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Gorbenko IV, Tarasenko VI, Garnik EY, Yakovleva TV, Katyshev AI, Belkov VI, Orlov YL, Konstantinov YM, Koulintchenko MV. Overexpression of RPOTmp Being Targeted to Either Mitochondria or Chloroplasts in Arabidopsis Leads to Overall Transcriptome Changes and Faster Growth. Int J Mol Sci 2024; 25:8164. [PMID: 39125738 PMCID: PMC11312007 DOI: 10.3390/ijms25158164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/18/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
The transcription of Arabidopsis organellar genes is performed by three nuclear-encoded RNA polymerases: RPOTm, RPOTmp, and RPOTp. The RPOTmp protein possesses ambiguous transit peptides, allowing participation in gene expression control in both mitochondria and chloroplasts, although its function in plastids is still under discussion. Here, we show that the overexpression of RPOTmp in Arabidopsis, targeted either to mitochondria or chloroplasts, disturbs the dormant seed state, and it causes the following effects: earlier germination, decreased ABA sensitivity, faster seedling growth, and earlier flowering. The germination of RPOTmp overexpressors is less sensitive to NaCl, while rpotmp knockout is highly vulnerable to salt stress. We found that mitochondrial dysfunction in the rpotmp mutant induces an unknown retrograde response pathway that bypasses AOX and ANAC017. Here, we show that RPOTmp transcribes the accD, clpP, and rpoB genes in plastids and up to 22 genes in mitochondria.
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Affiliation(s)
- Igor V. Gorbenko
- Siberian Institute of Plant Physiology and Biochemistry of Siberian Branch of Russian Academy of Sciences, Irkutsk 664033, Russia; (V.I.T.); (T.V.Y.); (A.I.K.); (Y.M.K.); (M.V.K.)
| | - Vladislav I. Tarasenko
- Siberian Institute of Plant Physiology and Biochemistry of Siberian Branch of Russian Academy of Sciences, Irkutsk 664033, Russia; (V.I.T.); (T.V.Y.); (A.I.K.); (Y.M.K.); (M.V.K.)
| | - Elena Y. Garnik
- Siberian Institute of Plant Physiology and Biochemistry of Siberian Branch of Russian Academy of Sciences, Irkutsk 664033, Russia; (V.I.T.); (T.V.Y.); (A.I.K.); (Y.M.K.); (M.V.K.)
| | - Tatiana V. Yakovleva
- Siberian Institute of Plant Physiology and Biochemistry of Siberian Branch of Russian Academy of Sciences, Irkutsk 664033, Russia; (V.I.T.); (T.V.Y.); (A.I.K.); (Y.M.K.); (M.V.K.)
| | - Alexander I. Katyshev
- Siberian Institute of Plant Physiology and Biochemistry of Siberian Branch of Russian Academy of Sciences, Irkutsk 664033, Russia; (V.I.T.); (T.V.Y.); (A.I.K.); (Y.M.K.); (M.V.K.)
| | - Vadim I. Belkov
- Siberian Institute of Plant Physiology and Biochemistry of Siberian Branch of Russian Academy of Sciences, Irkutsk 664033, Russia; (V.I.T.); (T.V.Y.); (A.I.K.); (Y.M.K.); (M.V.K.)
| | - Yuriy L. Orlov
- The Digital Health Center, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow 119991, Russia
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia, Moscow 117198, Russia
| | - Yuri M. Konstantinov
- Siberian Institute of Plant Physiology and Biochemistry of Siberian Branch of Russian Academy of Sciences, Irkutsk 664033, Russia; (V.I.T.); (T.V.Y.); (A.I.K.); (Y.M.K.); (M.V.K.)
- Biosoil Department, Irkutsk State University, Irkutsk 664003, Russia
| | - Milana V. Koulintchenko
- Siberian Institute of Plant Physiology and Biochemistry of Siberian Branch of Russian Academy of Sciences, Irkutsk 664033, Russia; (V.I.T.); (T.V.Y.); (A.I.K.); (Y.M.K.); (M.V.K.)
- Kazan Institute of Biochemistry and Biophysics of the Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences” (KIBB FRC KazSC RAS), Kazan 420111, Russia
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Hao Z, Jiang X, Pan L, Guo J, Chen Y, Li J, Liu B, Guo A, Luo L, Jia R. The complete mitochondrial genome of Pontederia crassipes: using HiFi reads to investigate genome recombination and gene transfer from chloroplast genome. FRONTIERS IN PLANT SCIENCE 2024; 15:1407309. [PMID: 39006960 PMCID: PMC11240117 DOI: 10.3389/fpls.2024.1407309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/12/2024] [Indexed: 07/16/2024]
Abstract
Water hyacinth (Pontederia crassipes Mart.) is a monocotyledonous aquatic plant renowned for its rapid growth, extensive proliferation, biological invasiveness, and ecological resilience to variations in pH, nutrients, and temperature. The International Union for Conservation of Nature (IUCN) has listed P. crassipes among the top 100 invasive species. However, comprehensive genomic information, particularly concerning its mitochondrial genome (mitogenome), remains surprisingly limited. In this study, the complete mitogenome of P. crassipes was analyzed using bioinformatics approaches. The mitogenome is 399,263 bp long and contains 38 protein-coding genes (PCGs), 24 tRNA genes, and 3 rRNA genes. Sequence analysis revealed that the complete mitogenome of the species contains 3,289 dispersed repeats, and 765 RNA editing sites in protein-coding genes. The P. crassipes mitogenome possessed un-conserved structures, including extensive sequence transfer between its chloroplasts and mitochondria. Our study on the mitogenome of P. crassipes offers critical insights into its evolutionary patterns and phylogenetic relationships with related taxa. This research enhances our understanding of this invasive species, known for its significant biomass and rapid overgrowth in aquatic environments.
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Affiliation(s)
- Zhigang Hao
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
- Hainan Seed Industry Laboratory, Sanya, Hainan, China
- Department of Plant Pathology, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Xiaoqi Jiang
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Lei Pan
- CAIQ Center for Biosafety in Sanya, Sanya, Hainan, China
| | - Jingyuan Guo
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Yi Chen
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Jianqiang Li
- Department of Plant Pathology, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Biao Liu
- Ministry of Ecology and Environment, Nanjing Institute of Environmental Sciences, Nanjing, China
| | - Anping Guo
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Laixin Luo
- Department of Plant Pathology, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Ruizong Jia
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
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Hao Z, Zhang Z, Zhang J, Cui X, Li J, Luo L, Li Y. The complete mitochondrial genome of Aglaia odorata, insights into its genomic structure and RNA editing sites. FRONTIERS IN PLANT SCIENCE 2024; 15:1362045. [PMID: 38510436 PMCID: PMC10950942 DOI: 10.3389/fpls.2024.1362045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/21/2024] [Indexed: 03/22/2024]
Abstract
Aglaia odorata, native to Guangdong, Guangxi, and Hainan provinces in China, has long been utilized as an herbal remedy in ancient China. In this study, we assembled and annotated the complete mitochondrial genome (mitogenome) of A. odorata, which spans a total length of 537,321 bp. Conformation of the A. odorata recombination was verified through PCR experiments and Sanger sequencing. We identified and annotated 35 protein-coding genes (PCGs), 22 tRNA genes, and 3 rRNA genes within the mitogenome. Analysis of repeated elements revealed the presence of 192 SSRs, 29 pairs of tandem repeats, and 333 pairs of dispersed repeats in the A. odorata mitogenome. Additionally, we analyzed codon usage and mitochondrial plastid DNAs (MTPTs). Twelve MTPTs between the plastome and mitogenome of A. odorata were identified, with a combined length of 2,501 bp, accounting for 0.47% of the mitogenome. Furthermore, 359 high-confidence C to U RNA editing sites were predicted on PCGs, and four selected RNA editing sites were specially examined to verify the creation of start and/or stop codons. Extensive genomic rearrangement was observed between A. odorata and related mitogenomes. Phylogenetic analysis based on mitochondrial PCGs were conducted to elucidate the evolutionary relationships between A. odorata and other angiosperms.
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Affiliation(s)
- Zhigang Hao
- Department of Pesticide Science, State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, China
- Sanya Institute of China Agricultural University, Sanya, Hainan, China
- Hainan Seed Industry Laboratory, Sanya, Hainan, China
| | - Zhiping Zhang
- Department of Pesticide Science, State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Jinan Zhang
- Sanya Institute of China Agricultural University, Sanya, Hainan, China
| | - Xiufen Cui
- Hainan Seed Industry Laboratory, Sanya, Hainan, China
- Department of Plant Pathology, Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, China
| | - Jianqiang Li
- Hainan Seed Industry Laboratory, Sanya, Hainan, China
- Department of Plant Pathology, Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, China
| | - Laixin Luo
- Hainan Seed Industry Laboratory, Sanya, Hainan, China
- MOA Key Lab of Pest Monitoring and Green Management, China Agricultural University, Beijing, China
| | - Yingbin Li
- Department of Pesticide Science, State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, China
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Liu J, Hu JY, Li DZ. Remarkable mitochondrial genome heterogeneity in Meniocus linifolius (Brassicaceae). PLANT CELL REPORTS 2024; 43:36. [PMID: 38200362 DOI: 10.1007/s00299-023-03102-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/06/2023] [Indexed: 01/12/2024]
Abstract
KEY MESSAGE Detailed analyses of 16 genomes identified a remarkable acceleration of mutation rate, hence mitochondrial sequence and structural heterogeneity, in Meniocus linifolius (Brassicaceae). The powerhouse, mitochondria, in plants feature high levels of structural variation, while the encoded genes are normally conserved. However, the substitution rates and spectra of mitochondria DNA within the Brassicaceae, a family with substantial scientific and economic importance, have not been adequately deciphered. Here, by analyzing three newly assembled and 13 known mitochondrial genomes (mitogenomes), we report the highly variable genome structure and mutation rates in Brassicaceae. The genome sizes and GC contents are 196,604 bp and 46.83%, 288,122 bp and 44.79%, and 287,054 bp and 44.93%, for Meniocus linifolius (Mli), Crucihimalaya lasiocarpa (Cla), and Lepidium sativum (Lsa), respectively. In total, 29, 33, and 34 protein-coding genes (PCGs) and 14, 18, and 18 tRNAs are annotated for Mli, Cla, and Lsa, respectively, while all mitogenomes contain one complete circular molecule with three rRNAs and abundant RNA editing sites. The Mli mitogenome features four conformations likely mediated by the two pairs of long repeats, while at the same time seems to have an unusual evolutionary history due to higher GC content, loss of more genes and sequences, but having more repeats and plastid DNA insertions. Corroborating with these, an ambiguous phylogenetic position with long branch length and elevated synonymous substitution rate in nearly all PCGs are observed for Mli. Taken together, our results reveal a high level of mitogenome heterogeneity at the family level and provide valuable resources for further understanding the evolutionary pattern of organelle genomes in Brassicaceae.
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Affiliation(s)
- Jie Liu
- CAS Key Laboratory for Plant Diversity, Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jin-Yong Hu
- CAS Key Laboratory for Plant Diversity, Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
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Wang M, Yu W, Yang J, Hou Z, Li C, Niu Z, Zhang B, Xue Q, Liu W, Ding X. Mitochondrial genome comparison and phylogenetic analysis of Dendrobium (Orchidaceae) based on whole mitogenomes. BMC PLANT BIOLOGY 2023; 23:586. [PMID: 37993773 PMCID: PMC10666434 DOI: 10.1186/s12870-023-04618-9] [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: 02/21/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023]
Abstract
BACKGROUND Mitochondrial genomes are essential for deciphering the unique evolutionary history of seed plants. However, the rules of their extreme variation in genomic size, multi-chromosomal structure, and foreign sequences remain unresolved in most plant lineages, which further hindered the application of mitogenomes in phylogenetic analyses. RESULTS Here, we took Dendrobium (Orchidaceae) which shows the great divergence of morphology and difficulty in species taxonomy as the study focus. We first de novo assembled two complete mitogenomes of Dendrobium wilsonii and Dendrobium henanense that were 763,005 bp and 807,551 bp long with multichromosomal structures. To understand the evolution of Dendrobium mitogenomes, we compared them with those of four other orchid species. The results showed great variations of repetitive and chloroplast-derived sequences in Dendrobium mitogenomes. Moreover, the intergenic content of Dendrobium mitogenomes has undergone expansion during evolution. We also newly sequenced mitogenomes of 26 Dendrobium species and reconstructed phylogenetic relationships of Dendrobium based on genomic mitochondrial and plastid data. The results indicated that the existence of chloroplast-derived sequences made the mitochondrial phylogeny display partial characteristics of the plastid phylogeny. Additionally, the mitochondrial phylogeny provided new insights into the phylogenetic relationships of Dendrobium species. CONCLUSIONS Our study revealed the evolution of Dendrobium mitogenomes and the potential of mitogenomes in deciphering phylogenetic relationships at low taxonomic levels.
