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Li L, Li X, Liu Y, Li J, Zhen X, Huang Y, Ye J, Fan L. Comparative analysis of the complete mitogenomes of Camellia sinensis var. sinensis and C. sinensis var. assamica provide insights into evolution and phylogeny relationship. FRONTIERS IN PLANT SCIENCE 2024; 15:1396389. [PMID: 39239196 PMCID: PMC11374768 DOI: 10.3389/fpls.2024.1396389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 07/29/2024] [Indexed: 09/07/2024]
Abstract
Introduction Among cultivated tea plants (Camellia sinensis), only four mitogenomes for C. sinensis var. assamica (CSA) have been reported so far but none for C. sinensis var. sinensis (CSS). Here, two mitogenomes of CSS (CSSDHP and CSSRG) have been sequenced and assembled. Methods Using a combination of Illumina and Nanopore data for the first time. Comparison between CSS and CSA mitogenomes revealed a huge heterogeneity. Results The number of the repetitive sequences was proportional to the mitogenome size and the repetitive sequences dominated the intracellular gene transfer segments (accounting for 88.7%- 92.8% of the total length). Predictive RNA editing analysis revealed that there might be significant editing in NADH dehydrogenase subunit transcripts. Codon preference analysis showed a tendency to favor A/T bases and T was used more frequently at the third base of the codon. ENc plots analysis showed that the natural selection play an important role in shaping the codon usage bias, and Ka/Ks ratios analysis indicated Nad1 and Sdh3 genes may have undergone positive selection. Further, phylogenetic analysis shows that six C. sinensis clustered together, with the CSA and CSS forming two distinct branches, suggesting two different evolutionary pathway. Discussion Altogether, this investigation provided an insight into evolution and phylogeny relationship of C. sinensis mitogenome, thereby enhancing comprehension of the evolutionary patterns within C. sinensis species.
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Affiliation(s)
- Li Li
- College of Tea and Food Science, Wuyi University, Wuyishan, China
| | - Xiangru Li
- College of Tea and Food Science, Wuyi University, Wuyishan, China
| | - Yun Liu
- College of Tea and Food Science, Wuyi University, Wuyishan, China
| | - Junda Li
- College of Tea and Food Science, Wuyi University, Wuyishan, China
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoyun Zhen
- College of Tea and Food Science, Wuyi University, Wuyishan, China
| | - Yu Huang
- College of Tea and Food Science, Wuyi University, Wuyishan, China
| | - Jianghua Ye
- College of Tea and Food Science, Wuyi University, Wuyishan, China
| | - Li Fan
- College of Tea and Food Science, Wuyi University, Wuyishan, China
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Miao X, Yang W, Li D, Wang A, Li J, Deng X, He L, Niu J. Assembly and comparative analysis of the complete mitochondrial and chloroplast genome of Cyperus stoloniferus (Cyperaceae), a coastal plant possessing saline-alkali tolerance. BMC PLANT BIOLOGY 2024; 24:628. [PMID: 38961375 PMCID: PMC11220973 DOI: 10.1186/s12870-024-05333-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024]
Abstract
BACKGROUND Cyperus stoloniferus is an important species in coastal ecosystems and possesses economic and ecological value. To elucidate the structural characteristics, variation, and evolution of the organelle genome of C. stoloniferus, we sequenced, assembled, and compared its mitochondrial and chloroplast genomes. RESULTS We assembled the mitochondrial and chloroplast genomes of C. stoloniferus. The total length of the mitochondrial genome (mtDNA) was 927,413 bp, with a GC content of 40.59%. It consists of two circular DNAs, including 37 protein-coding genes (PCGs), 22 tRNAs, and five rRNAs. The length of the chloroplast genome (cpDNA) was 186,204 bp, containing 93 PCGs, 40 tRNAs, and 8 rRNAs. The mtDNA and cpDNA contained 81 and 129 tandem repeats, respectively, and 