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Zhang J, Liu G, Wei J. Assembly and comparative analysis of the first complete mitochondrial genome of Setaria italica. PLANTA 2024; 260:23. [PMID: 38850310 DOI: 10.1007/s00425-024-04386-2] [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: 11/16/2023] [Accepted: 03/10/2024] [Indexed: 06/10/2024]
Abstract
MAIN CONCLUSION In this study, we assembled the first complete mitochondrial genome of Setaria italica and confirmed the multi-branched architecture. The foxtail millet (Setaria italica) holds significant agricultural importance, particularly in arid and semi-arid regions. It plays a pivotal role in diversifying dietary patterns and shaping planting strategies. Although the chloroplast genome of S. italica has been elucidated in recent studies, the complete mitochondrial genome remains largely unexplored. In this study, we employed PacBio HiFi sequencing platforms to sequence and assemble the complete mitochondrial genome. The mitochondrial genome spans a total length of 446,614 base pairs and harbors a comprehensive set of genetic elements, including 33 unique protein-coding genes (PCGs), encompassing 24 unique mitochondrial core genes and 9 variable genes, along with 20 transfer RNA (tRNA) genes and 3 ribosomal RNA (rRNA) genes. Our analysis of mitochondrial PCGs revealed a pronounced codon usage preference. For instance, the termination codon exhibits a marked preference for UAA, while alanine (Ala) exhibits a preference for GCU, and glutamine (Gln) favors CAA. Notably, the maximum Relative Synonymous Codon Usage (RSCU) values for cysteine (Cys) and phenylalanine (Phe) are both below 1.2, indicating a lack of strong codon usage preference for these amino acids. Phylogenetic analyses consistently place S. italica in close evolutionary proximity to Chrysopogon zizanioides, relative to other Panicoideae plants. Collinearity analysis showed that a total of 39 fragments were identified to display homology with both the mitochondrial and chloroplast genomes. A total of 417 potential RNA-editing sites were discovered across the 33 mitochondrial PCGs. Notably, all these editing events involved the conversion of cytosine (C) to uracil (U). Through the employment of PCR validation coupled with Sanger sequencing for the anticipated editing sites of these codons, RNA-editing events were conclusively identified at two specific loci: nad4L-2 and atp6-1030. The results of this study provide a pivotal foundation for advanced genomic breeding research in foxtail millet. Furthermore, they impart essential insights that will be instrumental for forthcoming investigations into the evolutionary and molecular dynamics of Panicoideae species.
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Affiliation(s)
- Jiewei Zhang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Guiming Liu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Jianhua Wei
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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Lu G, Li Q. Complete mitochondrial genome of Syzygium samarangense reveals genomic recombination, gene transfer, and RNA editing events. FRONTIERS IN PLANT SCIENCE 2024; 14:1301164. [PMID: 38264024 PMCID: PMC10803518 DOI: 10.3389/fpls.2023.1301164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024]
Abstract
Wax apple (Syzygium samarangense) is a commercial fruit that belongs to one of the most species-rich tree genera in the world. We report here the first complete S. samarangense mitogenome obtained using a hybrid assembly strategy. The mitogenome was a 530,242 bp circular molecule encoding 61 unique genes accounting for 7.99% of the full-length genome. Additionally, 167 simple sequence repeats, 19 tandem repeats, and 529 pairs of interspersed repeats were identified. Long read mapping and Sanger sequencing revealed the involvement of two forward repeats (35,843 bp and 22,925 bp) in mediating recombination. Thirteen homologous fragments in the chloroplast genome were identified, accounting for 1.53% of the mitogenome, and the longest fragment was 2,432 bp. An evolutionary analysis showed that S. samarangense underwent multiple genomic reorganization events and lost at least four protein-coding genes (PCGs) (rps2, rps7, rps11, and rps19). A total of 591 RNA editing sites were predicted in 37 PCGs, of which nad1-2, nad4L-2, and rps10-2 led to the gain of new start codons, while atp6-1156, ccmFC-1315 and rps10-331 created new stop codons. This study reveals the genetic features of the S. samarangense mitogenome and provides a scientific basis for further studies of traits with an epistatic basis and for germplasm identification.
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Affiliation(s)
- Guilong Lu
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
- College of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
| | - Qing Li
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
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Nicolia A, Scotti N, D'Agostino N, Festa G, Sannino L, Aufiero G, Arimura SI, Cardi T. Mitochondrial DNA editing in potato through mitoTALEN and mitoTALECD: molecular characterization and stability of editing events. PLANT METHODS 2024; 20:4. [PMID: 38183104 PMCID: PMC10768376 DOI: 10.1186/s13007-023-01124-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 12/04/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND The aim of this study was to evaluate and characterize the mutations induced by two TALE-based approaches, double-strand break (DSB) induction by the FokI nuclease (mitoTALEN) and targeted base editing by the DddA cytidine deaminase (mitoTALECD), to edit, for the first time, the mitochondrial genome of potato, a vegetatively propagated crop. The two methods were used to knock out the same mitochondrial target sequence (orf125). RESULTS Targeted chondriome deletions of different sizes (236-1066 bp) were induced by mitoTALEN due to DSB repair through ectopic homologous recombination of short direct repeats (11-12 bp) present in the target region. Furthermore, in one case, the induced DSB and subsequent repair resulted in the amplification of an already present substoichiometric molecule showing a 4288 bp deletion spanning the target sequence. With the mitoTALECD approach, both nonsense and missense mutations could be induced by base substitution. The deletions and single nucleotide mutations were either homoplasmic or heteroplasmic. The former were stably inherited in vegetative offspring. CONCLUSIONS Both editing approaches allowed us to obtain plants with precisely modified mitochondrial genomes at high frequency. The use of the same plant genotype and mtDNA region allowed us to compare the two methods for efficiency, accuracy, type of modifications induced and stability after vegetative propagation.
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Affiliation(s)
- Alessandro Nicolia
- CREA, Research Centre for Vegetable and Ornamental Crops, via Cavalleggeri 25, 84098, Pontecagnano, SA, Italy
| | - Nunzia Scotti
- CNR-IBBR, Institute of Biosciences and BioResources, 80055, Portici, NA, Italy
| | - Nunzio D'Agostino
- Department of Agricultural Sciences, University of Naples Federico II, 80055, Portici, Italy
| | - Giovanna Festa
- CREA, Research Centre for Vegetable and Ornamental Crops, via Cavalleggeri 25, 84098, Pontecagnano, SA, Italy
| | - Lorenza Sannino
- CNR-IBBR, Institute of Biosciences and BioResources, 80055, Portici, NA, Italy
| | - Gaetano Aufiero
- Department of Agricultural Sciences, University of Naples Federico II, 80055, Portici, Italy
| | - Shin-Ichi Arimura
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Teodoro Cardi
- CREA, Research Centre for Vegetable and Ornamental Crops, via Cavalleggeri 25, 84098, Pontecagnano, SA, Italy.
- CNR-IBBR, Institute of Biosciences and BioResources, 80055, Portici, NA, Italy.
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Ranaware AS, Kunchge NS, Lele SS, Ochatt SJ. Protoplast Technology and Somatic Hybridisation in the Family Apiaceae. PLANTS (BASEL, SWITZERLAND) 2023; 12:1060. [PMID: 36903923 PMCID: PMC10005591 DOI: 10.3390/plants12051060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/03/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Species of the family Apiaceae occupy a major market share but are hitherto dependent on open pollinated cultivars. This results in a lack of production uniformity and reduced quality that has fostered hybrid seed production. The difficulty in flower emasculation led breeders to use biotechnology approaches including somatic hybridization. We discuss the use of protoplast technology for the development of somatic hybrids, cybrids and in-vitro breeding of commercial traits such as CMS (cytoplasmic male sterility), GMS (genetic male sterility) and EGMS (environment-sensitive genic male sterility). The molecular mechanism(s) underlying CMS and its candidate genes are also discussed. Cybridization strategies based on enucleation (Gamma rays, X-rays and UV rays) and metabolically arresting protoplasts with chemicals such as iodoacetamide or iodoacetate are reviewed. Differential fluorescence staining of fused protoplast as routinely used can be replaced by new tagging approaches using non-toxic proteins. Here, we focused on the initial plant materials and tissue sources for protoplast isolation, the various digestion enzyme mixtures tested, and on the understanding of cell wall re-generation, all of which intervene in somatic hybrids regeneration. Although there are no alternatives to somatic hybridization, various approaches also discussed are emerging, viz., robotic platforms, artificial intelligence, in recent breeding programs for trait identification and selection.