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Grants
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
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Affiliation(s)
- Mengting Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
- Ningbo Key Laboratory of Agricultural Germplasm Resources Mining and Environmental Regulation, College of Science and Technology, Ningbo University, Cixi, China
| | - Wenhui Yu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jiapeng Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhenyu Hou
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Chao Li
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhitao Niu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Benhou Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qingyun Xue
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wei Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoyu Ding
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
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Zhu H, Shan Y, Li J, Zhang X, Yu J, Wang H. Assembly and comparative analysis of the complete mitochondrial genome of Viburnum chinshanense. BMC PLANT BIOLOGY 2023; 23:487. [PMID: 37821817 PMCID: PMC10566092 DOI: 10.1186/s12870-023-04493-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND Viburnum chinshanense is an endemic species found exclusively in the North-Central and South-Central regions of China. This species is a lush garden ornamental tree and is extensively utilized for vegetation restoration in rocky desertification areas. RESULTS In this study, we obtained 13.96 Gb of Oxford Nanopore data for the whole genome, and subsequently, by combining Illumina short-reads, we successfully assembled the complete mitochondrial genome (mitogenome) of the V. chinshanense using a hybrid assembly strategy. The assembled genome can be described as a circular genome. The total length of the V. chinshanense mitogenome measures 643,971 bp, with a GC content of 46.18%. Our annotation efforts have revealed a total of 39 protein-coding genes (PCGs), 28 tRNA genes, and 3 rRNA genes within the V. chinshanense mitogenome. The analysis of repeated elements has identified 212 SSRs, 19 long tandem repeat elements, and 325 pairs of dispersed repeats in the V. chinshanense mitogenome. Additionally, we have investigated mitochondrial plastid DNAs (MTPTs) and identified 21 MTPTs within the mitogenome and plastidial genome. These MTPTs collectively span a length of 9,902 bp, accounting for 1.54% of the mitogenome. Moreover, employing Deepred-mt, we have confidently predicted 623 C to U RNA editing sites across the 39 protein-coding genes. Furthermore, extensive genomic rearrangements have been observed between V. chinshanense and the mitogenomes of related species. Interestingly, we have also identified a bacterial-derived tRNA gene (trnC-GCA) in the V. chinshanense mitogenome. Lastly, we have inferred the phylogenetic relationships of V. chinshanense with other angiosperms based on mitochondrial PCGs. CONCLUSIONS This study marks the first report of a mitogenome from the Viburnum genus, offering a valuable genomic resource for exploring the evolution of mitogenomes within the Dipsacales order.
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Affiliation(s)
- Haoxiang Zhu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing, 400715, China
| | - Yuanyu Shan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Xue Zhang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China.
| | - Haiyang Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China.
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing, 400715, China.
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Ni Y, Zhang X, Li J, Lu Q, Chen H, Ma B, Liu C. Genetic diversity of Coffea arabica L. mitochondrial genomes caused by repeat- mediated recombination and RNA editing. FRONTIERS IN PLANT SCIENCE 2023; 14:1261012. [PMID: 37885664 PMCID: PMC10598636 DOI: 10.3389/fpls.2023.1261012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023]
Abstract
Background Coffea arabica L. is one of the most important crops widely cultivated in 70 countries across Asia, Africa, and Latin America. Mitochondria are essential organelles that play critical roles in cellular respiration, metabolism, and differentiation. C. arabica's nuclear and chloroplast genomes have been reported. However, its mitochondrial genome remained unreported. Here, we intended to sequence and characterize its mitochondrial genome to maximize the potential of its genomes for evolutionary studies, molecular breeding, and molecular marker developments. Results We sequenced the total DNA of C. arabica using Illumina and Nanopore platforms. We then assembled the mitochondrial genome with a hybrid strategy using Unicycler software. We found that the mitochondrial genome comprised two circular chromosomes with lengths of 867,678 bp and 153,529 bp, encoding 40 protein-coding genes, 26 tRNA genes, and three rRNA genes. We also detected 270 Simple Sequence Repeats and 34 tandem repeats in the mitochondrial genome. We found 515 high-scoring sequence pairs (HSPs) for a self-to-self similarity comparison using BLASTn. Three HSPs were found to mediate recombination by the mapping of long reads. Furthermore, we predicted 472 using deep-mt with the convolutional neural network model. Then we randomly validated 90 RNA editing events by PCR amplification and Sanger sequencing, with the majority being non-synonymous substitutions and only three being synonymous substitutions. These findings provide valuable insights into the genetic characteristics of the C. arabica mitochondrial genome, which can be helpful for future study on coffee breeding and mitochondrial genome evolution. Conclusion Our study sheds new light on the evolution of C. arabica organelle genomes and their potential use in genetic breeding, providing valuable data for developing molecular markers that can improve crop productivity and quality. Furthermore, the discovery of RNA editing events in the mitochondrial genome of C. arabica offers insights into the regulation of gene expression in this species, contributing to a better understanding of coffee genetics and evolution.
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Affiliation(s)
| | | | | | | | | | | | - Chang Liu
- Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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Liu H, Hou Z, Xu L, Ma Q, Wei M, Tembrock LR, Zhang S, Wu Z. Comparative analysis of organellar genomes between diploid and tetraploid Chrysanthemum indicum with its relatives. FRONTIERS IN PLANT SCIENCE 2023; 14:1228551. [PMID: 37662149 PMCID: PMC10471889 DOI: 10.3389/fpls.2023.1228551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/28/2023] [Indexed: 09/05/2023]
Abstract
Chrysanthemum indicum, a species native to Eastern Asia is well known as one of the progenitor species of the cultivated Chrysanthemum which is grown for its ornamental and medicinal value. Previous genomic studies on Chrysanthemum have largely ignored the dynamics of plastid genome (plastome) and mitochondria genome (mitogenome) evolution when analyzing this plant lineage. In this study, we sequenced and assembled the plastomes and mitogenomes of diploid and tetraploid C. indicum as well as the morphologically divergent variety C. indicum var. aromaticum. We used published data from 27 species with both plastome and mitogenome complete sequences to explore differences in sequence evolution between the organellar genomes. The size and structure of organellar genome between diploid and tetraploid C. indicum were generally similar but the tetraploid C. indicum and C. indicum var. aromaticum were found to contain unique sequences in the mitogenomes which also contained previously undescribed open reading frames (ORFs). Across Chrysanthemum mitogenome structure varied greatly but sequences transferred from plastomes in to the mitogenomes were conserved. Finally, differences observed between mitogenome and plastome gene trees may be the result of the difference in the rate of sequence evolution between genes in these two genomes. In total the findings presented here greatly expand the resources for studying Chrysanthemum organellar genome evolution with possible applications to conservation, breeding, and gene banking in the future.
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Affiliation(s)
- Huihui Liu
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen, China
| | - Zhuangwei Hou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Lei Xu
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen, China
| | - Qing Ma
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen, China
| | - Min Wei
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen, China
| | - Luke R. Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Shuo Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
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Shan Y, Li J, Zhang X, Yu J. The complete mitochondrial genome of Amorphophallus albus and development of molecular markers for five Amorphophallus species based on mitochondrial DNA. FRONTIERS IN PLANT SCIENCE 2023; 14:1180417. [PMID: 37416891 PMCID: PMC10322194 DOI: 10.3389/fpls.2023.1180417] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023]
Abstract
Introduction Amorphophallus albus is an herbaceous, cormous, perennial plant used as a food source and traditional medicine in Asia. Methods In this study, we assembled and annotated the complete mitochondrial genome (mitogenome) of A. albus. Then we analyzed the repeated elements and mitochondrial plastid sequences (MTPTs), predicted RNA editing sites in mitochondrial protein-coding genes (PCGs). Lastly, we inferred the phylogenetic relationships of A. albus and other angiosperms based on mitochondrial PCGs, and designed two molecular markers based on mitochondrial DNA. Results and discussion The complete mitogenome of A. albus consists of 19 circular chromosomes. And the total length of A. albus mitogenome is 537,044 bp, with the longest chromosome measuring 56,458 bp and the shortest measuring 12,040 bp. We identified and annotated a total of 36 protein-coding genes (PCGs), 21 tRNA genes, and 3 rRNA genes in the mitogenome. Additionally, we analyzed mitochondrial plastid DNAs (MTPTs) and identified 20 MTPTs between the two organelle genomes, with a combined length of 22,421 bp, accounting for 12.76% of the plastome. Besides, we predicted a total of 676 C to U RNA editing sites on 36 protein-coding genes of high confidence using Deepred-mt. Furthermore, extensive genomic rearrangement was observed between A. albus and the related mitogenomes. We conducted phylogenetic analyses based on mitochondrial PCGs to determine the evolutionary relationships between A. albus and other angiosperms. Finally, we developed and validated two molecular markers, Ai156 and Ai976, based on two intron regions (nad2i156 and nad4i976) respectively. The discrimination success rate was 100 % in validation experiments for five widely grown konjac species. Our results reveal the multi-chromosome mitogenome of A. albus, and the developed markers will facilitate molecular identification of this genus.
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Zhang X, Shan Y, Li J, Qin Q, Yu J, Deng H. Assembly of the Complete Mitochondrial Genome of Pereskia aculeata Revealed That Two Pairs of Repetitive Elements Mediated the Recombination of the Genome. Int J Mol Sci 2023; 24:ijms24098366. [PMID: 37176072 PMCID: PMC10179450 DOI: 10.3390/ijms24098366] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
Pereskia aculeata is a potential new crop species that has both food and medicinal (antinociceptive activity) properties. However, comprehensive genomic research on P. aculeata is still lacking, particularly concerning its organelle genome. In this study, P. aculeata was studied to sequence the mitochondrial genome (mitogenome) and to ascertain the assembly, informational content, and developmental expression of the mitogenome. The findings revealed that the mitogenome of P. aculeata is circular and measures 515,187 bp in length with a GC content of 44.05%. It contains 52 unique genes, including 33 protein-coding genes, 19 tRNA genes, and three rRNA genes. Additionally, the mitogenome analysis identified 165 SSRs, primarily consisting of tetra-nucleotides, and 421 pairs of dispersed repeats with lengths greater than or equal to 30, which were mainly forward repeats. Based on long reads and PCR experiments, we confirmed that two pairs of long-fragment repetitive elements were highly involved with the mitogenome recombination process. Furthermore, there were 38 homologous fragments detected between the mitogenome and chloroplast genome, and the longest fragment was 3962 bp. This is the first report on the mitogenome in the family Cactaceae. The decoding of the mitogenome of P. aculeata will provide important genetic materials for phylogenetic studies of Cactaceae and promote the utilization of species germplasm resources.
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Affiliation(s)
- Xue Zhang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
| | - Yuanyu Shan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
| | - Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
| | - Qiulin Qin
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Southwest University, Chongqing 400715, China
| | - Hongping Deng
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing 400715, China
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11
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Wang L, Fan L, Zhao Z, Zhang Z, Jiang L, Chai M, Tian C. The Capparis spinosa var. herbacea genome provides the first genomic instrument for a diversity and evolution study of the Capparaceae family. Gigascience 2022; 11:giac106. [PMID: 36310248 PMCID: PMC9618406 DOI: 10.1093/gigascience/giac106] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/17/2022] [Accepted: 10/13/2022] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND The caper bush Capparis spinosa L., one of the most economically important species of Capparaceae, is a xerophytic shrub that is well adapted to drought and harsh environments. However, genetic studies on this species are limited because of the lack of its reference genome. FINDINGS We sequenced and assembled the Capparis spinosa var. herbacea (Willd.) genome using data obtained from the combination of PacBio circular consensus sequencing and high-throughput chromosome conformation capture. The final genome assembly was approximately 274.53 Mb (contig N50 length of 9.36 Mb, scaffold N50 of 15.15 Mb), 99.23% of which was assigned to 21 chromosomes. In the whole-genome sequence, tandem repeats accounted for 19.28%, and transposable element sequences accounted for 43.98%. The proportion of tandem repeats in the C. spinosa var. herbacea genome was much higher than the average of 8.55% in plant genomes. A total of 21,577 protein-coding genes were predicted, with 98.82% being functionally annotated. The result of species divergence times showed that C. spinosa var. herbacea and Tarenaya hassleriana separated from a common ancestor 43.31 million years ago. CONCLUSIONS This study reported a high-quality reference genome assembly and genome features for the Capparaceae family. The assembled C. spinosa var. herbacea genome might provide a system for studying the diversity, speciation, and evolution of this family and serve as an important resource for understanding the mechanism of drought and high-temperature resistance.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liqiang Fan
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China
| | - Zhenyong Zhao
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhibin Zhang
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China
| | - Li Jiang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mao Chai
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China
| | - Changyan Tian
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Wu C, Chaw S. Evolution of mitochondrial RNA editing in extant gymnosperms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1676-1687. [PMID: 35877596 PMCID: PMC9545813 DOI: 10.1111/tpj.15916] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 06/01/2023]
Abstract
To unveil the evolution of mitochondrial RNA editing in gymnosperms, we characterized mitochondrial genomes (mitogenomes), plastid genomes, RNA editing sites, and pentatricopeptide repeat (PPR) proteins from 10 key taxa representing four of the five extant gymnosperm clades. The assembled mitogenomes vary in gene content due to massive gene losses in Gnetum and Conifer II clades. Mitochondrial gene expression levels also vary according to protein function, with the most highly expressed genes involved in the respiratory complex. We identified 9132 mitochondrial C-to-U editing sites, as well as 2846 P-class and 8530 PLS-class PPR proteins. Regains of editing sites were demonstrated in Conifer II rps3 transcripts whose corresponding mitogenomic sequences lack introns due to retroprocessing. Our analyses reveal that non-synonymous editing is efficient and results in more codons encoding hydrophobic amino acids. In contrast, synonymous editing, although performed with variable efficiency, can increase the number of U-ending codons that are preferentially utilized in gymnosperm mitochondria. The inferred loss-to-gain ratio of mitochondrial editing sites in gymnosperms is 2.1:1, of which losses of non-synonymous editing are mainly due to genomic C-to-T substitutions. However, such substitutions only explain a small fraction of synonymous editing site losses, indicating distinct evolutionary mechanisms. We show that gymnosperms have experienced multiple lineage-specific duplications in PLS-class PPR proteins. These duplications likely contribute to accumulated RNA editing sites, as a mechanistic correlation between RNA editing and PLS-class PPR proteins is statistically supported.
