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Štorchová H, Krüger M. Methods for assembling complex mitochondrial genomes in land plants. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5169-5174. [PMID: 38302086 DOI: 10.1093/jxb/erae034] [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: 11/22/2023] [Accepted: 01/29/2024] [Indexed: 02/03/2024]
Abstract
The large size and complex structural rearrangements inherent in the mitochondrial genomes of land plants pose challenges for their sequencing. Originally, the assembly of these genomes required the cloning of mitochondrial DNA fragments followed by Sanger sequencing. Subsequently, the advent of next-generation sequencing significantly expedited the process. This review highlights examples of plant mitochondrial genome assembly employing various technologies, including 454 sequencing, Illumina short sequencing reads, and Pacific Biosciences or Oxford Nanopore Technology long sequencing reads. The combination of short and long reads in hybrid assembly has proven to be the most efficient approach for achieving reliable assemblies of land plant mitochondrial genomes.
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Affiliation(s)
- Helena Štorchová
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 313, CZ-16502 Prague, Czech Republic
| | - Manuela Krüger
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 313, CZ-16502 Prague, Czech Republic
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Wang J, Kan S, Liao X, Zhou J, Tembrock LR, Daniell H, Jin S, Wu Z. Plant organellar genomes: much done, much more to do. TRENDS IN PLANT SCIENCE 2024; 29:754-769. [PMID: 38220520 DOI: 10.1016/j.tplants.2023.12.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 01/16/2024]
Abstract
Plastids and mitochondria are the only organelles that possess genomes of endosymbiotic origin. In recent decades, advances in sequencing technologies have contributed to a meteoric rise in the number of published organellar genomes, and have revealed greatly divergent evolutionary trajectories. In this review, we quantify the abundance and distribution of sequenced plant organellar genomes across the plant tree of life. We compare numerous genomic features between the two organellar genomes, with an emphasis on evolutionary trajectories, transfers, the current state of organellar genome editing by transcriptional activator-like effector nucleases (TALENs), transcription activator-like effector (TALE)-mediated deaminase, and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas), as well as genetic transformation. Finally, we propose future research to understand these different evolutionary trajectories, and genome-editing strategies to promote functional studies and eventually improve organellar genomes.
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Affiliation(s)
- Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6000-6999, Australia
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Marine College, Shandong University, Weihai, 264209, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jiawei Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Henry Daniell
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104-6030, USA.
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
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Shen B, Shen A, Liu L, Tan Y, Li S, Tan Z. Assembly and comparative analysis of the complete multichromosomal mitochondrial genome of Cymbidium ensifolium, an orchid of high economic and ornamental value. BMC PLANT BIOLOGY 2024; 24:255. [PMID: 38594641 PMCID: PMC11003039 DOI: 10.1186/s12870-024-04962-4] [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: 11/18/2023] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND Orchidaceae is one of the largest groups of angiosperms, and most species have high economic value and scientific research value due to their ornamental and medicinal properties. In China, Chinese Cymbidium is a popular ornamental orchid with high economic value and a long history. However, to date, no detailed information on the mitochondrial genome of any species of Chinese Cymbidium has been published. RESULTS Here, we present the complete assembly and annotation of the mitochondrial genome of Cymbidium ensifolium (L.) Sw. The mitogenome of C. ensifolium was 560,647 bp in length and consisted of 19 circular subgenomes ranging in size from 21,995 bp to 48,212 bp. The genome encoded 35 protein-coding genes, 36 tRNAs, 3 rRNAs, and 3405 ORFs. Repeat sequence analysis and prediction of RNA editing sites revealed a total of 915 dispersed repeats, 162 simple repeats, 45 tandem repeats, and 530 RNA editing sites. Analysis of codon usage showed a preference for codons ending in A/T. Interorganellar DNA transfer was identified in 13 of the 19 chromosomes, with plastid-derived DNA fragments representing 6.81% of the C. ensifolium mitochondrial genome. The homologous fragments of the mitochondrial genome and nuclear genome were also analysed. Comparative analysis showed that the GC content was conserved, but the size, structure, and gene content of the mitogenomes varied greatly among plants with multichromosomal mitogenome structure. Phylogenetic analysis based on the mitogenomes reflected the evolutionary and taxonomic statuses of C. ensifolium. Interestingly, compared with the mitogenomes of Cymbidium lancifolium Hook. and Cymbidium macrorhizon Lindl., the mitogenome of C. ensifolium lost 8 ribosomal protein-coding genes. CONCLUSION In this study, we assembled and annotated the mitogenome of C. ensifolium and compared it with the mitogenomes of other Liliidae and plants with multichromosomal mitogenome structures. Our findings enrich the mitochondrial genome database of orchid plants and reveal the rapid structural evolution of Cymbidium mitochondrial genomes, highlighting the potential for mitochondrial genes to help decipher plant evolutionary history.
