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Liu Q, Dai J, Chen J, Liu Z, Lin Y, Qiu G, Gao X, Zhang R, Zhu S. Comparative analysis the chloroplast genomes of Celastrus (Celastraceae) species: Provide insights into molecular evolution, species identification and phylogenetic relationships. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 131:155770. [PMID: 38851103 DOI: 10.1016/j.phymed.2024.155770] [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: 01/29/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND The genus Celastrus is an important medicinal plant resource. The similarity of morphology and the lack of complete chloroplast genome analysis have significantly impeded the exploration of species identification, molecular evolution and phylogeny of Celastrus. PURPOSE In order to resolve the phylogenic controversy of Celastrus species, the chloroplast genome comparative analysis was performed to provide genetic evidence. METHODS In this study, we collected and sequenced ten chloroplast genomes of Celastrus species from China and downloaded three chloroplast genomes from the databases. The chloroplast genomes were compared and analyzed to explore their characteristics and evolution. Furthermore, the phylogenetic relationships of Celastrus species were inferred based on the whole chloroplast genomes and protein-coding genes. RESULTS All the 13 Celastrus species chloroplast genomes showed a typical quadripartite structure with genome sizes ranging from 155,113 to 157,366 bp. The intron loss of the rps16 gene occurred in all the 13 Celastrus species. The GC content, gene sequence, repeat types and codon bias pattern were highly conserved. Ten highly variation regions were identified, which can be used as potential DNA markers in molecular identification of Celastrus species. Eight genes, including accD, atp4, ndhB, rpoC1, rbcL, rpl2, rpl20 and ycf1, were detected to experience positive selection. Phylogenetic analysis showed that Celastrus was a monophyletic group and Tripterygium was the closest sister-group. Noteworthy, C. gemmatus Loes. and C. orbiculatus Thunb. can be discriminated using the chloroplast genome as a super barcode. The comparative and phylogenetic analysis results proposed that C. tonkinensis Pitard. was the synonym of C. hindsii Benth. CONCLUSION The comparative analysis of the Celastrus chloroplast genomes can provide comprehensive genetic evidence for molecular evolution, species identification and phylogenetic relationships.
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Affiliation(s)
- Qiaozhen Liu
- School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Jiangpeng Dai
- School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Jie Chen
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Zhiwen Liu
- School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Yuexia Lin
- School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Xiaoxia Gao
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China.
| | - Rongxin Zhang
- School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, China.
| | - Shuang Zhu
- School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, China.
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Jia M, Ni Y, Zhao H, Liu X, Yan W, Zhao X, Wang J, He B, Liu H. Full-length transcriptome and RNA-Seq analyses reveal the resistance mechanism of sesame in response to Corynespora cassiicola. BMC PLANT BIOLOGY 2024; 24:64. [PMID: 38262910 PMCID: PMC10804834 DOI: 10.1186/s12870-024-04728-y] [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: 05/26/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024]
Abstract
BACKGROUND Corynespora leaf spot is a common leaf disease occurring in sesame, and the disease causes leaf yellowing and even shedding, which affects the growth quality of sesame. At present, the mechanism of sesame resistance to this disease is still unclear. Understanding the resistance mechanism of sesame to Corynespora leaf spot is highly important for the control of infection. In this study, the leaves of the sesame resistant variety (R) and the sesame susceptible variety (S) were collected at 0-48 hpi for transcriptome sequencing, and used a combined third-generation long-read and next-generation short-read technology approach to identify some key genes and main pathways related to resistance. RESULTS The gene expression levels of the two sesame varieties were significantly different at 0, 6, 12, 24, 36 and 48 hpi, indicating that the up-regulation of differentially expressed genes in the R might enhanced the resistance. Moreover, combined with the phenotypic observations of sesame leaves inoculated at different time points, we found that 12 hpi was the key time point leading to the resistance difference between the two sesame varieties at the molecular level. The WGCNA identified two modules significantly associated with disease resistance, and screened out 10 key genes that were highly expressed in R but low expressed in S, which belonged to transcription factors (WRKY, AP2/ERF-ERF, and NAC types) and protein kinases (RLK-Pelle_DLSV, RLK-Pelle_SD-2b, and RLK-Pelle_WAK types). These genes could be the key response factors in the response of sesame to infection by Corynespora cassiicola. GO and KEGG enrichment analysis showed that specific modules could be enriched, which manifested as enrichment in biologically important pathways, such as plant signalling hormone transduction, plant-pathogen interaction, carbon metabolism, phenylpropanoid biosynthesis, glutathione metabolism, MAPK and other stress-related pathways. CONCLUSIONS This study provides an important resource of genes contributing to disease resistance and will deepen our understanding of the regulation of disease resistance, paving the way for further molecular breeding of sesame.
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Affiliation(s)
- Min Jia
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Yunxia Ni
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China.
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China.
| | - Hui Zhao
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Xintao Liu
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Wenqing Yan
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Xinbei Zhao
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Jing Wang
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Bipo He
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Hongyan Liu
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China.
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China.
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Wang J, Xie QL, Feng EY, Liu XF. The complete chloroplast genome sequence of Rosa 'Limoncello' (Rosales: Rosaceae). Mitochondrial DNA B Resour 2023; 8:1386-1390. [PMID: 38189025 PMCID: PMC10768736 DOI: 10.1080/23802359.2023.2290854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 11/29/2023] [Indexed: 01/09/2024] Open
Abstract
Rosa 'Limoncello' finds applications in gardening and landscaping. In this study, we assembled and annotated the complete chloroplast genome of this variety for the first time. The length of its chloroplast genome was 156,493 bp, containing two short inverted repeat regions of 26,052 bp, each separated by a large single-copy region of 85,649 bp and a small single-copy region of 18,740 bp. The chloroplast DNA of R. 'Limoncello' consisted of 135 genes, including 90 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. On comparing the complete chloroplast sequence of R. 'Limoncello' with that of other Rosa species, R. 'Limoncello' was found to be closely related to Rosa cymosa. Thus, information on the chloroplast genome sequence of this rose variety can facilitate phylogenetic studies of the genus Rosa.
