automated Graph-Based Assembly Curator) that identifies recombinogenic repeat-pairs and reconstructs plant mitochondrial genomes. SAGBAC processes assembly outputs and applies our novel ISEIS (Iterative Sequence Ends Identity Search) algorithm to obtain a graph-based visualization. We applied this approach to three mitochondrial genomes of evening primrose (Oenothera), a plant genus used for cytoplasmic genetics studies. All identified repeat pairs were found to be flanked by two alternative and unique sequence-contigs defining so-called 'double forks', resulting in four possible contig-repeat-contig combinations for each repeat pair. Based on the inferred structural models, the stoichiometry of the different contig-repeat-contig combinations was analyzed using Illumina mate-pair and PacBio RSII data. This uncovered a remarkable structural diversity of the three closely related mitochondrial genomes, as well as substantial phylogenetic variation of the underlying repeats. Our model allows predicting all recombination events and, thus, all possible sub-genomes. In future work, the proposed methodology may prove useful for the investigation of the sub-genome organization and dynamics in different tissues and at various developmental stages.
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Affiliation(s)
- Axel Fischer
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jana Dotzek
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Stephan Greiner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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Tripathi D, Oldenburg DJ, Bendich AJ. Analysis of the Plastid Genome Sequence During Maize Seedling Development. Front Genet 2022; 13:870115. [PMID: 35559017 PMCID: PMC9086435 DOI: 10.3389/fgene.2022.870115] [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: 02/05/2022] [Accepted: 03/24/2022] [Indexed: 11/13/2022] Open
Abstract
Shoot development in maize progresses from small, non-pigmented meristematic cells to expanded cells in the green leaf. During this transition, large plastid DNA (ptDNA) molecules in proplastids become fragmented in the photosynthetically-active chloroplasts. The genome sequences were determined for ptDNA obtained from Zea mays B73 plastids isolated from four tissues: base of the stalk (the meristem region); fully-developed first green leaf; first three leaves from light-grown seedlings; and first three leaves from dark-grown (etiolated) seedlings. These genome sequences were then compared to the Z. mays B73 plastid reference genome sequence that was previously obtained from green leaves. The assembled plastid genome was identical among these four tissues to the reference genome. Furthermore, there was no difference among these tissues in the sequence at and around the previously documented 27 RNA editing sites. There were, however, more sequence variants (insertions/deletions and single-nucleotide polymorphisms) for leaves grown in the dark than in the light. These variants were tightly clustered into two areas within the inverted repeat regions of the plastid genome. We propose a model for how these variant clusters could be generated by replication-transcription conflict.
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Affiliation(s)
- Diwaker Tripathi
- Department of Biology, University of Washington, Seattle, WA, United States
| | - Delene J Oldenburg
- Department of Biology, University of Washington, Seattle, WA, United States
| | - Arnold J Bendich
- Department of Biology, University of Washington, Seattle, WA, United States
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Choi IS, Wojciechowski MF, Steele KP, Hunter SG, Ruhlman TA, Jansen RK. Born in the mitochondrion and raised in the nucleus: evolution of a novel tandem repeat family in Medicago polymorpha (Fabaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:389-406. [PMID: 35061308 DOI: 10.1111/tpj.15676] [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: 05/07/2021] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
Plant nuclear genomes harbor sequence elements derived from the organelles (mitochondrion and plastid) through intracellular gene transfer (IGT). Nuclear genomes also show a dramatic range of repeat content, suggesting that any sequence can be readily amplified. These two aspects of plant nuclear genomes are well recognized but have rarely been linked. Through investigation of 31 Medicago taxa we detected exceptionally high post-IGT amplification of mitochondrial (mt) DNA sequences containing rps10 in the nuclear genome of Medicago polymorpha and closely related species. The amplified sequences were characterized as tandem arrays of five distinct repeat motifs (2157, 1064, 987, 971, and 587 bp) that have diverged from the mt genome (mitogenome) in the M. polymorpha nuclear genome. The mt rps10-like arrays were identified in seven loci (six intergenic and one telomeric) of the nuclear chromosome assemblies and were the most abundant tandem repeat family, representing 1.6-3.0% of total genomic DNA, a value approximately three-fold greater than the entire mitogenome in M. polymorpha. Compared to a typical mt gene, the mt rps10-like sequence coverage level was 691.5-7198-fold higher in M. polymorpha and closely related species. In addition to the post-IGT amplification, our analysis identified the canonical telomeric repeat and the species-specific satellite arrays that are likely attributable to an ancestral chromosomal fusion in M. polymorpha. A possible relationship between chromosomal instability and the mt rps10-like tandem repeat family in the M. polymorpha clade is discussed.