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Affiliation(s)
- Chung‐Shien Wu
- Biodiversity Research CenterAcademia SinicaTaipei11529Taiwan
| | - Shu‐Miaw Chaw
- Biodiversity Research CenterAcademia SinicaTaipei11529Taiwan
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Characterization of the mitochondrial genome of Cucumis hystrix and comparison with other cucurbit crops. Gene 2022; 823:146342. [PMID: 35219813 DOI: 10.1016/j.gene.2022.146342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/28/2022] [Accepted: 02/14/2022] [Indexed: 11/20/2022]
Abstract
The mitochondria ofCucumis genus contain several intriguing features such as paternal inheritance and three-ring genome structure. However, the evolutionary relationships of mitochondria inCucumisremain elusive. Here, we assembled the mitochondrial genome ofC. hystrixand performed a comparative genomic analysis with other crops inthe Cucurbitaceae. The mitochondrial genome ofC. hystrixhas three circular-mapping chromosomes of lengths 1,113,461 bp, 110,683 bp, and 92,288 bp, which contain 73 genes including 38 protein-coding genes, 31tRNAgenes, and 4rRNAgenes. Repeat sequences, RNA editing, and horizontal gene transfer events were identified. The results of phylogenetic analyses, collinearity and gene clusters revealed thatC. hystrixis closer toC. sativus than to C. melo. Meanwhile, wedemonstrated mitochondrial paternal inheritance inC. hystrixbymolecular markers. In comparison with other cucurbitcrops, wefound amarker foridentification of germplasm resources ofCucumis. Collectively, our findings provide a tool to help clarify the paternal lineage within that genus in the evolution of Cucumis.
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Liu H, Zhao W, Hua W, Liu J. A large-scale population based organelle pan-genomes construction and phylogeny analysis reveal the genetic diversity and the evolutionary origins of chloroplast and mitochondrion in Brassica napus L. BMC Genomics 2022; 23:339. [PMID: 35501686 PMCID: PMC9063048 DOI: 10.1186/s12864-022-08573-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 04/19/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Allotetraploid oilseed rape (Brassica napus L.) is an important worldwide oil-producing crop. The origin of rapeseed is still undetermined due to the lack of wild resources. Despite certain genetic architecture and phylogenetic studies have been done focus on large group of Brassica nuclear genomes, the organelle genomes information under global pattern is largely unknown, which provide unique material for phylogenetic studies of B. napus. Here, based on de novo assemblies of 1,579 B. napus accessions collected globally, we constructed the chloroplast and mitochondrial pan-genomes of B. napus, and investigated the genetic diversity, phylogenetic relationships of B. napus, B. rapa and B. oleracea. RESULTS Based on mitotype-specific markers and mitotype-variant ORFs, four main cytoplasmic haplotypes were identified in our groups corresponding the nap, pol, ole, and cam mitotypes, among which the structure of chloroplast genomes was more conserved without any rearrangement than mitochondrial genomes. A total of 2,092 variants were detected in chloroplast genomes, whereas only 326 in mitochondrial genomes, indicating that chloroplast genomes exhibited a higher level of single-base polymorphism than mitochondrial genomes. Based on whole-genome variants diversity analysis, eleven genetic difference regions among different cytoplasmic haplotypes were identified on chloroplast genomes. The phylogenetic tree incorporating accessions of the B. rapa, B. oleracea, natural and synthetic populations of B. napus revealed multiple origins of B. napus cytoplasm. The cam-type and pol-type were both derived from B. rapa, while the ole-type was originated from B. oleracea. Notably, the nap-type cytoplasm was identified in both the B. rapa population and the synthetic B. napus, suggesting that B. rapa might be the maternal ancestor of nap-type B. napus. CONCLUSIONS The phylogenetic results provide novel insights into the organelle genomic evolution of Brassica species. The natural rapeseeds contained at least four cytoplastic haplotypes, of which the predominant nap-type might be originated from B. rapa. Besides, the organelle pan-genomes and the overall variation data offered useful resources for analysis of cytoplasmic inheritance related agronomical important traits of rapeseed, which can substantially facilitate the cultivation and improvement of rapeseed varieties.
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Affiliation(s)
- Hongfang Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Wei Zhao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Wei Hua
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
| | - Jing Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
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Mower JP, Hanley L, Wolff K, Pabón-Mora N, González F. Complete Mitogenomes of Two Aragoa Species and Phylogeny of Plantagineae (Plantaginaceae, Lamiales) Using Mitochondrial Genes and the Nuclear Ribosomal RNA Repeat. PLANTS 2021; 10:plants10122673. [PMID: 34961143 PMCID: PMC8707427 DOI: 10.3390/plants10122673] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022]
Abstract
Aragoa, comprising 19 high-altitude North Andean species, is one of three genera in the Plantagineae (Plantaginaceae, Lamiales), along with Littorella and Plantago. Based primarily on plastid data and nuclear ITS, Aragoa is sister to a clade of Littorella + Plantago, but Plantagineae relationships have yet to be assessed using multigene datasets from the nuclear and mitochondrial genomes. Here, complete mitogenomes were assembled for two species of Aragoa (A. abietina and A. cleefii). The mitogenomes of both species have a typical suite of genes for 34 proteins, 17 tRNAs, and three rRNAs. The A. abietina mitogenome assembled into a simple circular map, with no large repeats capable of producing alternative isoforms. The A. cleefii mitogenomic map was more complex, involving two circular maps bridged by a substoichiometric linear fragment. Phylogenetics of three mitochondrial genes or the nuclear rRNA repeat placed Aragoa as sister to Littorella + Plantago, consistent with previous studies. However, P. nubicola, the sole representative of subg. Bougueria, was nested within subg. Psyllium based on the mitochondrial and nuclear data, conflicting with plastid-based analyses. Phylogenetics of the nuclear rRNA repeat provided better resolution overall, whereas relationships from mitochondrial data were hindered by extensive substitution rate variation among lineages.
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Affiliation(s)
- Jeffrey P. Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA;
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
- Correspondence:
| | - Lilly Hanley
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA;
| | - Kirsten Wolff
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK;
| | - Natalia Pabón-Mora
- Instituto de Biología, Universidad de Antioquia, Medellín 050010, Colombia;
| | - Favio González
- Sede Bogotá, Facultad de Ciencias, Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá 111321, Colombia;
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Transcriptional Landscape and Splicing Efficiency in Arabidopsis Mitochondria. Cells 2021; 10:cells10082054. [PMID: 34440822 PMCID: PMC8392254 DOI: 10.3390/cells10082054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/23/2021] [Accepted: 07/30/2021] [Indexed: 12/18/2022] Open
Abstract
Plant mitochondrial transcription is initiated from multiple promoters without an apparent motif, which precludes their identification in other species based on sequence comparisons. Even though coding regions take up only a small fraction of plant mitochondrial genomes, deep RNAseq studies uncovered that these genomes are fully or nearly fully transcribed with significantly different RNA read depth across the genome. Transcriptomic analysis can be a powerful tool to understand the transcription process in diverse angiosperms, including the identification of potential promoters and co-transcribed genes or to study the efficiency of intron splicing. In this work, we analyzed the transcriptional landscape of the Arabidopsis mitochondrial genome (mtDNA) based on large-scale RNA sequencing data to evaluate the use of RNAseq to study those aspects of the transcription process. We found that about 98% of the Arabidopsis mtDNA is transcribed with highly different RNA read depth, which was elevated in known genes. The location of a sharp increase in RNA read depth upstream of genes matched the experimentally identified promoters. The continuously high RNA read depth across two adjacent genes agreed with the known co-transcribed units in Arabidopsis mitochondria. Most intron-containing genes showed a high splicing efficiency with no differences between cis and trans-spliced introns or between genes with distinct splicing mechanisms. Deep RNAseq analyses of diverse plant species will be valuable to recognize general and lineage-specific characteristics related to the mitochondrial transcription process.
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17
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Mohd Saad NS, Severn-Ellis AA, Pradhan A, Edwards D, Batley J. Genomics Armed With Diversity Leads the Way in Brassica Improvement in a Changing Global Environment. Front Genet 2021; 12:600789. [PMID: 33679880 PMCID: PMC7930750 DOI: 10.3389/fgene.2021.600789] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/15/2021] [Indexed: 12/14/2022] Open
Abstract
Meeting the needs of a growing world population in the face of imminent climate change is a challenge; breeding of vegetable and oilseed Brassica crops is part of the race in meeting these demands. Available genetic diversity constituting the foundation of breeding is essential in plant improvement. Elite varieties, land races, and crop wild species are important resources of useful variation and are available from existing genepools or genebanks. Conservation of diversity in genepools, genebanks, and even the wild is crucial in preventing the loss of variation for future breeding efforts. In addition, the identification of suitable parental lines and alleles is critical in ensuring the development of resilient Brassica crops. During the past two decades, an increasing number of high-quality nuclear and organellar Brassica genomes have been assembled. Whole-genome re-sequencing and the development of pan-genomes are overcoming the limitations of the single reference genome and provide the basis for further exploration. Genomic and complementary omic tools such as microarrays, transcriptomics, epigenetics, and reverse genetics facilitate the study of crop evolution, breeding histories, and the discovery of loci associated with highly sought-after agronomic traits. Furthermore, in genomic selection, predicted breeding values based on phenotype and genome-wide marker scores allow the preselection of promising genotypes, enhancing genetic gains and substantially quickening the breeding cycle. It is clear that genomics, armed with diversity, is set to lead the way in Brassica improvement; however, a multidisciplinary plant breeding approach that includes phenotype = genotype × environment × management interaction will ultimately ensure the selection of resilient Brassica varieties ready for climate change.
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Affiliation(s)
| | | | | | | | - Jacqueline Batley
- School of Biological Sciences Western Australia and UWA Institute of Agriculture, University of Western Australia, Perth, WA, Australia
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18
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Garcia LE, Edera AA, Palmer JD, Sato H, Sanchez-Puerta MV. Horizontal gene transfers dominate the functional mitochondrial gene space of a holoparasitic plant. THE NEW PHYTOLOGIST 2021; 229:1701-1714. [PMID: 32929737 DOI: 10.1111/nph.16926] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
Although horizontal gene transfer (HGT) is common in angiosperm mitochondrial DNAs (mtDNAs), few cases of functional foreign genes have been identified. The one outstanding candidate for large-scale functional HGT is the holoparasite Lophophytum mirabile, whose mtDNA has lost most native genes but contains intact foreign homologs acquired from legume host plants. To investigate the extent to which this situation results from functional replacement of native by foreign genes, functional mitochondrial gene transfer to the nucleus, and/or loss of mitochondrial biochemical function in the context of extreme parasitism, we examined the Lophophytum mitochondrial and nuclear transcriptomes by deep paired-end RNA sequencing. Most foreign mitochondrial genes in Lophophytum are highly transcribed, accurately spliced, and efficiently RNA edited. By contrast, we found no evidence for functional gene transfer to the nucleus or loss of mitochondrial functions in Lophophytum. Many functional replacements occurred via the physical replacement of native genes by foreign genes. Some of these events probably occurred as the final act of HGT itself. Lophophytum mtDNA has experienced an unprecedented level of functional replacement of native genes by foreign copies. This raises important questions concerning population-genetic and molecular regimes that underlie such a high level of foreign gene takeover.