346 and 1,170 dispersed repeats, respectively, both of which have 270 simple sequence repeats. The third high-frequency codon (RSCU > 1) in the organellar genome tended to end at A or U, whereas the low-frequency codon (RSCU < 1) tended to end at G or C. The RNA editing sites of the PCGs were relatively few, with only 9 and 23 sites in the mtDNA and cpDNA, respectively. A total of 28 mitochondrial plastid DNAs (MTPTs) in the mtDNA were derived from cpDNA, including three complete trnT-GGU, trnH-GUG, and trnS-GCU. Phylogeny and collinearity indicated that the relationship between C. stoloniferus and C. rotundus are closest. The mitochondrial rns gene exhibited the greatest nucleotide variability, whereas the chloroplast gene with the greatest nucleotide variability was infA. Most PCGs in the organellar genome are negatively selected and highly evolutionarily conserved. Only six mitochondrial genes and two chloroplast genes exhibited Ka/Ks > 1; in particular, atp9, atp6, and rps7 may have undergone potential positive selection. CONCLUSION We assembled and validated the mtDNA of C. stoloniferus, which contains a 15,034 bp reverse complementary sequence. The organelle genome sequence of C. stoloniferus provides valuable genomic resources for species identification, evolution, and comparative genomic research in Cyperaceae.
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Affiliation(s)
- Xiaorong Miao
- College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Wenwen Yang
- College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Donghai Li
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin, 537000, China
| | - Aiqin Wang
- College of Agriculture, Guangxi University, Nanning, 530004, China.
| | - Juanyun Li
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin, 537000, China
| | - Xu Deng
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin, 537000, China
| | - Longfei He
- College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Junqi Niu
- College of Agriculture, Guangxi University, Nanning, 530004, China.
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin, 537000, China.
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Sanita Lima M, Silva Domingues D, Rossi Paschoal A, Smith DR. Long-read RNA sequencing can probe organelle genome pervasive transcription. Brief Funct Genomics 2024:elae026. [PMID: 38880995 DOI: 10.1093/bfgp/elae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/20/2024] [Accepted: 05/30/2024] [Indexed: 06/18/2024] Open
Abstract
40 years ago, organelle genomes were assumed to be streamlined and, perhaps, unexciting remnants of their prokaryotic past. However, the field of organelle genomics has exposed an unparallel diversity in genome architecture (i.e. genome size, structure, and content). The transcription of these eccentric genomes can be just as elaborate - organelle genomes are pervasively transcribed into a plethora of RNA types. However, while organelle protein-coding genes are known to produce polycistronic transcripts that undergo heavy posttranscriptional processing, the nature of organelle noncoding transcriptomes is still poorly resolved. Here, we review how wet-lab experiments and second-generation sequencing data (i.e. short reads) have been useful to determine certain types of organelle RNAs, particularly noncoding RNAs. We then explain how third-generation (long-read) RNA-Seq data represent the new frontier in organelle transcriptomics. We show that public repositories (e.g. NCBI SRA) already contain enough data for inter-phyla comparative studies and argue that organelle biologists can benefit from such data. We discuss the prospects of using publicly available sequencing data for organelle-focused studies and examine the challenges of such an approach. We highlight that the lack of a comprehensive database dedicated to organelle genomics/transcriptomics is a major impediment to the development of a field with implications in basic and applied science.