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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
| | | | - Kelly P Steele
- Division of Science and Mathematics, Arizona State University, Mesa, AZ, 85212, USA
| | - Sarah G Hunter
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, 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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Nadeem M, Wu J, Ghaffari H, Kedir AJ, Saleem S, Mollier A, Singh J, Cheema M. Understanding the Adaptive Mechanisms of Plants to Enhance Phosphorus Use Efficiency on Podzolic Soils in Boreal Agroecosystems. FRONTIERS IN PLANT SCIENCE 2022; 13:804058. [PMID: 35371179 PMCID: PMC8965363 DOI: 10.3389/fpls.2022.804058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Being a macronutrient, phosphorus (P) is the backbone to complete the growth cycle of plants. However, because of low mobility and high fixation, P becomes the least available nutrient in podzolic soils; hence, enhancing phosphorus use efficiency (PUE) can play an important role in different cropping systems/crop production practices to meet ever-increasing demands in food, fiber, and fuel. Additionally, the rapidly decreasing mineral phosphate rocks/stocks forced to explore alternative resources and methods to enhance PUE either through improved seed P reserves and their remobilization, P acquisition efficiency (PAE), or plant's internal P utilization efficiency (IPUE) or both for sustainable P management strategies. The objective of this review article is to explore and document important domains to enhance PUE in crop plants grown on Podzol in a boreal agroecosystem. We have discussed P availabilities in podzolic soils, root architecture and morphology, root exudates, phosphate transporters and their role in P uptake, different contributors to enhance PAE and IPUE, and strategies to improve plant PUE in crops grown on podzolic soils deficient in P and acidic in nature.
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Affiliation(s)
- Muhammad Nadeem
- School of Science and the Environment, Memorial University of Newfoundland, Corner Brook, NL, Canada
| | - Jiaxu Wu
- School of Science and the Environment, Memorial University of Newfoundland, Corner Brook, NL, Canada
| | | | - Amana Jemal Kedir
- School of Science and the Environment, Memorial University of Newfoundland, Corner Brook, NL, Canada
- Environmental Science Program, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Shamila Saleem
- Department of Agriculture Extension, Government of Punjab, Khanewal, Pakistan
| | - Alain Mollier
- INRAE, UMR 1391 ISPA, Bordeaux Science Agro, Villenave d'Ornon, France
| | - Jaswinder Singh
- Department of Plant Science, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Mumtaz Cheema
- School of Science and the Environment, Memorial University of Newfoundland, Corner Brook, NL, Canada
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Pagano L, Marmiroli M, Villani M, Magnani J, Rossi R, Zappettini A, White JC, Marmiroli N. Engineered Nanomaterial Exposure Affects Organelle Genetic Material Replication in Arabidopsis thaliana. ACS NANO 2022; 16:2249-2260. [PMID: 35048688 DOI: 10.1021/acsnano.1c08367] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Mitochondria and chloroplasts not only are cellular energy sources but also have important regulatory and developmental roles in cell function. CeO2, FeOx ENMs, ZnS, CdS QDs, and relative metal salts were utilized in Murashige-Skoog (MS) synthetic growth medium at different concentrations (80-500 mg L-1) and times of exposures (0-20 days). Analysis of physiological and molecular response of A. thaliana chloroplasts and mitochondrion demonstrates that ENMs increase or decrease functionality and organelle genome replication. Exposure to nanoscale CeO2 and FeOx causes an 81-105% increase in biomass, whereas ZnS and CdS