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Affiliation(s)
- Laura E Garcia
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, Mendoza, M5502JMA, Argentina
| | - Alejandro A Edera
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Argentina
| | - Jeffrey D Palmer
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Hector Sato
- Facultad de Ciencias Agrarias (UNJu), Cátedra de Botánica General-Herbario JUA, Alberdi 47, Jujuy, CP 4600, Argentina
| | - M Virginia Sanchez-Puerta
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, Mendoza, M5502JMA, Argentina
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Plant Mitochondria are a Riddle Wrapped in a Mystery Inside an Enigma. J Mol Evol 2021; 89:151-156. [PMID: 33486550 DOI: 10.1007/s00239-020-09980-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 12/03/2020] [Indexed: 12/23/2022]
Abstract
A fundamental paradox motivates the study of plant mitochondrial genomics: the mutation rate is very low (lower than in the nucleus) but the rearrangement rate is high. A landmark paper published in Journal of Molecular Evolution in 1988 established these facts and revealed the paradox. Jeffrey Palmer and Laura Herbon did a prodigious amount of work in the pre-genome sequencing era to identify both the high frequency of rearrangements between closely related species, and the low frequency of mutations, observations that have now been confirmed many times by sequencing. This paper was also the first to use molecular data on rearrangements as a phylogenetic trait to build a parsimonious tree. The work was a technical tour-de-force, its findings are still at the heart of plant mitochondrial genomics, and the underlying molecular mechanisms that produce this paradox are still not completely understood.
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Shtratnikova VY, Schelkunov MI, Penin AA, Logacheva MD. Mitochondrial genome of the nonphotosynthetic mycoheterotrophic plant Hypopitys monotropa, its structure, gene expression and RNA editing. PeerJ 2020; 8:e9309. [PMID: 32601550 PMCID: PMC7307570 DOI: 10.7717/peerj.9309] [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: 06/13/2019] [Accepted: 05/17/2020] [Indexed: 01/05/2023] Open
Abstract
Heterotrophic plants—plants that have lost the ability to photosynthesize—are characterized by a number of changes at all levels of organization. Heterotrophic plants are divided into two large categories—parasitic and mycoheterotrophic (MHT). The question of to what extent such changes are similar in these two categories is still open. The plastid genomes of nonphotosynthetic plants are well characterized, and they exhibit similar patterns of reduction in the two groups. In contrast, little is known about the mitochondrial genomes of MHT plants. We report the structure of the mitochondrial genome of Hypopitys monotropa, a MHT member of Ericaceae, and the expression of its genes. In contrast to its highly reduced plastid genome, the mitochondrial genome of H. monotropa is larger than that of its photosynthetic relative Vaccinium macrocarpon, and its complete size is ~810 Kb. We observed an unusually long repeat-rich structure of the genome that suggests the existence of linear fragments. Despite this unique feature, the gene content of the H. monotropa mitogenome is typical of flowering plants. No acceleration of substitution rates is observed in mitochondrial genes, in contrast to previous observations in parasitic non-photosynthetic plants. Transcriptome sequencing revealed the trans-splicing of several genes and RNA editing in 33 of 38 genes. Notably, we did not find any traces of horizontal gene transfer from fungi, in contrast to plant parasites, which extensively integrate genetic material from their hosts.
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Affiliation(s)
- Viktoria Yu Shtratnikova
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail I Schelkunov
- Skolkovo Institute of Science and Technology, Moscow, Russia.,Laboratory of Plant Genomics, Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Aleksey A Penin
- Laboratory of Plant Genomics, Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
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Choi IS, Ruhlman TA, Jansen RK. Comparative Mitogenome Analysis of the Genus Trifolium Reveals Independent Gene Fission of ccmFn and Intracellular Gene Transfers in Fabaceae. Int J Mol Sci 2020; 21:E1959. [PMID: 32183014 PMCID: PMC7139807 DOI: 10.3390/ijms21061959] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 02/15/2020] [Accepted: 02/17/2020] [Indexed: 01/30/2023] Open
Abstract
The genus Trifolium is the largest of the tribe Trifolieae in the subfamily Papilionoideae (Fabaceae). The paucity of mitochondrial genome (mitogenome) sequences has hindered comparative analyses among the three genomic compartments of the plant cell (nucleus, mitochondrion and plastid). We assembled four mitogenomes from the two subgenera (Chronosemium and Trifolium) of the genus. The four Trifolium mitogenomes were compact (294,911-348,724 bp in length) and contained limited repetitive (6.6-8.6%) DNA. Comparison of organelle repeat content highlighted the distinct evolutionary trajectory of plastid genomes in a subset of Trifolium species. Intracellular gene transfer (IGT) was analyzed among the three genomic compartments revealing functional transfer of mitochondrial rps1 to nuclear genome along with other IGT events. Phylogenetic analysis based on mitochondrial and nuclear rps1 sequences revealed that the functional transfer in Trifolieae was independent from the event that occurred in robinioid clade that includes genus Lotus. A novel, independent fission event of ccmFn in Trifolium was identified, caused by a 59 bp deletion. Fissions of this gene reported previously in land plants were reassessed and compared with Trifolium.
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Affiliation(s)
- In-Su Choi
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA; (T.A.R.); (R.K.J.)
| | - Tracey A. Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA; (T.A.R.); (R.K.J.)
| | - Robert K. Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA; (T.A.R.); (R.K.J.)
- Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Murik O, Chandran SA, Nevo-Dinur K, Sultan LD, Best C, Stein Y, Hazan C, Ostersetzer-Biran O. Topologies of N 6 -adenosine methylation (m 6 A) in land plant mitochondria and their putative effects on organellar gene expression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1269-1286. [PMID: 31657869 DOI: 10.1111/tpj.14589] [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: 04/13/2019] [Revised: 10/03/2019] [Accepted: 10/17/2019] [Indexed: 06/10/2023]
Abstract
Mitochondria serve as major sites of ATP production and play key roles in many other metabolic processes that are critical to the cell. As relicts of an ancient bacterial endosymbiont, mitochondria contain their own hereditary material (i.e. mtDNA, or mitogenome) and a machinery for protein biosynthesis. The expression of the mtDNA in plants is complex, particularly at the post-transcriptional level. Following transcription, the polycistronic pre-RNAs undergo extensive modifications, including trimming, splicing and editing, before being translated by organellar ribosomes. Our study focuses on N6 -methylation of adenosine ribonucleotides (m6 A-RNA) in plant mitochondria. m6 A is a prevalent modification in nuclear-encoded mRNAs. The biological significance of this dynamic modification is under investigation, but it is widely accepted that m6 A mediates structural switches that affect RNA stability and/or activity. Using m6 A-pulldown/RNA-seq (m6 A-RIP-seq) assays of Arabidopsis and cauliflower mitochondria, we provide information on the m6 A-RNA landscapes in Arabidopsis thaliana and Brassica oleracea mitochondria. The results show that m6 A targets different types of mitochondrial transcripts, including known genes, mtORFs, as well as non-coding (transcribed intergenic) RNA species. While ncRNAs undergo multiple m6 A modifications, N6 -methylation of adenosine residues with mRNAs seem preferably positioned near start codons and may modulate their translatability.
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Affiliation(s)
- Omer Murik
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Sam Aldrin Chandran
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Keren Nevo-Dinur
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Laure D Sultan
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Corinne Best
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Yuval Stein
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Carina Hazan
- Analytical Chemistry Laboratory, The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Oren Ostersetzer-Biran
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
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Small ID, Schallenberg-Rüdinger M, Takenaka M, Mireau H, Ostersetzer-Biran O. Plant organellar RNA editing: what 30 years of research has revealed. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1040-1056. [PMID: 31630458 DOI: 10.1111/tpj.14578] [Citation(s) in RCA: 176] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/25/2019] [Accepted: 10/08/2019] [Indexed: 05/21/2023]
Abstract
The central dogma in biology defines the flow of genetic information from DNA to RNA to protein. Accordingly, RNA molecules generally accurately follow the sequences of the genes from which they are transcribed. This rule is transgressed by RNA editing, which creates RNA products that differ from their DNA templates. Analyses of the RNA landscapes of terrestrial plants have indicated that RNA editing (in the form of C-U base transitions) is highly prevalent within organelles (that is, mitochondria and chloroplasts). Numerous C→U conversions (and in some plants also U→C) alter the coding sequences of many of the organellar transcripts and can also produce translatable mRNAs by creating AUG start sites or eliminating premature stop codons, or affect the RNA structure, influence splicing and alter the stability of RNAs. RNA-binding proteins are at the heart of post-transcriptional RNA expression. The C-to-U RNA editing process in plant mitochondria involves numerous nuclear-encoded factors, many of which have been identified as pentatricopeptide repeat (PPR) proteins that target editing sites in a sequence-specific manner. In this review we report on major discoveries on RNA editing in plant organelles, since it was first documented 30 years ago.
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Affiliation(s)
- Ian D Small
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Mareike Schallenberg-Rüdinger
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abt. Molekulare Evolution, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Mizuki Takenaka
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hakim Mireau
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
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Choi IS, Schwarz EN, Ruhlman TA, Khiyami MA, Sabir JSM, Hajarah NH, Sabir MJ, Rabah SO, Jansen RK. Fluctuations in Fabaceae mitochondrial genome size and content are both ancient and recent. BMC PLANT BIOLOGY 2019; 19:448. [PMID: 31653201 PMCID: PMC6814987 DOI: 10.1186/s12870-019-2064-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/02/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Organelle genome studies of Fabaceae, an economically and ecologically important plant family, have been biased towards the plastid genome (plastome). Thus far, less than 15 mitochondrial genome (mitogenome) sequences of Fabaceae have been published, all but four of which belong to the subfamily Papilionoideae, limiting the understanding of size variation and content across the family. To address this, four mitogenomes were sequenced and assembled from three different subfamilies (Cercidoideae, Detarioideae and Caesalpinioideae). RESULTS Phylogenetic analysis based on shared mitochondrial protein coding regions produced a fully resolved and well-supported phylogeny that was completely congruent with the plastome tree. Comparative analyses suggest that two kinds of mitogenome expansions have occurred in Fabaceae. Size expansion of four genera (Tamarindus, Libidibia, Haematoxylum, and Leucaena) in two subfamilies (Detarioideae and Caesalpinioideae) occurred in relatively deep nodes, and was mainly caused by intercellular gene transfer and/or interspecific horizontal gene transfer (HGT). The second, more recent expansion occurred in the Papilionoideae as a result of duplication of native mitochondrial sequences. Family-wide gene content analysis revealed 11 gene losses, four (rps2, 7, 11 and 13) of which occurred in the ancestor of Fabaceae. Losses of the remaining seven genes (cox2, rpl2, rpl10, rps1, rps19, sdh3, sdh4) were restricted to specific lineages or occurred independently in different clades. Introns of three genes (cox2, ccmFc and rps10) showed extensive lineage-specific length variation due to large sequence insertions and deletions. Shared DNA analysis among Fabaceae mitogenomes demonstrated a substantial decay of intergenic spacers and provided further insight into HGT between the mimosoid clade of Caesalpinioideae and the holoparasitic Lophophytum (Balanophoraceae). CONCLUSION This study represents the most exhaustive analysis of Fabaceae mitogenomes so far, and extends the understanding the dynamic variation in size and gene/intron content. The four newly sequenced mitogenomes reported here expands the phylogenetic coverage to four subfamilies. The family has experienced multiple mitogenome size fluctuations in both ancient and recent times. The causes of these size variations are distinct in different lineages. Fabaceae mitogenomes experienced extensive size fluctuation by recruitment of exogenous DNA and duplication of native mitochondrial DNA.
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Affiliation(s)
- In-Su Choi
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712 USA
| | - Erika N. Schwarz
- Department of Biological Sciences, St. Edward’s University, Austin, TX 78704 USA
| | - Tracey A. Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712 USA
| | - Mohammad A. Khiyami
- King Abdulaziz City for Science and Technology (KACST), Riyadh, 11442 Saudi Arabia
| | - Jamal S. M. Sabir
- Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Nahid H. Hajarah
- Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Mernan J. Sabir
- Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Samar O. Rabah
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Robert K. Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712 USA
- Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
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Zhang F, Li W, Gao CW, Zhang D, Gao LZ. Deciphering tea tree chloroplast and mitochondrial genomes of Camellia sinensis var. assamica. Sci Data 2019; 6:209. [PMID: 31624267 PMCID: PMC6797725 DOI: 10.1038/s41597-019-0201-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/10/2019] [Indexed: 11/10/2022] Open
Abstract
Tea is the most popular non-alcoholic caffeine-containing and the oldest beverage in the world. In this study, we de novo assembled the chloroplast (cp) and mitochondrial (mt) genomes of C. sinensis var. assamica cv. Yunkang10 into a circular contig of 157,100 bp and two complete circular scaffolds (701719 bp and 177329 bp), respectively. We correspondingly annotated a total of 141 cp genes and 71 mt genes. Comparative analysis suggests repeat-rich nature of the mt genome compared to the cp genome, for example, with the characterization of 37,878 bp and 149 bp of long repeat sequences and 665 and 214 SSRs, respectively. We also detected 478 RNA-editing sites in 42 protein-coding mt genes, which are ~4.4-fold more than 54 RNA-editing sites detected in 21 protein-coding cp genes. The high-quality cp and mt genomes of C. sinensis var. assamica presented in this study will become an important resource for a range of genetic, functional, evolutionary and comparative genomic studies in tea tree and other Camellia species of the Theaceae family.