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Affiliation(s)
- Jing Wang
- Zhanjiang University of Science and Technology, Zhanjiang, China
| | - Qiu-lan Xie
- Zhanjiang University of Science and Technology, Zhanjiang, China
| | - En-you Feng
- Zhanjiang Academy of Agricultural Sciences, Zhanjiang, China
| | - Xiao-fei Liu
- Zhanjiang Academy of Agricultural Sciences, Zhanjiang, China
- Environmental Horticulture Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Key Laboratory of Urban Agriculture in South China, Ministry of Agriculture, Guangzhou, 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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Xia Y, Wu H, Li S. The first chloroplast sequence of Rosa davurica Pall. var. Davurica. Mitochondrial DNA B Resour 2023; 8:668-672. [PMID: 37325773 PMCID: PMC10266123 DOI: 10.1080/23802359.2023.2220431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 05/25/2023] [Indexed: 06/17/2023] Open
Abstract
Rosa davurica Pall. var. davurica is a member of the plant family Rosaceae. Although R. davurica has high application value, its chloroplast genome sequence has not been reported. This study aims to reveal the genetic characteristics of the chloroplast genome of Rosa roxburghii. The length of its total chloroplast DNA is 156,971 bp, with 37.22% G/C content. Its chloroplast genome has two inverted repeat (IRa and IRb) regions totaling 26,051 bp which are separated by a large single copy (LSC) region of 86,032 bp and a small single copy (SSC) region of 18,837 bp. The genome contains 131 independent genes (86 protein-coding, 37 tRNA, and 8 rRNA), and there are 18 repeated genes within the IR region. Among these genes, 17 genes contained one or two introns. The phylogenetic analysis showed that R. davurica was relatively close to other Rosa species, such as the Rosa hybrid.
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Affiliation(s)
- Yongxiu Xia
- State Key Laboratory of Tree Genetics and Breeding, Experimental Center of Forestry in North China, National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiulong Mountain in Beijing, Chinese Academy of Forestry, Beijing, China
| | - Hua Wu
- Management Center of Songshushan Nature Reserve, Inner Mongolia, China (Songshushan Forestry Center, Wengniute Banner)
| | - Shaofeng Li
- State Key Laboratory of Tree Genetics and Breeding, Experimental Center of Forestry in North China, National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiulong Mountain in Beijing, Chinese Academy of Forestry, Beijing, China
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Pan H, Zagorchev L, Chen L, Tao Y, Cai C, Jiang M, Sun Z, Li J. Complete chloroplast genomes of five Cuscuta species and their evolutionary significance in the Cuscuta genus. BMC Genomics 2023; 24:310. [PMID: 37291497 DOI: 10.1186/s12864-023-09427-w] [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: 02/03/2023] [Accepted: 06/03/2023] [Indexed: 06/10/2023] Open
Abstract
BACKGROUND Cuscuta, a parasitic plant species in the Convolvulaceae family, grows in many countries and regions. However, the relationship between some species is still unclear. Therefore, more studies are needed to assess the variation of the chloroplast (cp) genome in Cuscuta species and their relationship with subgenera or sections, thus, providing important information on the evolution of Cuscuta species. RESULTS In the present study, we identified the whole cp genomes of C. epithymum, C. europaea, C. gronovii, C. chinensis and C. japonica, and then constructed a phylogenetic tree of 23 Cuscuta species based on the complete genome sequences and protein-coding genes. The complete cp genome sequences of C. epithymum and C. europaea were 96,292 and 97,661 bp long, respectively, and lacked an inverted repeat region. Most cp genomes of Cuscuta spp. have tetragonal and circular structures except for C. epithymum, C. europaea, C. pedicellata and C. approximata. Based on the number of genes and the structure of cp genome and the patterns of gene reduction, we found that C. epithymum and C. europaea belonged to subgenus Cuscuta. Most of the cp genomes of the 23 Cuscuta species had single nucleotide repeats of A and T. The inverted repeat region boundaries among species were similar in the same subgenera. Several cp genes were lost. In addition, the numbers and types of the lost genes in the same subgenus were similar. Most of the lost genes were related to photosynthesis (ndh, rpo, psa, psb, pet, and rbcL), which could have gradually caused the plants to lose the ability to photosynthesize. CONCLUSION Our results enrich the data on cp. genomes of genus Cuscuta. This study provides new insights into understanding the phylogenetic relationships and variations in the cp genome of Cuscuta species.
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Affiliation(s)
- Hangkai Pan
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
- School of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Lyuben Zagorchev
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
- Department of Biochemistry, Faculty of Biology, Sofia University "St. Kliment Ohridski", 8 Dragan Tsankov Blvd., Sofia, 1164, Bulgaria
| | - Luxi Chen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
| | - Yutian Tao
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
- School of Electronics and Information Engineering, Taizhou University, Taizhou, 318000, China
| | - Chaonan Cai
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
- School of Advanced Study, Taizhou University, Taizhou, 318000, China
| | - Ming Jiang
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
| | - Zhongshuai Sun
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
- School of Advanced Study, Taizhou University, Taizhou, 318000, China
| | - Junmin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China.
- School of Advanced Study, Taizhou University, Taizhou, 318000, China.
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Mu Z, Zhang Y, Zhang B, Cheng Y, Shang F, Wang H. Intraspecific Chloroplast Genome Variation and Domestication Origins of Major Cultivars of Styphnolobium japonicum. Genes (Basel) 2023; 14:1156. [PMID: 37372336 DOI: 10.3390/genes14061156] [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: 04/17/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Styphnolobium japonicum is a significant resource of ornamental and medicinal plants. In this study, we employed high-throughput sequencing to assemble nine chloroplast genomes of S. japonicum. We compared and reconstructed the phylogenetic relationships of these genomes, along with three publicly available chloroplast genomes. Our results showed that the length of the 12 S. japonicum chloroplast genomes ranged from 158,613 bp to 158,837 bp, all containing 129 unique functional genes. The genetic diversity within S. japonicum chloroplast genomes was relatively low, with π = 0.00029, Theta-W = 0.00028, and an indel frequency of 0.62 indels/1 kb. Among the four regions, the SSC region exhibited the highest genetic diversity and indel frequency, while the IR region had the lowest. Non-coding regions displayed greater genetic variation compared to coding regions, with a few highly variable regions identified. The phylogenetic tree constructed revealed that the major cultivars of S. japonicum originated from two genetic 'sources. S. japonicum 'JinhuaiJ2' had an independent origin and showed close relatedness to S. japonicum var. violacea, S. japonicum var. japonicum, and S. japonicum f. oligophylla. On the other hand, other major cultivars shared a common genetic origin and were closely related to S. japonicum f. pendula. This study highlights the variability of chloroplast genomes within S. japonicum and provides insights into the genetic origins of major cultivars and their relationships with different varieties and forma.
