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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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Chen G, Kang R, Wang Z, Jiang Y, Zhou H, Abuduaini A, Suo F, Huang L. The complete mitochondrial genome of Cuminum cyminum (Apiales: Apiaceae) and phylogenetic analysis. Mitochondrial DNA B Resour 2023; 8:760-765. [PMID: 37521907 PMCID: PMC10375935 DOI: 10.1080/23802359.2023.2238357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 07/13/2023] [Indexed: 08/01/2023] Open
Abstract
Cumin (Cuminum cyminum L). belongs to the family Apiaceae and the order Apiales, which is a widely grown spice and medicinal plant in Xinjiang province, China. In the current study, whole genome sequencing of C. cyminum was performed using the Illumina HiSeq 4000 platform, and the complete mitogenome sequence was assembled and annotated. We found that the single circular mitogenome of C. cyminum was 246,721 bp in length, and has about 45.5% GC content. It comprised 73 genes in the coding region (35 protein-coding genes, 18 tRNA genes, 3 rRNA genes, and 15 open-reading frames) and a non-coding region. Phylogenetic analysis indicated that C. cyminum is closely related to Daucus carota and the subtribes Daucinae. The mitogenome of C. cyminum revealed its phylogenetic relationships with other species in the Apiaceae family, which would further help in understanding its evolution.
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Affiliation(s)
- Ge Chen
- College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Ruiping Kang
- College of Life Science and Technology, Xinjiang University, Urumchi, Xinjiang, China
| | - Zihao Wang
- College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Yu Jiang
- College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Huiying Zhou
- College of Life Science and Technology, Xinjiang University, Urumchi, Xinjiang, China
| | - Aifeire Abuduaini
- College of Life Science and Technology, Xinjiang University, Urumchi, Xinjiang, China
| | - Feiya Suo
- College of Life Science and Technology, Xinjiang University, Urumchi, Xinjiang, China
| | - Luodong Huang
- College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
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Tian R, Aou X, Song B, Li Z, He X, Zhou S. Plastid Phylogenomic Analyses Reveal a Cryptic Species of Ligusticopsis (Apiaceae, Angiosperms). Int J Mol Sci 2023; 24:ijms24087419. [PMID: 37108580 PMCID: PMC10138589 DOI: 10.3390/ijms24087419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/06/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Ligusticopsis litangensis is identified and described as a cryptic species from Sichuan Province, China. Although the distribution of this cryptic species overlaps with that of Ligusticopsis capillacea and Ligusticopsis dielsiana, the morphological boundaries between them are explicit and have obviously distinguishable characters. The main distinguishing features of the cryptic species are as follows: long conical multi-branched roots, very short pedicels in compound umbels, unequal rays, oblong-globose fruits, 1-2 vittae per furrow and 3-4 vittae on the commissure. The above-mentioned features differ somewhat from other species within the genus Ligusticopsis, but generally coincide with the morphological boundaries defined for the genus Ligusticopsis. To determine the taxonomic position of L. litangensis, we sequenced and assembled the plastomes of L. litangensis and compared them with the plastomes of 11 other species of the genus Ligusticopsis. Notably, both phylogenetic analyses based on ITS sequences and the complete chloroplast genome robustly supported that three accessions of L. litangensis are monophyletic clade and then nested in Ligusticopsis genus. Moreover, the plastid genomes of 12 Ligusticopsis species, including the new species, were highly conserved in terms of gene order, gene content, codon bias, IR boundaries and SSR content. Overall, the integration of morphological, comparative genomic and phylogenetic evidence indicates that Ligusticopsis litangensis actually represents a new species.