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Affiliation(s)
- Fen Zhang
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, 510642, China
| | - Wei Li
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, 510642, China
| | - Cheng-Wen Gao
- Affiliated Hospital, Qingdao University, Qingdao, 266003, China
| | - Dan Zhang
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, 510642, China
| | - Li-Zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, 510642, China.
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China.
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Transcriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value. Sci Rep 2019; 9:10411. [PMID: 31320697 PMCID: PMC6639398 DOI: 10.1038/s41598-019-46613-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/27/2019] [Indexed: 01/08/2023] Open
Abstract
Caper (Capparis spinosa L.) is a xerophytic shrub cultivated for its flower buds and fruits, used as food and for their medicinal properties. Breeding programs and even proper taxonomic classification of the genus Capparis has been hampered so far by the lack of reliable genetic information and molecular markers. Here, we present the first genomic resource for C. spinosa, generated by transcriptomic approach and de novo assembly. The sequencing effort produced nearly 80 million clean reads assembled into 124,723 unitranscripts. Careful annotation and comparison with public databases revealed homologs to genes with a key role in important metabolic pathways linked to abiotic stress tolerance and bio-compounds production, such purine, thiamine and phenylpropanoid biosynthesis, α-linolenic acid and lipid metabolism. Additionally, a panel of genes involved in stomatal development/distribution and encoding for Stress Associated Proteins (SAPs) was also identified. We also used the transcriptomic data to uncover novel molecular markers for caper. Out of 50 SSRs tested, 14 proved polymorphic and represent the first set of SSR markers for the genus Capparis. This transcriptome will be an important contribution to future studies and breeding programs for this orphan crop, aiding to the development of improved varieties to sustain agriculture in arid conditions.
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The Shared and Specific Genes and a Comparative Genomics Analysis within Three Hanseniaspora Strains. Int J Genomics 2019; 2019:7910865. [PMID: 31281829 PMCID: PMC6589277 DOI: 10.1155/2019/7910865] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/17/2019] [Accepted: 04/16/2019] [Indexed: 11/21/2022] Open
Abstract
Kloeckera apiculata plays an important role in the inhibition of citrus postharvest blue and green mould diseases. This study was based on the previous genome sequencing of K. apiculata strain 34-9. After homologous comparison, scaffold 27 was defined as the mitochondrial (mt) sequence of K. apiculata 34-9. The comparison showed a high level of sequence identity between scaffold 27 and the known mtDNA of Hanseniaspora uvarum. The genome sequence of H. vineae T02/19AF showed several short and discontinuous fragments homologous to the mtDNA of H. uvarum. The shared and specific genes of K. apiculata, H. uvarum, and H. vineae were analysed by family using the TreeFam methodology. GO analysis was used to classify the shared and specific genes. Most of the gene families were classified into the functional categories of cellular component and metabolic processes. The whole-genome phylogram and genome synteny analysis showed that K. apiculata was more closely related to H. uvarum than to H. vineae. The genomic comparisons clearly displayed the locations of the homologous regions in each genome. This analysis could contribute to discovering the genomic similarities and differences within the genus Hanseniaspora. In addition, some regions were not collinearity-matched in the genome of K. apiculata compared with that of H. uvarum or H. vineae, and these sequences might have resulted from evolutionary variations.
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Wu Z, Hu K, Yan M, Song L, Wen J, Ma C, Shen J, Fu T, Yi B, Tu J. Mitochondrial genome and transcriptome analysis of five alloplasmic male-sterile lines in Brassica juncea. BMC Genomics 2019; 20:348. [PMID: 31068124 PMCID: PMC6507029 DOI: 10.1186/s12864-019-5721-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 04/22/2019] [Indexed: 01/15/2023] Open
Abstract
Background Alloplasmic lines, in which the nuclear genome is combined with wild cytoplasm, are often characterized by cytoplasmic male sterility (CMS), regardless of whether it was derived from sexual or somatic hybridization with wild relatives. In this study, we sequenced and analyzed the mitochondrial genomes of five such alloplasmic lines in Brassica juncea. Results The assembled and annotated mitochondrial genomes of the five alloplasmic lines were found to have virtually identical gene contents. They preserved most of the ancestral mitochondrial segments, and the same candidate male sterility gene (orf108) was found harbored in mitotype-specific sequences. We also detected promiscuous sequences of chloroplast origin that were conserved among plants of the Brassicaceae, and found the RNA editing profiles to vary across the five mitochondrial genomes. Conclusions On the basis of our characterization of the genetic nature of five alloplasmic mitochondrial genomes, we speculated that the putative candidate male sterility gene orf108 may not be responsible for the CMS observed in Brassica oxyrrhina and Diplotaxis catholica. Furthermore, we propose the potential coincidence of CMS in alloplasmic lines. Our findings lay the foundation for further elucidation of male sterility gene. Electronic supplementary material The online version of this article (10.1186/s12864-019-5721-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zengxiang Wu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kaining Hu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mengjiao Yan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liping Song
- Institute of Vegetables, Wuhan Academy of Agricultural Sciences, Wuhan, 430070, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China.
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Repeats of Unusual Size in Plant Mitochondrial Genomes: Identification, Incidence and Evolution. G3-GENES GENOMES GENETICS 2019; 9:549-559. [PMID: 30563833 PMCID: PMC6385970 DOI: 10.1534/g3.118.200948] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Plant mitochondrial genomes have excessive size relative to coding capacity, a low mutation rate in genes and a high rearrangement rate. They also have abundant non-tandem repeats often including pairs of large repeats which cause isomerization of the genome by recombination, and numerous repeats of up to several hundred base pairs that recombine only when the genome is stressed by DNA damaging agents or mutations in DNA repair pathway genes. Early work on mitochondrial genomes led to the suggestion that repeats in the size range from several hundred to a few thousand base pair are underrepresented. The repeats themselves are not well-conserved between species, and are not always annotated in mitochondrial sequence assemblies. We systematically identified and compared these repeats, which are important clues to mechanisms of DNA maintenance in mitochondria. We developed a tool to find and curate non-tandem repeats larger than 50bp and analyzed the complete mitochondrial sequences from 157 plant species. We observed an interesting difference between taxa: the repeats are larger and more frequent in the vascular plants. Analysis of closely related species also shows that plant mitochondrial genomes evolve in dramatic bursts of breakage and rejoining, complete with DNA sequence gain and loss. We suggest an adaptive explanation for the existence of the repeats and their evolution.
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Li S, Chen Z, Zhao N, Wang Y, Nie H, Hua J. The comparison of four mitochondrial genomes reveals cytoplasmic male sterility candidate genes in cotton. BMC Genomics 2018; 19:775. [PMID: 30367630 PMCID: PMC6204043 DOI: 10.1186/s12864-018-5122-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/26/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The mitochondrial genomes of higher plants vary remarkably in size, structure and sequence content, as demonstrated by the accumulation and activity of repetitive DNA sequences. Incompatibility between mitochondrial genome and nuclear genome leads to non-functional male reproductive organs and results in cytoplasmic male sterility (CMS). CMS has been used to produce F1 hybrid seeds in a variety of plant species. RESULTS Here we compared the mitochondrial genomes (mitogenomes) of Gossypium hirsutum sterile male lines CMS-2074A and CMS-2074S, as well as their restorer and maintainer lines. First, we noticed the mitogenome organization and sequences were conserved in these lines. Second, we discovered the mitogenomes of 2074A and 2074S underwent large-scale substitutions and rearrangements. Actually, there were five and six unique chimeric open reading frames (ORFs) in 2074A and 2074S, respectively, which were derived from the recombination between unique repetitive sequences and nearby functional genes. Third, we found out four chimeric ORFs that were differentially transcribed in sterile line (2074A) and fertile-restored line. CONCLUSIONS These four novel and recombinant ORFs are potential candidates that confer CMS character in 2074A. In addition, our observations suggest that CMS in cotton is associated with the accelerated rates of rearrangement, and that novel expression products are derived from recombinant ORFs.
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Affiliation(s)
- Shuangshuang Li
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhiwen Chen
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Nan Zhao
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yumei Wang
- Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
| | - Hushuai Nie
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jinping Hua
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
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Kovar L, Nageswara-Rao M, Ortega-Rodriguez S, Dugas DV, Straub S, Cronn R, Strickler SR, Hughes CE, Hanley KA, Rodriguez DN, Langhorst BW, Dimalanta ET, Bailey CD. PacBio-Based Mitochondrial Genome Assembly of Leucaena trichandra (Leguminosae) and an Intrageneric Assessment of Mitochondrial RNA Editing. Genome Biol Evol 2018; 10:2501-2517. [PMID: 30137422 PMCID: PMC6161758 DOI: 10.1093/gbe/evy179] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2018] [Indexed: 12/31/2022] Open
Abstract
Reconstructions of vascular plant mitochondrial genomes (mt-genomes) are notoriously complicated by rampant recombination that has resulted in comparatively few plant mt-genomes being available. The dearth of plant mitochondrial resources has limited our understanding of mt-genome structural diversity, complex patterns of RNA editing, and the origins of novel mt-genome elements. Here, we use an efficient long read (PacBio) iterative assembly pipeline to generate mt-genome assemblies for Leucaena trichandra (Leguminosae: Caesalpinioideae: mimosoid clade), providing the first assessment of non-papilionoid legume mt-genome content and structure to date. The efficiency of the assembly approach facilitated the exploration of alternative structures that are common place among plant mitochondrial genomes. A compact version (729 kbp) of the recovered assemblies was used to investigate sources of mt-genome size variation among legumes and mt-genome sequence similarity to the legume associated root holoparasite Lophophytum. The genome and an associated suite of transcriptome data from select species of Leucaena permitted an in-depth exploration of RNA editing in a diverse clade of closely related species that includes hybrid lineages. RNA editing in the allotetraploid, Leucaena leucocephala, is consistent with co-option of nearly equal maternal and paternal C-to-U edit components, generating novel combinations of RNA edited sites. A preliminary investigation of L. leucocephala C-to-U edit frequencies identified the potential for a hybrid to generate unique pools of alleles from parental variation through edit frequencies shared with one parental lineage, those intermediate between parents, and transgressive patterns.
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Affiliation(s)
- Lynsey Kovar
- Department of Biology, New Mexico State University
| | | | | | | | - Shannon Straub
- Department of Biology, Hobart and William Smith Colleges, Geneva, New York
| | - Richard Cronn
- Pacific Northwest Research Station, Corvallis, Oregon
| | | | - Colin E Hughes
- Department of Systematic & Evolutionary Botany, University of Zurich, Switzerland
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Shevtsov S, Nevo-Dinur K, Faigon L, Sultan LD, Zmudjak M, Markovits M, Ostersetzer-Biran O. Control of organelle gene expression by the mitochondrial transcription termination factor mTERF22 in Arabidopsis thaliana plants. PLoS One 2018; 13:e0201631. [PMID: 30059532 PMCID: PMC6066234 DOI: 10.1371/journal.pone.0201631] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/18/2018] [Indexed: 11/28/2022] Open
Abstract
Mitochondria are key sites for cellular energy metabolism and are essential to cell survival. As descendants of eubacterial symbionts (specifically α-proteobacteria), mitochondria contain their own genomes (mtDNAs), RNAs and ribosomes. Plants need to coordinate their energy demands during particular growth and developmental stages. The regulation of mtDNA expression is critical for controlling the oxidative phosphorylation capacity in response to physiological or environmental signals. The mitochondrial transcription termination factor (mTERF) family has recently emerged as a central player in mitochondrial gene expression in various eukaryotes. Interestingly, the number of mTERFs has been greatly expanded in the nuclear genomes of plants, with more than 30 members in different angiosperms. The majority of the annotated mTERFs in plants are predicted to be plastid- or mitochondria-localized. These are therefore expected to play important roles in organellar gene expression in angiosperms. Yet, functions have been assigned to only a small fraction of these factors in plants. Here, we report the characterization of mTERF22 (At5g64950) which functions in the regulation of mtDNA transcription in Arabidopsis thaliana. GFP localization assays indicate that mTERF22 resides within the mitochondria. Disruption of mTERF22 function results in reduced mtRNA accumulation and altered organelle biogenesis. Transcriptomic and run-on experiments suggest that the phenotypes of mterf22 mutants are attributable, at least in part, to altered mitochondria transcription, and indicate that mTERF22 affects the expression of numerous mitochondrial genes in Arabidopsis plants.