QDs yielded neutral or a 59% decrease in growth, respectively. Differential effects between ENMs and their corresponding metal salts highlight nanoscale-specific response pathways, which include energy production and oxidative stress response. Differences may be ascribed to ENM and the metal salt dissolution rate and the toxicity of the metal ion, which suggests eventual biotransformation processes occurring within the plant. With regard to specific effects on plastid (pt) and mitochondrial (mt) DNA, CdS QD exposure triggered potential variations at the substoichiometric level in the two organellar genomes, while nanoscale FeOx and ZnS QDs caused a 1- to 3-fold increase in ptDNA and mtDNA copy numbers. Nanoparticle CeO2 exposure did not affect ptDNA and mtDNA stoichiometry. These findings suggest that modification in stoichiometry is a potential morpho-functional adaptive response to ENM exposure, triggered by modifications of bioenergetic redox balance, which leads to reducing the photosynthesis or cellular respiration rate.
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Affiliation(s)
- Luca Pagano
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Marta Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Marco Villani
- IMEM-CNR, Parco Area Delle Scienze 37/A, 43124 Parma, Italy
| | - Jacopo Magnani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Riccardo Rossi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | | | - Jason C White
- The Connecticut Agricultural Experiment Station, 123 Huntington Street, New Haven, Connecticut 06504, United States
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
- Consorzio Interuniversitario Nazionale per le Scienze Ambientali (CINSA), University of Parma, 43124 Parma, Italy
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Niu Y, Gao C, Liu J. Complete mitochondrial genomes of three Mangifera species, their genomic structure and gene transfer from chloroplast genomes. BMC Genomics 2022; 23:147. [PMID: 35183120 PMCID: PMC8857841 DOI: 10.1186/s12864-022-08383-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/11/2022] [Indexed: 01/30/2023] Open
Abstract
Abstract
Background
Among the Mangifera species, mango (Mangifera indica) is an important commercial fruit crop. However, very few studies have been conducted on the Mangifera mitochondrial genome. This study reports and compares the newly sequenced mitochondrial genomes of three Mangifera species.
Results
Mangifera mitochondrial genomes showed partial similarities in the overall size, genomic structure, and gene content. Specifically, the genomes are circular and contain about 63–69 predicted functional genes, including five ribosomal RNA (rRNA) genes and 24–27 transfer RNA (tRNA) genes. The GC contents of the Mangifera mitochondrial genomes are similar, ranging from 44.42–44.66%. Leucine (Leu) and serine (Ser) are the most frequently used, while tryptophan (Trp) and cysteine (Cys) are the least used amino acids among the protein-coding genes in Mangifera mitochondrial genomes. We also identified 7–10 large chloroplast genomic fragments in the mitochondrial genome, ranging from 1407 to 6142 bp. Additionally, four intact mitochondrial tRNAs genes (tRNA-Cys, tRNA-Trp, tRNA-Pro, and tRNA-Met) and intergenic spacer regions were identified. Phylogenetic analysis based on the common protein-coding genes of most branches provided a high support value.
Conclusions
We sequenced and compared the mitochondrial genomes of three Mangifera species. The results showed that the gene content and the codon usage pattern of Mangifera mitochondrial genomes is similar across various species. Gene transfer from the chloroplast genome to the mitochondrial genome were identified. This study provides valuable information for evolutionary and molecular studies of Mangifera and a basis for further studies on genomic breeding of mango.