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Affiliation(s)
- Rongming Tian
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xueyimu Aou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Boni Song
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Zixuan Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xingjin He
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Songdong Zhou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
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Ni Y, Li J, Chen H, Yue J, Chen P, Liu C. Comparative analysis of the chloroplast and mitochondrial genomes of Saposhnikovia divaricata revealed the possible transfer of plastome repeat regions into the mitogenome. BMC Genomics 2022; 23:570. [PMID: 35945507 PMCID: PMC9364500 DOI: 10.1186/s12864-022-08821-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 08/04/2022] [Indexed: 11/23/2022] Open
Abstract
Background Saposhnikovia divaricata (Turcz.) Schischk. is a perennial herb whose dried roots are commonly used as a source of traditional medicines. To elucidate the organelle-genome-based phylogeny of Saposhnikovia species and the transfer of DNA between organelle genomes, we sequenced and characterised the mitochondrial genome (mitogenome) of S. divaricata. Results The mitogenome of S. divaricata is a circular molecule of 293,897 bp. The nucleotide composition of the mitogenome is as follows: A, 27.73%; T, 27.03%; C, 22.39%; and G, 22.85. The entire gene content is 45.24%. A total of 31 protein-coding genes, 20 tRNAs and 4 rRNAs, including one pseudogene (rpl16), were annotated in the mitogenome. Phylogenetic analysis of the organelle genomes from S. divaricata and 10 related species produced congruent phylogenetic trees. Selection pressure analysis revealed that most of the mitochondrial genes of related species are highly conserved. Moreover, 2 and 46 RNA-editing sites were found in the chloroplast genome (cpgenome) and mitogenome protein-coding regions, respectively. Finally, a comparison of the cpgenome and the mitogenome assembled from the same dataset revealed 10 mitochondrial DNA fragments with sequences similar to those in the repeat regions of the cpgenome, suggesting that the repeat regions might be transferred into the mitogenome. Conclusions In this study, we assembled and annotated the mitogenome of S. divaricata. This study provides valuable information on the taxonomic classification and molecular evolution of members of the family Apiaceae. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08821-0.
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Affiliation(s)
- Yang Ni
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, 100193, Beijing, P. R. China
| | - Jingling Li
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, 100193, Beijing, P. R. China
| | - Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, 100193, Beijing, P. R. China
| | - Jingwen Yue
- College of Agriculture, Fujian Agriculture and Forestry University, No.15, Shang Xiadian Road, Fuzhou, Fujian Province, 350002, P. R. China
| | - Pinghua Chen
- College of Agriculture, Fujian Agriculture and Forestry University, No.15, Shang Xiadian Road, Fuzhou, Fujian Province, 350002, P. R. China.
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, 100193, Beijing, P. R. China.
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Huang R, Xie X, Chen A, Li F, Tian E, Chao Z. The chloroplast genomes of four Bupleurum (Apiaceae) species endemic to Southwestern China, a diversity center of the genus, as well as their evolutionary implications and phylogenetic inferences. BMC Genomics 2021; 22:714. [PMID: 34600494 PMCID: PMC8487540 DOI: 10.1186/s12864-021-08008-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 09/13/2021] [Indexed: 11/28/2022] Open
Abstract
Background As one of the largest genera in Apiaceae, Bupleurum L. is well known for its high medicinal value. The genus has frequently attracted the attention of evolutionary biologist and taxonomist for its distinctive characteristics in the Apiaceae family. Although some chloroplast genomes data have been now available, the changes in the structure of chloroplast genomes and selective pressure in the genus have not been fully understood. In addition, few of the species are endemic to Southwest China, a distribution and diversity center of Chinese Bupleurum. Endemic species are key components of biodiversity and ecosystems, and investigation of the chloroplast genomes features of endemic species in Bupleurum will be helpful to develop a better understanding of evolutionary process and phylogeny of the genus. In this study, we analyzed the sequences of whole chloroplast genomes of 4 Southwest China endemic Bupleurum species in comparison with the published data of 17 Bupleurum species to determine the evolutionary characteristics of the genus and the phylogenetic relationships of Asian Bupleurum. Results The complete chloroplast genome sequences of the 4 endemic Bupleurum species are 155,025 bp to 155,323 bp in length including a SSC and a LSC region separated by a pair of IRs. Comparative analysis revealed an identical chloroplast gene content across the 21 Bupleurum species, including a total of 114 unique genes (30 tRNA genes, 4 rRNA genes and 80 protein-coding genes). Chloroplast genomes of the 21 Bupleurum species showed no rearrangements and a high sequence identity (96.4–99.2%). They also shared a similar tendency of SDRs and SSRs, but differed in number (59–83). In spite of their high conservation, they contained some mutational hotspots, which can be potentially exploited as high-resolution DNA barcodes for species discrimination. Selective pressure analysis showed that four genes were under positive selection. Phylogenetic analysis revealed that the 21 Bupleurum formed two major clades, which are likely to correspond to their geographical distribution. Conclusions The chloroplast genome data of the four endemic Bupleurum species provide important insights into the characteristics and evolution of chloroplast genomes of this genu, and the phylogeny of Bupleurum. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08008-z.