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Affiliation(s)
- Baoming Shen
- Institute of Forest and Grass Cultivation, Hunan Academy of Forestry, 658 Shaoshan South Road, Tianxin District, Changsha City, 410004, China
| | - Airong Shen
- Institute of Forest and Grass Cultivation, Hunan Academy of Forestry, 658 Shaoshan South Road, Tianxin District, Changsha City, 410004, China
| | - Lina Liu
- Institute of Forest and Grass Cultivation, Hunan Academy of Forestry, 658 Shaoshan South Road, Tianxin District, Changsha City, 410004, China
| | - Yun Tan
- Institute of Forest and Grass Cultivation, Hunan Academy of Forestry, 658 Shaoshan South Road, Tianxin District, Changsha City, 410004, China
| | - Sainan Li
- Institute of Forest and Grass Cultivation, Hunan Academy of Forestry, 658 Shaoshan South Road, Tianxin District, Changsha City, 410004, China
| | - Zhuming Tan
- Institute of Forest and Grass Cultivation, Hunan Academy of Forestry, 658 Shaoshan South Road, Tianxin District, Changsha City, 410004, China.
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Tang P, Ni Y, Li J, Lu Q, Liu C, Guo J. The Complete Mitochondrial Genome of Paeonia lactiflora Pall. (Saxifragales: Paeoniaceae): Evidence of Gene Transfer from Chloroplast to Mitochondrial Genome. Genes (Basel) 2024; 15:239. [PMID: 38397228 PMCID: PMC10888214 DOI: 10.3390/genes15020239] [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: 01/10/2024] [Revised: 02/10/2024] [Accepted: 02/11/2024] [Indexed: 02/25/2024] Open
Abstract
Paeonia lactiflora (P. lactiflora), a perennial plant renowned for its medicinal roots, provides a unique case for studying the phylogenetic relationships of species based on organelle genomes, as well as the transference of DNA across organelle genomes. In order to investigate this matter, we sequenced and characterized the mitochondrial genome (mitogenome) of P. lactiflora. Similar to the chloroplast genome (cpgenome), the mitogenome of P. lactiflora extends across 181,688 base pairs (bp). Its unique quadripartite structure results from a pair of extensive inverted repeats, each measuring 25,680 bp in length. The annotated mitogenome includes 27 protein-coding genes, 37 tRNAs, 8 rRNAs, and two pseudogenes (rpl5, rpl16). Phylogenetic analysis was performed to identify phylogenetic trees consistent with Paeonia species phylogeny in the APG Ⅳ system. Moreover, a total of 12 MTPT events were identified and 32 RNA editing sites were detected during mitogenome analysis of P. lactiflora. Our research successfully compiled and annotated the mitogenome of P. lactiflora. The study provides valuable insights regarding the taxonomic classification and molecular evolution within the Paeoniaceae family.
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Affiliation(s)
- Pan Tang
- Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China;
- Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100093, China; (Y.N.); (J.L.); (Q.L.)
| | - Yang Ni
- Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100093, China; (Y.N.); (J.L.); (Q.L.)
| | - Jingling Li
- Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100093, China; (Y.N.); (J.L.); (Q.L.)
| | - Qianqi Lu
- Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100093, China; (Y.N.); (J.L.); (Q.L.)
| | - Chang Liu
- Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100093, China; (Y.N.); (J.L.); (Q.L.)