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Affiliation(s)
- Ankush S. Ranaware
- Institute of Chemical Technology, Marathwada Campus, Jalna 431203, Maharashtra, India
| | - Nandkumar S. Kunchge
- Research and Development Division, Kalash Seeds Pvt. Ltd., Jalna 431203, Maharashtra, India
| | - Smita S. Lele
- Institute of Chemical Technology, Marathwada Campus, Jalna 431203, Maharashtra, India
| | - Sergio J. Ochatt
- Agroécologie, InstitutAgro Dijon, INRAE, Université Bourgogne Franche-Comté, 21000 Dijon, France
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Maliga P. Engineering the plastid and mitochondrial genomes of flowering plants. NATURE PLANTS 2022; 8:996-1006. [PMID: 36038655 DOI: 10.1038/s41477-022-01227-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Engineering the plastid genome based on homologous recombination is well developed in a few model species. Homologous recombination is also the rule in mitochondria, but transformation of the mitochondrial genome has not been realized in the absence of selective markers. The application of transcription activator-like (TAL) effector-based tools brought about a dramatic change because they can be deployed from nuclear genes and targeted to plastids or mitochondria by an N-terminal targeting sequence. Recognition of the target site in the organellar genomes is ensured by the modular assembly of TALE repeats. In this paper, I review the applications of TAL effector nucleases and TAL effector cytidine deaminases for gene deletion, base editing and mutagenesis in plastids and mitochondria. I also review emerging technologies such as post-transcriptional RNA modification to regulate gene expression, Agrobacterium- and nanoparticle-mediated organellar genome transformation, and self-replicating organellar vectors as production platforms.
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Affiliation(s)
- Pal Maliga
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, USA.
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, USA.
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Cho KS, Lee HO, Lee SC, Park HJ, Seo JH, Cho JH, Park YE, Choi JG, Yang TJ. Mitochondrial genome recombination in somatic hybrids of Solanum commersonii and S. tuberosum. Sci Rep 2022; 12:8659. [PMID: 35606486 PMCID: PMC9127095 DOI: 10.1038/s41598-022-12661-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/12/2022] [Indexed: 11/19/2022] Open
Abstract
Interspecific somatic hybridization has been performed in potato breeding experiments to increase plant resistance against biotic and abiotic stress conditions. We analyzed the mitochondrial and plastid genomes and 45S nuclear ribosomal DNA (45S rDNA) for the cultivated potato (S. tuberosum, St), wild potato (S. commersonii, Sc), and their somatic hybrid (StSc). Complex genome components and structure, such as the hybrid form of 45S rDNA in StSc, unique plastome in Sc, and recombinant mitogenome were identified. However, the mitogenome exhibited dynamic multipartite structures in both species as well as in the somatic hybrid. In St, the mitogenome is 756,058 bp and is composed of five subgenomes ranging from 297,014 to 49,171 bp. In Sc, it is 552,103 bp long and is composed of two sub-genomes of 338,427 and 213,676 bp length. StSc has 447,645 bp long mitogenome with two subgenomes of length 398,439 and 49,206 bp. The mitogenome structure exhibited dynamic recombination mediated by tandem repeats; however, it contained highly conserved genes in the three species. Among the 35 protein-coding genes of the StSc mitogenome, 21 were identical for all the three species, and 12 and 2 were unique in Sc and St, respectively. The recombinant mitogenome might be derived from homologous recombination between both species during somatic hybrid development.
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Affiliation(s)
- Kwang-Soo Cho
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, 50424, Republic of Korea.
| | - Hyun-Oh Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.,Phyzen Genomics Institute, Baekgoong Plaza 1, Bundang-gu, Seongnam, 13558, Republic of Korea
| | - Sang-Choon Lee
- Phyzen Genomics Institute, Baekgoong Plaza 1, Bundang-gu, Seongnam, 13558, Republic of Korea
| | - Hyun-Jin Park
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Jin-Hee Seo
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Ji-Hong Cho
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Young-Eun Park
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Jang-Gyu Choi
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
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Chen L, Ren W, Zhang B, Chen W, Fang Z, Yang L, Zhuang M, Lv H, Wang Y, Ji J, Zhang Y. Organelle Comparative Genome Analysis Reveals Novel Alloplasmic Male Sterility with orf112 in Brassica oleracea L. Int J Mol Sci 2021; 22:ijms222413230. [PMID: 34948024 PMCID: PMC8703919 DOI: 10.3390/ijms222413230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 11/16/2022] Open
Abstract
B. oleracea Ogura CMS is an alloplasmic male-sterile line introduced from radish by interspecific hybridization and protoplast fusion. The introduction of alien cytoplasm resulted in many undesirable traits, which affected the yield of hybrids. Therefore, it is necessary to identify the composition and reduce the content of alien cytoplasm in B. oleracea Ogura CMS. In the present study, we sequenced, assembled, and compared the organelle genomes of Ogura CMS cabbage and its maintainer line. The chloroplast genome of Ogura-type cabbage was completely derived from normal-type cabbage, whereas the mitochondrial genome was recombined from normal-type cabbage and Ogura-type radish. Nine unique regions derived from radish were identified in the mitochondrial genome of Ogura-type cabbage, and the total length of these nine regions was 35,618 bp, accounting for 13.84% of the mitochondrial genome. Using 32 alloplasmic markers designed according to the sequences of these nine regions, one novel sterile source with less alien cytoplasm was discovered among 305 materials and named Bel CMS. The size of the alien cytoplasm in Bel CMS was 21,587 bp, accounting for 8.93% of its mtDNA, which was much less than that in Ogura CMS. Most importantly, the sterility gene orf138 was replaced by orf112, which had a 78-bp deletion, in Bel CMS. Interestingly, Bel CMS cabbage also maintained 100% sterility, although orf112 had 26 fewer amino acids than orf138. Field phenotypic observation showed that Bel CMS was an excellent sterile source with stable 100% sterility and no withered buds at the early flowering stage, which could replace Ogura CMS in cabbage heterosis utilization.
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Affiliation(s)
- Li Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenjing Ren
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Bin Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wendi Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Zhiyuan Fang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Limei Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Mu Zhuang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Honghao Lv
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Yong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Jialei Ji
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Yangyong Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
- Correspondence:
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Fertet A, Graindorge S, Koechler S, de Boer GJ, Guilloteau-Fonteny E, Gualberto JM. Sequence of the Mitochondrial Genome of Lactuca virosa Suggests an Unexpected Role in Lactuca sativa's Evolution. FRONTIERS IN PLANT SCIENCE 2021; 12:697136. [PMID: 34381482 PMCID: PMC8350775 DOI: 10.3389/fpls.2021.697136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
The involvement of the different Lactuca species in the domestication and diversification of cultivated lettuce is not totally understood. Lactuca serriola is considered as the direct ancestor and the closest relative to Lactuca sativa, while the other wild species that can be crossed with L. sativa, Lactuca virosa, and Lactuca saligna, would have just contributed to the latter diversification of cultivated typologies. To contribute to the study of Lactuca evolution, we assembled the mtDNA genomes of nine Lactuca spp. accessions, among them three from L. virosa, whose mtDNA had not been studied so far. Our results unveiled little to no intraspecies variation among Lactuca species, with the exception of L. serriola where the accessions we sequenced diverge significantly from the mtDNA of a L. serriola accession already reported. Furthermore, we found a remarkable phylogenetic closeness between the mtDNA of L. sativa and the mtDNA of L. virosa, contrasting to the L. serriola origin of the nuclear and plastidial genomes. These results suggest that a cross between L. virosa and the ancestor of cultivated lettuce is at the origin of the actual mitochondrial genome of L. sativa.