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Affiliation(s)
- Zhiqiang Mu
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Yu Zhang
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Bin Zhang
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Yueqin Cheng
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Fude Shang
- College of Life Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Hongwei Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
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Abe Y, Ide T, Matsuo K, Maeto K, Wu Y. Extinction Threat to a Previously Undescribed Species of Gall Wasp (Hymenoptera: Cynipidae) and Two Associated Parasitoid Species (Hymenoptera: Braconidae and Eulophidae) on a Threatened Rose. ANNALS OF THE ENTOMOLOGICAL SOCIETY OF AMERICA 2023; 116:154-161. [PMID: 37201158 PMCID: PMC10187585 DOI: 10.1093/aesa/saad004] [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: 09/28/2022] [Indexed: 05/20/2023]
Abstract
Diplolepis ogawai Abe and Ide sp. nov. (Hymenoptera: Cynipidae) induces galls on Rosa hirtula (Regel) Nakai (Rosales: Rosaceae), which is endemic to a restricted area of Honshu, the main island of Japan. The gall is induced mainly on the leaf of R. hirtula in spring and the mature gall falls to the ground in early summer. The gall-inducing wasp emerges from the gall on the ground in the following spring, suggesting that D. ogawai is univoltine. From spring to summer, the braconid Syntomernus flavus Samartsev and Ku and the eulophid Aprostocetus sp. are parasitic on the larva of D. ogawai in the gall, and the adult wasp of both parasitoid species emerges from the gall on the ground in summer. For S. flavus, this is the first distribution record in Japan and the first host record. Since R. hirtula is threatened with extinction by succession and deforestation, D. ogawai and its two parasitoid wasp species are considered to be at risk of coextinction with the threatened rose. In the event that the population size of this rose species is further reduced, D. ogawai and its parasitoids may -become extinct prior to the extinction of R. hirtula. To conserve these three wasp species associated with R. hirtula, protection of remnant vegetation where individuals of this threatened rose species grow is necessary.
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Affiliation(s)
| | - Tatsuya Ide
- Department of Zoology, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki 305-0005, Japan
| | - Kazunori Matsuo
- Faculty of Social and Cultural Studies, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Kaoru Maeto
- Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Yajiao Wu
- Graduate School of Integrated Sciences for Global Society, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
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Xu Y, Liu Y, Yu Z, Jia X. Complete Chloroplast Genome Sequence of the Long Blooming Cultivar Camellia 'Xiari Qixin': Genome Features, Comparative and Phylogenetic Analysis. Genes (Basel) 2023; 14:460. [PMID: 36833387 PMCID: PMC9956581 DOI: 10.3390/genes14020460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
The camellia flower is a famous woody plant with a long-cultivated history and high ornamental value. It is extensively planted and utilized around the world and owns a massive germplasm resource. Camellia 'Xiari Qixin' belongs to one of the typical cultivars in the four seasons camellia hybrids series. Due to its long flowering period, this kind of cultivar is identified as a precious resource of camellia flowers. In this study, the complete chloroplast genome sequence of C. 'Xiari Qixin' was first reported. Its whole chloroplast genome is 157,039 bp in length with an overall GC content of 37.30%, composed of a large single copy region (LSC, 86,674 bp), a small single copy region (SSC, 18,281 bp), and a pair of inverted repeat regions (IRs, 26,042 bp each). A total of 134 genes were predicted in this genome, including 8 ribosomal RNA genes, 37 transfer RNA genes, and 89 protein-coding genes. In addition, 50 simple sequence repeats (SSRs) and 36 long repeat sequences were detected. By comparing C. 'Xiari Qixin' and seven Camellia species on the chloroplast genome, seven mutation hotspot regions were identified, including psbK, trnS (GCU)-trnG(GCC), trnG(GCC), petN-psbM, trnF(GAA)-ndhJ, trnP(UGG)-psaJ, and ycf1. Phylogenetic analysis of 30 chloroplast genomes showed that the genetic relationship between C. 'Xiari Qixin' and Camellia azalea is quite close in evolution. These results could not only provide a valuable database for determining the maternal origin of Camellia cultivars, but also contribute to the exploration of the phylogenetic relationship and utilization of germplasm resources for Camellia.
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Affiliation(s)
| | | | | | - Xiaocheng Jia
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
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Park JM, Koo J. The complete chloroplast genome sequence of Berchemia racemosa Siebold & Zucc. (Rhamnaceae), a rare plant species in Korea. Mitochondrial DNA B Resour 2023; 8:69-72. [PMID: 36620322 PMCID: PMC9817123 DOI: 10.1080/23802359.2022.2161329] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Berchemia racemosa Siebold & Zucc., 1845 is a rare species distributed in restricted areas in the western Korean peninsula. In this study, the complete chloroplast genome (plastome) of B. racemosa was sequenced and assembled by Illumina paired-end sequencing. The plastome of B. racemosa was 161,187 bp in length and was quadripartite in structure, including a large single-copy (LSC) region of 89,503 bp, a small single-copy (SSC) region of 18,214 bp, and two inverted repeats of 26,735 bp. The GC content was 37.2%. The plastome of B. racemosa contains 130 genes, including eight ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes, and 85 protein-coding genes. Phylogenetic analysis using complete genome sequences showed that B. racemosa is most closely related to Berchemia flavescens.
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Affiliation(s)
- Joon Moh Park
- Forest Resource Research Division, Jeollabuk-do Forest Environment Research Institute, Jinan, South Korea
| | - Jachoon Koo
- Division of Science Education and Institute of Fusion Science, College of Education, Jeonbuk National University, Jeonju, South Korea,CONTACT Jachoon Koo Division of Science Education and Institute of Fusion Science, College of Education, Jeonbuk National University, Jeonju, South Korea
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The Complete Chloroplast Genome Sequence of Machilus chuanchienensis (Lauraceae): Genome Structure and Phylogenetic Analysis. Genes (Basel) 2022; 13:genes13122402. [PMID: 36553669 PMCID: PMC9778441 DOI: 10.3390/genes13122402] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Machilus chuanchienensis is an ecological tree distributed in southwestern China. It has a significant valuation with making Hawk tea using its leaves, an ethnic traditional tea-like beverage with a long history in Chinese tea culture. The whole chloroplast (cp) genome is an ideal model for the phylogenetic study of Lauraceae because of its simple structure and highly conserved features. There have been numerous reports of complete cp genome sequences in Lauraceae, but little is known about M. chuanchienensis. Here, the next-generation sequencing (NGS) was used to sequence the M. chuanchienensis cp genome. Then, a comprehensive comparative genome analysis was performed. The results revealed that the M. chuanchienensis's cp genome measured 152,748 base pairs (bp) with a GC content of 39.15% and coded 126 genes annotated, including comprising eight ribosomal RNA (rRNA), 36 transporter RNA (tRNA), and 82 protein-coding genes. In addition, the cp genome presented a typical quadripartite structure comprising a large single-copy (LSC; 93,811) region, a small single-copy (SSC; 18,803) region, and the inverted repeats (IRs; 20,067) region and contained 92 simple sequence repeat (SSR) locus in total. Phylogenetic relationships of 37 species indicated that M. chuanchienensis was a sister to M. balansae, M. melanophylla, and M. minutiflora. Further research on this crucial species may benefit significantly from these findings.