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Affiliation(s)
- Matheus Sanita Lima
- Department of Biology, Western University, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Douglas Silva Domingues
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Avenida Padua Dias 11, Piracicaba, SP 13418-900, Brazil
| | - Alexandre Rossi Paschoal
- Department of Computer Science, Bioinformatics and Pattern Recognition Group (BIOINFO-CP), Federal University of Technology - Paraná - UTFPR, Avenida Alberto Carazzai 1640, Cornélio Procópio, PR 86300000, Brazil
| | - David Roy Smith
- Department of Biology, Western University, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
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Zhang J, Liu G, Wei J. Assembly and comparative analysis of the first complete mitochondrial genome of Setaria italica. PLANTA 2024; 260:23. [PMID: 38850310 DOI: 10.1007/s00425-024-04386-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/10/2024] [Indexed: 06/10/2024]
Abstract
MAIN CONCLUSION In this study, we assembled the first complete mitochondrial genome of Setaria italica and confirmed the multi-branched architecture. The foxtail millet (Setaria italica) holds significant agricultural importance, particularly in arid and semi-arid regions. It plays a pivotal role in diversifying dietary patterns and shaping planting strategies. Although the chloroplast genome of S. italica has been elucidated in recent studies, the complete mitochondrial genome remains largely unexplored. In this study, we employed PacBio HiFi sequencing platforms to sequence and assemble the complete mitochondrial genome. The mitochondrial genome spans a total length of 446,614 base pairs and harbors a comprehensive set of genetic elements, including 33 unique protein-coding genes (PCGs), encompassing 24 unique mitochondrial core genes and 9 variable genes, along with 20 transfer RNA (tRNA) genes and 3 ribosomal RNA (rRNA) genes. Our analysis of mitochondrial PCGs revealed a pronounced codon usage preference. For instance, the termination codon exhibits a marked preference for UAA, while alanine (Ala) exhibits a preference for GCU, and glutamine (Gln) favors CAA. Notably, the maximum Relative Synonymous Codon Usage (RSCU) values for cysteine (Cys) and phenylalanine (Phe) are both below 1.2, indicating a lack of strong codon usage preference for these amino acids. Phylogenetic analyses consistently place S. italica in close evolutionary proximity to Chrysopogon zizanioides, relative to other Panicoideae plants. Collinearity analysis showed that a total of 39 fragments were identified to display homology with both the mitochondrial and chloroplast genomes. A total of 417 potential RNA-editing sites were discovered across the 33 mitochondrial PCGs. Notably, all these editing events involved the conversion of cytosine (C) to uracil (U). Through the employment of PCR validation coupled with Sanger sequencing for the anticipated editing sites of these codons, RNA-editing events were conclusively identified at two specific loci: nad4L-2 and atp6-1030. The results of this study provide a pivotal foundation for advanced genomic breeding research in foxtail millet. Furthermore, they impart essential insights that will be instrumental for forthcoming investigations into the evolutionary and molecular dynamics of Panicoideae species.
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Affiliation(s)
- Jiewei Zhang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Guiming Liu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Jianhua Wei
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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Gao C, Li T, Zhao X, Wu C, Zhang Q, Zhao X, Wu M, Lian Y, Li Z. Comparative analysis of the chloroplast genomes of Rosa species and RNA editing analysis. BMC PLANT BIOLOGY 2023; 23:318. [PMID: 37316771 DOI: 10.1186/s12870-023-04338-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 06/08/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND The genus Rosa (Rosaceae) contains approximately 200 species, most of which have high ecological and economic values. Chloroplast genome sequences are important for studying species differentiation, phylogeny, and RNA editing. RESULTS In this study, the chloroplast genomes of three Rosa species, Rosa hybrida, Rosa acicularis, and Rosa rubiginosa, were assembled and compared with other reported Rosa chloroplast genomes. To investigate the RNA editing sites in R. hybrida (commercial rose cultivar), we mapped RNA-sequencing data to the chloroplast genome and analyzed their post-transcriptional features. Rosa chloroplast genomes presented a quadripartite structure and had highly conserved gene order and gene content. We identified four mutation hotspots (ycf3-trnS, trnT-trnL, psbE-petL, and ycf1) as candidate molecular markers for differentiation in the Rosa species. Additionally, 22 chloroplast genomic fragments with a total length of 6,192 bp and > 90% sequence similarity with their counterparts were identified in the mitochondrial genome, representing 3.96% of the chloroplast genome. Phylogenetic analysis including all sections and all subgenera revealed that the earliest divergence in the chloroplast phylogeny roughly distinguished species of sections Pimpinellifoliae and Rosa and subgenera Hulthemia. Moreover, DNA- and RNA-sequencing data revealed 19 RNA editing sites, including three synonymous and 16 nonsynonymous, in the chloroplast genome of R. hybrida that were distributed among 13 genes. CONCLUSIONS The genome structure and gene content of Rosa chloroplast genomes are similar across various species. Phylogenetic analysis based on the Rosa chloroplast genomes has high resolution. Additionally, a total of 19 RNA editing sites were validated by RNA-Seq mapping in R. hybrida. The results provide valuable information for RNA editing and evolutionary studies of Rosa and a basis for further studies on genomic breeding of Rosa species.