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Affiliation(s)
- Arnaud Fertet
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Stéfanie Graindorge
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Sandrine Koechler
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Gert-Jan de Boer
- Enza Zaden Research and Development B.V., Enkhuizen, Netherlands
| | | | - José M. Gualberto
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
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Vasupalli N, Kumar V, Bhattacharya R, Bhat SR. Analysis of mitochondrial recombination in the male sterile Brassica juncea cybrid Og1 and identification of the molecular basis of fertility reversion. PLANT MOLECULAR BIOLOGY 2021; 106:109-122. [PMID: 33638768 DOI: 10.1007/s11103-021-01132-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 02/12/2021] [Indexed: 06/12/2023]
Abstract
Recombinations between the parental genomes produced a novel mitochondrial genome in the cytoplasmic male sterile Brassica juncea cybrid Og1. A mitochondrial stoichiometric shift greatly reduced the molecule containing male-sterility-inducing orf138 gene leading to reversion to male fertility. An improved, chlorosis-corrected, cytoplasmic male sterile Brassica juncea cybrid Og1 derived from Ogura cytoplasm shows frequent reversion to male fertility. To determine the nature of mitochondrial recombination in the cybrid and to uncover the molecular mechanism of male fertility reversion, we sequenced the mitochondrial genomes of Og1, its isonuclear parental lines (OgRLM and Brassica juncea RLM198) and the revertant line (Og1-rt). Assembly of Og1 mitochondrial genome gave two circular molecules, Og1a (250.999 kbp) and Og1b (96.185 kbp) sharing two large direct repeat regions capable of recombining to form a single circular molecule. Og1a contains all essential mitochondrial genes, but the male-sterility-causing orf138 was uniquely present in Og1b along with 16 other complete or partial genes already represented in Og1a. Eleven and four recombinations between the parental mitochondrial genomes produced the Og1a and the Og1b molecules, respectively. Five genes were duplicated within Og1a, of which trnfM was inherited from both the parents while the other four genes, atp4, cox1 nad4L and trnM, were inherited from RLM198. RFLP analysis revealed that orf138-containing molecules were less abundant than Og1a in the male-sterile plants while og1b bearing molecules were undetectable in the revertant line. However, orf138 transcripts were amplified in RT-PCR and were also detected in northern blots revealing that Og1b molecules are not completely lost in the revertant plants. This is the first report where the mitochondrial genome of a cybrid is compared with its actual parents. The findings are discussed in the light of previous reports on mitochondrial genome recombination in cybrids.
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Affiliation(s)
- Naresh Vasupalli
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Vajinder Kumar
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | | | - Shripad R Bhat
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India.
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10
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Roulet ME, Garcia LE, Gandini CL, Sato H, Ponce G, Sanchez-Puerta MV. Multichromosomal structure and foreign tracts in the Ombrophytum subterraneum (Balanophoraceae) mitochondrial genome. PLANT MOLECULAR BIOLOGY 2020; 103:623-638. [PMID: 32440763 DOI: 10.1007/s11103-020-01014-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Horizontal gene transfer (HGT) is frequent in parasitic plant mitochondria as a result of vascular connections established in host-parasite relationships. Recent studies of the holoparasitic plant Lophophytum mirabile (Balanophoraceae) revealed the unprecedented acquisition of a large amount of mitochondrial sequences from its legume host. We focused on a close relative, the generalist holoparasite Ombrophytum subterraneum, to examine the incidence of HGT events in the mitochondrial genome (mtDNA). The mtDNA of O. subterraneum assembles into 54 circular chromosomes, only 34 of which contain the 51 full-length coding regions. Numerous foreign tracts (totaling almost 100 kb, ~ 14% of the mtDNA), including 12 intact genes, were acquired by HGT from the Asteraceae hosts. Nine chromosomes concentrate most of those regions and eight are almost entirely foreign. Native homologs of each foreign gene coexist in the mtDNA and are potentially functional. A large proportion of shorter regions were related to the Fabaceae (a total of ~ 110 kb, 15.4%), some of which were shared with L. mirabile. We also found evidence of foreign sequences donated by angiosperm lineages not reported as hosts (Apocynaceae, Euphorbiaceae, Lamiaceae, and Malvales). We propose an evolutionary hypothesis that involves ancient transfers from legume hosts in the common ancestor of Ombrophytum and Lophophytum followed by more recent transfer events in L. mirabile. Besides, the O. subterraneum mtDNA was also subjected to additional HGT events from diverse angiosperm lineages, including large and recent transfers from the Asteraceae, and also from Lamiaceae.
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Affiliation(s)
- M Emilia Roulet
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
| | - Laura E Garcia
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina
| | - Carolina L Gandini
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
| | - Hector Sato
- Facultad de Ciencias Agrarias, Universidad Nacional de Jujuy, Cátedra de Botánica General-Herbario JUA, Alberdi 47, 4600, San Salvador de Jujuy, Jujuy, Argentina
| | - Gabriela Ponce
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina
| | - M Virginia Sanchez-Puerta
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina.
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina.
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11
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Qiao J, Zhang X, Chen B, Huang F, Xu K, Huang Q, Huang Y, Hu Q, Wu X. Comparison of the cytoplastic genomes by resequencing: insights into the genetic diversity and the phylogeny of the agriculturally important genus Brassica. BMC Genomics 2020; 21:480. [PMID: 32660507 PMCID: PMC7359470 DOI: 10.1186/s12864-020-06889-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 07/07/2020] [Indexed: 12/18/2022] Open
Abstract
Background The genus Brassica mainly comprises three diploid and three recently derived allotetraploid species, most of which are highly important vegetable, oil or ornamental crops cultivated worldwide. Despite being extensively studied, the origination of B. napus and certain detailed interspecific relationships within Brassica genus remains undetermined and somewhere confused. In the current high-throughput sequencing era, a systemic comparative genomic study based on a large population is necessary and would be crucial to resolve these questions. Results The chloroplast DNA and mitochondrial DNA were synchronously resequenced in a selected set of Brassica materials, which contain 72 accessions and maximally integrated the known Brassica species. The Brassica genomewide cpDNA and mtDNA variations have been identified. Detailed phylogenetic relationships inside and around Brassica genus have been delineated by the cpDNA- and mtDNA- variation derived phylogenies. Different from B. juncea and B. carinata, the natural B. napus contains three major cytoplasmic haplotypes: the cam-type which directly inherited from B. rapa, polima-type which is close to cam-type as a sister, and the mysterious but predominant nap-type. Certain sparse C-genome wild species might have primarily contributed the nap-type cytoplasm and the corresponding C subgenome to B. napus, implied by their con-clustering in both phylogenies. The strictly concurrent inheritance of mtDNA and cpDNA were dramatically disturbed in the B. napus cytoplasmic male sterile lines (e.g., mori and nsa). The genera Raphanus, Sinapis, Eruca, Moricandia show a strong parallel evolutional relationships with Brassica. Conclusions The overall variation data and elaborated phylogenetic relationships provide further insights into genetic understanding of Brassica, which can substantially facilitate the development of novel Brassica germplasms.