| | - Jinlin Guo
- Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China;
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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Jiang M, Ni Y, Li J, Liu C. Characterisation of the complete mitochondrial genome of Taraxacum mongolicum revealed five repeat-mediated recombinations. PLANT CELL REPORTS 2023; 42:775-789. [PMID: 36774424 DOI: 10.1007/s00299-023-02994-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
We reported the mitochondrial genome of Taraxacum mongolicum for the first time. Five pairs of repeats that can mediate recombination were validated, leading to multiple conformations of genome. Taraxacum mongolicum belongs to the Asteraceae family and has important pharmaceutical value. To explore the possible interaction between the organelle genomes, we assembled the complete mitochondrial genome (mitogenome) of T. mongolicum using Illumina and Oxford Nanopore sequencing data. This genome corresponded to a circular molecule 304,467 bp long. It encodes 52 unique genes including 31 protein-coding, 3 ribosomal RNA (rRNA) and 18 transfer RNA (tRNA) genes. In addition to the single circular conformation, the existence of alternative conformations mediated by five repetitive sequences in the mitogenome was identified and validated. Recombination mediated by the inverted repeats resulted in two conformations. Conversely, recombination mediated by the two direct repeats broke one large circular molecule into two subgenomic circular molecules. Furthermore, we identified 12 homologous fragments by comparing the sequences of mitogenome and plastome, including eight complete tRNA genes. Lastly, we identified a total of 278 RNA-editing sites in protein-coding sequences based on RNA-seq data. Among them, cox1 and nad5 gene has the most sites (21), followed by the nad2 gene with 19 sites. We successfully validated 213 predicted RNA-editing sites using PCR amplification and Sanger sequencing. This project reported the first mitogenome of T. mongolicum and demonstrated its multiple conformations generated by repeat-mediated recombination. This genome could provide critical information for the molecular breeding of T. mongolicum, and also be used as a reference genome for other species of the genus Taraxacum.
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Affiliation(s)
- Mei Jiang
- School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, People's Republic of China
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, People's Republic of China
| | - Yang Ni
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, People's Republic of China
| | - Jingling Li
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, People's Republic of China
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, People's Republic of China.
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Wei L, Liu TJ, Hao G, Ge XJ, Yan HF. Comparative analyses of three complete Primula mitogenomes with insights into mitogenome size variation in Ericales. BMC Genomics 2022; 23:770. [PMID: 36424546 PMCID: PMC9686101 DOI: 10.1186/s12864-022-08983-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 11/01/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Although knowledge of the sizes, contents, and forms of plant mitochondrial genomes (mitogenomes) is increasing, little is known about the mechanisms underlying their structural diversity. Evolutionary information on the mitogenomes of Primula, an important ornamental taxon, is more limited than the information on their nuclear and plastid counterparts, which has hindered the comprehensive understanding of Primula mitogenomic diversity and evolution. The present study reported and compared three Primula mitogenomes and discussed the size expansion of mitogenomes in Ericales. RESULTS Mitogenome master circles were sequenced and successfully assembled for three Primula taxa and were compared with publicly available Ericales mitogenomes. The three mitogenomes contained similar gene contents and varied primarily in their structures. The Primula mitogenomes possessed relatively high nucleotide diversity among all examined plant lineages. In addition, high nucleotide diversity was found among Primula species between the Mediterranean and Himalaya-Hengduan Mountains. Most predicted RNA editing sites appeared in the second amino acid codon, increasing the hydrophobic character of the protein. An early stop in atp6 caused by RNA editing was conserved across all examined Ericales species. The interfamilial relationships within Ericales and interspecific relationships within Primula could be well resolved based on mitochondrial data. Transfer of the two longest mitochondrial plastid sequences (MTPTs) occurred before the divergence of Primula and its close relatives, and multiple independent transfers could also occur in a single MTPT sequence. Foreign sequence [MTPTs and mitochondrial nuclear DNA sequences (NUMTs)] uptake and repeats were to some extent associated with changes in Ericales mitogenome size, although none of these relationships were significant overall. CONCLUSIONS The present study revealed relatively conserved gene contents, gene clusters, RNA editing, and MTPTs but considerable structural variation in Primula mitogenomes. Relatively high nucleotide diversity was found in the Primula mitogenomes. In addition, mitogenomic genes, collinear gene clusters, and locally collinear blocks (LCBs) all showed phylogenetic signals. The evolutionary history of MTPTs in Primula was complicated, even in a single MTPT sequence. Various reasons for the size variation observed in Ericales mitogenomes were found.
