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Wang R, Luo Y, Lan Z, Qiu D. Insights into structure, codon usage, repeats, and RNA editing of the complete mitochondrial genome of Perilla frutescens (Lamiaceae). Sci Rep 2024; 14:13940. [PMID: 38886463 DOI: 10.1038/s41598-024-64509-3] [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: 03/01/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
Perilla frutescens (L.) Britton, a member of the Lamiaceae family, stands out as a versatile plant highly valued for its unique aroma and medicinal properties. Additionally, P. frutescens seeds are rich in Îś-linolenic acid, holding substantial economic importance. While the nuclear and chloroplast genomes of P. frutescens have already been documented, the complete mitochondrial genome sequence remains unreported. To this end, the sequencing, annotation, and assembly of the entire Mitochondrial genome of P. frutescens were hereby conducted using a combination of Illumina and PacBio data. The assembled P. frutescens mitochondrial genome spanned 299,551 bp and exhibited a typical circular structure, involving a GC content of 45.23%. Within the genome, a total of 59 unique genes were identified, encompassing 37 protein-coding genes, 20 tRNA genes, and 2 rRNA genes. Additionally, 18 introns were observed in 8 protein-coding genes. Notably, the codons of the P. frutescens mitochondrial genome displayed a notable A/T bias. The analysis also revealed 293 dispersed repeat sequences, 77 simple sequence repeats (SSRs), and 6 tandem repeat sequences. Moreover, RNA editing sites preferentially produced leucine at amino acid editing sites. Furthermore, 70 sequence fragments (12,680 bp) having been transferred from the chloroplast to the mitochondrial genome were identified, accounting for 4.23% of the entire mitochondrial genome. Phylogenetic analysis indicated that among Lamiaceae plants, P. frutescens is most closely related to Salvia miltiorrhiza and Platostoma chinense. Meanwhile, inter-species Ka/Ks results suggested that Ka/Ks < 1 for 28 PCGs, indicating that these genes were evolving under purifying selection. Overall, this study enriches the mitochondrial genome data for P. frutescens and forges a theoretical foundation for future molecular breeding research.
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Affiliation(s)
- Ru Wang
- Hubei Minzu University, School of Forestry and Horticulture, Enshi, 445000, China
| | - Yongjian Luo
- Hubei Minzu University, School of Forestry and Horticulture, Enshi, 445000, China
| | - Zheng Lan
- Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Daoshou Qiu
- Key Laboratory of Crops Genetics and Improvement of Guangdong Province, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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Gong Y, Xie X, Zhou G, Chen M, Chen Z, Li P, Huang H. Assembly and comparative analysis of the complete mitochondrial genome of Brassica rapa var. Purpuraria. BMC Genomics 2024; 25:546. [PMID: 38824587 PMCID: PMC11143693 DOI: 10.1186/s12864-024-10457-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 05/26/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Purple flowering stalk (Brassica rapa var. purpuraria) is a widely cultivated plant with high nutritional and medicinal value and exhibiting strong adaptability during growing. Mitochondrial (mt) play important role in plant cells for energy production, developing with an independent genetic system. Therefore, it is meaningful to assemble and annotate the functions for the mt genome of plants independently. Though there have been several reports referring the mt genome of in Brassica species, the genome of mt in B. rapa var. purpuraria and its functional gene variations when compared to its closely related species has not yet been addressed. RESULTS The mt genome of B. rapa var. purpuraria was assembled through the Illumina and Nanopore sequencing platforms, which revealed a length of 219,775 bp with a typical circular structure. The base composition of the whole B. rapa var. purpuraria mt genome revealed A (27.45%), T (27.31%), C (22.91%), and G (22.32%). 59 functional genes, composing of 33 protein-coding genes (PCGs), 23 tRNA genes, and 3 rRNA genes, were annotated. The sequence repeats, codon usage, RNA editing, nucleotide diversity and gene transfer between the cp genome and mt genome were examined in the B. rapa var. purpuraria mt genome. Phylogenetic analysis show that B. rapa var. Purpuraria was closely related to B. rapa subsp. Oleifera and B. juncea. Ka/Ks analysis reflected that most of the PCGs in the B. rapa var. Purpuraria were negatively selected, illustrating that those mt genes were conserved during evolution. CONCLUSIONS The results of our findings provide valuable information on the B.rapa var. Purpuraria genome, which might facilitate molecular breeding, genetic variation and evolutionary researches for Brassica species in the future.