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Affiliation(s)
- Jiangwei Qiao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
| | - Xiaojun Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Biyun Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | | | - Kun Xu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Qian Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yi Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Qiong Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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12
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The draft mitochondrial genome of Magnolia biondii and mitochondrial phylogenomics of angiosperms. PLoS One 2020; 15:e0231020. [PMID: 32294100 PMCID: PMC7159230 DOI: 10.1371/journal.pone.0231020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/13/2020] [Indexed: 12/15/2022] Open
Abstract
The mitochondrial genomes of flowering plants are well known for their large size, variable coding-gene set and fluid genome structure. The available mitochondrial genomes of the early angiosperms show extreme genetic diversity in genome size, structure, and sequences, such as rampant HGTs in Amborella mt genome, numerous repeated sequences in Nymphaea mt genome, and conserved gene evolution in Liriodendron mt genome. However, currently available early angiosperm mt genomes are still limited, hampering us from obtaining an overall picture of the mitogenomic evolution in angiosperms. Here we sequenced and assembled the draft mitochondrial genome of Magnolia biondii Pamp. from Magnoliaceae (magnoliids) using Oxford Nanopore sequencing technology. We recovered a single linear mitochondrial contig of 967,100 bp with an average read coverage of 122 × and a GC content of 46.6%. This draft mitochondrial genome contains a rich 64-gene set, similar to those of Liriodendron and Nymphaea, including 41 protein-coding genes, 20 tRNAs, and 3 rRNAs. Twenty cis-spliced and five trans-spliced introns break ten protein-coding genes in the Magnolia mt genome. Repeated sequences account for 27% of the draft genome, with 17 out of the 1,145 repeats showing recombination evidence. Although partially assembled, the approximately 1-Mb mt genome of Magnolia is still among the largest in angiosperms, which is possibly due to the expansion of repeated sequences, retention of ancestral mtDNAs, and the incorporation of nuclear genome sequences. Mitochondrial phylogenomic analysis of the concatenated datasets of 38 conserved protein-coding genes from 91 representatives of angiosperm species supports the sister relationship of magnoliids with monocots and eudicots, which is congruent with plastid evidence.
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13
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Wang R, Cai X, Hu S, Li Y, Fan Y, Tan S, Liu Q, Zhou W. Comparative Analysis of the Mitochondrial Genomes of Nicotiana tabacum: Hints Toward the Key Factors Closely Related to the Cytoplasmic Male Sterility Mechanism. Front Genet 2020; 11:257. [PMID: 32265988 PMCID: PMC7100274 DOI: 10.3389/fgene.2020.00257] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/03/2020] [Indexed: 02/02/2023] Open
Abstract
Background Cytoplasmic male sterility (CMS) is a complex phenomenon of plant sterility that can produce non-functional pollen. It is caused by mutation, rearrangement or recombination in the mitochondrial genome. So far, the systematic structural characteristics of the changes in the mitochondrial genome from the maintainer lines to the CMS lines have not been reported in tobacco. Results The mitochondrial genomes of the flower buds from both CMS lines and maintainer lines of two Nicotiana tabacum cultivars (YY85, sYY85, ZY90, and sZY90) were sequenced using the PacBio and Illumina Hiseq technology, and several findings were produced by comparative analysis based on the de novo sequencing. (1) The genomes of the CMS lines were larger, and the different areas were mostly non-coding regions. (2) A large number of rearrangement regions were detected in the CMS lines, with many translocation regions. (3) Thirteen gene clusters were shared by the four mitochondrial genomes, among which two of the gene clusters, nad2-sdh3 and nad6-rps4, were far from each other in the CMS lines. (4) Thirty-three protein-coding genes were conserved in four mitochondrial genomes. However, nad3 was detected one additional copy in the maintainer lines, and sequence differences were revealed in the four candidate genes (atp6, cox2, nad2, and sdh3). Importantly, the evolutionary tree based on the four genes could be used to distinguish the CMS lines and the maintainer lines well for the sequenced mitochondrial genomes of the tobacco. (5) Sixteen CMS-specific open reading frames (ORFs) were found, three of which (orf91, orf115b, and orf100) were previously reported. (6) The differences in intensity of the protein–protein (PPI) interaction in ATP6 were further verified using the yeast two-hybrid analysis. Conclusion Although the majority of the sequences, genes and gene clusters were shared by the mitochondrial genomes of the maintainer and the CMS lines in tobacco, extensive structural variations identified with comprehensive analysis based on the mitochondrial genomes, including rearrangement, gene order, the mitochondrial genome expansion and shrinkage events, might be related to CMS. Additionally, the candidate protein-coding genes and CMS-specific ORFs were closely associated with the CMS mechanism. Verification experiments of one of the candidate genes were performed, and the validity of our research results was supported.
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Affiliation(s)
- Ruyi Wang
- Hunan Engineering and Technology Research Center for Agricultural Big Data Analysis and Decision-Making, Changsha, China.,Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Xunhui Cai
- School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, China
| | - Shengnan Hu
- Hunan Engineering and Technology Research Center for Agricultural Big Data Analysis and Decision-Making, Changsha, China.,Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Ying Li
- Hunan Engineering and Technology Research Center for Agricultural Big Data Analysis and Decision-Making, Changsha, China.,Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Yanjun Fan
- Hunan Engineering and Technology Research Center for Agricultural Big Data Analysis and Decision-Making, Changsha, China.,Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Siqiao Tan
- Hunan Engineering and Technology Research Center for Agricultural Big Data Analysis and Decision-Making, Changsha, China.,Hunan Engineer Research Center for Information Technology in Agriculture, Changsha, China
| | - Qiyuan Liu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Wei Zhou
- Hunan Engineering and Technology Research Center for Agricultural Big Data Analysis and Decision-Making, Changsha, China.,Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha, China
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14
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Dujon B. Mitochondrial genetics revisited. Yeast 2020; 37:191-205. [DOI: 10.1002/yea.3445] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 10/05/2019] [Accepted: 10/08/2019] [Indexed: 12/17/2022] Open
Affiliation(s)
- Bernard Dujon
- Department Genomes and GeneticsInstitut Pasteur Paris France
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15
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Chevigny N, Schatz-Daas D, Lotfi F, Gualberto JM. DNA Repair and the Stability of the Plant Mitochondrial Genome. Int J Mol Sci 2020; 21:E328. [PMID: 31947741 PMCID: PMC6981420 DOI: 10.3390/ijms21010328] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/27/2019] [Accepted: 01/01/2020] [Indexed: 12/13/2022] Open
Abstract
The mitochondrion stands at the center of cell energy metabolism. It contains its own genome, the mtDNA, that is a relic of its prokaryotic symbiotic ancestor. In plants, the mitochondrial genetic information influences important agronomic traits including fertility, plant vigor, chloroplast function, and cross-compatibility. Plant mtDNA has remarkable characteristics: It is much larger than the mtDNA of other eukaryotes and evolves very rapidly in structure. This is because of recombination activities that generate alternative mtDNA configurations, an important reservoir of genetic diversity that promotes rapid mtDNA evolution. On the other hand, the high incidence of ectopic recombination leads to mtDNA instability and the expression of gene chimeras, with potential deleterious effects. In contrast to the structural plasticity of the genome, in most plant species the mtDNA coding sequences evolve very slowly, even if the organization of the genome is highly variable. Repair mechanisms are probably responsible for such low mutation rates, in particular repair by homologous recombination. Herein we review some of the characteristics of plant organellar genomes and of the repair pathways found in plant mitochondria. We further discuss how homologous recombination is involved in the evolution of the plant mtDNA.
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Affiliation(s)
| | | | | | - José Manuel Gualberto
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67081 Strasbourg, France; (N.C.); (D.S.-D.); (F.L.)
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16
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Aguirre-Dugua X, Castellanos-Morales G, Paredes-Torres LM, Hernández-Rosales HS, Barrera-Redondo J, Sánchez-de la Vega G, Tapia-Aguirre F, Ruiz-Mondragón KY, Scheinvar E, Hernández P, Aguirre-Planter E, Montes-Hernández S, Lira-Saade R, Eguiarte LE. Evolutionary Dynamics of Transferred Sequences Between Organellar Genomes in Cucurbita. J Mol Evol 2019; 87:327-342. [PMID: 31701178 DOI: 10.1007/s00239-019-09916-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 10/28/2019] [Indexed: 12/12/2022]
Abstract
Twenty-nine DNA regions of plastid origin have been previously identified in the mitochondrial genome of Cucurbita pepo (pumpkin; Cucurbitaceae). Four of these regions harbor homolog sequences of rbcL, matK, rpl20-rps12 and trnL-trnF, which are widely used as molecular markers for phylogenetic and phylogeographic studies. We extracted the mitochondrial copies of these regions based on the mitochondrial genome of C. pepo and, along with published sequences for these plastome markers from 13 Cucurbita taxa, we performed phylogenetic molecular analyses to identify inter-organellar transfer events in the Cucurbita phylogeny and changes in their nucleotide substitution rates. Phylogenetic reconstruction and tree selection tests suggest that rpl20 and rbcL mitochondrial paralogs arose before Cucurbita diversification whereas the mitochondrial matK and trnL-trnF paralogs emerged most probably later, in the mesophytic Cucurbita clade. Nucleotide substitution rates increased one order of magnitude in all the mitochondrial paralogs compared to their original plastid sequences. Additionally, mitochondrial trnL-trnF sequences obtained by PCR from nine Cucurbita taxa revealed higher nucleotide diversity in the mitochondrial than in the plastid copies, likely related to the higher nucleotide substitution rates in the mitochondrial region and loss of functional constraints in its tRNA genes.