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Affiliation(s)
- Chengwen Gao
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China.
| | - Teng Li
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China
- School of Public Health, Qingdao University, Qingdao, 266000, Shangdong, China
| | - Xia Zhao
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China
| | - Chuanhong Wu
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China
| | - Qian Zhang
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China
| | - Xiangzhong Zhao
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China
| | - Mingxuan Wu
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China
| | - Yihong Lian
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China
| | - Zhiqiang Li
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China.
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Wei L, Liu TJ, Hao G, Ge XJ, Yan HF. Comparative analyses of three complete Primula mitogenomes with insights into mitogenome size variation in Ericales. BMC Genomics 2022; 23:770. [PMID: 36424546 PMCID: PMC9686101 DOI: 10.1186/s12864-022-08983-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 11/01/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Although knowledge of the sizes, contents, and forms of plant mitochondrial genomes (mitogenomes) is increasing, little is known about the mechanisms underlying their structural diversity. Evolutionary information on the mitogenomes of Primula, an important ornamental taxon, is more limited than the information on their nuclear and plastid counterparts, which has hindered the comprehensive understanding of Primula mitogenomic diversity and evolution. The present study reported and compared three Primula mitogenomes and discussed the size expansion of mitogenomes in Ericales. RESULTS Mitogenome master circles were sequenced and successfully assembled for three Primula taxa and were compared with publicly available Ericales mitogenomes. The three mitogenomes contained similar gene contents and varied primarily in their structures. The Primula mitogenomes possessed relatively high nucleotide diversity among all examined plant lineages. In addition, high nucleotide diversity was found among Primula species between the Mediterranean and Himalaya-Hengduan Mountains. Most predicted RNA editing sites appeared in the second amino acid codon, increasing the hydrophobic character of the protein. An early stop in atp6 caused by RNA editing was conserved across all examined Ericales species. The interfamilial relationships within Ericales and interspecific relationships within Primula could be well resolved based on mitochondrial data. Transfer of the two longest mitochondrial plastid sequences (MTPTs) occurred before the divergence of Primula and its close relatives, and multiple independent transfers could also occur in a single MTPT sequence. Foreign sequence [MTPTs and mitochondrial nuclear DNA sequences (NUMTs)] uptake and repeats were to some extent associated with changes in Ericales mitogenome size, although none of these relationships were significant overall. CONCLUSIONS The present study revealed relatively conserved gene contents, gene clusters, RNA editing, and MTPTs but considerable structural variation in Primula mitogenomes. Relatively high nucleotide diversity was found in the Primula mitogenomes. In addition, mitogenomic genes, collinear gene clusters, and locally collinear blocks (LCBs) all showed phylogenetic signals. The evolutionary history of MTPTs in Primula was complicated, even in a single MTPT sequence. Various reasons for the size variation observed in Ericales mitogenomes were found.