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Affiliation(s)
- Sofia Shevtsov
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem, Israel
| | - Keren Nevo-Dinur
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem, Israel
| | - Lior Faigon
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem, Israel
| | - Laure D. Sultan
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem, Israel
| | - Michal Zmudjak
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem, Israel
| | - Mark Markovits
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem, Israel
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem, Israel
- * E-mail:
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Edera AA, Gandini CL, Sanchez-Puerta MV. Towards a comprehensive picture of C-to-U RNA editing sites in angiosperm mitochondria. PLANT MOLECULAR BIOLOGY 2018; 97:215-231. [PMID: 29761268 DOI: 10.1007/s11103-018-0734-9] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 05/02/2018] [Indexed: 06/08/2023]
Abstract
Our understanding of the dynamic and evolution of RNA editing in angiosperms is in part limited by the few editing sites identified to date. This study identified 10,217 editing sites from 17 diverse angiosperms. Our analyses confirmed the universality of certain features of RNA editing, and offer new evidence behind the loss of editing sites in angiosperms. RNA editing is a post-transcriptional process that substitutes cytidines (C) for uridines (U) in organellar transcripts of angiosperms. These substitutions mostly take place in mitochondrial messenger RNAs at specific positions called editing sites. By means of publicly available RNA-seq data, this study identified 10,217 editing sites in mitochondrial protein-coding genes of 17 diverse angiosperms. Even though other types of mismatches were also identified, we did not find evidence of non-canonical editing processes. The results showed an uneven distribution of editing sites among species, genes, and codon positions. The analyses revealed that editing sites were conserved across angiosperms but there were some species-specific sites. Non-synonymous editing sites were particularly highly conserved (~ 80%) across the plant species and were efficiently edited (80% editing extent). In contrast, editing sites at third codon positions were poorly conserved (~ 30%) and only partially edited (~ 40% editing extent). We found that the loss of editing sites along angiosperm evolution is mainly occurring by replacing editing sites with thymidines, instead of a degradation of the editing recognition motif around editing sites. Consecutive and highly conserved editing sites had been replaced by thymidines as result of retroprocessing, by which edited transcripts are reverse transcribed to cDNA and then integrated into the genome by homologous recombination. This phenomenon was more pronounced in eudicots, and in the gene cox1. These results suggest that retroprocessing is a widespread driving force underlying the loss of editing sites in angiosperm mitochondria.
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Affiliation(s)
- Alejandro A Edera
- IBAM, Facultad de Ciencias Agrarias, CONICET, Universidad Nacional de Cuyo, M5528AHB, Chacras de Coria, Argentina.
| | - Carolina L Gandini
- IBAM, Facultad de Ciencias Agrarias, CONICET, Universidad Nacional de Cuyo, M5528AHB, Chacras de Coria, Argentina
| | - M Virginia Sanchez-Puerta
- IBAM, Facultad de Ciencias Agrarias, CONICET, Universidad Nacional de Cuyo, M5528AHB, Chacras de Coria, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, 5500, Mendoza, Argentina
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Jabaily RS, Shepherd KA, Michener PS, Bush CJ, Rivero R, Gardner AG, Sessa EB. Employing hypothesis testing and data from multiple genomic compartments to resolve recalcitrant backbone nodes in Goodenia s.l. (Goodeniaceae). Mol Phylogenet Evol 2018; 127:502-512. [PMID: 29758275 DOI: 10.1016/j.ympev.2018.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/22/2018] [Accepted: 05/07/2018] [Indexed: 11/30/2022]
Abstract
Goodeniaceae is a primarily Australian flowering plant family with a complex taxonomy and evolutionary history. Previous phylogenetic analyses have successfully resolved the backbone topology of the largest clade in the family, Goodenia s.l., but have failed to clarify relationships within the species-rich and enigmatic Goodenia clade C, a prerequisite for taxonomic revision of the group. We used genome skimming to retrieve sequences for chloroplast, mitochondrial, and nuclear markers for 24 taxa representing Goodenia s.l., with a particular focus on Goodenia clade C. We performed extensive hypothesis tests to explore incongruence in clade C and evaluate statistical support for clades within this group, using datasets from all three genomic compartments. The mitochondrial dataset is comparable to the chloroplast dataset in providing resolution within Goodenia clade C, though backbone support values within this clade remain low. The hypothesis tests provided an additional, complementary means of evaluating support for clades. We propose that the major subclades of Goodenia clade C (C1-C3 + Verreauxia) are the result of a rapid radiation, and each represents a distinct lineage.
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Affiliation(s)
- Rachel S Jabaily
- Department of Organismal Biology & Ecology, Colorado College, Colorado Springs, CO 80903, USA; Department of Biology, Rhodes College, Memphis, TN 38112, USA.
| | - Kelly A Shepherd
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Kensington, WA 6151, Australia.
| | | | - Caroline J Bush
- Department of Biology, Rhodes College, Memphis, TN 38112, USA.
| | - Rodrigo Rivero
- Department of Biology, University of Florida, Gainesville, FL 32607, USA; Department of Natural Resources and Environmental Management, University of Hawaii- Mānoa, Honolulu, HI 96822, USA.
| | - Andrew G Gardner
- Department of Biological Sciences, California State University, Stanislaus, One University Circle, Turlock, CA 95382, USA.
| | - Emily B Sessa
- Department of Biology, University of Florida, Gainesville, FL 32607, USA; Genetics Institute, University of Florida, Gainesville, FL 32607, USA.
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Yang K, Nath UK, Biswas MK, Kayum MA, Yi GE, Lee J, Yang TJ, Nou IS. Whole-genome sequencing of Brassica oleracea var. capitata reveals new diversity of the mitogenome. PLoS One 2018; 13:e0194356. [PMID: 29547671 PMCID: PMC5856397 DOI: 10.1371/journal.pone.0194356] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 03/01/2018] [Indexed: 11/24/2022] Open
Abstract
Plant mitochondrial genomes (mtDNAs) vary in sequence structure. We assembled the Brassica oleracea var. capitata mtDNA using a mean coverage depth of 25X whole genome sequencing (WGS) and confirmed the presence of eight contigs/fragments by BLASTZ using the previously reported KJ820683 and AP012988 mtDNA as reference. Assembly of the mtDNA sequence reads resulted in a circular structure of 219,975 bp. Our assembled mtDNA, NCBI acc. no. KU831325, contained 34 protein-coding genes, 3 rRNA genes, and 19 tRNA genes with similarity to the KJ820683 and AP012988 reference mtDNA. No large repeats were found in the KU831325 assembly. However, KU831325 showed differences in the arrangement of bases at different regions compared to the previously reported mtDNAs. In the reference mtDNAs KJ820683 and AP012988, contig/fragment number 4 is partitioned into two contigs/fragments, 4a and 4b. However, contig/fragment number 4 was a single contig/fragment with 29,661 bp in KU831325. PCR and qRT-PCR using flanking markers from separate parts of contig/fragment number 4 confirmed it to be a single contig/fragment. In addition, genome re-alignment of the plastid genome and mtDNAs supported the presence of heteroplasmy and reverse arrangement of the heteroplasmic blocks within the other mtDNAs compared to KU831325 that might be one of the causal factors for its diversity. Our results thus confirm the existence of different mtDNAs in diverse B. oleracea subspecies.
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Affiliation(s)
- Kiwoung Yang
- Department of Horticulture, Sunchon National University, Suncheon, Korea
| | - Ujjal Kumar Nath
- Department of Horticulture, Sunchon National University, Suncheon, Korea
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | | | - Md Abdul Kayum
- Department of Horticulture, Sunchon National University, Suncheon, Korea
| | - Go-eun Yi
- Department of Horticulture, Sunchon National University, Suncheon, Korea
| | - Jonghoon Lee
- Joeun Seed, Goesan-Gun, Chungcheongbuk-Do, Republic of Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- * E-mail: (ISN); (TJY)
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, Suncheon, Korea
- * E-mail: (ISN); (TJY)
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Heng S, Gao J, Wei C, Chen F, Li X, Wen J, Yi B, Ma C, Tu J, Fu T, Shen J. Transcript levels of orf288 are associated with the hau cytoplasmic male sterility system and altered nuclear gene expression in Brassica juncea. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:455-466. [PMID: 29301015 PMCID: PMC5853284 DOI: 10.1093/jxb/erx443] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/17/2017] [Indexed: 05/22/2023]
Abstract
Cytoplasmic male sterility (CMS) is primarily caused by chimeric genes located in the mitochondrial genomes. In Brassica juncea, orf288 has been identified as a CMS-associated gene in the hau CMS line; however, neither the specific abortive stage nor the molecular function of the gene have been determined. We therefore characterized the hau CMS line, and found that defective mitochondria affect the development of archesporial cells during the L2 stage, leading to male sterility. The expression level of the orf288 transcript was higher in the male-sterility line than in the fertility-restorer line, although no significant differences were apparent at the protein level. The toxicity region of ORF288 was found to be located near the N-terminus and repressed growth of Escherichia coli. However, transgenic expression of different portions of ORF288 indicated that the region that causes male sterility resides between amino acids 73 and 288, the expression of which in E. coli did not result in growth inhibition. Transcriptome analysis revealed a wide range of genes involved in anther development and mitochondrial function that were differentially expressed in the hau CMS line. This study provides new insights into the hau CMS mechanism by which orf288 affects the fertility of Brassica juncea.
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Affiliation(s)
- Shuangping Heng
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
- College of Life Science, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, P.R. China
| | - Jie Gao
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Chao Wei
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Fengyi Chen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Xianwen Li
- College of Life Science, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, P.R. China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
- Correspondence:
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Yu T, Sun L, Cui H, Liu S, Men J, Chen S, Chen Y, Lu C. The complete mitochondrial genome of a tertiary relict evergreen woody plant Ammopiptanthus mongolicus. MITOCHONDRIAL DNA PART B-RESOURCES 2017; 3:9-11. [PMID: 33474049 PMCID: PMC7800826 DOI: 10.1080/23802359.2017.1413301] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ammopiptanthus mongolicus is a tertiary relict evergreen broad-leaf shrub in family Fabaceae with remarkable tolerance to desiccation and low temperature. In this study, we report the complete mitochondrial genome of A. mongolicus. The total genome length was 475,396 bp and contained a total of 127 genes, including 79 protein-coding genes (28 novel genes, 45 known functional genes, and six known orf genes), three rRNA genes, and 45 tRNA genes. Most of the genes were single-copy genes, only six were duplicated and two were multi-copy. The mitochondrial genome also contained ‘promiscuous’ sequences from the chloroplast, 16 intact tRNAs of mitochondrial origin, and 29 intact and potentially functional chloroplast-derived tRNAs. The overall GC content of the mitochondrial DNA was 42.75%. A neighbour-joining phylogenomic analysis showed that A. mongolicus was closely related to Medicago truncatula, which also belongs to family Leguminosae.
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Affiliation(s)
- Tingqiao Yu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Lichun Sun
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Hongwei Cui
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Shengli Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Jingyu Men
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Shaoliang Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yuzhen Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Cunfu Lu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
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Chen Z, Nie H, Wang Y, Pei H, Li S, Zhang L, Hua J. Rapid evolutionary divergence of diploid and allotetraploid Gossypium mitochondrial genomes. BMC Genomics 2017; 18:876. [PMID: 29132310 PMCID: PMC5683544 DOI: 10.1186/s12864-017-4282-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/07/2017] [Indexed: 12/31/2022] Open
Abstract
Background Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups and an allotetraploid genomic group, AD. The mitochondrial genomes supply new information to understand both the evolution process and the mechanism of cytoplasmic male sterility. Based on previously released mitochondrial genomes of G. hirsutum (AD1), G. barbadense (AD2), G. raimondii (D5) and G. arboreum (A2), together with data of six other mitochondrial genomes, to elucidate the evolution and diversity of mitochondrial genomes within Gossypium. Results Six Gossypium mitochondrial genomes, including three diploid species from D and three allotetraploid species from AD genome groups (G. thurberi D1, G. davidsonii D3-d and G. trilobum D8; G. tomentosum AD3, G. mustelinum AD4 and G. darwinii AD5), were assembled as the single circular molecules of lengths about 644 kb in diploid species and 677 kb in allotetraploid species, respectively. The genomic structures of mitochondrial in D group species were identical but differed from the mitogenome of G. arboreum (A2), as well as from the mitogenomes of five species of the AD group. There mainly existed four or six large repeats in the mitogenomes of the A + AD or D group species, respectively. These variations in repeat sequences caused the major inversions and translocations within the mitochondrial genome. The mitochondrial genome complexity in Gossypium presented eight unique segments in D group species, three specific fragments in A + AD group species and a large segment (more than 11 kb) in diploid species. These insertions or deletions were most probably generated from crossovers between repetitive or homologous regions. Unlike the highly variable genome structure, evolutionary distance of mitochondrial genes was 1/6th the frequency of that in chloroplast genes of Gossypium. RNA editing events were conserved in cotton mitochondrial genes. We confirmed two near full length of the integration of the mitochondrial genome into chromosome 1 of G. raimondii and chromosome A03 of G. hirsutum, respectively, with insertion time less than 1.03 MYA. Conclusion Ten Gossypium mitochondrial sequences highlight the insights to the evolution of cotton mitogenomes. Electronic supplementary material The online version of this article (10.1186/s12864-017-4282-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhiwen Chen
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Hushuai Nie
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yumei Wang
- Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, 430064, China
| | - Haili Pei
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Shuangshuang Li
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Lida Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jinping Hua
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
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Wang C, Aubé F, Planchard N, Quadrado M, Dargel-Graffin C, Nogué F, Mireau H. The pentatricopeptide repeat protein MTSF2 stabilizes a nad1 precursor transcript and defines the 3΄ end of its 5΄-half intron. Nucleic Acids Res 2017; 45:6119-6134. [PMID: 28334831 PMCID: PMC5449624 DOI: 10.1093/nar/gkx162] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 02/28/2017] [Indexed: 12/14/2022] Open
Abstract
RNA expression in plant mitochondria implies a large number of post-transcriptional events in which transcript processing and stabilization are essential. In this study, we analyzed the function of the Arabidopsis mitochondrial stability factor 2 gene (MTSF2) and show that the encoded pentatricopeptide repeat protein is essential for the accumulation of stable nad1 mRNA. The production of mature nad1 requires the assembly of three independent RNA precursors via two trans-splicing reactions. Genetic analyses revealed that the lack of nad1 in mtsf2 mutants results from the specific destabilization of the nad1 exons 2-3 precursor transcript. We further demonstrated that MTSF2 binds to its 3΄ extremity with high affinity, suggesting a protective action by blocking exoribonuclease progression. By defining the 3΄ end of nad1 exons 2-3 precursor, MTSF2 concomitantly determines the 3΄ extremity of the first half of the trans-intron found at the end of the transcript. Therefore, binding of the MTSF2 protein to nad1 exons 2-3 precursor evolved both to stabilize the transcript and to define a 3΄ extremity compatible with the trans-splicing reaction needed to reconstitute mature nad1. We thus reveal that the range of transcripts stabilized by association with protective protein on their 3΄ end concerns also mitochondrial precursor transcripts.