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Affiliation(s)
- Rong Huang
- Department of Pharmacy, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China
| | - Xuena Xie
- Department of Pharmacy, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China
| | - Aimin Chen
- Department of Pharmacy, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China
| | - Fang Li
- Department of Pharmacy, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China
| | - Enwei Tian
- Department of Pharmacy, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China
| | - Zhi Chao
- Department of Pharmacy, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China. .,Faculty of Medicinal Plants and Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China. .,Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou, 510515, China.
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Wang Y, Lan Q, Zhao X, Wang L, Yu W, Wang B, Wang Y. The complete mitochondrial genome of Coriandrum sativum. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2391-2392. [PMID: 34345704 PMCID: PMC8288116 DOI: 10.1080/23802359.2021.1951131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Using Oxford Nanopore and Illumina sequencing technologies, we reported the first complete mitochondrial genome of the important medicinal and edible plant Coriandrum sativum. The complete mitogenome was assembled into two circular-mapping forms of 82,926 bp (cir1) and 224,590 bp (cir2), respectively. There were 28 genes identified in the cir1 mitogenome, which included 14 protein-coding genes, 2 rRNA genes and 12 tRNA genes. There were 62 genes identified in the cir2 mitogenome, which included 41 protein-coding genes, 5 rRNA genes and 16 tRNA genes. Phylogenetic analysis showed that Coriandrum sativum was most closely related to Daucus carota.
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Affiliation(s)
- Yiheng Wang
- Biotechnology Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Qingkuo Lan
- Biotechnology Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Xin Zhao
- Biotechnology Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Luping Wang
- Biotechnology Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Wancong Yu
- Biotechnology Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Bo Wang
- Biotechnology Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Yong Wang
- Biotechnology Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
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Wang ZF, Cao HL. The complete mitochondrial genome sequence of Aquilaria sinensis. Mitochondrial DNA B Resour 2021; 6:381-383. [PMID: 33628874 PMCID: PMC7889115 DOI: 10.1080/23802359.2020.1869609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/19/2020] [Indexed: 11/19/2022] Open
Abstract
Aquilaria sinensis, endemic to China, is an economically important evergreen tree species and a source of agarwood. Due to the high market demand for agarwood, this species is heavily overexploited in the wild and is now listed as an endangered species. Although its nuclear and chloroplast genomes have been previously reported, little is known about its mitochondrial genome. Using the paired-end short reads generated by the Illumina sequencing platform, we assembled and herein report the mitochondrial genome of A. sinensis for future phylogenetic, evolutionary, and preservative studies. The length of the A. sinensis mitochondrial genome was found to be 341,829 bp and the GC content was 45.01%. A total of 32 protein-coding genes, 19 tRNA genes, and three rRNA genes were annotated. The phylogenetic tree indicated that A. sinensis is most closely genetically related to Vigna radiata.
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Affiliation(s)
- Zheng-Feng Wang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Hong-Lin Cao
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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