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Affiliation(s)
- Xitlali Aguirre-Dugua
- Unidad de Biotecnología Y Prototipos, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De Los Barrios 1, Col. Los Reyes Iztacala, 54090, Tlalnepantla, Estado de México, Mexico.
| | - Gabriela Castellanos-Morales
- Departamento de Conservación de La Biodiversidad, El Colegio de La Frontera Sur, Unidad Villahermosa, Carretera Villahermosa-Reforma km. 15.5, Ranchería El Guineo 2a Sección, 86280, Villahermosa, Tabasco, Mexico
| | - Leslie M Paredes-Torres
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Helena S Hernández-Rosales
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Josué Barrera-Redondo
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Guillermo Sánchez-de la Vega
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Fernando Tapia-Aguirre
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Karen Y Ruiz-Mondragón
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Enrique Scheinvar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Paulina Hernández
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Erika Aguirre-Planter
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Salvador Montes-Hernández
- Campo Experimental Bajío, Instituto Nacional de Investigaciones Forestales, Agrícolas Y Pecuarias (INIFAP), Km 6.5 Carretera Celaya-San Miguel de Allende, 38110, Celaya, Gto., Mexico
| | - Rafael Lira-Saade
- Unidad de Biotecnología Y Prototipos, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De Los Barrios 1, Col. Los Reyes Iztacala, 54090, Tlalnepantla, Estado de México, Mexico.
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico.
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17
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Sang SF, Mei DS, Liu J, Zaman QU, Zhang HY, Hao MY, Fu L, Wang H, Cheng HT, Hu Q. Organelle genome composition and candidate gene identification for Nsa cytoplasmic male sterility in Brassica napus. BMC Genomics 2019; 20:813. [PMID: 31694534 PMCID: PMC6836354 DOI: 10.1186/s12864-019-6187-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 10/15/2019] [Indexed: 12/29/2022] Open
Abstract
Background Nsa cytoplasmic male sterility (CMS) is a novel alloplasmic male sterility system derived from somatic hybridization between Brassica napus and Sinapis arvensis. Identification of the CMS-associated gene is a prerequisite for a better understanding of the origin and molecular mechanism of this CMS. With the development of genome sequencing technology, organelle genomes of Nsa CMS line and its maintainer line were sequenced by pyro-sequencing technology, and comparative analysis of the organelle genomes was carried out to characterize the organelle genome composition of Nsa CMS as well as to identify the candidate Nsa CMS-associated genes. Results Nsa CMS mitochondrial genome showed a higher collinearity with that of S. arvensis than B. napus, indicating that Nsa CMS mitochondrial genome was mainly derived from S. arvensis. However, mitochondrial genome recombination of parental lines was clearly detected. In contrast, the chloroplast genome of Nsa CMS was highly collinear with its B. napus parent, without any evidence of recombination of the two parental chloroplast genomes or integration from S. arvensis. There were 16 open reading frames (ORFs) specifically existed in Nsa CMS mitochondrial genome, which could not be identified in the maintainer line. Among them, three ORFs (orf224, orf309, orf346) possessing chimeric and transmembrane structure are most likely to be the candidate CMS genes. Sequences of all three candidate CMS genes in Nsa CMS line were found to be 100% identical with those from S. arvensis mitochondrial genome. Phylogenetic and homologous analysis showed that all the mitochondrial genes were highly conserved during evolution. Conclusions Nsa CMS contains a recombined mitochondrial genome of its two parental species with the majority form S. arvensis. Three candidate Nsa CMS genes were identified and proven to be derived from S. arvensis other than recombination of its two parental species. Further functional study of the candidate genes will help to identify the gene responsible for the CMS and the underlying molecular mechanism.
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Affiliation(s)
- Shi-Fei Sang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - De-Sheng Mei
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Jia Liu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Qamar U Zaman
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Hai-Yan Zhang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Meng-Yu Hao
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Li Fu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Hui Wang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Hong-Tao Cheng
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China.
| | - Qiong Hu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China.
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18
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Sinn BT, Barrett CF. Ancient Mitochondrial Gene Transfer between Fungi and the Orchids. Mol Biol Evol 2019; 37:44-57. [PMID: 31504747 DOI: 10.1093/molbev/msz198] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
AbstractThe mitochondrial genomes (mitogenomes) of plants are known to incorporate and accumulate DNA from intra- and extracellular donors. Despite the intimate relationships formed between flowing plants (angiosperms) and fungi, lengthy fungal-like sequence has not been identified in angiosperm mitogenomes to date. Here, we present multiple lines of evidence documenting horizontal gene transfer (HGT) between the mitogenomes of fungi and the ancestors of the orchids, plants that are obligate parasites of fungi during their early development. We show that the ancestor of the orchids acquired an ∼270-bp fungal mitogenomic region containing three transfer RNA genes. We propose that the short HGT was later replaced by a second HGT event transferring >8 kb and 14 genes from a fungal mitogenome to that of the ancestor of the largest orchid subfamily, Epidendroideae. Our results represent the first evidence of genomic-scale HGT between fungal and angiosperm mitogenomes and demonstrate that the length intergenic spacer regions of angiosperm mitogenomes can effectively fossilize the genomic remains of ancient, nonplant organisms.
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Affiliation(s)
- Brandon T Sinn
- Department of Biology, West Virginia University, Morgantown, WV
- Department of Biology and Earth Science, Otterbein University, Westerville, OH
| | - Craig F Barrett
- Department of Biology, West Virginia University, Morgantown, WV
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19
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Garcia LE, Zubko MK, Zubko EI, Sanchez-Puerta MV. Elucidating genomic patterns and recombination events in plant cybrid mitochondria. PLANT MOLECULAR BIOLOGY 2019; 100:433-450. [PMID: 30968307 DOI: 10.1007/s11103-019-00869-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/01/2019] [Indexed: 05/17/2023]
Abstract
KEY MESSAGE Cybrid plant mitochondria undergo homologous recombination, mainly BIR, keep a single allele for each gene, and maintain exclusive sequences of each parent and a single copy of the homologous regions. The maintenance of a dynamic equilibrium between the mitochondrial and nuclear genomes requires continuous communication and a high level of compatibility between them, so that alterations in one genetic compartment need adjustments in the other. The co-evolution of nuclear and mitochondrial genomes has been poorly studied, even though the consequences and effects of this interaction are highly relevant for human health, as well as for crop improvement programs and for genetic engineering. The mitochondria of plants represent an excellent system to understand the mechanisms of genomic rearrangements, chimeric gene formation, incompatibility between nucleus and cytoplasm, and horizontal gene transfer. We carried out detailed analyses of the mtDNA of a repeated cybrid between the solanaceae Nicotiana tabacum and Hyoscyamus niger. The mtDNA of the cybrid was intermediate between the size of the parental mtDNAs and the sum of them. Noticeably, most of the homologous sequences inherited from both parents were lost. In contrast, the majority of the sequences exclusive of a single parent were maintained. The mitochondrial gene content included a majority of N. tabacum derived genes, but also chimeric, two-parent derived, and H. niger-derived genes in a tobacco nuclear background. Any of these alterations in the gene content could be the cause of CMS in the cybrid. The parental mtDNAs interacted through 28 homologous recombination events and a single case of illegitimate recombination. Three main homologous recombination mechanisms were recognized in the cybrid mitochondria. Break induced replication (BIR) pathway was the most frequent. We propose that BIR could be one of the mechanisms responsible for the loss of the majority of the repeated regions derived from H. niger.