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Han S, Ding H, Bi D, Zhang S, Yi R, Gao J, Yang J, Ye Y, Wu L, Kan X. Structural Diversities and Phylogenetic Signals in Plastomes of the Early-Divergent Angiosperms: A Case Study in Saxifragales. PLANTS (BASEL, SWITZERLAND) 2022; 11:3544. [PMID: 36559654 PMCID: PMC9787361 DOI: 10.3390/plants11243544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
As representative of the early-divergent groups of angiosperms, Saxifragales is extremely divergent in morphology, comprising 15 families. Within this order, our previous case studies observed significant structural diversities among the plastomes of several lineages, suggesting a possible role in elucidating their deep phylogenetic relationships. Here, we collected 208 available plastomes from 11 constituent families to explore the evolutionary patterns among Saxifragales. With thorough comparisons, the losses of two genes and three introns were found in several groups. Notably, 432 indel events have been observed from the introns of all 17 plastomic intron-containing genes, which could well play an important role in family barcoding. Moreover, numerous heterogeneities and strong intrafamilial phylogenetic implications were revealed in pttRNA (plastomic tRNA) structures, and the unique structural patterns were also determined for five families. Most importantly, based on the well-supported phylogenetic trees, evident phylogenetic signals were detected in combinations with the identified pttRNAs features and intron indels, demonstrating abundant lineage-specific characteristics for Saxifragales. Collectively, the results reported here could not only provide a deeper understanding into the evolutionary patterns of Saxifragales, but also provide a case study for exploring the plastome evolution at a high taxonomic level of angiosperms.
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Affiliation(s)
- Shiyun Han
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Hengwu Ding
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - De Bi
- College of Landscape Engineering, Suzhou Polytechnic Institute of Agriculture, Suzhou 215000, China
| | - Sijia Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Ran Yi
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jinming Gao
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jianke Yang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Yuanxin Ye
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Longhua Wu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xianzhao Kan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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Tang C, Chen X, Deng Y, Geng L, Ma J, Wei X. Complete chloroplast genomes of Sorbus sensu stricto (Rosaceae): comparative analyses and phylogenetic relationships. BMC PLANT BIOLOGY 2022; 22:495. [PMID: 36273120 PMCID: PMC9587547 DOI: 10.1186/s12870-022-03858-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Sorbus sensu stricto (Sorbus s.s.) is a genus with important economical values because of its beautiful leaves, and flowers and especially the colorful fruits. It belongs to the tribe Maleae of the family Rosaceae, and comprises about 90 species mainly distributed in China. There is on-going dispute about its infrageneric classification and species delimitation as the species are morphologically similar. With the aim of shedding light on the circumscription of taxa within the genus, phylogenetic analyses were performed using 29 Sorbus s.s. chloroplast (cp) genomes (16 newly sequenced) representing two subgenera and eight sections. RESULTS The 16 cp genomes newly sequenced range between 159,646 bp and 160,178 bp in length. All the samples examined and 22 taxa re-annotated in Sorbus sensu lato (Sorbus s.l.) contain 113 unique genes with 19 of these duplicated in the inverted repeat (IR). Six hypervariable regions including trnR-atpA, petN-psbM, rpl32-trnL, trnH-psbA, trnT-trnL and ndhC-trnV were screened and 44-53 SSRs and 14-31 dispersed repeats were identified as potential molecular markers. Phylogenetic analyses under ML/BI indicated that Sorbus s.l. is polyphyletic, but Sorbus s.s. and the other five segregate genera, Aria, Chamaemespilus, Cormus, Micromeles and Torminalis are monophyletic. Two major clades and four sub-clades resolved with full-support within Sorbus s.s. are not consistent with the existing infrageneric classification. Two subgenera, subg. Sorbus and subg. Albocarmesinae are supported as monophyletic when S. tianschanica is transferred to subg. Albocarmesinae from subg. Sorbus and S. hupehensis var. paucijuga transferred to subg. Sorbus from subg. Albocarmesinae, respectively. The current classification at sectional level is not supported by analysis of cp genome phylogeny. CONCLUSION Phylogenomic analyses of the cp genomes are useful for inferring phylogenetic relationships in Sorbus s.s. Though genome structure is highly conserved in the genus, hypervariable regions and repeat sequences used are the most promising molecule makers for population genetics, species delimitation and phylogenetic studies.
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Affiliation(s)
- Chenqian Tang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Xin Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
| | - Yunfei Deng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Liyang Geng
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Jianhui Ma
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Xueyan Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
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Huang Y, Li J, Yang Z, An W, Xie C, Liu S, Zheng X. Comprehensive analysis of complete chloroplast genome and phylogenetic aspects of ten Ficus species. BMC PLANT BIOLOGY 2022; 22:253. [PMID: 35606691 PMCID: PMC9125854 DOI: 10.1186/s12870-022-03643-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The large genus Ficus comprises approximately 800 species, most of which possess high ornamental and ecological values. However, its evolutionary history remains largely unknown. Plastome (chloroplast genome) analysis had become an essential tool for species identification and for unveiling evolutionary relationships between species, genus and other rank groups. In this work we present the plastomes of ten Ficus species. RESULTS The complete chloroplast (CP) genomes of eleven Ficus specimens belonging to ten species were determined and analysed. The full length of the Ficus plastome was nearly 160 kbp with a similar overall GC content, ranging from 35.88 to 36.02%. A total of 114 unique genes, distributed in 80 protein-coding genes, 30 tRNAs, and 4 rRNAs, were annotated in each of the Ficus CP genome. In addition, these CP genomes showed variation in their inverted repeat regions (IR). Tandem repeats and mononucleotide simple sequence repeat (SSR) are widely distributed across the Ficus CP genome. Comparative genome analysis showed low sequence variability. In addition, eight variable regions to be used as potential molecular markers were proposed for future Ficus species identification. According to the phylogenetic analysis, these ten Ficus species were clustered together and further divided into three clades based on different subgenera. Simultaneously, it also showed the relatedness between Ficus and Morus. CONCLUSION The chloroplast genome structure of 10 Ficus species was similar to that of other angiosperms, with a typical four-part structure. Chloroplast genome sizes vary slightly due to expansion and contraction of the IR region. And the variation of noncoding regions of the chloroplast genome is larger than that of coding regions. Phylogenetic analysis showed that these eleven sampled CP genomes were divided into three clades, clustered with species from subgenus Urostigma, Sycomorus, and Ficus, respectively. These results support the Berg classification system, in which the subgenus Ficus was further decomposed into the subgenus Sycomorus. In general, the sequencing and analysis of Ficus plastomes, especially the ones of species with no or limited sequences available yet, contribute to the study of genetic diversity and species evolution of Ficus, while providing useful information for taxonomic and phylogenetic studies of Ficus.