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Affiliation(s)
- Yihui Gong
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China.
| | - Xin Xie
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Guihua Zhou
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Meiyu Chen
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Zhiyin Chen
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Peng Li
- Xiangtan Agricultural Science Research Institute, Xiangtan, 411100, China
| | - Hua Huang
- Institute of Fruit Tree Research, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, 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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Chen L, Ren W, Zhang B, Guo H, Fang Z, Yang L, Zhuang M, Lv H, Wang Y, Ji J, Hou X, Zhang Y. Comparative Transcriptome Analysis Reveals a Potential Regulatory Network for Ogura Cytoplasmic Male Sterility in Cabbage (Brassica oleracea L.). Int J Mol Sci 2023; 24:ijms24076703. [PMID: 37047676 PMCID: PMC10094764 DOI: 10.3390/ijms24076703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/02/2023] [Accepted: 04/02/2023] [Indexed: 04/07/2023] Open
Abstract
Ogura cytoplasmic male sterility (CMS) lines are widely used breeding materials in cruciferous crops and play important roles in heterosis utilization; however, the sterility mechanism remains unclear. To investigate the microspore development process and gene expression changes after the introduction of orf138 and Rfo, cytological observation and transcriptome analysis were performed using a maintainer line, an Ogura CMS line, and a restorer line. Semithin sections of microspores at different developmental stages showed that the degradation of tapetal cells began at the tetrad stage in the Ogura CMS line, while it occurred at the bicellular microspore stage to the tricellular microspore stage in the maintainer and restorer lines. Therefore, early degradation of tapetal cells may be the cause of pollen abortion. Transcriptome analysis results showed that a total of 1287 DEGs had consistent expression trends in the maintainer line and restorer line, but were significantly up- or down-regulated in the Ogura CMS line, indicating that they may be closely related to pollen abortion. Functional annotation showed that the 1287 core DEGs included a large number of genes related to pollen development, oxidative phosphorylation, carbohydrate, lipid, and protein metabolism. In addition, further verification elucidated that down-regulated expression of genes related to energy metabolism led to decreased ATP content and excessive ROS accumulation in the anthers of Ogura CMS. Based on these results, we propose a transcriptome-mediated induction and regulatory network for cabbage Ogura CMS. Our research provides new insights into the mechanism of pollen abortion and fertility restoration in Ogura CMS.
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Affiliation(s)
- Li Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China
| | - Wenjing Ren
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China
| | - Bin Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China
| | - Huiling Guo
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China
| | - Zhiyuan Fang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China
| | - Limei Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China
| | - Mu Zhuang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China
| | - Honghao Lv
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China
| | - Yong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China
| | - Jialei Ji
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangyong Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China
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Niu Y, Gao C, Liu J. Complete mitochondrial genomes of three Mangifera species, their genomic structure and gene transfer from chloroplast genomes. BMC Genomics 2022; 23:147. [PMID: 35183120 PMCID: PMC8857841 DOI: 10.1186/s12864-022-08383-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/11/2022] [Indexed: 01/30/2023] Open
Abstract
Abstract
Background
Among the Mangifera species, mango (Mangifera indica) is an important commercial fruit crop. However, very few studies have been conducted on the Mangifera mitochondrial genome. This study reports and compares the newly sequenced mitochondrial genomes of three Mangifera species.
Results
Mangifera mitochondrial genomes showed partial similarities in the overall size, genomic structure, and gene content. Specifically, the genomes are circular and contain about 63–69 predicted functional genes, including five ribosomal RNA (rRNA) genes and 24–27 transfer RNA (tRNA) genes. The GC contents of the Mangifera mitochondrial genomes are similar, ranging from 44.42–44.66%. Leucine (Leu) and serine (Ser) are the most frequently used, while tryptophan (Trp) and cysteine (Cys) are the least used amino acids among the protein-coding genes in Mangifera mitochondrial genomes. We also identified 7–10 large chloroplast genomic fragments in the mitochondrial genome, ranging from 1407 to 6142 bp. Additionally, four intact mitochondrial tRNAs genes (tRNA-Cys, tRNA-Trp, tRNA-Pro, and tRNA-Met) and intergenic spacer regions were identified. Phylogenetic analysis based on the common protein-coding genes of most branches provided a high support value.