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Affiliation(s)
- Lei Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tong-Jian Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
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Zluvova J, Kubat Z, Hobza R, Janousek B. Adaptive changes of the autosomal part of the genome in a dioecious clade of Silene. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210228. [PMID: 35306886 PMCID: PMC8935319 DOI: 10.1098/rstb.2021.0228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The genus Silene brings many opportunities for the study of various processes involved in the evolution of dioecy and young sex chromosomes. Here we focus on a dioecious clade in Silene subgenus Silene and closely related species. This study provides improved support for monophyly of this clade (based on inclusion of further dioecious species) and a new estimate of its age (ca 2.3 million years). We observed a rise in adaptive evolution in the autosomal and pseudoautosomal parts of the genome on the branch where dioecy originated. This increase is not a result of the accumulation of sexually antagonistic genes in the pseudoautosomal region. It is also not caused by the coevolution of genes acting in mitochondria (despite the possibility that dioecy along this branch could have evolved from a nucleo-cytoplasmic male sterility-based system). After considering other possibilities, the most parsimonious explanation for the increase seen in the number of positively selected codons is the adaptive evolution of genes involved in the adaptation of the autosomal part of the genome to dioecy, as described in Charnov's sex-allocation theory. As the observed coincidence cannot prove causality, studies in other dioecious clades are necessary to allow the formation of general conclusions. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.
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Affiliation(s)
- Jitka Zluvova
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno CZ - 612 65, Czech Republic
| | - Zdenek Kubat
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno CZ - 612 65, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno CZ - 612 65, Czech Republic
| | - Bohuslav Janousek
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno CZ - 612 65, Czech Republic
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Edera AA, Small I, Milone DH, Sanchez-Puerta MV. Deepred-Mt: Deep representation learning for predicting C-to-U RNA editing in plant mitochondria. Comput Biol Med 2021; 136:104682. [PMID: 34343887 DOI: 10.1016/j.compbiomed.2021.104682] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 10/20/2022]
Abstract
In land plant mitochondria, C-to-U RNA editing converts cytidines into uridines at highly specific RNA positions called editing sites. This editing step is essential for the correct functioning of mitochondrial proteins. When using sequence homology information, edited positions can be computationally predicted with high precision. However, predictions based on the sequence contexts of such edited positions often result in lower precision, which is limiting further advances on novel genetic engineering techniques for RNA regulation. Here, a deep convolutional neural network called Deepred-Mt is proposed. It predicts C-to-U editing events based on the 40 nucleotides flanking a given cytidine. Unlike existing methods, Deepred-Mt was optimized by using editing extent information, novel strategies of data augmentation, and a large-scale training dataset, constructed with deep RNA sequencing data of 21 plant mitochondrial genomes. In comparison to predictive methods based on sequence homology, Deepred-Mt attains significantly better predictive performance, in terms of average precision as well as F1 score. In addition, our approach is able to recognize well-known sequence motifs linked to RNA editing, and shows that the local RNA structure surrounding editing sites may be a relevant factor regulating their editing. These results demonstrate that Deepred-Mt is an effective tool for predicting C-to-U RNA editing in plant mitochondria. Source code, datasets, and detailed use cases are freely available at https://github.com/aedera/deepredmt.
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Affiliation(s)
- Alejandro A Edera
- Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH-UNL/CONICET, Ciudad Universitaria, Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, Santa Fe, 3000, Argentina
| | - Ian Small
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Diego H Milone
- Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH-UNL/CONICET, Ciudad Universitaria, Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, Santa Fe, 3000, Argentina.
| | - M Virginia Sanchez-Puerta
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Argentina; Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, Mendoza, M5502JMA, Argentina.