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Glycation damage to organelles and their DNA increases during maize seedling development. Sci Rep 2022; 12:2688. [PMID: 35177666 PMCID: PMC8854438 DOI: 10.1038/s41598-022-06454-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/31/2022] [Indexed: 11/17/2022] Open
Abstract
Shoot development in maize begins when meristematic, non-pigmented cells at leaf base stop dividing and proceeds toward the expanded green cells of the leaf blade. During this transition, promitochondria and proplastids develop into mature organelles and their DNA becomes fragmented. Changes in glycation damage during organelle development were measured for protein and DNA, as well as the glycating agent methyl glyoxal and the glycation-defense protein DJ-1 (known as Park7 in humans). Maize seedlings were grown under normal, non-stressful conditions. Nonetheless, we found that glycation damage, as well as defenses against glycation, follow the same developmental pattern we found previously for reactive oxygen species (ROS): as damage increases, damage-defense measures decrease. In addition, light-grown leaves had more glycation and less DJ-1 compared to dark-grown leaves. The demise of maize organellar DNA during development may therefore be attributed to both oxidative and glycation damage that is not repaired. The coordination between oxidative and glycation damage, as well as damage-response from the nucleus is also discussed.
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Sielemann K, Pucker B, Schmidt N, Viehöver P, Weisshaar B, Heitkam T, Holtgräwe D. Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives. BMC Genomics 2022; 23:113. [PMID: 35139817 PMCID: PMC8830136 DOI: 10.1186/s12864-022-08336-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/20/2022] [Indexed: 12/24/2022] Open
Abstract
Background As the major source of sugar in moderate climates, sugar-producing beets (Beta vulgaris subsp. vulgaris) have a high economic value. However, the low genetic diversity within cultivated beets requires introduction of new traits, for example to increase their tolerance and resistance attributes – traits that often reside in the crop wild relatives. For this, genetic information of wild beet relatives and their phylogenetic placements to each other are crucial. To answer this need, we sequenced and assembled the complete plastome sequences from a broad species spectrum across the beet genera Beta and Patellifolia, both embedded in the Betoideae (order Caryophyllales). This pan-plastome dataset was then used to determine the wild beet phylogeny in high-resolution. Results We sequenced the plastomes of 18 closely related accessions representing 11 species of the Betoideae subfamily and provided high-quality plastome assemblies which represent an important resource for further studies of beet wild relatives and the diverse plant order Caryophyllales. Their assembly sizes range from 149,723 bp (Beta vulgaris subsp. vulgaris) to 152,816 bp (Beta nana), with most variability in the intergenic sequences. Combining plastome-derived phylogenies with read-based treatments based on mitochondrial information, we were able to suggest a unified and highly confident phylogenetic placement of the investigated Betoideae species. Our results show that the genus Beta can be divided into the two clearly separated sections Beta and Corollinae. Our analysis confirms the affiliation of B. nana with the other Corollinae species, and we argue against a separate placement in the Nanae section. Within the Patellifolia genus, the two diploid species Patellifolia procumbens and Patellifolia webbiana are, regarding the plastome sequences, genetically more similar to each other than to the tetraploid Patellifolia patellaris. Nevertheless, all three Patellifolia species are clearly separated. Conclusion In conclusion, our wild beet plastome assemblies represent a new resource to understand the molecular base of the beet germplasm. Despite large differences on the phenotypic level, our pan-plastome dataset is highly conserved. For the first time in beets, our whole plastome sequences overcome the low sequence variation in individual genes and provide the molecular backbone for highly resolved beet phylogenomics. Hence, our plastome sequencing strategy can also guide genomic approaches to unravel other closely related taxa. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08336-8.
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Affiliation(s)
- Katharina Sielemann
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany.,Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, 33615, Bielefeld, Germany
| | - Boas Pucker
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany.,Evolution and Diversity, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.,Institute of Plant Biology, TU Braunschweig, Braunschweig, Germany
| | - Nicola Schmidt
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Prisca Viehöver
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Bernd Weisshaar
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Tony Heitkam
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany.
| | - Daniela Holtgräwe
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany.