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Affiliation(s)
- Chuande Wang
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
- Paris-Sud University, Université Paris-Saclay, 91405 Orsay Cedex, France
- These authors contributed equally to the paper as first authors
| | - Fabien Aubé
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
- These authors contributed equally to the paper as first authors
| | - Noelya Planchard
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
- Paris-Sud University, Université Paris-Saclay, 91405 Orsay Cedex, France
- These authors contributed equally to the paper as first authors
| | - Martine Quadrado
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
| | - Céline Dargel-Graffin
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
| | - Hakim Mireau
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
- To whom correspondence should be addressed. Tel: +33 130 833 070; Fax: +33 130 833 319;
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Hatono S, Nishimura K, Murakami Y, Tsujimura M, Yamagishi H. Complete mitochondrial genome sequences of Brassica rapa (Chinese cabbage and mizuna), and intraspecific differentiation of cytoplasm in B. rapa and Brassica juncea. BREEDING SCIENCE 2017; 67:357-362. [PMID: 29085245 PMCID: PMC5654463 DOI: 10.1270/jsbbs.17023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 05/04/2017] [Indexed: 06/07/2023]
Abstract
The complete sequence of the mitochondrial genome was determined for two cultivars of Brassica rapa. After determining the sequence of a Chinese cabbage variety, 'Oushou hakusai', the sequence of a mizuna variety, 'Chusei shiroguki sensuji kyomizuna', was mapped against the sequence of Chinese cabbage. The precise sequences where the two varieties demonstrated variation were ascertained by direct sequencing. It was found that the mitochondrial genomes of the two varieties are identical over 219,775 bp, with a single nucleotide polymorphism (SNP) between the genomes. Because B. rapa is the maternal species of an amphidiploid crop species, Brassica juncea, the distribution of the SNP was observed both in B. rapa and B. juncea. While the mizuna type SNP was restricted mainly to cultivars of mizuna (japonica group) in B. rapa, the mizuna type was widely distributed in B. juncea. The finding that the two Brassica species have these SNP types in common suggests that the nucleotide substitution occurred in wild B. rapa before both mitotypes were domesticated. It was further inferred that the interspecific hybridization between B. rapa and B. nigra took place twice and resulted in the two mitotypes of cultivated B. juncea.
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Affiliation(s)
- Saki Hatono
- Graduate School of Life Sciences, Kyoto Sangyo University,
Kamigamo, Motoyama, Kita, Kyoto 603-8555,
Japan
| | - Kaori Nishimura
- Faculty of Life Sciences, Kyoto Sangyo University,
Kamigamo, Motoyama, Kita, Kyoto 603-8555,
Japan
| | - Yoko Murakami
- Faculty of Life Sciences, Kyoto Sangyo University,
Kamigamo, Motoyama, Kita, Kyoto 603-8555,
Japan
| | - Mai Tsujimura
- Plant Organelle Genome Research Center, Kyoto Sangyo University,
Kamigamo, Motoyama, Kita, Kyoto 603-8555,
Japan
| | - Hiroshi Yamagishi
- Faculty of Life Sciences, Kyoto Sangyo University,
Kamigamo, Motoyama, Kita, Kyoto 603-8555,
Japan
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Wu Z, Sloan DB, Brown CW, Rosenblueth M, Palmer JD, Ong HC. Mitochondrial Retroprocessing Promoted Functional Transfers of rpl5 to the Nucleus in Grasses. Mol Biol Evol 2017; 34:2340-2354. [PMID: 28541477 PMCID: PMC5850859 DOI: 10.1093/molbev/msx170] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Functional gene transfers from the mitochondrion to the nucleus are ongoing in angiosperms and have occurred repeatedly for all 15 ribosomal protein genes, but it is not clear why some of these genes are transferred more often than others nor what the balance is between DNA- and RNA-mediated transfers. Although direct insertion of mitochondrial DNA into the nucleus occurs frequently in angiosperms, case studies of functional mitochondrial gene transfer have implicated an RNA-mediated mechanism that eliminates introns and RNA editing sites, which would otherwise impede proper expression of mitochondrial genes in the nucleus. To elucidate the mechanisms that facilitate functional gene transfers and the evolutionary dynamics of the coexisting nuclear and mitochondrial gene copies that are established during these transfers, we have analyzed rpl5 genes from 90 grasses (Poaceae) and related monocots. Multiple lines of evidence indicate that rpl5 has been functionally transferred to the nucleus at least three separate times in the grass family and that at least seven species have intact and transcribed (but not necessarily functional) copies in both the mitochondrion and nucleus. In two grasses, likely functional nuclear copies of rpl5 have been subject to recent gene conversion events via secondarily transferred mitochondrial copies in what we believe are the first described cases of mitochondrial-to-nuclear gene conversion. We show that rpl5 underwent a retroprocessing event within the mitochondrial genome early in the evolution of the grass family, which we argue predisposed the gene towards successful, DNA-mediated functional transfer by generating a "pre-edited" sequence.
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Affiliation(s)
- Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins, CO
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, Fort Collins, CO
| | - Colin W. Brown
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX
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Multiple origins of endosymbionts in Chlorellaceae with no reductive effects on the plastid or mitochondrial genomes. Sci Rep 2017; 7:10101. [PMID: 28855622 PMCID: PMC5577192 DOI: 10.1038/s41598-017-10388-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 08/08/2017] [Indexed: 11/20/2022] Open
Abstract
Ancient endosymbiotic relationships have led to extreme genomic reduction in many bacterial and eukaryotic algal endosymbionts. Endosymbionts in more recent and/or facultative relationships can also experience genomic reduction to a lesser extent, but little is known about the effects of the endosymbiotic transition on the organellar genomes of eukaryotes. To understand how the endosymbiotic lifestyle has affected the organellar genomes of photosynthetic green algae, we generated the complete plastid genome (plastome) and mitochondrial genome (mitogenome) sequences from three green algal endosymbionts (Chlorella heliozoae, Chlorella variabilis and Micractinium conductrix). The mitogenomes and plastomes of the three newly sequenced endosymbionts have a standard set of genes compared with free-living trebouxiophytes, providing no evidence for functional genomic reduction. Instead, their organellar genomes are generally larger and more intron rich. Intron content is highly variable among the members of Chlorella, suggesting very high rates of gain and/or loss of introns during evolution. Phylogenetic analysis of plastid and mitochondrial genes demonstrated that the three endosymbionts do not form a monophyletic group, indicating that the endosymbiotic lifestyle has evolved multiple times in Chlorellaceae. In addition, M. conductrix is deeply nested within the Chlorella clade, suggesting that taxonomic revision is needed for one or both genera.
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Heng S, Chen F, Wei C, Hu K, Yang Z, Wen J, Yi B, Ma C, Tu J, Si P, Fu T, Shen J. Identification of different cytoplasms based on newly developed mitotype-specific markers for marker-assisted selection breeding in Brassica napus L. PLANT CELL REPORTS 2017; 36:901-909. [PMID: 28265748 DOI: 10.1007/s00299-017-2121-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/15/2017] [Indexed: 06/06/2023]
Abstract
Different mitotype-specific markers were developed to distinguish different cytoplasms in Brassica napus L. Mitotype-specific markers have been developed to distinguish different mitotypes in plant. And use of molecular markers to identify different mitotypes in Brassica napus would enhance breeding efficiency. Here, we comparatively analyzed six sequenced mitochondrial genomes in Brassica napus and identified collinear block sequences and mitotype-specific sequences (MSSs) of these mitochondrial genomes. The collinear block sequences between mitochondrial genomes of nap, cam, and pol cytoplasmic male sterility (CMS) lines were higher than those of other lines. After comparative analysis of the six sequenced mitochondrial genomes (cam, nap, ole, pol CMS, ogu CMS, and hau CMS), 90 MSSs with sizes ranging from 101 to 9981 bp and a total length of 103,756 bp (accounting for 6.77% of the mitochondrial genome sequences) were identified. Additionally, 12 mitotype-specific markers were developed based on the mitochondrial genome-specific sequences in order to distinguish among these different mitotypes. Cytoplasms of 570 different inbred lines collected across scientific research institutes in China were identified using the MSS markers developed in our study. In addition to confirming the accuracy of the cytoplasmic identification, we also identified mitotypes that have not been reported in Brassica napus. Our study may provide guidance for the classification of different mitotypes in B. napus breeding.
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Affiliation(s)
- Shuangping Heng
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- College of Life Science, Xinyang Normal University, Xinyang, 464000, People's Republic of China
| | - Fengyi Chen
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Chao Wei
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Kaining Hu
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Zonghui Yang
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Ping Si
- Centre for Plant Genetics and Breeding, School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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Petersen G, Cuenca A, Zervas A, Ross GT, Graham SW, Barrett CF, Davis JI, Seberg O. Mitochondrial genome evolution in Alismatales: Size reduction and extensive loss of ribosomal protein genes. PLoS One 2017; 12:e0177606. [PMID: 28545148 PMCID: PMC5435185 DOI: 10.1371/journal.pone.0177606] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 04/28/2017] [Indexed: 11/18/2022] Open
Abstract
The order Alismatales is a hotspot for evolution of plant mitochondrial genomes characterized by remarkable differences in genome size, substitution rates, RNA editing, retrotranscription, gene loss and intron loss. Here we have sequenced the complete mitogenomes of Zostera marina and Stratiotes aloides, which together with previously sequenced mitogenomes from Butomus and Spirodela, provide new evolutionary evidence of genome size reduction, gene loss and transfer to the nucleus. The Zostera mitogenome includes a large portion of DNA transferred from the plastome, yet it is the smallest known mitogenome from a non-parasitic plant. Using a broad sample of the Alismatales, the evolutionary history of ribosomal protein gene loss is analyzed. In Zostera almost all ribosomal protein genes are lost from the mitogenome, but only some can be found in the nucleus.
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Affiliation(s)
- Gitte Petersen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Argelia Cuenca
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Athanasios Zervas
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Gregory T. Ross
- Department of Botany, 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, 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
- L. H. Bailey Hortorium and Plant Biology Section, Cornell University, Ithaca, New York, United States of America
| | - Jerrold I. Davis
- L. H. Bailey Hortorium and Plant Biology Section, Cornell University, Ithaca, New York, United States of America
| | - Ole Seberg
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Chen Z, Nie H, Grover CE, Wang Y, Li P, Wang M, Pei H, Zhao Y, Li S, Wendel JF, Hua J. Entire nucleotide sequences of Gossypium raimondii and G. arboreum mitochondrial genomes revealed A-genome species as cytoplasmic donor of the allotetraploid species. PLANT BIOLOGY (STUTTGART, GERMANY) 2017; 19:484-493. [PMID: 28008701 DOI: 10.1111/plb.12536] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 12/16/2016] [Indexed: 05/20/2023]
Abstract
Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups, designated A-G and K, and an allotetraploid genomic group, AD. Gossypium raimondii (D5 ) and G. arboreum (A2 ) are the putative contributors to the progenitor of G. hirsutum (AD1 ), the economically important fibre-producing cotton species. Mitochondrial DNA from week-old etiolated seedlings was extracted from isolated organelles using discontinuous sucrose density gradient method. Mitochondrial genomes were sequenced, assembled, annotated and analysed in orderly. Gossypium raimondii (D5 ) and G. arboreum (A2 ) mitochondrial genomes were provided in this study. The mitochondrial genomes of two diploid species harboured circular genome of 643,914 bp (D5 ) and 687,482 bp (A2 ), respectively. They differ in size and number of repeat sequences, both contain illuminating triplicate sequences with 7317 and 10,246 bp, respectively, demonstrating dynamic difference and rearranged genome organisations. Comparing the D5 and A2 mitogenomes with mitogenomes of tetraploid Gossypium species (AD1 , G. hirsutum; AD2 , G. barbadense), a shared 11 kbp fragment loss was detected in allotetraploid species, three regions shared by G. arboreum (A2 ), G. hirsutum (AD1 ) and G. barbadense (AD2 ), while eight regions were specific to G. raimondii (D5 ). The presence/absence variations and gene-based phylogeny supported that A-genome is a cytoplasmic donor to the progenitor of allotetraploid species G. hirsutum and G. barbadense. The results present structure variations and phylogeny of Gossypium mitochondrial genome evolution.