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Affiliation(s)
- Laura E Garcia
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown 500, M5528AHB, Chacras de Coria, Argentina.
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, 5500, Mendoza, Argentina.
| | - Mikhajlo K Zubko
- Centre for Bioscience, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, M1 5GD, UK
| | - Elena I Zubko
- Centre for Bioscience, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, M1 5GD, UK
| | - M Virginia Sanchez-Puerta
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown 500, M5528AHB, Chacras de Coria, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, 5500, Mendoza, Argentina
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The complete organelle genomes of Physochlaina orientalis: Insights into short sequence repeats across seed plant mitochondrial genomes. Mol Phylogenet Evol 2019; 137:274-284. [PMID: 31112782 DOI: 10.1016/j.ympev.2019.05.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/14/2019] [Accepted: 05/17/2019] [Indexed: 11/24/2022]
Abstract
Short repeats (SR) play an important role in shaping seed plant mitochondrial genomes (mtDNAs). However, their origin, distribution, and relationships across the different plant lineages remain unresolved. We focus on the angiosperm family Solanaceae that shows great variation in repeat content and extend the study to a wide diversity of seed plants. We determined the complete nucleotide sequences of the organellar genomes of the medicinal plant Physochlaina orientalis (Solanaceae), member of the tribe Hyoscyameae. To understand the evolution of the P. orientalis mtDNA we made comparisons with those of five other Solanaceae. P. orientalis mtDNA presents the largest mitogenome (∼685 kb in size) among the Solanaceae and has an unprecedented 8-copy repeat family of ∼8.2 kb in length and a great number of SR arranged in tandem-like structures. We found that the SR in the Solanaceae share a common origin, but these only expanded in members of the tribe Hyoscyameae. We discuss a mechanism that could explain SR formation and expansion in P. orientalis and Hyoscyamus niger. Finally, the great increase in plant mitochondrial data allowed us to systematically extend our repeat analysis to a total of 136 seed plants to characterize and analyze for the first time families of SR among seed plant mtDNAs.
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Genome-scale transfer of mitochondrial DNA from legume hosts to the holoparasite Lophophytum mirabile (Balanophoraceae). Mol Phylogenet Evol 2019; 132:243-250. [DOI: 10.1016/j.ympev.2018.12.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 12/06/2018] [Accepted: 12/06/2018] [Indexed: 11/23/2022]
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Dong S, Zhao C, Chen F, Liu Y, Zhang S, Wu H, Zhang L, Liu Y. The complete mitochondrial genome of the early flowering plant Nymphaea colorata is highly repetitive with low recombination. BMC Genomics 2018; 19:614. [PMID: 30107780 PMCID: PMC6092842 DOI: 10.1186/s12864-018-4991-4] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 08/02/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Mitochondrial genomes of flowering plants (angiosperms) are highly dynamic in genome structure. The mitogenome of the earliest angiosperm Amborella is remarkable in carrying rampant foreign DNAs, in contrast to Liriodendron, the other only known early angiosperm mitogenome that is described as 'fossilized'. The distinctive features observed in the two early flowering plant mitogenomes add to the current confusions of what early flowering plants look like. Expanded sampling would provide more details in understanding the mitogenomic evolution of early angiosperms. Here we report the complete mitochondrial genome of water lily Nymphaea colorata from Nymphaeales, one of the three orders of the earliest angiosperms. RESULTS Assembly of data from Pac-Bio long-read sequencing yielded a circular mitochondria chromosome of 617,195 bp with an average depth of 601×. The genome encoded 41 protein coding genes, 20 tRNA and three rRNA genes with 25 group II introns disrupting 10 protein coding genes. Nearly half of the genome is composed of repeated sequences, which contributed substantially to the intron size expansion, making the gross intron length of the Nymphaea mitochondrial genome one of the longest among angiosperms, including an 11.4-Kb intron in cox2, which is the longest organellar intron reported to date in plants. Nevertheless, repeat mediated homologous recombination is unexpectedly low in Nymphaea evidenced by 74 recombined reads detected from ten recombinationally active repeat pairs among 886,982 repeat pairs examined. Extensive gene order changes were detected in the three early angiosperm mitogenomes, i.e. 38 or 44 events of inversions and translocations are needed to reconcile the mitogenome of Nymphaea with Amborella or Liriodendron, respectively. In contrast to Amborella with six genome equivalents of foreign mitochondrial DNA, not a single horizontal gene transfer event was observed in the Nymphaea mitogenome. CONCLUSIONS The Nymphaea mitogenome resembles the other available early angiosperm mitogenomes by a similarly rich 64-coding gene set, and many conserved gene clusters, whereas stands out by its highly repetitive nature and resultant remarkable intron expansions. The low recombination level in Nymphaea provides evidence for the predominant master conformation in vivo with a highly substoichiometric set of rearranged molecules.
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Affiliation(s)
- Shanshan Dong
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chaoxian Zhao
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
- Department of Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Fei Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanhui Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shouzhou Zhang
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Hong Wu
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Liangsheng Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yang Liu
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
- BGI-Shenzhen, Shenzhen, 518083 China
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Arimura SI, Yanase S, Tsutsumi N, Koizuka N. The mitochondrial genome of an asymmetrically cell-fused rapeseed, Brassica napus, containing a radish-derived cytoplasmic male sterility-associated gene. Genes Genet Syst 2018; 93:143-148. [DOI: 10.1266/ggs.18-00005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Shin-ichi Arimura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Shungo Yanase
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Nobuhiro Tsutsumi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
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Arimura SI. Fission and Fusion of Plant Mitochondria, and Genome Maintenance. PLANT PHYSIOLOGY 2018; 176:152-161. [PMID: 29138352 PMCID: PMC5761811 DOI: 10.1104/pp.17.01025] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/07/2017] [Indexed: 05/18/2023]
Abstract
Dynamic changes maintain a multipartite mitochondrial genome meets the changing needs of plant cells.
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Affiliation(s)
- Shin-Ichi Arimura
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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Gualberto JM, Newton KJ. Plant Mitochondrial Genomes: Dynamics and Mechanisms of Mutation. ANNUAL REVIEW OF PLANT BIOLOGY 2017; 68:225-252. [PMID: 28226235 DOI: 10.1146/annurev-arplant-043015-112232] [Citation(s) in RCA: 231] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The large mitochondrial genomes of angiosperms are unusually dynamic because of recombination activities involving repeated sequences. These activities generate subgenomic forms and extensive genomic variation even within the same species. Such changes in genome structure are responsible for the rapid evolution of plant mitochondrial DNA and for the variants associated with cytoplasmic male sterility and abnormal growth phenotypes. Nuclear genes modulate these processes, and over the past decade, several of these genes have been identified. They are involved mainly in pathways of DNA repair by homologous recombination and mismatch repair, which appear to be essential for the faithful replication of the mitogenome. Mutations leading to the loss of any of these activities release error-prone repair pathways, resulting in increased ectopic recombination, genome instability, and heteroplasmy. We review the present state of knowledge of the genes and pathways underlying mitochondrial genome stability.