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Choi KS, Park S. Complete Plastid and Mitochondrial Genomes of Aeginetia indica Reveal Intracellular Gene Transfer (IGT), Horizontal Gene Transfer (HGT), and Cytoplasmic Male Sterility (CMS). Int J Mol Sci 2021; 22:6143. [PMID: 34200260 PMCID: PMC8201098 DOI: 10.3390/ijms22116143] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/01/2021] [Accepted: 06/05/2021] [Indexed: 11/16/2022] Open
Abstract
Orobanchaceae have become a model group for studies on the evolution of parasitic flowering plants, and Aeginetia indica, a holoparasitic plant, is a member of this family. In this study, we assembled the complete chloroplast and mitochondrial genomes of A. indica. The chloroplast and mitochondrial genomes were 56,381 bp and 401,628 bp long, respectively. The chloroplast genome of A. indica shows massive plastid genes and the loss of one IR (inverted repeat). A comparison of the A. indica chloroplast genome sequence with that of a previous study demonstrated that the two chloroplast genomes encode a similar number of proteins (except atpH) but differ greatly in length. The A. indica mitochondrial genome has 53 genes, including 35 protein-coding genes (34 native mitochondrial genes and one chloroplast gene), 15 tRNA (11 native mitochondrial genes and four chloroplast genes) genes, and three rRNA genes. Evidence for intracellular gene transfer (IGT) and horizontal gene transfer (HGT) was obtained for plastid and mitochondrial genomes. ψndhB and ψcemA in the A. indica mitogenome were transferred from the plastid genome of A. indica. The atpH gene in the plastid of A. indica was transferred from another plastid angiosperm plastid and the atpI gene in mitogenome A. indica was transferred from a host plant like Miscanthus siensis. Cox2 (orf43) encodes proteins containing a membrane domain, making ORF (Open Reading Frame) the most likely candidate gene for CMS development in A. indica.
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Affiliation(s)
- Kyoung-Su Choi
- Institute of Natural Science, Yeungnam Univiersity, Gyeongsan-si 38541, Gyeongbuk-do, Korea;
- Department of Life Sciences, Yeungnam University, Gyeongsan-si 38541, Gyeongbuk-do, Korea
| | - Seonjoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan-si 38541, Gyeongbuk-do, Korea
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Krüger M, Abeyawardana OAJ, Krüger C, Juříček M, Štorchová H. Differentially Expressed Genes Shared by Two Distinct Cytoplasmic Male Sterility (CMS) Types of Silene vulgaris Suggest the Importance of Oxidative Stress in Pollen Abortion. Cells 2020; 9:cells9122700. [PMID: 33339225 PMCID: PMC7766179 DOI: 10.3390/cells9122700] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 12/14/2020] [Indexed: 11/25/2022] Open
Abstract
Cytoplasmic male sterility (CMS), encoded by the interacting mitochondrial and nuclear genes, causes pollen abortion or non-viability. CMS is widely used in agriculture and extensively studied in crops. Much less is known about CMS in wild species. We performed a comparative transcriptomic analysis of male sterile and fertile individuals of Silene vulgaris, a model plant for the study of gynodioecy, to reveal the genes responsible for pollen abortion in this species. We used RNA-seq datasets previously employed for the analysis of mitochondrial and plastid transcriptomes of female and hermaphrodite flower buds, making it possible to compare the transcriptomes derived from three genomes in the same RNA specimen. We assembled de novo transcriptomes for two haplotypes of S. vulgaris and identified differentially expressed genes between the females and hermaphrodites, associated with stress response or pollen development. The gene for alternative oxidase was downregulated in females. The genetic pathways controlling CMS in S. vulgaris are similar to those in crops. The high number of the differentially expressed nuclear genes contrasts with the uniformity of organellar transcriptomes across genders, which suggests these pathways are evolutionarily conserved and that selective mechanisms may shield organellar transcription against changes in the cytoplasmic transcriptome.
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Affiliation(s)
- Manuela Krüger
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic; (M.K.); (O.A.J.A.); (C.K.); (M.J.)
| | - Oushadee A. J. Abeyawardana
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic; (M.K.); (O.A.J.A.); (C.K.); (M.J.)
- Department of Horticulture, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 16500 Prague 6-Suchdol, Czech Republic
| | - Claudia Krüger
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic; (M.K.); (O.A.J.A.); (C.K.); (M.J.)
| | - Miloslav Juříček
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic; (M.K.); (O.A.J.A.); (C.K.); (M.J.)
| | - Helena Štorchová
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic; (M.K.); (O.A.J.A.); (C.K.); (M.J.)