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Affiliation(s)
- Yuying Huang
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuangdong Road, Higher Education Mega Center, Panyu District, Guangzhou, Guangdong, China
| | - Jing Li
- Traditional Chinese Medicine Gynecology Laboratory in Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, 510410, China
| | - Zerui Yang
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuangdong Road, Higher Education Mega Center, Panyu District, Guangzhou, Guangdong, China
| | - Wenli An
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuangdong Road, Higher Education Mega Center, Panyu District, Guangzhou, Guangdong, China
| | - Chunzhu Xie
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuangdong Road, Higher Education Mega Center, Panyu District, Guangzhou, Guangdong, China
| | - Shanshan Liu
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuangdong Road, Higher Education Mega Center, Panyu District, Guangzhou, Guangdong, China
| | - Xiasheng Zheng
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuangdong Road, Higher Education Mega Center, Panyu District, Guangzhou, Guangdong, China.
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Infrageneric Plastid Genomes of Cotoneaster (Rosaceae): Implications for the Plastome Evolution and Origin of C. wilsonii on Ulleung Island. Genes (Basel) 2022; 13:genes13050728. [PMID: 35627113 PMCID: PMC9141645 DOI: 10.3390/genes13050728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 12/31/2022] Open
Abstract
Cotoneaster is a taxonomically and ornamentally important genus in the family Rosaceae; however, phylogenetic relationships among its species are complicated owing to insufficient morphological diagnostic characteristics and hybridization associated with polyploidy and apomixis. In this study, we sequenced the complete plastomes of seven Cotoneaster species (C. dielsianus, C. hebephyllus, C. integerrimus, C. mongolicus, C. multiflorus, C. submultiflorus, and C. tenuipes) and included the available complete plastomes in a phylogenetic analysis to determine the origin of C. wilsonii, which is endemic to Ulleung Island, Korea. Furthermore, based on 15 representative lineages within the genus, we carried out the first comparative analysis of Cotoneaster plastid genomes to gain an insight into their molecular evolution. The plastomes were highly conserved, with sizes ranging from 159,595 bp (C. tenuipes) to 160,016 bp (C. hebephyllus), and had a GC content of 36.6%. The frequency of codon usage showed similar patterns among the 15 Cotoneaster species, and 24 of the 35 protein-coding genes were predicted to undergo RNA editing. Eight of the 76 common protein-coding genes, including ccsA, matK, ndhD, ndhF, ndhK, petA, rbcL, and rpl16, were positively selected, implying their potential roles in adaptation and speciation. Of the 35 protein-coding genes, 24 genes (15 photosynthesis-related, seven self-replications, and three others) were found to harbor RNA editing sites. Furthermore, several mutation hotspots were identified, including trnG-UCC/trnR-UCU/atpA and trnT-UGU/trnL-UAA. Maximum likelihood analysis based on 57 representative plastomes of Cotoneaster and two Heteromeles plastomes as outgroups revealed two major lineages within the genus, which roughly correspond to two subgenera, Chaenopetalum and Cotoneaster. The Ulleung Island endemic, C. wilsonii, shared its most recent common ancestor with two species, C. schantungensis and C. zabelii, suggesting its potential origin from geographically close members of the subgenus Cotoneaster, section Integerrimi.
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Comparative Chloroplast Genome Analysis of Wax Gourd (Benincasa hispida) with Three Benincaseae Species, Revealing Evolutionary Dynamic Patterns and Phylogenetic Implications. Genes (Basel) 2022; 13:genes13030461. [PMID: 35328015 PMCID: PMC8954987 DOI: 10.3390/genes13030461] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/01/2022] [Indexed: 12/13/2022] Open
Abstract
Benincasa hispida (wax gourd) is an important Cucurbitaceae crop, with enormous economic and medicinal importance. Here, we report the de novo assembly and annotation of the complete chloroplast genome of wax gourd with 156,758 bp in total. The quadripartite structure of the chloroplast genome comprises a large single-copy (LSC) region with 86,538 bp and a small single-copy (SSC) region with 18,060 bp, separated by a pair of inverted repeats (IRa and IRb) with 26,080 bp each. Comparison analyses among B. hispida and three other species from Benincaseae presented a significant conversion regarding nucleotide content, genome structure, codon usage, synonymous and non-synonymous substitutions, putative RNA editing sites, microsatellites, and oligonucleotide repeats. The LSC and SSC regions were found to be much more varied than the IR regions through a divergent analysis of the species within Benincaseae. Notable IR contractions and expansions were observed, suggesting a difference in genome size, gene duplication and deletion, and the presence of pseudogenes. Intronic gene sequences, such as trnR-UCU–atpA and atpH–atpI, were observed as highly divergent regions. Two types of phylogenetic analysis based on the complete cp genome and 72 genes suggested sister relationships between B. hispida with the Citrullus, Lagenaria, and Cucumis. Variations and consistency with previous studies regarding phylogenetic relationships are discussed. The cp genome of B. hispida provides valuable genetic information for the detection of molecular markers, research on taxonomic discrepancies, and the inference of the phylogenetic relationships of Cucurbitaceae.
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Yu J, Fu J, Fang Y, Xiang J, Dong H. Complete chloroplast genomes of Rubus species (Rosaceae) and comparative analysis within the genus. BMC Genomics 2022; 23:32. [PMID: 34991463 PMCID: PMC8740016 DOI: 10.1186/s12864-021-08225-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/01/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Rubus is the largest genus of the family Rosaceae and is valued as medicinal, edible, and ornamental plants. Here, we sequenced and assembled eight chloroplast (cp) genomes of Rubus from the Dabie Mountains in Central China. Fifty-one Rubus species were comparatively analyzed for the cp genomes including the eight newly discovered genomes and forty-three previously reported in GenBank database (NCBI). RESULTS The eight newly obtained cp genomes had the same quadripartite structure as the other cp genomes in Rubus. The length of the eight plastomes ranged from 155,546 bp to 156,321 bp with similar GC content (37.0 to 37.3%). The results indicated 133-134 genes were annotated for the Rubus plastomes, which contained 88 or 89 protein coding genes (PCGs), 37 transfer RNA genes (tRNAs), and eight ribosomal RNA genes (rRNAs). Among them, 16 (or 18) of the genes were duplicated in the IR region. Structural comparative analysis results showed that the gene content and order were relatively preserved. Nucleotide variability analysis identified nine hotspot regions for genomic divergence and multiple simple sequences repeats (SSRs), which may be used as markers for genetic diversity and phylogenetic analysis. Phylogenetic relationships were highly supported within the family Rosaceae, as evidenced by sub-clade taxa cp genome sequences. CONCLUSION Thus, the whole plastome may be used as a super-marker in phylogenetic studies of this genus.
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Affiliation(s)
- Jiaojun Yu
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang Normal University, Huanggang, Hubei, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Xingang Road No. 146, Huanggang, 438000, Hubei, China
| | - Jun Fu
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang Normal University, Huanggang, Hubei, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Xingang Road No. 146, Huanggang, 438000, Hubei, China
| | - Yuanping Fang
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang Normal University, Huanggang, Hubei, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Xingang Road No. 146, Huanggang, 438000, Hubei, China
| | - Jun Xiang
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang Normal University, Huanggang, Hubei, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Xingang Road No. 146, Huanggang, 438000, Hubei, China
| | - Hongjin Dong
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang Normal University, Huanggang, Hubei, China.