Conclusions
We sequenced and compared the mitochondrial genomes of three Mangifera species. The results showed that the gene content and the codon usage pattern of Mangifera mitochondrial genomes is similar across various species. Gene transfer from the chloroplast genome to the mitochondrial genome were identified. This study provides valuable information for evolutionary and molecular studies of Mangifera and a basis for further studies on genomic breeding of mango.
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Kuwabara K, Harada I, Matsuzawa Y, Ariizumi T, Shirasawa K. Organelle genome assembly uncovers the dynamic genome reorganization and cytoplasmic male sterility associated genes in tomato. HORTICULTURE RESEARCH 2021; 8:250. [PMID: 34848681 PMCID: PMC8632925 DOI: 10.1038/s41438-021-00676-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/21/2021] [Accepted: 08/02/2021] [Indexed: 05/11/2023]
Abstract
To identify cytoplasmic male sterility (CMS)-associated genes in tomato, we determined the genome sequences of mitochondria and chloroplasts in three CMS tomato lines derived from independent asymmetric cell fusions, their nuclear and cytoplasmic donors, and male fertile weedy cultivated tomato and wild relatives. The structures of the CMS mitochondrial genomes were highly divergent from those of the nuclear and cytoplasmic donors, and genes of the donors were mixed up in these genomes. On the other hand, the structures of CMS chloroplast genomes were moderately conserved across the donors, but CMS chloroplast genes were unexpectedly likely derived from the nuclear donors. Comparative analysis of the structures and contents of organelle genes and transcriptome analysis identified three genes that were uniquely present in the CMS lines, but not in the donor or fertile lines. RNA-sequencing analysis indicated that these three genes transcriptionally expressed in anther, and identified different RNA editing levels in one gene, orf265, that was partially similar to ATP synthase subunit 8, between fertile and sterile lines. The orf265 was a highly potential candidate for CMS-associated gene. This study suggests that organelle reorganization mechanisms after cell fusion events differ between mitochondria and chloroplasts, and provides insight into the development of new F1 hybrid breeding programs employing the CMS system in tomato.
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Affiliation(s)
- Kosuke Kuwabara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Issei Harada
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | | | - Tohru Ariizumi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan.
- Tsukuba Plant Innovation Research Center, Tsukuba, Ibaraki, 305-8577, Japan.
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan.
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Hong Z, Liao X, Ye Y, Zhang N, Yang Z, Zhu W, Gao W, Sharbrough J, Tembrock LR, Xu D, Wu Z. A complete mitochondrial genome for fragrant Chinese rosewood (Dalbergia odorifera, Fabaceae) with comparative analyses of genome structure and intergenomic sequence transfers. BMC Genomics 2021; 22:672. [PMID: 34536995 PMCID: PMC8449883 DOI: 10.1186/s12864-021-07967-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/27/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Dalbergia odorifera is an economically and culturally important species in the Fabaceae because of the high-quality lumber and traditional Chinese medicines made from this plant, however, overexploitation has increased the scarcity of D. odorifera. Given the rarity and the multiple uses of this species, it is important to expand the genomic resources for utilizing in applications such as tracking illegal logging, determining effective population size of wild stands, delineating pedigrees in marker assisted breeding programs, and resolving gene networks in functional genomics studies. Even the nuclear and chloroplast genomes have been published for D. odorifera, the complete mitochondrial genome has not been assembled or assessed for sequence transfer to other genomic compartments until now. Such work is essential in understanding structural and functional genome evolution in a lineage (Fabaceae) with frequent intergenomic sequence transfers. RESULTS We integrated Illumina short-reads and PacBio CLR long-reads to assemble and annotate the complete mitochondrial genome of D. odorifera. The mitochondrial genome was organized as a single circular structure of 435 Kb in length containing 33 protein coding genes, 4 rRNA and 17 tRNA genes. Nearly 4.0% (17,386 bp) of the genome was annotated as repetitive DNA. From the sequence transfer analysis, it was found that 114 Kb of DNA originating from the mitochondrial genome has been transferred to the nuclear genome, with most of the transfer events having taken place relatively recently. The high frequency of sequence transfers from the mitochondria to the nuclear genome was similar to that of sequence transfer from the chloroplast to the nuclear genome. CONCLUSION For the first-time, the complete mitochondrial genome of D. odorifera was assembled in this study, which will provide a baseline resource in understanding genomic evolution in the highly specious Fabaceae. In particular, the assessment of intergenomic sequence transfer suggests that transfers have been common and recent indicating a possible role in environmental adaptation as has been found in other lineages. The high turnover rate of genomic colinearly and large differences in mitochondrial genome size found in the comparative analyses herein providing evidence for the rapid evolution of mitochondrial genome structure compared to chloroplasts in Faboideae. While phylogenetic analyses using functional genes indicate that mitochondrial genes are very slowly evolving compared to chloroplast genes.