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Huang CH, Liu YC, Shen JY, Lu FI, Shaw SY, Huang HJ, Chang CC. Repairing TALEN-mediated double-strand break by microhomology-mediated recombination in tobacco plastids generates abundant subgenomic DNA. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 313:111028. [PMID: 34763881 DOI: 10.1016/j.plantsci.2021.111028] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Transcription activator-like effector nuclease (TALEN) technology has been widely used to edit nuclear genomes in plants but rarely for editing organellar genomes. In addition, ciprofloxacin, commonly used to cause the double-strand break of organellar DNA for studying the repair mechanism in plants, confers no organellar selectivity and site-specificity. To demonstrate the feasibility of TALEN-mediated chloroplast DNA editing and to use it for studying the repair mechanism in plastids, we developed a TALEN-mediated editing technology fused with chloroplast transit peptide (cpTALEN) to site-specifically edit the rpoB gene via Agrobacteria-mediated transformation of tobacco leaf. Transgenic plants showed various degrees of chlorotic phenotype. Repairing damaged plastid DNA resulted in point mutation, large deletion and small inversion surrounding the rpoB gene by homologous recombination and/or microhomology-mediated recombination. In an albino line, microhomology-mediated recombination via a pair of 12-bp direct repeats between rpoC2 and ycf2 genes generated the chimeric ycf2-rpoC2 subgenome, with the level about 3- to 5-fold higher for subgenomic DNA than ycf2. Additionally, the expression of chimeric ycf2-rpoC2 transcripts versus ycf2 mRNA agreed well with the level of corresponding DNA. The ycf2-rpoC2 subgenomic DNA might independently and preferentially replicate in plastids.
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Affiliation(s)
- Chih-Hao Huang
- Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan; Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Yu-Chang Liu
- Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan; Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Jia-Yi Shen
- Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan; Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Fu-I Lu
- Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan; Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Shyh-Yu Shaw
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan; Department of Chemistry, National Cheng Kung University, Tainan, 701, Taiwan
| | - Hao-Jen Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan; Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
| | - Ching-Chun Chang
- Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan; Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan; Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan.
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Charboneau JLM, Cronn RC, Liston A, Wojciechowski MF, Sanderson MJ. Plastome Structural Evolution and Homoplastic Inversions in Neo-Astragalus (Fabaceae). Genome Biol Evol 2021; 13:evab215. [PMID: 34534296 PMCID: PMC8486006 DOI: 10.1093/gbe/evab215] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2021] [Indexed: 12/23/2022] Open
Abstract
The plastid genomes of photosynthetic green plants have largely maintained conserved gene content and order as well as structure over hundreds of millions of years of evolution. Several plant lineages, however, have departed from this conservation and contain many plastome structural rearrangements, which have been associated with an abundance of repeated sequences both overall and near rearrangement endpoints. We sequenced the plastomes of 25 taxa of Astragalus L. (Fabaceae), a large genus in the inverted repeat-lacking clade of legumes, to gain a greater understanding of the connection between repeats and plastome inversions. We found plastome repeat structure has a strong phylogenetic signal among these closely related taxa mostly in the New World clade of Astragalus called Neo-Astragalus. Taxa without inversions also do not differ substantially in their overall repeat structure from four taxa each with one large-scale inversion. For two taxa with inversion endpoints between the same pairs of genes, differences in their exact endpoints indicate the inversions occurred independently. Our proposed mechanism for inversion formation suggests the short inverted repeats now found near the endpoints of the four inversions may be there as a result of these inversions rather than their cause. The longer inverted repeats now near endpoints may have allowed the inversions first mediated by shorter microhomologous sequences to propagate, something that should be considered in explaining how any plastome rearrangement becomes fixed regardless of the mechanism of initial formation.