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Xingang Road No. 146, Huanggang, 438000, Hubei, China.
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Park J, Lee J, Park J. The investigation of intraspecific characteristics and comparative analyses of the complete mitochondrial genome of Stegobium paniceum (Linnaeus, 1758) (Coleoptera: Ptinidae) assembled from public NGS raw reads of the black truffle, Tuber melanosporum. Sci Prog 2022; 105:368504211072355. [PMID: 35040745 PMCID: PMC10358573 DOI: 10.1177/00368504211072355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Due to the rapid development of NGS technologies, a huge amount of NGS raw reads have been accumulated in public repositories, such as the Short Read Archive of NCBI. We successfully rescued the complete mitochondrial genome of Stegobium paniceum, a drug store beetle, from public NGS raw reads of truffle generated from the whole genome project. The circular mitogenome of S. paniceum is 15,474 bp long including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 803 bp. Intraspecific transfer RNAs structure and sequence variations were investigated and simple sequence repeats identified from three S. paniceum mitochondrial genomes were compared showing their diversities as fundamental data to utilize them in various aspects including developing efficient molecular markers in the family, Ptinidae. Phylogenetic analysis of 23 Bostrichoidea mitochondrial genomes presented better species identification based on phylogenetic analyses and the optimal options for constructing phylogenetic trees based on Bostrichoidea mitochondrial genomes. Our results present not only utilization of public NGS raw read sequences but also intraspecific features of S. paniceum mitochondrial genomes and comparative analysis of Bostrichoidea mitochondrial genomes in various aspects.
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Affiliation(s)
- Jongsun Park
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Jungmo Lee
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Jonghyun Park
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
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Tian X, Shi L, Guo J, Fu L, Du P, Huang B, Wu Y, Zhang X, Wang Z. Chloroplast Phylogenomic Analyses Reveal a Maternal Hybridization Event Leading to the Formation of Cultivated Peanuts. FRONTIERS IN PLANT SCIENCE 2021; 12:804568. [PMID: 34975994 PMCID: PMC8718879 DOI: 10.3389/fpls.2021.804568] [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: 10/29/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Peanuts (Arachis hypogaea L.) offer numerous healthy benefits, and the production of peanuts has a prominent role in global food security. As a result, it is in the interest of society to improve the productivity and quality of peanuts with transgenic means. However, the lack of a robust phylogeny of cultivated and wild peanut species has limited the utilization of genetic resources in peanut molecular breeding. In this study, a total of 33 complete peanut plastomes were sequenced, analyzed and used for phylogenetic analyses. Our results suggest that sect. Arachis can be subdivided into two lineages. All the cultivated species are contained in Lineage I with AABB and AA are the two predominant genome types present, while species in Lineage II possess diverse genome types, including BB, KK, GG, etc. Phylogenetic studies also indicate that all allotetraploid cultivated peanut species have been derived from a possible maternal hybridization event with one of the diploid Arachis duranensis accessions being a potential AA sub-genome ancestor. In addition, Arachis monticola, a tetraploid wild species, is placed in the same group with all the cultivated peanuts, and it may represent a transitional species, which has been through the recent hybridization event. This research could facilitate a better understanding of the taxonomic status of various Arachis species/accessions and the evolutionary relationship among them, and assists in the correct and efficient use of germplasm resources in breeding efforts to improve peanuts for the benefit of human beings.
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Affiliation(s)
- Xiangyu Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Luye Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Jia Guo
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Liuyang Fu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Pei Du
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Bingyan Huang
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yue Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Xinyou Zhang
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Zhenlong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
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Li C, Cai C, Tao Y, Sun Z, Jiang M, Chen L, Li J. Variation and Evolution of the Whole Chloroplast Genomes of Fragaria spp. (Rosaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:754209. [PMID: 34721483 PMCID: PMC8551639 DOI: 10.3389/fpls.2021.754209] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/21/2021] [Indexed: 06/02/2023]
Abstract
Species identification is vital for protecting species diversity and selecting high-quality germplasm resources. Wild Fragaria spp. comprise rich and excellent germplasm resources; however, the variation and evolution of the whole chloroplast (cp) genomes in the genus Fragaria have been ignored. In the present study, 27 complete chloroplast genomes of 11 wild Fragaria species were sequenced using the Illumina platform. Then, the variation among complete cp genomes of Fragaria was analyzed, and phylogenetic relationships were reconstructed from those genome sequences. There was an overall high similarity of sequences, with some divergence. According to analysis with mVISTA, non-coding regions were more variable than coding regions. Inverted repeats (IRs) were observed to contract or expand to different degrees, which resulted in different sizes of cp genomes. Additionally, five variable loci, trnS-trnG, trnR-atpA, trnC-petN, rbcL-accD, and psbE-petL, were identified that could be used to develop DNA barcoding for identification of Fragaria species. Phylogenetic analyses based on the whole cp genomes supported clustering all species into two groups (A and B). Group A species were mainly distributed in western China, while group B contained several species from Europe and Americas. These results support allopolyploid origins of the octoploid species F. chiloensis and F. virginiana and the tetraploid species F. moupinensis and F. tibetica. The complete cp genomes of these Fragaria spp. provide valuable information for selecting high-quality Fragaria germplasm resources in the future.
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Affiliation(s)
- Chenxin Li
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Chaonan Cai
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- School of Advanced Study, Taizhou University, Taizhou, China
| | - Yutian Tao
- School of Advanced Study, Taizhou University, Taizhou, China
| | - Zhongshuai Sun
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- School of Advanced Study, Taizhou University, Taizhou, China
| | - Ming Jiang
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Luxi Chen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Junmin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- School of Advanced Study, Taizhou University, Taizhou, China
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The complete chloroplast genome sequence of Rubus hirsutus Thunb. and a comparative analysis within Rubus species. Genetica 2021; 149:299-311. [PMID: 34546501 DOI: 10.1007/s10709-021-00131-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 08/18/2021] [Indexed: 11/27/2022]
Abstract
Rubus hirsutus is a type of tonifying kidney-essence herb that belongs to the Rosaceae family, and has been commonly used to treat multiple diseases, such as polyuria, impotence, and infertility. In this study, we determined the complete chloroplast sequence of R. hirsutus and conduced a comparative analysis within the genus Rubus. The assembled chloroplast (cp.) genome is 156,380 bp in length with a GC content of 37.0% and shares a conserved quadripartite structure within the other cp. genomes in this genus. A total of 132 unique genes were annotated in the cp. genome of R. hirsutus, which contained 87 protein-coding genes, 37 tRNAs, and eight rRNAs. Seventeen duplicated genes were identified in the inverted repeats region. Furthermore, 70 simple sequence repeats and 35 long repeats were detected in total in the R. hirsutus chloroplast genome. Eight mutational hotspots were identified in the cp. genome of this species with higher nucleotide variations in non-coding regions than those of coding regions. Furthermore, the gene order, codon usage, and repeat sequence distribution were highly consistent in Rubus according to the results of a comparative analysis. A phylogenetic analysis indicated that there was a sister relationship between R. hirsutus and R. chingii. Overall, the complete chloroplast genome of R. hirsutus and the comparative analysis will help to further the evolutionary study, conservation, phylogenetic reconstruction, and development of molecular barcodes for the genus Rubus.