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Affiliation(s)
- Zhou Hong
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Xuezhu Liao
- 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, 518120, China
| | - Yuanjun Ye
- Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Ningnan Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Zengjiang Yang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Weidong Zhu
- 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, 518120, China
| | - Wei Gao
- 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, 518120, China.,College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Joel Sharbrough
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, 87801, USA
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Daping Xu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, 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, 518120, China.
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Shao D, Ma Y, Li X, Ga S, Ren Y. The sequence structure and phylogenetic analysis by complete mitochondrial genome of kohlrabi ( Brassica oleracea var. gongylodes L.). Mitochondrial DNA B Resour 2021; 6:2714-2716. [PMID: 34435131 PMCID: PMC8382015 DOI: 10.1080/23802359.2021.1966341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Dengkui Shao
- Qinghai University (Qinghai Academy of Agriculture and Forestry Sciences), Xining, PR China
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining, PR China
| | - Yidong Ma
- Qinghai University (Qinghai Academy of Agriculture and Forestry Sciences), Xining, PR China
| | - Xiaojuan Li
- Qinghai University (Qinghai Academy of Agriculture and Forestry Sciences), Xining, PR China
| | - Sang Ga
- Comprehensive Agriculture and Animal Husbandry Service Center of Yushu Tibetan Autonomous Prefecture, Yushu, PR China
| | - Yanjing Ren
- Qinghai University (Qinghai Academy of Agriculture and Forestry Sciences), Xining, PR China
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining, PR China
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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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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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12
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Masutani B, Arimura SI, Morishita S. Investigating the mitochondrial genomic landscape of Arabidopsis thaliana by long-read sequencing. PLoS Comput Biol 2021; 17:e1008597. [PMID: 33434206 PMCID: PMC7833223 DOI: 10.1371/journal.pcbi.1008597] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 01/25/2021] [Accepted: 12/01/2020] [Indexed: 11/18/2022] Open
Abstract
Plant mitochondrial genomes have distinctive features compared to those of animals; namely, they are large and divergent, with sizes ranging from hundreds of thousands of to a few million bases. Recombination among repetitive regions is thought to produce similar structures that differ slightly, known as "multipartite structures," which contribute to different phenotypes. Although many reference plant mitochondrial genomes represent almost all the genes in mitochondria, the full spectrum of their structures remains largely unknown. The emergence of long-read sequencing technology is expected to yield this landscape; however, many studies aimed to assemble only one representative circular genome, because properly understanding multipartite structures using existing assemblers is not feasible. To elucidate multipartite structures, we leveraged the information in existing reference genomes and classified long reads according to their corresponding structures. We developed a method that exploits two classic algorithms, partial order alignment (POA) and the hidden Markov model (HMM) to construct a sensitive read classifier. This method enables us to represent a set of reads as a POA graph and analyze it using the HMM. We can then calculate the likelihood of a read occurring in a given cluster, resulting in an iterative clustering algorithm. For synthetic data, our proposed method reliably detected one variation site out of 9,000-bp synthetic long reads with a 15% sequencing-error rate and produced accurate clustering. It was also capable of clustering long reads from six very similar sequences containing only slight differences. For real data, we assembled putative multipartite structures of mitochondrial genomes of Arabidopsis thaliana from nine accessions sequenced using PacBio Sequel. The results indicated that there are recurrent and strain-specific structures in A. thaliana mitochondrial genomes.