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Affiliation(s)
- Z Chen
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology, Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - H Nie
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology, Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - C E Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Y Wang
- Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - P Li
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology, Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - M Wang
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology, Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - H Pei
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology, Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Y Zhao
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology, Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - S Li
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology, Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - J F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | - J Hua
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology, Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
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Guo W, Zhu A, Fan W, Mower JP. Complete mitochondrial genomes from the ferns Ophioglossum californicum and Psilotum nudum are highly repetitive with the largest organellar introns. THE NEW PHYTOLOGIST 2017; 213:391-403. [PMID: 27539928 DOI: 10.1111/nph.14135] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 07/06/2016] [Indexed: 05/07/2023]
Abstract
Currently, complete mitochondrial genomes (mitogenomes) are available from all major land plant lineages except ferns. Sequencing of fern mitogenomes could shed light on the major evolutionary transitions that established mitogenomic diversity among extant lineages. In this study, we generated complete mitogenomes from the adder's tongue fern (Ophioglossum californicum) and the whisk fern (Psilotum nudum). The Psilotum mitogenome (628 kb) contains a rich complement of genes and introns, some of which are the largest of any green plant organellar genome. In the Ophioglossum mitogenome (372 kb), gene and intron content is slightly reduced, including the loss of all four mitochondrial ccm genes. Transcripts of nuclear Ccm genes also were not detected, suggesting loss of the entire mitochondrial cytochrome c maturation pathway from Ophioglossum. Both fern mitogenomes are highly repetitive, yet they show extremely low levels of active recombination. Transcriptomic sequencing uncovered ˜1000 sites of C-to-U RNA editing in both species, plus a small number (< 60) of U-to-C edit sites. Overall, the first mitochondrial genomes of ferns show a mix of features shared with lycophytes and/or seed plants and several novel genomic features, enabling a robust reconstruction of the mitogenome in the common ancestor of vascular plants.
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Affiliation(s)
- Wenhu Guo
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA
- ACGT Inc., Wheeling, IL, 60090, USA
| | - Andan Zhu
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Weishu Fan
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
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Grewe F, Zhu A, Mower JP. Loss of a Trans-Splicing nad1 Intron from Geraniaceae and Transfer of the Maturase Gene matR to the Nucleus in Pelargonium. Genome Biol Evol 2016; 8:3193-3201. [PMID: 27664178 PMCID: PMC5174742 DOI: 10.1093/gbe/evw233] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The mitochondrial nad1 gene of seed plants has a complex structure, including four introns in cis or trans configurations and a maturase gene (matR) hosted within the final intron. In the geranium family (Geraniaceae), however, sequencing of representative species revealed that three of the four introns, including one in a trans configuration and another that hosts matR, were lost from the nad1 gene in their common ancestor. Despite the loss of the host intron, matR has been retained as a freestanding gene in most genera of the family, indicating that this maturase has additional functions beyond the splicing of its host intron. In the common ancestor of Pelargonium, matR was transferred to the nuclear genome, where it was split into two unlinked genes that encode either its reverse transcriptase or maturase domain. Both nuclear genes are transcribed and contain predicted mitochondrial targeting signals, suggesting that they express functional proteins that are imported into mitochondria. The nuclear localization and split domain structure of matR in the Pelargonium nuclear genome offers a unique opportunity to assess the function of these two domains using transgenic approaches.
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Affiliation(s)
- Felix Grewe
- Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska.,Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska.,Integrative Research Center, The Field Museum of Natural History, Chicago, Illinois
| | - Andan Zhu
- Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska.,Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska .,Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska
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Yang J, Liu G, Zhao N, Chen S, Liu D, Ma W, Hu Z, Zhang M. Comparative mitochondrial genome analysis reveals the evolutionary rearrangement mechanism in Brassica. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:527-536. [PMID: 27079962 DOI: 10.1111/plb.12414] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 11/09/2015] [Indexed: 06/05/2023]
Abstract
The genus Brassica has many species that are important for oil, vegetable and other food products. Three mitochondrial genome types (mitotype) originated from its common ancestor. In this paper, a B. nigra mitochondrial main circle genome with 232,407 bp was generated through de novo assembly. Synteny analysis showed that the mitochondrial genomes of B. rapa and B. oleracea had a better syntenic relationship than B. nigra. Principal components analysis and development of a phylogenetic tree indicated maternal ancestors of three allotetraploid species in Us triangle of Brassica. Diversified mitotypes were found in allotetraploid B. napus, in which napus-type B. napus was derived from B. oleracea, while polima-type B. napus was inherited from B. rapa. In addition, the mitochondrial genome of napus-type B. napus was closer to botrytis-type than capitata-type B. oleracea. The sub-stoichiometric shifting of several mitochondrial genes suggested that mitochondrial genome rearrangement underwent evolutionary selection during domestication and/or plant breeding. Our findings clarify the role of diploid species in the maternal origin of allotetraploid species in Brassica and suggest the possibility of breeding selection of the mitochondrial genome.
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Affiliation(s)
- J Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, China
| | - G Liu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - N Zhao
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - S Chen
- School of Plant Biology (M084), The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - D Liu
- Biomarker Technologies Corporation, Beijing, China
| | - W Ma
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Z Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, China
| | - M Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, China
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49
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Kim B, Kim K, Yang TJ, Kim S. Completion of the mitochondrial genome sequence of onion (Allium cepa L.) containing the CMS-S male-sterile cytoplasm and identification of an independent event of the ccmF N gene split. Curr Genet 2016; 62:873-885. [PMID: 27016941 DOI: 10.1007/s00294-016-0595-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/14/2016] [Accepted: 03/15/2016] [Indexed: 01/16/2023]
Abstract
Cytoplasmic male-sterility (CMS) conferred by the CMS-S cytoplasm has been most commonly used for onion (Allium cepa L.) F1 hybrid seed production. We first report the complete mitochondrial genome sequence containing CMS-S cytoplasm in this study. Initially, seven contigs were de novo assembled from 150-bp paired-end raw reads produced from the total genomic DNA using the Illumina NextSeq500 platform. These contigs were connected into a single circular genome consisting of 316,363 bp (GenBank accession: KU318712) by PCR amplification. Although all 24 core protein-coding genes were present, no ribosomal protein-coding genes, except rps12, were identified in the onion mitochondrial genome. Unusual trans-splicing of the cox2 gene was verified, and the cox1 gene was identified as part of the chimeric orf725 gene, which is a candidate gene responsible for inducing CMS. In addition to orf725, two small chimeric genes were identified, but no transcripts were detected for these two open reading frames. Thirteen chloroplast-derived sequences, with sizes of 126-13,986 bp, were identified in the intergenic regions. Almost 10 % of the onion mitochondrial genome was composed of repeat sequences. The vast majority of repeats were short repeats of <100 base pairs. Interestingly, the gene encoding ccmFN was split into two genes. The ccmF N gene split is first identified outside the Brassicaceae family. The breakpoint in the onion ccmF N gene was different from that of other Brassicaceae species. This split of the ccmF N gene was also present in 30 other Allium species. The complete onion mitochondrial genome sequence reported in this study would be fundamental information for elucidation of onion CMS evolution.
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Affiliation(s)
- Bongju Kim
- Department of Plant Biotechnology, Biotechnology Research Institute, Chonnam National University, Gwangju, 500-757, Republic of Korea
| | - Kyunghee Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.,Phyzen Genomics Institute, 501-1, Gwanak Century Tower, Gwanak-gu, Seoul, 151-836, Republic of Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Sunggil Kim
- Department of Plant Biotechnology, Biotechnology Research Institute, Chonnam National University, Gwangju, 500-757, Republic of Korea.
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50
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Lee J, Kim J, Choi JP, Lee M, Kim MK, Lee YH, Hur Y, Nou IS, Park SU, Min SR, Kim H. Intracellular Ca(2+) and K(+) concentration in Brassica oleracea leaf induces differential expression of transporter and stress-related genes. BMC Genomics 2016; 17:211. [PMID: 26955874 PMCID: PMC4784358 DOI: 10.1186/s12864-016-2512-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 02/23/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND One of the most important members of the genus Brassica, cabbage, requires a relatively high level of calcium for normal growth (Plant Cell Environ 7: 397-405, 1984; Plant Physiol 60: 854-856, 1977). Localized Ca(2+) deficiency in cabbage leaves causes tip-burn, bringing about serious economic losses (Euphytica 9:203-208, 1960; Ann Bot 43:363-372, 1979; Sci Hortic 14:131-138, 1981). Although it has been known that the occurrence of tip-burn is related to Ca(2+) deficiency, there is limited information on the underlying mechanisms of tip-burn or the relationship between Ca(2+) and tip-burn incidence. To obtain more information on the genetic control of tip-burn symptoms, we focused on the identification of genes differentially expressed in response to increasing intracellular Ca(2+) and K(+) concentrations in B. oleracea lines derived from tip-burn susceptible, tip-burn resistant cabbages (B. oleracea var. capitata), and kale (B. oleracea var. acephala). RESULTS We compared the levels of major macronutrient cations, including Ca(2+) and K(+), in three leaf segments, the leaf apex (LA), middle of leaf (LM), and leaf base (LB), of tip-burn susceptible, tip-burn resistant cabbages, and kale. Ca(2+) and K(+) concentrations were highest in kale, followed by tip-burn resistant and then tip-burn susceptible cabbages. These cations generally accumulated to a greater extent in the LB than in the LA. Transcriptome analysis identified 58,096 loci as putative non-redundant genes in the three leaf segments of the three B. oleracea lines and showed significant changes in expression of 27,876 loci based on Ca(2+) and K(+) levels. Among these, 1844 loci were identified as tip-burn related phenotype-specific genes. Tip-burn resistant cabbage and kale-specific genes were largely related to stress and transport activity based on GO annotation. Tip-burn resistant cabbage and kale plants showed phenotypes clearly indicative of heat-shock, freezing, and drought stress tolerance compared to tip-burn susceptible cabbages, demonstrating a correlation between intracellular Ca(2+) and K(+) concentrations and tolerance of abiotic stress with differential gene expression. We selected 165 genes that were up- or down-regulated in response to increasing Ca(2+) and K(+) concentrations in the three leaf segments of the three plant lines. Gene ontology enrichment analysis indicated that these genes participated in regulatory metabolic processes or stress responses. CONCLUSIONS Our results indicate that the genes involved in regulatory metabolic processes or stress responses were differentially expressed in response to increasing Ca(2+) and K(+) concentrations in the B. oleracea leaf. Our transcriptome data and the genes identified may serve as a starting point for understanding the mechanisms underlying essential macronutrient deficiencies in plants, as well as the features of tip-burn in cabbage and other Brassica species.
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Affiliation(s)
- Jeongyeo Lee
- Korea Research Institute of Bioscience and Biotechnology, 125 Gwahangno, Yuseong-gu, Daejeon, 305-806, Republic of Korea.
| | - Jungeun Kim
- Korea Research Institute of Bioscience and Biotechnology, 125 Gwahangno, Yuseong-gu, Daejeon, 305-806, Republic of Korea.
| | - Jae-Pil Choi
- Korea Research Institute of Bioscience and Biotechnology, 125 Gwahangno, Yuseong-gu, Daejeon, 305-806, Republic of Korea.
| | - MiYe Lee
- Korea Research Institute of Bioscience and Biotechnology, 125 Gwahangno, Yuseong-gu, Daejeon, 305-806, Republic of Korea.
| | - Min Keun Kim
- Environment-friendly Agriculture Research Division, Gyeongsangnam-do Agricultural Research and Extension Service, Jinju, 660-360, Republic of Korea.
| | - Young Han Lee
- Environment-friendly Agriculture Research Division, Gyeongsangnam-do Agricultural Research and Extension Service, Jinju, 660-360, Republic of Korea.
| | - Yoonkang Hur
- Department of Biological Sciences, College of Biological Sciences, Chungnam National University, Daejeon, 305-764, Republic of Korea.
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, Jeonnam, 540-742, Republic of Korea.
| | - Sang Un Park
- Department of Crop Science, College of Agriculture & Life Sciences, Chungnam National University, Daejeon, 305-764, Republic of Korea.
| | - Sung Ran Min
- Korea Research Institute of Bioscience and Biotechnology, 125 Gwahangno, Yuseong-gu, Daejeon, 305-806, Republic of Korea.
| | - HyeRan Kim
- Korea Research Institute of Bioscience and Biotechnology, 125 Gwahangno, Yuseong-gu, Daejeon, 305-806, Republic of Korea. .,Systems and Bioengineering, University of Science and Technology, 217 Gajung-ro, Daejeon, Republic of Korea.
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