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Yang J, Choi MJ, Kim SH, Choi HJ, Kim SC. Plastome Characterization and Phylogenomic Analysis Yield New Insights into the Evolutionary Relationships among the Species of the Subgenus Bryocles ( Hosta; Asparagaceae) in East Asia. PLANTS 2021; 10:plants10101980. [PMID: 34685791 PMCID: PMC8538707 DOI: 10.3390/plants10101980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 11/23/2022]
Abstract
The genus Hosta, which has a native distribution in temperate East Asia and a number of species ranging from 23 to 40, represents a taxonomically important and ornamentally popular plant. Despite its taxonomic and horticultural importance, the genus Hosta has remained taxonomically challenging owing to insufficient diagnostic features, continuous morphological variation, and the process of hybridization and introgression, making species circumscription and phylogenetic inference difficult. In this study, we sequenced 11 accessions of Hosta plastomes, including members of three geographically defined subgenera, Hosta, Bryocles, and Giboshi, determined the characteristics of plastomes, and inferred their phylogenetic relationships. We found highly conserved plastomes among the three subgenera, identified several mutation hotspots that can be used as barcodes, and revealed the patterns of codon usage bias and RNA editing sites. Five positively selected plastome genes (rbcL, rpoB, rpoC2, rpl16, and rpl20) were identified. Phylogenetic analysis suggested (1) the earliest divergence of subg. Hosta, (2) non-monophyly of subg. Bryocles and its two sections (Lamellatae and Stoloniferae), (3) a sister relationship between H. sieboldiana (subg. Giboshi) and H. ventricosa (subg. Bryocles), and (4) reciprocally monophyletic and divergent lineages of H. capitata in Korea and Japan, requiring further studies of their taxonomic distinction.
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Affiliation(s)
- JiYoung Yang
- Research Institute for Ulleung-do & Dok-do, College of Natural Sciences, Kyungpook National University, Daegu 41566, Korea;
| | - Mi-Jung Choi
- Department of Biology and Chemistry, Changwon National University, Changwon 51140, Korea;
| | - Seon-Hee Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea;
| | - Hyeok-Jae Choi
- Department of Biology and Chemistry, Changwon National University, Changwon 51140, Korea;
- Correspondence: (H.-J.C.); (S.-C.K.); Tel.: +82-55-213-3457 (H.-J.C.); +82-31-299-4499 (S.-C.K.)
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea;
- Correspondence: (H.-J.C.); (S.-C.K.); Tel.: +82-55-213-3457 (H.-J.C.); +82-31-299-4499 (S.-C.K.)
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A Comparative Analyses of the Complete Mitochondrial Genomes of Fungal Endosymbionts in Sogatella furcifera, White-Backed Planthoppers. Int J Genomics 2021; 2021:6652508. [PMID: 34212028 PMCID: PMC8208876 DOI: 10.1155/2021/6652508] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/03/2021] [Accepted: 05/08/2021] [Indexed: 12/20/2022] Open
Abstract
Sogatella furcifera Horvath, commonly known as the white-backed planthoppers (WBPH), is an important pest in East Asian rice fields. Fungal endosymbiosis is widespread among planthoppers in the infraorder Fulgoromorpha and suborder Auchenorrhyncha. We successfully obtained complete mitogenome of five WBPH fungal endosymbionts, belonging to the Ophiocordycipitaceae family, from next-generation sequencing (NGS) reads obtained from S. furcifera samples. These five mitogenomes range in length from 55,390 bp to 55,406 bp, which is shorter than the mitogenome of the fungal endosymbiont found in Ricania speculum, black planthoppers. Twenty-eight protein-coding genes (PCGs), 12 tRNAs, and 2 rRNAs were found in the mitogenomes. Two single-nucleotide polymorphisms, two insertions, and three deletions were identified among the five mitogenomes, which were fewer in number than those of four species of Ophiocordycipitaceae, Ophiocordyceps sinensis, Hirsutella thompsonii, Hirsutella rhossiliensis, and Tolypocladium inflatum. Noticeably short lengths (up to 18 bp) of simple sequence repeats were identified in the five WBPH fungal endosymbiont mitogenomes. Phylogenetic analysis based on conserved PCGs across 25 Ophiocordycipitaceae mitogenomes revealed that the five mitogenomes were clustered with that of R. speculum, forming an independent clade. In addition to providing the full mitogenome sequences, obtaining complete mitogenomes of WBPH endosymbionts can provide insights into their phylogenetic positions without needing to isolate the mtDNA from the host. This advantage is of value to future studies involving fungal endosymbiont mitogenomes.
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Tang Y, Zhao Y, Li C, Yang G, Peng J, Xu Z. New insights into the evolutionary characteristic between the New World and Old World Lupinus species using complete chloroplast genomes. ALL LIFE 2021. [DOI: 10.1080/26895293.2021.1926341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Yiwang Tang
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, People’s Republic of China
| | - Yunlin Zhao
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, People’s Republic of China
| | - Chaoyang Li
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, People’s Republic of China
| | - Guiyan Yang
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, People’s Republic of China
- College of Forestry, Northwest A & F University, Yangling, People’s Republic of China
| | - Jiao Peng
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, People’s Republic of China
| | - Zhenggang Xu
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, People’s Republic of China
- College of Forestry, Northwest A & F University, Yangling, People’s Republic of China
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Yang J, Chiang YC, Hsu TW, Kim SH, Pak JH, Kim SC. Characterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan. Sci Rep 2021; 11:1152. [PMID: 33441744 PMCID: PMC7806662 DOI: 10.1038/s41598-020-80143-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 11/27/2020] [Indexed: 12/13/2022] Open
Abstract
Genus Rubus represents the second largest genus of the family Rosaceae in Taiwan, with 41 currently recognized species across three subgenera (Chamaebatus, Idaoeobatus, and Malochobatus). Despite previous morphological and cytological studies, little is known regarding the overall phylogenetic relationships among the Rubus species in Taiwan, and their relationships to congeneric species in continental China. We characterized eight complete plastomes of Taiwan endemic Rubus species: subg. Idaeobatus (R. glandulosopunctatus, R. incanus, R. parviaraliifolius, R rubroangustifolius, R. taitoensis, and R. taiwanicolus) and subg. Malachobatus (R. kawakamii and R. laciniastostipulatus) to determine their phylogenetic relationships. The plastomes were highly conserved and the size of the complete plastome sequences ranged from 155,566 to 156,236 bp. The overall GC content ranged from 37.0 to 37.3%. The frequency of codon usage showed similar patterns among species, and 29 of the 73 common protein-coding genes were positively selected. The comparative phylogenomic analysis identified four highly variable intergenic regions (rps16/trnQ, petA/psbJ, rpl32/trnL-UAG, and trnT-UGU/trnL-UAA). Phylogenetic analysis of 31 representative complete plastomes within the family Rosaceae revealed three major lineages within Rubus in Taiwan. However, overall phylogenetic relationships among endemic species require broader taxon sampling to gain new insights into infrageneric relationships and their plastome evolution.
