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Sun J, Dong X, Cao Q, Xu T, Zhu M, Sun J, Dong T, Ma D, Han Y, Li Z. A systematic comparison of eight new plastome sequences from Ipomoea L. PeerJ 2019; 7:e6563. [PMID: 30881765 PMCID: PMC6417408 DOI: 10.7717/peerj.6563] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 02/04/2019] [Indexed: 11/20/2022] Open
Abstract
Background Ipomoea is the largest genus in the family Convolvulaceae. The species in this genus have been widely used in many fields, such as agriculture, nutrition, and medicine. With the development of next-generation sequencing, more than 50 chloroplast genomes of Ipomoea species have been sequenced. However, the repeats and divergence regions in Ipomoea have not been well investigated. In the present study, we sequenced and assembled eight chloroplast genomes from sweet potato's close wild relatives. By combining these with 32 published chloroplast genomes, we conducted a detailed comparative analysis of a broad range of Ipomoea species. Methods Eight chloroplast genomes were assembled using short DNA sequences generated by next-generation sequencing technology. By combining these chloroplast genomes with 32 other published Ipomoea chloroplast genomes downloaded from GenBank and the Oxford Research Archive, we conducted a comparative analysis of the repeat sequences and divergence regions across the Ipomoea genus. In addition, separate analyses of the Batatas group and Quamoclit group were also performed. Results The eight newly sequenced chloroplast genomes ranged from 161,225 to 161,721 bp in length and displayed the typical circular quadripartite structure, consisting of a pair of inverted repeat (IR) regions (30,798-30,910 bp each) separated by a large single copy (LSC) region (87,575-88,004 bp) and a small single copy (SSC) region (12,018-12,051 bp). The average guanine-cytosine (GC) content was approximately 40.5% in the IR region, 36.1% in the LSC region, 32.2% in the SSC regions, and 37.5% in complete sequence for all the generated plastomes. The eight chloroplast genome sequences from this study included 80 protein-coding genes, four rRNAs (rrn23, rrn16, rrn5, and rrn4.5), and 37 tRNAs. The boundaries of single copy regions and IR regions were highly conserved in the eight chloroplast genomes. In Ipomoea, 57-89 pairs of repetitive sequences and 39-64 simple sequence repeats were found. By conducting a sliding window analysis, we found six relatively high variable regions (ndhA intron, ndhH-ndhF, ndhF-rpl32, rpl32-trnL, rps16-trnQ, and ndhF) in the Ipomoea genus, eight (trnG, rpl32-trnL, ndhA intron, ndhF-rpl32, ndhH-ndhF, ccsA-ndhD, trnG-trnR, and pasA-ycf3) in the Batatas group, and eight (ndhA intron, petN-psbM, rpl32-trnL, trnG-trnR, trnK-rps16, ndhC-trnV, rps16-trnQ, and trnG) in the Quamoclit group. Our maximum-likelihood tree based on whole chloroplast genomes confirmed the phylogenetic topology reported in previous studies. Conclusions The chloroplast genome sequence and structure were highly conserved in the eight newly-sequenced Ipomoea species. Our comparative analysis included a broad range of Ipomoea chloroplast genomes, providing valuable information for Ipomoea species identification and enhancing the understanding of Ipomoea genetic resources.
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Affiliation(s)
- Jianying Sun
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China.,Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, China
| | - Xiaofeng Dong
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China.,Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, China
| | - Qinghe Cao
- Jiangsu Xuhuai Regional Xuzhou Institute of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Xuzhou, China
| | - Tao Xu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China.,Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, China
| | - Mingku Zhu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China.,Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, China
| | - Jian Sun
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China.,Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, China
| | - Tingting Dong
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China.,Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, China
| | - Daifu Ma
- Jiangsu Xuhuai Regional Xuzhou Institute of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Xuzhou, China
| | - Yonghua Han
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China.,Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, China
| | - Zongyun Li
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China.,Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, China
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Li ZH, Ma X, Wang DY, Li YX, Wang CW, Jin XH. Evolution of plastid genomes of Holcoglossum (Orchidaceae) with recent radiation. BMC Evol Biol 2019; 19:63. [PMID: 30808310 DOI: 10.1186/s12862-019-1384-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 02/11/2019] [Indexed: 01/08/2023] Open
Abstract
Background The plastid is a semiautonomous organelle with its own genome. Plastid genomes have been widely used as models for studying phylogeny, speciation and adaptive evolution. However, most studies focus on comparisons of plastid genome evolution at high taxonomic levels, and comparative studies of the process of plastome evolution at the infrageneric or intraspecific level remain elusive. Holcoglossum is a small genus of Orchidaceae, consisting of approximately 20 species of recent radiation. This made it an ideal group to explore the plastome mutation mode at the infrageneric or intraspecific level. Results In this paper, we reported 15 complete plastid genomes from 12 species of Holcoglossum and 1 species of Vanda. The plastid genomes of Holcoglossum have a total length range between 145 kb and 148 kb, encoding a set of 102 genes. The whole set of ndh-gene families in Holcoglossum have been truncated or pseudogenized. Hairpin inversion in the coding region of the plastid gene ycf2 has been found. Conclusions Using a comprehensive comparative plastome analysis, we found that all the indels between different individuals of the same species resulted from the copy number variation of the short repeat sequence, which may be caused by replication slippage. Annotation of tandem repeats shows that the variation introduced by tandem repeats is widespread in plastid genomes. The hairpin inversion found in the plastid gene ycf2 occurred randomly in the Orchidaceae. Electronic supplementary material The online version of this article (10.1186/s12862-019-1384-5) contains supplementary material, which is available to authorized users.
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Abstract
BACKGROUND The plastid is a semiautonomous organelle with its own genome. Plastid genomes have been widely used as models for studying phylogeny, speciation and adaptive evolution. However, most studies focus on comparisons of plastid genome evolution at high taxonomic levels, and comparative studies of the process of plastome evolution at the infrageneric or intraspecific level remain elusive. Holcoglossum is a small genus of Orchidaceae, consisting of approximately 20 species of recent radiation. This made it an ideal group to explore the plastome mutation mode at the infrageneric or intraspecific level. RESULTS In this paper, we reported 15 complete plastid genomes from 12 species of Holcoglossum and 1 species of Vanda. The plastid genomes of Holcoglossum have a total length range between 145 kb and 148 kb, encoding a set of 102 genes. The whole set of ndh-gene families in Holcoglossum have been truncated or pseudogenized. Hairpin inversion in the coding region of the plastid gene ycf2 has been found. CONCLUSIONS Using a comprehensive comparative plastome analysis, we found that all the indels between different individuals of the same species resulted from the copy number variation of the short repeat sequence, which may be caused by replication slippage. Annotation of tandem repeats shows that the variation introduced by tandem repeats is widespread in plastid genomes. The hairpin inversion found in the plastid gene ycf2 occurred randomly in the Orchidaceae.
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Affiliation(s)
- Zhang-Hai Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Ma
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - De-Yi Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yun-Xia Li
- Fujian Agriculture and Forest University, Shanxiadian Road 15, Changshan District, Fuzhou, 350002, Fujian, China
| | - Cheng-Wang Wang
- Nanchang University, Xuefu Road 999, Honggutang District, Nanchang, Jiangxi, China
| | - Xiao-Hua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Science (CAS-SEABRI), Nay Pyi Taw, Myanmar.
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