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Affiliation(s)
- Lei Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tong-Jian Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
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Huang KY, Kan SL, Shen TT, Gong P, Feng YY, Du H, Zhao YP, Wan T, Wang XQ, Ran JH. A Comprehensive Evolutionary Study of Chloroplast RNA Editing in Gymnosperms: A Novel Type of G-to-A RNA Editing Is Common in Gymnosperms. Int J Mol Sci 2022; 23:ijms231810844. [PMID: 36142757 PMCID: PMC9505161 DOI: 10.3390/ijms231810844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 12/05/2022] Open
Abstract
Although more than 9100 plant plastomes have been sequenced, RNA editing sites of the whole plastome have been experimentally verified in only approximately 21 species, which seriously hampers the comprehensive evolutionary study of chloroplast RNA editing. We investigated the evolutionary pattern of chloroplast RNA editing sites in 19 species from all 13 families of gymnosperms based on a combination of genomic and transcriptomic data. We found that the chloroplast C-to-U RNA editing sites of gymnosperms shared many common characteristics with those of other land plants, but also exhibited many unique characteristics. In contrast to that noted in angiosperms, the density of RNA editing sites in ndh genes was not the highest in the sampled gymnosperms, and both loss and gain events at editing sites occurred frequently during the evolution of gymnosperms. In addition, GC content and plastomic size were positively correlated with the number of chloroplast RNA editing sites in gymnosperms, suggesting that the increase in GC content could provide more materials for RNA editing and facilitate the evolution of RNA editing in land plants or vice versa. Interestingly, novel G-to-A RNA editing events were commonly found in all sampled gymnosperm species, and G-to-A RNA editing exhibits many different characteristics from C-to-U RNA editing in gymnosperms. This study revealed a comprehensive evolutionary scenario for chloroplast RNA editing sites in gymnosperms, and reported that a novel type of G-to-A RNA editing is prevalent in gymnosperms.
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Affiliation(s)
- Kai-Yuan Huang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sheng-Long Kan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ting-Ting Shen
- School of Earth Sciences, East China University of Technology, Nanchang 330013, China
| | - Pin Gong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yuan-Yuan Feng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Du
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yun-Peng Zhao
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Tao Wan
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence:
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Li J, Li J, Ma Y, Kou L, Wei J, Wang W. The complete mitochondrial genome of okra (Abelmoschus esculentus): using nanopore long reads to investigate gene transfer from chloroplast genomes and rearrangements of mitochondrial DNA molecules. BMC Genomics 2022; 23:481. [PMID: 35768783 PMCID: PMC9245263 DOI: 10.1186/s12864-022-08706-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/13/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Okra (Abelmoschus esculentus L. Moench) is an economically important crop and is known for its slimy juice, which has significant scientific research value. The A. esculentus chloroplast genome has been reported; however, the sequence of its mitochondrial genome is still lacking. RESULTS We sequenced the plastid and mitochondrial genomes of okra based on Illumina short reads and Nanopore long reads and conducted a comparative study between the two organelle genomes. The plastid genome of okra is highly structurally conserved, but the mitochondrial genome of okra has been confirmed to have abundant subgenomic configurations. The assembly results showed that okra's mitochondrial genome existed mainly in the form of two independent molecules, which could be divided into four independent molecules through two pairs of long repeats. In addition, we found that four pairs of short repeats could mediate the integration of the two independent molecules into one complete molecule at a low frequency. Subsequently, we also found extensive sequence transfer between the two organelles of okra, where three plastid-derived genes (psaA, rps7 and psbJ) remained intact in the mitochondrial genome. Furthermore, psbJ, psbF, psbE and psbL were integrated into the mitochondrial genome as a conserved gene cluster and underwent pseudogenization as nonfunctional genes. Only psbJ retained a relatively complete sequence, but its expression was not detected in the transcriptome data, and we speculate that it is still nonfunctional. Finally, we characterized the RNA editing events of protein-coding genes located in the organelle genomes of okra. CONCLUSIONS In the current study, our results not only provide high-quality organelle genomes for okra but also advance our understanding of the gene dialogue between organelle genomes and provide information to breed okra cultivars efficiently.