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Affiliation(s)
- José M Gualberto
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, 67084 Strasbourg, France;
| | - Kathleen J Newton
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211;
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26
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Kang L, Li P, Wang A, Ge X, Li Z. A Novel Cytoplasmic Male Sterility in Brassica napus (inap CMS) with Carpelloid Stamens via Protoplast Fusion with Chinese Woad. FRONTIERS IN PLANT SCIENCE 2017; 8:529. [PMID: 28428799 PMCID: PMC5382163 DOI: 10.3389/fpls.2017.00529] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 03/24/2017] [Indexed: 05/29/2023]
Abstract
A novel cytoplasmic male sterility (CMS) in Brassica napus (inap CMS) was selected from the somatic hybrid with Isatis indigotica (Chinese woad) by recurrent backcrossing. The male sterility was caused by the conversion of tetradynamous stamens into carpelloid structures with stigmatoid tissues at their tips and ovule-like tissues in the margins, and the two shorter stamens into filaments without anthers. The feminized development of the stamens resulted in the complete lack of pollen grains, which was stable in different years and environments. The pistils of inap CMS displayed normal morphology and good seed-set after pollinated by B. napus. Histological sections showed that the developmental alteration of the stamens initiated at the stage of stamen primordium differentiation. AFLP analysis of the nuclear genomic composition with 23 pairs of selective primers detected no woad DNA bands in inap CMS. Twenty out of 25 mitochondrial genes originated from I. indigotica, except for cox2-2 which was the recombinant between cox2 from woad and cox2-2 from rapeseed. The novel cox2-2 was transcribed in flower buds of inap CMS weakly and comparatively with the fertile B. napus addition line Me harboring one particular woad chromosome. The restorers of other autoplasmic and alloplasmic CMS systems in rapeseed failed to restore the fertility of inap CMS and the screening of B. napus wide resources found no fertility restoration variety, showing its distinct origin and the related mechanism of sterility. The reasons for the mitochondrial rearrangements and the breeding of the restorer for the novel CMS system were discussed.
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27
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Sanchez-Puerta MV, García LE, Wohlfeiler J, Ceriotti LF. Unparalleled replacement of native mitochondrial genes by foreign homologs in a holoparasitic plant. THE NEW PHYTOLOGIST 2017; 214:376-387. [PMID: 27905116 DOI: 10.1111/nph.14361] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 10/27/2016] [Indexed: 05/26/2023]
Abstract
Horizontal gene transfer (HGT) among flowering plant mitochondria occurs frequently and, in most cases, leads to nonfunctional transgenes in the recipient genome. Parasitic plants are particularly prone to this phenomenon, but their mitochondrial genomes (mtDNA) have been largely unexplored. We undertook a large-scale mitochondrial genomic study of the holoparasitic plant Lophophytum mirabile (Balanophoraceae). Comprehensive phylogenetic analyses were performed to address the frequency, origin, and impact of HGT. The sequencing of the complete mtDNA of L. mirabile revealed the unprecedented acquisition of host-derived mitochondrial genes, representing 80% of the protein-coding gene content. All but two of these foreign genes replaced the native homologs and are probably functional in energy metabolism. The genome consists of 54 circular-mapping chromosomes, 25 of which carry no intact genes. The likely functional replacement of up to 26 genes in L. mirabile represents a stunning example of the potential effect of rampant HGT on plant mitochondria. The use of host-derived genes may have a positive effect on the host-parasite relationship, but could also be the result of nonadaptive forces.
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Affiliation(s)
- M Virginia Sanchez-Puerta
- IBAM, Facultad de Ciencias Agrarias, CONICET, Universidad Nacional de Cuyo, Almirante Brown 500, M5528AHB, Chacras de Coria, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, 5500, Mendoza, Argentina
| | - Laura E García
- IBAM, Facultad de Ciencias Agrarias, CONICET, Universidad Nacional de Cuyo, Almirante Brown 500, M5528AHB, Chacras de Coria, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, 5500, Mendoza, Argentina
| | - Josefina Wohlfeiler
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, 5500, Mendoza, Argentina
| | - Luis F Ceriotti
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, 5500, Mendoza, Argentina
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Liberatore KL, Dukowic-Schulze S, Miller ME, Chen C, Kianian SF. The role of mitochondria in plant development and stress tolerance. Free Radic Biol Med 2016; 100:238-256. [PMID: 27036362 DOI: 10.1016/j.freeradbiomed.2016.03.033] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/25/2016] [Accepted: 03/28/2016] [Indexed: 01/03/2023]
Abstract
Eukaryotic cells require orchestrated communication between nuclear and organellar genomes, perturbations in which are linked to stress response and disease in both animals and plants. In addition to mitochondria, which are found across eukaryotes, plant cells contain a second organelle, the plastid. Signaling both among the organelles (cytoplasmic) and between the cytoplasm and the nucleus (i.e. nuclear-cytoplasmic interactions (NCI)) is essential for proper cellular function. A deeper understanding of NCI and its impact on development, stress response, and long-term health is needed in both animal and plant systems. Here we focus on the role of plant mitochondria in development and stress response. We compare and contrast features of plant and animal mitochondrial genomes (mtDNA), particularly highlighting the large and highly dynamic nature of plant mtDNA. Plant-based tools are powerful, yet underutilized, resources for enhancing our fundamental understanding of NCI. These tools also have great potential for improving crop production. Across taxa, mitochondria are most abundant in cells that have high energy or nutrient demands as well as at key developmental time points. Although plant mitochondria act as integrators of signals involved in both development and stress response pathways, little is known about plant mtDNA diversity and its impact on these processes. In humans, there are strong correlations between particular mitotypes (and mtDNA mutations) and developmental differences (or disease). We propose that future work in plants should focus on defining mitotypes more carefully and investigating their functional implications as well as improving techniques to facilitate this research.
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Affiliation(s)
- Katie L Liberatore
- United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108, United States; Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, United States.
| | | | - Marisa E Miller
- United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108, United States; Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, United States
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, United States
| | - Shahryar F Kianian
- United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108, United States; Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, United States
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Cuenca A, Ross TG, Graham SW, Barrett CF, Davis JI, Seberg O, Petersen G. Localized Retroprocessing as a Model of Intron Loss in the Plant Mitochondrial Genome. Genome Biol Evol 2016; 8:2176-89. [PMID: 27435795 PMCID: PMC4987113 DOI: 10.1093/gbe/evw148] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2016] [Indexed: 12/23/2022] Open
Abstract
Loss of introns in plant mitochondrial genes is commonly explained by retroprocessing. Under this model, an mRNA is reverse transcribed and integrated back into the genome, simultaneously affecting the contents of introns and edited sites. To evaluate the extent to which retroprocessing explains intron loss, we analyzed patterns of intron content and predicted RNA editing for whole mitochondrial genomes of 30 species in the monocot order Alismatales. In this group, we found an unusually high degree of variation in the intron content, even expanding the hitherto known variation among angiosperms. Some species have lost some two-third of the cis-spliced introns. We found a strong correlation between intron content and editing frequency, and detected 27 events in which intron loss is consistent with the presence of nucleotides in an edited state, supporting retroprocessing. However, we also detected seven cases of intron loss not readily being explained by retroprocession. Our analyses are also not consistent with the entire length of a fully processed cDNA copy being integrated into the genome, but instead indicate that retroprocessing usually occurs for only part of the gene. In some cases, several rounds of retroprocessing may explain intron loss in genes completely devoid of introns. A number of taxa retroprocessing seem to be very common and a possibly ongoing process. It affects the entire mitochondrial genome.
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Affiliation(s)
- Argelia Cuenca
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - T Gregory Ross
- Department of Botany, 6270 University Boulevard, University of British Columbia, Vancouver, British Columbia, Canada UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean W Graham
- Department of Botany, 6270 University Boulevard, University of British Columbia, Vancouver, British Columbia, Canada UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Craig F Barrett
- Department of Biological Sciences, California State University, Los Angeles, California
| | - Jerrold I Davis
- L.H. Bailey Hortorium and Plant Biology Section, Cornell University, Ithaca, New York
| | - Ole Seberg
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Gitte Petersen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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30
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Abstract
We report cell-to-cell movement of mitochondria through a graft junction. Mitochondrial movement was discovered in an experiment designed to select for chloroplast transfer from Nicotiana sylvestris into Nicotiana tabacum cells. The alloplasmic N. tabacum line we used carries Nicotiana undulata cytoplasmic genomes, and its flowers are male sterile due to the foreign mitochondrial genome. Thus, rare mitochondrial DNA transfer from N. sylvestris to N. tabacum could be recognized by restoration of fertile flower anatomy. Analyses of the mitochondrial genomes revealed extensive recombination, tentatively linking male sterility to orf293, a mitochondrial gene causing homeotic conversion of anthers into petals. Demonstrating cell-to-cell movement of mitochondria reconstructs the evolutionary process of horizontal mitochondrial DNA transfer and enables modification of the mitochondrial genome by DNA transmitted from a sexually incompatible species. Conversion of anthers into petals is a visual marker that can be useful for mitochondrial transformation.