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Affiliation(s)
- Joseph L M Charboneau
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Richard C Cronn
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, Oregon, USA
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | | | - Michael J Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
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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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Mahapatra K, Banerjee S, De S, Mitra M, Roy P, Roy S. An Insight Into the Mechanism of Plant Organelle Genome Maintenance and Implications of Organelle Genome in Crop Improvement: An Update. Front Cell Dev Biol 2021; 9:671698. [PMID: 34447743 PMCID: PMC8383295 DOI: 10.3389/fcell.2021.671698] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/21/2021] [Indexed: 12/19/2022] Open
Abstract
Besides the nuclear genome, plants possess two small extra chromosomal genomes in mitochondria and chloroplast, respectively, which contribute a small fraction of the organelles’ proteome. Both mitochondrial and chloroplast DNA have originated endosymbiotically and most of their prokaryotic genes were either lost or transferred to the nuclear genome through endosymbiotic gene transfer during the course of evolution. Due to their immobile nature, plant nuclear and organellar genomes face continuous threat from diverse exogenous agents as well as some reactive by-products or intermediates released from various endogenous metabolic pathways. These factors eventually affect the overall plant growth and development and finally productivity. The detailed mechanism of DNA damage response and repair following accumulation of various forms of DNA lesions, including single and double-strand breaks (SSBs and DSBs) have been well documented for the nuclear genome and now it has been extended to the organelles also. Recently, it has been shown that both mitochondria and chloroplast possess a counterpart of most of the nuclear DNA damage repair pathways and share remarkable similarities with different damage repair proteins present in the nucleus. Among various repair pathways, homologous recombination (HR) is crucial for the repair as well as the evolution of organellar genomes. Along with the repair pathways, various other factors, such as the MSH1 and WHIRLY family proteins, WHY1, WHY2, and WHY3 are also known to be involved in maintaining low mutation rates and structural integrity of mitochondrial and chloroplast genome. SOG1, the central regulator in DNA damage response in plants, has also been found to mediate endoreduplication and cell-cycle progression through chloroplast to nucleus retrograde signaling in response to chloroplast genome instability. Various proteins associated with the maintenance of genome stability are targeted to both nuclear and organellar compartments, establishing communication between organelles as well as organelles and nucleus. Therefore, understanding the mechanism of DNA damage repair and inter compartmental crosstalk mechanism in various sub-cellular organelles following induction of DNA damage and identification of key components of such signaling cascades may eventually be translated into strategies for crop improvement under abiotic and genotoxic stress conditions. This review mainly highlights the current understanding as well as the importance of different aspects of organelle genome maintenance mechanisms in higher plants.
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Affiliation(s)
- Kalyan Mahapatra
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Burdwan, India
| | - Samrat Banerjee
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Burdwan, India
| | - Sayanti De
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Burdwan, India
| | - Mehali Mitra
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Burdwan, India
| | - Pinaki Roy
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Burdwan, India
| | - Sujit Roy
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Burdwan, India
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45
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Lee C, Choi IS, Cardoso D, de Lima HC, de Queiroz LP, Wojciechowski MF, Jansen RK, Ruhlman TA. The chicken or the egg? Plastome evolution and an independent loss of the inverted repeat in papilionoid legumes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:861-875. [PMID: 34021942 DOI: 10.1111/tpj.15351] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/22/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
The plastid genome (plastome), while surprisingly constant in gene order and content across most photosynthetic angiosperms, exhibits variability in several unrelated lineages. During the diversification history of the legume family Fabaceae, plastomes have undergone many rearrangements, including inversions, expansion, contraction and loss of the typical inverted repeat (IR), gene loss and repeat accumulation in both shared and independent events. While legume plastomes have been the subject of study for some time, most work has focused on agricultural species in the IR-lacking clade (IRLC) and the plant model Medicago truncatula. The subfamily Papilionoideae, which contains virtually all of the agricultural legume species, also comprises most of the plastome variation detected thus far in the family. In this study three non-papilioniods were included among 34 newly sequenced legume plastomes, along with 33 publicly available sequences, to assess plastome structural evolution in the subfamily. In an effort to examine plastome variation across the subfamily, approximately 20% of the sampling represents the IRLC with the remainder selected to represent the early-branching papilionoid clades. A number of IR-related and repeat-mediated changes were identified and examined in a phylogenetic context. Recombination between direct repeats associated with ycf2 resulted in intraindividual plastome heteroplasmy. Although loss of the IR has not been reported in legumes outside of the IRLC, one genistoid taxon was found to completely lack the typical plastome IR. The role of the IR and non-IR repeats in the progression of plastome change is discussed.