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Affiliation(s)
- Jihan Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
| | - Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
| | - Yubo Ma
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
| | - Lu Kou
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
| | - Juanjuan Wei
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, No.2 Tiansheng Road, Beibei District, Chongqing, 400716 China
| | - Weixing Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, No.2 Tiansheng Road, Beibei District, Chongqing, 400716 China
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9
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Yang Z, Ni Y, Lin Z, Yang L, Chen G, Nijiati N, Hu Y, Chen X. De novo assembly of the complete mitochondrial genome of sweet potato (Ipomoea batatas [L.] Lam) revealed the existence of homologous conformations generated by the repeat-mediated recombination. BMC PLANT BIOLOGY 2022; 22:285. [PMID: 35681138 PMCID: PMC9185937 DOI: 10.1186/s12870-022-03665-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/30/2022] [Indexed: 05/27/2023]
Abstract
Sweet potato (Ipomoea batatas [L.] Lam) is an important food crop, an excellent fodder crop, and a new type of industrial raw material crop. The lack of genomic resources could affect the process of industrialization of sweet potato. Few detailed reports have been completed on the mitochondrial genome of sweet potato. In this research, we sequenced and assembled the mitochondrial genome of sweet potato and investigated its substructure. The mitochondrial genome of sweet potato is 270,304 bp with 23 unique core genes and 12 variable genes. We detected 279 pairs of repeat sequences and found that three pairs of direct repeats could mediate the homologous recombination into four independent circular molecules. We identified 70 SSRs in the whole mitochondrial genome of sweet potato. The longest dispersed repeat in mitochondrial genome was a palindromic repeat with a length of 915 bp. The homologous fragments between the chloroplast and mitochondrial genome account for 7.35% of the mitochondrial genome. We also predicted 597 RNA editing sites and found that the rps3 gene was edited 54 times, which occurred most frequently. This study further demonstrates the existence of multiple conformations in sweet potato mitochondrial genomes and provides a theoretical basis for the evolution of higher plants and cytoplasmic male sterility breeding.
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Affiliation(s)
- Zhijian Yang
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yang Ni
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zebin Lin
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
| | - Liubin Yang
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
| | - Guotai Chen
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
| | - Nuerla Nijiati
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
| | - Yunzhuo Hu
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
| | - Xuanyang Chen
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fuzhou, Fujian China
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Fang B, Li J, Zhao Q, Liang Y, Yu J. Assembly of the Complete Mitochondrial Genome of Chinese Plum ( Prunus salicina): Characterization of Genome Recombination and RNA Editing Sites. Genes (Basel) 2021; 12:genes12121970. [PMID: 34946920 PMCID: PMC8701122 DOI: 10.3390/genes12121970] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 12/28/2022] Open
Abstract
Despite the significant progress that has been made in the genome sequencing of Prunus, this area of research has been lacking a systematic description of the mitochondrial genome of this genus for a long time. In this study, we assembled the mitochondrial genome of the Chinese plum (Prunus salicina) using Illumina and Oxford Nanopore sequencing data. The mitochondrial genome size of P. salicina was found to be 508,035 base pair (bp), which is the largest reported in the Rosaceae family to date, and P. salicina was shown to be 63,453 bp longer than sweet cherry (P. avium). The P. salicina mitochondrial genome contained 37 protein-coding genes (PCGs), 3 ribosomal RNA (rRNA) genes, and 16 transfer RNA (tRNA) genes. Two plastid-derived tRNA were identified. We also found two short repeats that captured the nad3 and nad6 genes and resulted in two copies. In addition, nine pairs of repeat sequences were identified as being involved in the mediation of genome recombination. This is crucial for the formation of subgenomic configurations. To characterize RNA editing sites, transcriptome data were used, and we identified 480 RNA editing sites in protein-coding sequences. Among them, the initiation codon of the nad1 gene confirmed that an RNA editing event occurred, and the genomic encoded ACG was edited as AUG in the transcript. Combined with previous reports on the chloroplast genome, our data complemented our understanding of the last part of the organelle genome of plum, which will facilitate our understanding of the evolution of organelle genomes.
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Affiliation(s)
- Bo Fang
- Fruit Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China; (B.F.); (Q.Z.)
| | - Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China;
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, Chongqing 400716, China
| | - Qian Zhao
- Fruit Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China; (B.F.); (Q.Z.)
| | - Yuping Liang
- College of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China;
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China;
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, Chongqing 400716, China
- Correspondence:
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