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31
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Wu Z, Stone JD, Štorchová H, Sloan DB. High transcript abundance, RNA editing, and small RNAs in intergenic regions within the massive mitochondrial genome of the angiosperm Silene noctiflora. BMC Genomics 2015; 16:938. [PMID: 26573088 PMCID: PMC4647634 DOI: 10.1186/s12864-015-2155-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 10/27/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Species within the angiosperm genus Silene contain the largest mitochondrial genomes ever identified. The enormity of these genomes (up to 11 Mb in size) appears to be the result of increased non-coding DNA, which represents >99 % of the genome content. These genomes are also fragmented into dozens of circular-mapping chromosomes, some of which contain no identifiable genes, raising questions about if and how these 'empty' chromosomes are maintained by selection. To assess the possibility that they contain novel and unannotated functional elements, we have performed RNA-seq to analyze the mitochondrial transcriptome of Silene noctiflora. RESULTS We identified regions of high transcript abundance in almost every chromosome in the mitochondrial genome including those that lack any annotated genes. In some cases, these transcribed regions exhibited higher expression levels than some core mitochondrial protein-coding genes. We also identified RNA editing sites throughout the genome, including 97 sites that were outside of protein-coding gene sequences and found in pseudogenes, introns, UTRs, and transcribed intergenic regions. Unlike in protein-coding sequences, however, most of these RNA editing sites were only edited at intermediate frequencies. Finally, analysis of mitochondrial small RNAs indicated that most were likely degradation products from longer transcripts, but we did identify candidates for functional small RNAs that mapped to intergenic regions and were not associated with longer RNA transcripts. CONCLUSIONS Our findings demonstrate transcriptional activity in many localized regions within the extensive intergenic sequence content in the S. noctiflora mitochondrial genome, supporting the possibility that the genome contains previously unidentified functional elements. However, transcription by itself is not proof of functional importance, and we discuss evidence that some of the observed transcription and post-transcriptional modifications are non-adaptive. Therefore, further investigations are required to determine whether any of the identified transcribed regions have played a functional role in the proliferation and maintenance of the enormous non-coding regions in Silene mitochondrial genomes.
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Affiliation(s)
- Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - James D Stone
- Institute of Experimental Botany v.v.i, Czech Academy of Sciences, Prague, Lysolaje, 16502, Czech Republic
| | - Helena Štorchová
- Institute of Experimental Botany v.v.i, Czech Academy of Sciences, Prague, Lysolaje, 16502, Czech Republic
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA.
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Tang M, Chen Z, Grover CE, Wang Y, Li S, Liu G, Ma Z, Wendel JF, Hua J. Rapid evolutionary divergence of Gossypium barbadense and G. hirsutum mitochondrial genomes. BMC Genomics 2015; 16:770. [PMID: 26459858 PMCID: PMC4603758 DOI: 10.1186/s12864-015-1988-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 10/06/2015] [Indexed: 11/10/2022] Open
Abstract
Background The mitochondrial genome from upland cotton, G. hirsutum, was previously sequenced. To elucidate the evolution of mitochondrial genomic diversity within a single genus, we sequenced the mitochondrial genome from Sea Island cotton (Gossypium barbadense L.). Methods Mitochondrial DNA from week-old etiolated seedlings was extracted from isolated organelles using discontinuous sucrose density gradient method. Mitochondrial genome was sequenced with Solexa using paired-end, 90 bp read. The clean reads were assembled into contigs using ABySS and finished via additional fosmid and BAC sequencing. Finally, the genome was annotated and analyzed using different softwares. Results The G. barbadense (Sea Island cotton) mitochondrial genome was fully sequenced (677,434-bp) and compared to the mitogenome of upland cotton. The G. barbadense mitochondrial DNA contains seven more genes than that of upland cotton, with a total of 40 protein coding genes (excluding possible pseudogenes), 6 rRNA genes, and 29 tRNA genes. Of these 75 genes, atp1, mttB, nad4, nad9, rrn5, rrn18, and trnD(GTC)-cp were each represented by two identical copies. A single 64 kb repeat was largely responsible for the 9 % difference in genome size between the two mtDNAs. Comparison of genome structures between the two mitochondrial genomes revealed 8 rearranged syntenic regions and several large repeats. The largest repeat was missing from the master chromosome in G. hirsutum. Both mitochondrial genomes contain a duplicated copy of rps3 (rps3-2) in conjunction with a duplication of repeated sequences. Phylogenetic and divergence considerations suggest that a 544-bp fragment of rps3 was transferred to the nuclear genome shortly after divergence of the A- and D- genome diploid cottons. Conclusion These results highlight the insights to the evolution of structural variation between Sea Island and upland cotton mitochondrial genomes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1988-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mingyong Tang
- Department of Plant Genetics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education /Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
| | - Zhiwen Chen
- Department of Plant Genetics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education /Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
| | - Corrinne E Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA50011, USA.
| | - Yumei Wang
- Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China.
| | - Shuangshuang Li
- Present address: Saskatchewan Cancer Agency, Division of Oncology, Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
| | - Guozheng Liu
- Present address: Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt, Seeland, Germany.
| | - Zhiying Ma
- College of Agronomy, Hebei Agricultural University, Baoding, 071001, Hebei, China.
| | - Jonathan F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA50011, USA.
| | - Jinping Hua
- Department of Plant Genetics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education /Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
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Govindarajulu R, Parks M, Tennessen JA, Liston A, Ashman TL. Comparison of nuclear, plastid, and mitochondrial phylogenies and the origin of wild octoploid strawberry species. AMERICAN JOURNAL OF BOTANY 2015; 102:544-554. [PMID: 25878088 DOI: 10.3732/ajb.1500026] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/05/2015] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY Molecular phylogenies derived from all three plant genomes can provide insight into the evolutionary history of plant groups influenced by reticulation. We sought to reconstruct mitochondrial exome, chloroplast, and nuclear genome phylogenies for octoploid Fragaria and their diploid ancestors and to document patterns of incongruence between and within the cytoplasmic genomes and interpret these in the context of evolutionary origin of the octoploid strawberries. METHODS Using a genome-skimming approach, we assembled chloroplast genomes and mitochondrial exomes, and we used the POLiMAPS method to assemble nuclear sequence for octoploid species and constructed phylogenies from all three genomes. We assessed incongruence between and within cytoplasmic genomes using topology-based phylogenetic incongruence tests. KEY RESULTS The incongruent cytoplasmic genome phylogeny with respect to the placement of octoploids suggests potential breakage in linkage disequilibrium of cytoplasmic genomes during allopolyploid origin of the octoploids. Furthermore, a single mitochondrial chimeric gene with a putative role in cytoplasmic male sterility yields a phylogeny that is inconsistent with the rest of the mitochondrial genome but consistent with the chloroplast phylogeny, suggesting intracellular gene transfer between heteroplasmic mitochondria, possibly driven by selection to overcome the effects of mito-nuclear incompatibility in octoploid origins. CONCLUSIONS This work expands on the current understanding of evolutionary history of the octoploid ancestors of cultivated strawberry. It demonstrates phylogenetic incongruence between cytoplasmic genomes in octoploids with respect to diploid ancestors, indicating breakage in linkage disequilibrium of cytoplasmic genomes. We discuss potential organism-level processes that may have contributed to the observed incongruence in Fragaria.
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Affiliation(s)
| | - Matthew Parks
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 USA
| | - Jacob A Tennessen
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon 97331 USA
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260 USA
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Yant L. When two is a crowd: mitochondrial genome merger and its aftermath. THE NEW PHYTOLOGIST 2015; 206:8-9. [PMID: 25711245 DOI: 10.1111/nph.13321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Levi Yant
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA
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