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Affiliation(s)
- Bansho Masutani
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- * E-mail:
| | - Shin-ichi Arimura
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
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Palumbo F, Vitulo N, Vannozzi A, Magon G, Barcaccia G. The Mitochondrial Genome Assembly of Fennel ( Foeniculum vulgare) Reveals Two Different atp6 Gene Sequences in Cytoplasmic Male Sterile Accessions. Int J Mol Sci 2020; 21:E4664. [PMID: 32630002 PMCID: PMC7370444 DOI: 10.3390/ijms21134664] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 06/29/2020] [Accepted: 06/29/2020] [Indexed: 01/12/2023] Open
Abstract
Cytoplasmic male sterility (CMS) has always aroused interest among researchers and breeders, being a valuable resource widely exploited not only to breed F1 hybrid varieties but also to investigate genes that control stamen and pollen development. With the aim of identifying candidate genes for CMS in fennel, we adopted an effective strategy relying on the comparison between mitochondrial genomes (mtDNA) of both fertile and sterile genotypes. mtDNA raw reads derived from a CMS genotype were assembled in a single molecule (296,483 bp), while a draft mtDNA assembly (166,124 nucleotides, 94 contigs) was performed using male fertile sample (MF) sequences. From their annotation and alignment, two atp6-like sequences were identified. atp6-, the putative mutant copy with a 300 bp truncation at the 5'-end, was found only in the mtDNA of CMS samples, while the wild type copy (atp6+) was detected only in the MF mtDNA. Further analyses (i.e., reads mapping and Sanger sequencing), revealed an atp6+ copy also in CMS samples, probably in the nuclear DNA. However, qPCRs performed on different tissues proved that, despite its availability, atp6+ is expressed only in MF samples, while apt6- mRNA was always detected in CMS individuals. In the light of these findings, the energy deficiency model could explain the pollen deficiency observed in male sterile flower. atp6- could represent a gene whose mRNA is translated into a not-fully functional protein leading to suboptimal ATP production that guarantees essential cellular processes but not a high energy demand process such as pollen development. Our study provides novel insights into the fennel mtDNA genome and its atp6 genes, and paves the way for further studies aimed at understanding their functional roles in the determination of male sterility.
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Affiliation(s)
- Fabio Palumbo
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, Viale dell’Università 16, 35020 Legnaro, PD, Italy; (A.V.); (G.M.); (G.B.)
| | - Nicola Vitulo
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy;
| | - Alessandro Vannozzi
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, Viale dell’Università 16, 35020 Legnaro, PD, Italy; (A.V.); (G.M.); (G.B.)
| | - Gabriele Magon
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, Viale dell’Università 16, 35020 Legnaro, PD, Italy; (A.V.); (G.M.); (G.B.)
| | - Gianni Barcaccia
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, Viale dell’Università 16, 35020 Legnaro, PD, Italy; (A.V.); (G.M.); (G.B.)
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14
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Sang SF, Mei DS, Liu J, Zaman QU, Zhang HY, Hao MY, Fu L, Wang H, Cheng HT, Hu Q. Organelle genome composition and candidate gene identification for Nsa cytoplasmic male sterility in Brassica napus. BMC Genomics 2019; 20:813. [PMID: 31694534 PMCID: PMC6836354 DOI: 10.1186/s12864-019-6187-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 10/15/2019] [Indexed: 12/29/2022] Open
Abstract
Background Nsa cytoplasmic male sterility (CMS) is a novel alloplasmic male sterility system derived from somatic hybridization between Brassica napus and Sinapis arvensis. Identification of the CMS-associated gene is a prerequisite for a better understanding of the origin and molecular mechanism of this CMS. With the development of genome sequencing technology, organelle genomes of Nsa CMS line and its maintainer line were sequenced by pyro-sequencing technology, and comparative analysis of the organelle genomes was carried out to characterize the organelle genome composition of Nsa CMS as well as to identify the candidate Nsa CMS-associated genes. Results Nsa CMS mitochondrial genome showed a higher collinearity with that of S. arvensis than B. napus, indicating that Nsa CMS mitochondrial genome was mainly derived from S. arvensis. However, mitochondrial genome recombination of parental lines was clearly detected. In contrast, the chloroplast genome of Nsa CMS was highly collinear with its B. napus parent, without any evidence of recombination of the two parental chloroplast genomes or integration from S. arvensis. There were 16 open reading frames (ORFs) specifically existed in Nsa CMS mitochondrial genome, which could not be identified in the maintainer line. Among them, three ORFs (orf224, orf309, orf346) possessing chimeric and transmembrane structure are most likely to be the candidate CMS genes. Sequences of all three candidate CMS genes in Nsa CMS line were found to be 100% identical with those from S. arvensis mitochondrial genome. Phylogenetic and homologous analysis showed that all the mitochondrial genes were highly conserved during evolution. Conclusions Nsa CMS contains a recombined mitochondrial genome of its two parental species with the majority form S. arvensis. Three candidate Nsa CMS genes were identified and proven to be derived from S. arvensis other than recombination of its two parental species. Further functional study of the candidate genes will help to identify the gene responsible for the CMS and the underlying molecular mechanism.