- Correspondence: ; Tel.: +420-225-106-828
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Krüger M, Abeyawardana OAJ, Juříček M, Krüger C, Štorchová H. Variation in plastid genomes in the gynodioecious species Silene vulgaris. BMC PLANT BIOLOGY 2019; 19:568. [PMID: 31856730 PMCID: PMC6921581 DOI: 10.1186/s12870-019-2193-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 12/10/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND Gynodioecious species exist in two sexes - male-sterile females and hermaphrodites. Male sterility in higher plants often results from mitonuclear interaction between the CMS (cytoplasmic male sterility) gene(s) encoded by mitochondrial genome and by nuclear-encoded restorer genes. Mitochondrial and nuclear-encoded transcriptomes in females and hermaphrodites are intensively studied, but little is known about sex-specific gene expression in plastids. We have compared plastid transcriptomes between females and hermaphrodites in two haplotypes of a gynodioecious species Silene vulgaris with known CMS candidate genes. RESULTS We generated complete plastid genome sequences from five haplotypes S. vulgaris including the haplotypes KRA and KOV, for which complete mitochondrial genome sequences were already published. We constructed a phylogenetic tree based on plastid sequences of S. vulgaris. Whereas lowland S. vulgaris haplotypes including KRA and KOV clustered together, the accessions from high European mountains diverged early in the phylogram. S. vulgaris belongs among Silene species with slowly evolving plastid genomes, but we still detected 212 substitutions and 112 indels between two accessions of this species. We estimated elevated Ka/Ks in the ndhF gene, which may reflect the adaptation of S. vulgaris to high altitudes, or relaxed selection. We compared depth of coverage and editing rates between female and hermaphrodite plastid transcriptomes and found no significant differences between the two sexes. We identified 51 unique C to U editing sites in the plastid genomes of S. vulgaris, 38 of them in protein coding regions, 2 in introns, and 11 in intergenic regions. The editing site in the psbZ gene was edited only in one of two plastid genomes under study. CONCLUSIONS We revealed no significant differences between the sexes in plastid transcriptomes of two haplotypes of S. vulgaris. It suggests that gene expression of plastid genes is not affected by CMS in flower buds of S. vulgaris, although both sexes may still differ in plastid gene expression in specific tissues. We revealed the difference between the plastid transcriptomes of two S. vulgaris haplotypes in editing rate and in the coverage of several antisense transcripts. Our results document the variation in plastid genomes and transcriptomes in S. vulgaris.
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Affiliation(s)
- Manuela Krüger
- Plant Reproduction Laboratory, Institute of Experimental Botany v.v.i, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic
| | - Oushadee A. J. Abeyawardana
- Plant Reproduction Laboratory, Institute of Experimental Botany v.v.i, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic
| | - Miloslav Juříček
- Plant Reproduction Laboratory, Institute of Experimental Botany v.v.i, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic
| | | | - Helena Štorchová
- Plant Reproduction Laboratory, Institute of Experimental Botany v.v.i, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic
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Havird JC, Noe GR, Link L, Torres A, Logan DC, Sloan DB, Chicco AJ. Do angiosperms with highly divergent mitochondrial genomes have altered mitochondrial function? Mitochondrion 2019; 49:1-11. [PMID: 31229574 PMCID: PMC6885534 DOI: 10.1016/j.mito.2019.06.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 06/07/2019] [Accepted: 06/17/2019] [Indexed: 02/06/2023]
Abstract
Angiosperm mitochondrial (mt) genes are generally slow-evolving, but multiple lineages have undergone dramatic accelerations in rates of nucleotide substitution and extreme changes in mt genome structure. While molecular evolution in these lineages has been investigated, very little is known about their mt function. Some studies have suggested altered respiration in individual taxa, although there are several reasons why mt variation might be neutral in others. Here, we develop a new protocol to characterize respiration in isolated plant mitochondria and apply it to species of Silene with mt genomes that are rapidly evolving, highly fragmented, and exceptionally large (~11 Mbp). This protocol, complemented with traditional measures of plant fitness, cytochrome c oxidase activity assays, and fluorescence microscopy, was also used to characterize inter- and intraspecific variation in mt function. Contributions of the individual "classic" OXPHOS complexes, the alternative oxidase, and external NADH dehydrogenases to overall mt respiratory flux were found to be similar to previously studied angiosperms with more typical mt genomes. Some differences in mt function could be explained by inter- and intraspecific variation. This study suggests that Silene species with peculiar mt genomes still show relatively normal mt respiration. This may be due to strong purifying selection on mt variants, coevolutionary responses in the nucleus, or a combination of both. Future experiments should explore such questions using a comparative framework and investigating other lineages with unusual mitogenomes.