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Affiliation(s)
- Chaehee Lee
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - In-Su Choi
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-4501, USA
| | - Domingos Cardoso
- Instituto de Biologia, Universidade Federal de Bahia (UFBA), Rua Barão de Jeremoabo, s.n., Ondina, Salvador, Bahia, 40170-115, Brazil
| | - Haroldo C de Lima
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rua Pacheco Leão, Rio de Janeiro, 915 22460-030, Brazil
| | - Luciano P de Queiroz
- Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Novo Horizonte, Feira de Santana, Bahia, 44036-900, Brazil
| | | | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
- Center of Excellence for Bionanoscience Research, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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46
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Gureev AP, Mashkina OS, Shabanova EA, Vitkalova IY, Sitnikov VV, Popov VN. Study of the amount of oxidative damage to mitochondrial and chloroplast DNA in clones of white poplar (Populus alba L.) during long-term in vitro cultivation for 26 years. PLANT MOLECULAR BIOLOGY 2021; 106:479-489. [PMID: 33970418 DOI: 10.1007/s11103-021-01157-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Artem P Gureev
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia, 394018.
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, Voronezh, Russia, 394036.
| | - Olga S Mashkina
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia, 394018
- Breeding and Biotechnology, All-Russian Research Institute of Forest Genetics, Voronezh, Russia, 394087
| | - Ekaterina A Shabanova
- Breeding and Biotechnology, All-Russian Research Institute of Forest Genetics, Voronezh, Russia, 394087
| | - Inna Yu Vitkalova
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia, 394018
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, Voronezh, Russia, 394036
| | - Vadim V Sitnikov
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia, 394018
- Breeding and Biotechnology, All-Russian Research Institute of Forest Genetics, Voronezh, Russia, 394087
| | - Vasily N Popov
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia, 394018
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, Voronezh, Russia, 394036
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47
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Jackman SD, Coombe L, Warren RL, Kirk H, Trinh E, MacLeod T, Pleasance S, Pandoh P, Zhao Y, Coope RJ, Bousquet J, Bohlmann J, Jones SJM, Birol I. Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates a Complex Physical Structure. Genome Biol Evol 2021; 12:1174-1179. [PMID: 32449750 PMCID: PMC7486957 DOI: 10.1093/gbe/evaa108] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2020] [Indexed: 12/12/2022] Open
Abstract
Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled the complete 5.5-Mb mitochondrial genome of Sitka spruce (Picea sitchensis), to date, one of the largest mitochondrial genomes of a gymnosperm. We sequenced the whole genome using Oxford Nanopore MinION, and then identified contigs of mitochondrial origin assembled from these long reads based on sequence homology to the white spruce mitochondrial genome. The assembly graph shows a multipartite genome structure, composed of one smaller 168-kb circular segment of DNA, and a larger 5.4-Mb single component with a branching structure. The assembly graph gives insight into a putative complex physical genome structure, and its branching points may represent active sites of recombination.