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Affiliation(s)
- Shi-Fei Sang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - De-Sheng Mei
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Jia Liu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Qamar U Zaman
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Hai-Yan Zhang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Meng-Yu Hao
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Li Fu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Hui Wang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Hong-Tao Cheng
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China.
| | - Qiong Hu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China.
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Makarenko MS, Usatov AV, Tatarinova TV, Azarin KV, Logacheva MD, Gavrilova VA, Kornienko IV, Horn R. Organization Features of the Mitochondrial Genome of Sunflower ( Helianthus annuus L.) with ANN2-Type Male-Sterile Cytoplasm. PLANTS (BASEL, SWITZERLAND) 2019; 8:E439. [PMID: 31652744 PMCID: PMC6918226 DOI: 10.3390/plants8110439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 10/18/2019] [Accepted: 10/19/2019] [Indexed: 12/24/2022]
Abstract
This study provides insights into the flexibility of the mitochondrial genome in sunflower (Helianthus annuus L.) as well as into the causes of ANN2-type cytoplasmic male sterility (CMS). De novo assembly of the mitochondrial genome of male-sterile HA89(ANN2) sunflower line was performed using high-throughput sequencing technologies. Analysis of CMS ANN2 mitochondrial DNA sequence revealed the following reorganization events: twelve rearrangements, seven insertions, and nine deletions. Comparisons of coding sequences from the male-sterile line with the male-fertile line identified a deletion of orf777 and seven new transcriptionally active open reading frames (ORFs): orf324, orf327, orf345, orf558, orf891, orf933, orf1197. Three of these ORFs represent chimeric genes involving atp6 (orf1197), cox2 (orf558), and nad6 (orf891). In addition, orf558, orf891, orf1197, as well as orf933, encode proteins containing membrane domain(s), making them the most likely candidate genes for CMS development in ANN2. Although the investigated CMS phenotype may be caused by simultaneous action of several candidate genes, we assume that orf1197 plays a major role in developing male sterility in ANN2. Comparative analysis of mitogenome organization in sunflower lines representing different CMS sources also allowed identification of reorganization hot spots in the mitochondrial genome of sunflower.
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Affiliation(s)
- Maksim S Makarenko
- Department of Genetics, Southern Federal University, Rostov-on-Don 344006, Russia.
- The Institute for Information Transmission Problems, Moscow 127051, Russia.
| | - Alexander V Usatov
- Department of Genetics, Southern Federal University, Rostov-on-Don 344006, Russia.
| | - Tatiana V Tatarinova
- The Institute for Information Transmission Problems, Moscow 127051, Russia.
- Department of Biology, University of La Verne, La Verne, CA 91750, USA.
- Vavilov Institute of General Genetics, Moscow 119333, Russia.
- School of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk 660041, Russia.
| | - Kirill V Azarin
- Department of Genetics, Southern Federal University, Rostov-on-Don 344006, Russia.
| | - Maria D Logacheva
- The Institute for Information Transmission Problems, Moscow 127051, Russia.
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia.
| | - Vera A Gavrilova
- The N.I. Vavilov All-Russian Institute of Plant Genetic Resources, Saint Petersburg 190121, Russia.
| | - Igor V Kornienko
- Department of Genetics, Southern Federal University, Rostov-on-Don 344006, Russia.
- Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don 344006, Russia.
| | - Renate Horn
- Institute of Biological Sciences, Plant Genetics, University of Rostock, 18059 Rostock, Germany.
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