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Affiliation(s)
- Justin C Havird
- Department of Biology, Colorado State University, Fort Collins, CO, USA; Department of Integrative Biology, The University of Texas, Austin, TX, USA.
| | - Gregory R Noe
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Luke Link
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Amber Torres
- Department of Biology, Colorado State University, Fort Collins, CO, USA.
| | - David C Logan
- IRHS, INRA, Université d'Angers, AGROCAMPUS-Ouest, SFR 4207 QUASAV, 49071 Beaucouzé cedex, France
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA.
| | - Adam J Chicco
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.
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Makarenko MS, Usatov AV, Tatarinova TV, Azarin KV, Logacheva MD, Gavrilova VA, Kornienko IV, Horn R. Organization Features of the Mitochondrial Genome of Sunflower ( Helianthus annuus L.) with ANN2-Type Male-Sterile Cytoplasm. PLANTS (BASEL, SWITZERLAND) 2019; 8:E439. [PMID: 31652744 PMCID: PMC6918226 DOI: 10.3390/plants8110439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 10/18/2019] [Accepted: 10/19/2019] [Indexed: 12/24/2022]
Abstract
This study provides insights into the flexibility of the mitochondrial genome in sunflower (Helianthus annuus L.) as well as into the causes of ANN2-type cytoplasmic male sterility (CMS). De novo assembly of the mitochondrial genome of male-sterile HA89(ANN2) sunflower line was performed using high-throughput sequencing technologies. Analysis of CMS ANN2 mitochondrial DNA sequence revealed the following reorganization events: twelve rearrangements, seven insertions, and nine deletions. Comparisons of coding sequences from the male-sterile line with the male-fertile line identified a deletion of orf777 and seven new transcriptionally active open reading frames (ORFs): orf324, orf327, orf345, orf558, orf891, orf933, orf1197. Three of these ORFs represent chimeric genes involving atp6 (orf1197), cox2 (orf558), and nad6 (orf891). In addition, orf558, orf891, orf1197, as well as orf933, encode proteins containing membrane domain(s), making them the most likely candidate genes for CMS development in ANN2. Although the investigated CMS phenotype may be caused by simultaneous action of several candidate genes, we assume that orf1197 plays a major role in developing male sterility in ANN2. Comparative analysis of mitogenome organization in sunflower lines representing different CMS sources also allowed identification of reorganization hot spots in the mitochondrial genome of sunflower.
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Affiliation(s)
- Maksim S Makarenko
- Department of Genetics, Southern Federal University, Rostov-on-Don 344006, Russia.
- The Institute for Information Transmission Problems, Moscow 127051, Russia.
| | - Alexander V Usatov
- Department of Genetics, Southern Federal University, Rostov-on-Don 344006, Russia.
| | - Tatiana V Tatarinova
- The Institute for Information Transmission Problems, Moscow 127051, Russia.
- Department of Biology, University of La Verne, La Verne, CA 91750, USA.
- Vavilov Institute of General Genetics, Moscow 119333, Russia.
- School of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk 660041, Russia.
| | - Kirill V Azarin
- Department of Genetics, Southern Federal University, Rostov-on-Don 344006, Russia.
| | - Maria D Logacheva
- The Institute for Information Transmission Problems, Moscow 127051, Russia.
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia.
| | - Vera A Gavrilova
- The N.I. Vavilov All-Russian Institute of Plant Genetic Resources, Saint Petersburg 190121, Russia.
| | - Igor V Kornienko
- Department of Genetics, Southern Federal University, Rostov-on-Don 344006, Russia.
- Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don 344006, Russia.
| | - Renate Horn
- Institute of Biological Sciences, Plant Genetics, University of Rostock, 18059 Rostock, Germany.
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