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Affiliation(s)
- Shaun D Jackman
- Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Lauren Coombe
- Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - René L Warren
- Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Heather Kirk
- Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Eva Trinh
- Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Tina MacLeod
- Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Stephen Pleasance
- Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Pawan Pandoh
- Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Yongjun Zhao
- Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Robin J Coope
- Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Jean Bousquet
- Forest Genomics, Institute for Systems and Integrative Biology, Université Laval, Quebec, Quebec, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Inanc Birol
- Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
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48
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Maheswari P, Kunhikannan C, Yasodha R. Chloroplast genome analysis of Angiosperms and phylogenetic relationships among Lamiaceae members with particular reference to teak (Tectona grandis L.f). J Biosci 2021. [DOI: 10.1007/s12038-021-00166-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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49
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Rose RJ. Contribution of Massive Mitochondrial Fusion and Subsequent Fission in the Plant Life Cycle to the Integrity of the Mitochondrion and Its Genome. Int J Mol Sci 2021; 22:5429. [PMID: 34063907 PMCID: PMC8196625 DOI: 10.3390/ijms22115429] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/24/2022] Open
Abstract
Plant mitochondria have large genomes to house a small number of key genes. Most mitochondria do not contain a whole genome. Despite these latter characteristics, the mitochondrial genome is faithfully maternally inherited. To maintain the mitochondrial genes-so important for energy production-the fusion and fission of mitochondria are critical. Fission in plants is better understood than fusion, with the dynamin-related proteins (DRP 3A and 3B) driving the constriction of the mitochondrion. How the endoplasmic reticulum and the cytoskeleton are linked to the fission process is not yet fully understood. The fusion mechanism is less well understood, as obvious orthologues are not present. However, there is a recently described gene, MIRO2, that appears to have a significant role, as does the ER and cytoskeleton. Massive mitochondrial fusion (MMF or hyperfusion) plays a significant role in plants. MMF occurs at critical times of the life cycle, prior to flowering, in the enlarging zygote and at germination, mixing the cells' mitochondrial population-the so-called "discontinuous whole". MMF in particular aids genome repair, the conservation of critical genes and possibly gives an energy boost to important stages of the life cycle. MMF is also important in plant regeneration, an important component of plant biotechnology.
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Affiliation(s)
- Ray J Rose
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia
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50
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Edwards DM, Røyrvik EC, Chustecki JM, Giannakis K, Glastad RC, Radzvilavicius AL, Johnston IG. Avoiding organelle mutational meltdown across eukaryotes with or without a germline bottleneck. PLoS Biol 2021; 19:e3001153. [PMID: 33891583 PMCID: PMC8064548 DOI: 10.1371/journal.pbio.3001153] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/23/2021] [Indexed: 11/25/2022] Open
Abstract
Mitochondrial DNA (mtDNA) and plastid DNA (ptDNA) encode vital bioenergetic apparatus, and mutations in these organelle DNA (oDNA) molecules can be devastating. In the germline of several animals, a genetic “bottleneck” increases cell-to-cell variance in mtDNA heteroplasmy, allowing purifying selection to act to maintain low proportions of mutant mtDNA. However, most eukaryotes do not sequester a germline early in development, and even the animal bottleneck remains poorly understood. How then do eukaryotic organelles avoid Muller’s ratchet—the gradual buildup of deleterious oDNA mutations? Here, we construct a comprehensive and predictive genetic model, quantitatively describing how different mechanisms segregate and decrease oDNA damage across eukaryotes. We apply this comprehensive theory to characterise the animal bottleneck with recent single-cell observations in diverse mouse models. Further, we show that gene conversion is a particularly powerful mechanism to increase beneficial cell-to-cell variance without depleting oDNA copy number, explaining the benefit of observed oDNA recombination in diverse organisms which do not sequester animal-like germlines (for example, sponges, corals, fungi, and plants). Genomic, transcriptomic, and structural datasets across eukaryotes support this mechanism for generating beneficial variance without a germline bottleneck. This framework explains puzzling oDNA differences across taxa, suggesting how Muller’s ratchet is avoided in different eukaryotes. A comprehensive model for mitochondrial and plasmid DNA segregation, supported by with genomic, transcriptomic, and single-cell data, shows how the attritional effects of Muller’s ratchet can be avoided in the organelles of diverse eukaryotes.
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Affiliation(s)
| | | | | | | | | | | | - Iain G. Johnston
- Department of Mathematics, University of Bergen, Norway
- Computational Biology Unit, University of Bergen, Norway
- * E-mail:
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