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Affiliation(s)
- JiYoung Yang
- Department of Biology, School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan
| | - Tsai-Wen Hsu
- Taiwan Endemic Species Research Institute, 1 Mingshen East Road, Chichi Township, Nantou, 55244, Taiwan
| | - Seon-Hee Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon, Gyeonggi-do, 16419, Republic of Korea
| | - Jae-Hong Pak
- Department of Biology, School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon, Gyeonggi-do, 16419, Republic of Korea.
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Yang J, Takayama K, Youn JS, Pak JH, Kim SC. Plastome Characterization and Phylogenomics of East Asian Beeches with a Special Emphasis on Fagus multinervis on Ulleung Island, Korea. Genes (Basel) 2020; 11:E1338. [PMID: 33198274 PMCID: PMC7697516 DOI: 10.3390/genes11111338] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 01/18/2023] Open
Abstract
Beech trees of the genus Fagus (Fagaceae) are monoecious and distributed in the Northern Hemisphere. They represent an important component of mixed broad-leaved evergreen-deciduous forests and are an economically important source of timber. Despite their ecological and economical importance, however, little is known regarding the overall plastome evolution among Fagus species in East Asia. In particular, the taxonomic position and status of F. multinervis, a beech species endemic to Ulleung Island of Korea, remains unclear even today. Therefore, in this study, we characterized four newly completed plastomes of East Asian Fagus species (one accession each of F. crenata and F. multinervis and two accessions of F. japonica). Moreover, we performed phylogenomic analyses comparing these four plastomes with F. sylvatica (European beech) plastome. The four plastomes were highly conserved, and their size ranged from 158,163 to 158,348 base pair (bp). The overall GC content was 37.1%, and the sequence similarity ranged from 99.8% to 99.99%. Codon usage patterns were similar among species, and 7 of 77 common protein-coding genes were under positive selection. Furthermore, we identified five highly variable hotspot regions of the Fagus plastomes (ccsA/ndhD, ndhD/psaC, ndhF/rpl32, trnS-GCU/trnG-UCC, and ycf1). Phylogenetic analysis revealed the monophyly of Fagus as well as early divergence of the subgenus Fagus and monophyletic Engleriana. Finally, phylogenetic results supported the taxonomic distinction of F. multinervis from its close relatives F. engleriana and F. japonica. However, the sister species and geographic origin of F. multinervis on Ulleung Island could not be determined.
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Affiliation(s)
- JiYoung Yang
- Research Institute for Dok-do and Ulleung-do Island, Department of Biology, School of Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Gyeongsangbuk-do, Daegu 41566, Korea; (J.Y.); (J.-S.Y.)
| | - Koji Takayama
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan;
| | - Jin-Suk Youn
- Research Institute for Dok-do and Ulleung-do Island, Department of Biology, School of Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Gyeongsangbuk-do, Daegu 41566, Korea; (J.Y.); (J.-S.Y.)
| | - Jae-Hong Pak
- Research Institute for Dok-do and Ulleung-do Island, Department of Biology, School of Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Gyeongsangbuk-do, Daegu 41566, Korea; (J.Y.); (J.-S.Y.)
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Gyeonggi-do, Suwon 16419, Korea
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Park J, Xi H, Kim Y. The Complete Chloroplast Genome of Arabidopsis thaliana Isolated in Korea (Brassicaceae): An Investigation of Intraspecific Variations of the Chloroplast Genome of Korean A. thaliana. Int J Genomics 2020; 2020:3236461. [PMID: 32964010 PMCID: PMC7492873 DOI: 10.1155/2020/3236461] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/02/2020] [Accepted: 08/17/2020] [Indexed: 01/18/2023] Open
Abstract
Arabidopsis thaliana (L.) Heynh. is a model organism of plant molecular biology. More than 1,700 whole genome sequences have been sequenced, but no Korean isolate genomes have been sequenced thus far despite the fact that many A. thaliana isolated in Japan and China have been sequenced. To understand the genetic background of Korean natural A. thaliana (named as 180404IB4), we presented its complete chloroplast genome, which is 154,464 bp long and has four subregions: 85,164 bp of large single copy (LSC) and 17,781 bp of small single copy (SSC) regions are separated by 26,257 bp of inverted repeat (IRs) regions including 130 genes (85 protein-coding genes, eight rRNAs, and 37 tRNAs). Fifty single nucleotide polymorphisms (SNPs) and 14 insertion and deletions (INDELs) are identified between 180404IB4 and Col0. In addition, 101 SSRs and 42 extendedSSRs were identified on the Korean A. thaliana chloroplast genome, indicating a similar number of SSRs on the rest five chloroplast genomes with a preference of sequence variations toward the SSR region. A nucleotide diversity analysis revealed two highly variable regions on A. thaliana chloroplast genomes. Phylogenetic trees with three more chloroplast genomes of East Asian natural isolates show that Korean and Chinese natural isolates are clustered together, whereas two Japanese isolates are not clustered, suggesting the need for additional investigations of the chloroplast genomes of East Asian isolates.
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Affiliation(s)
- Jongsun Park
- InfoBoss Inc., 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
| | - Hong Xi
- InfoBoss Inc., 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
| | - Yongsung Kim
- InfoBoss Inc., 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
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Lee J, Park J, Xi H, Park J. Comprehensive Analyses of the Complete Mitochondrial Genome of Figulus binodulus (Coleoptera: Lucanidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2020; 20:10. [PMID: 32976575 PMCID: PMC7583265 DOI: 10.1093/jisesa/ieaa090] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Indexed: 05/06/2023]
Abstract
Figulus binodulus Waterhouse is a small stag beetle distributed in East Asia. We determined the first mitochondrial genome of F. binodulus of which is 16,261-bp long including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large noncoding region of 1,717 bp. Gene order of F. binodulus is identical to the ancestral insect mitochondrial gene order as in most other stag beetle species. All of 22 tRNAs could be shaped into typical clover-leaf structure except trnSer1. Comparative analyses of 21 Lucanidae mitochondrial genomes was conducted in aspect of their length and AT-GC ratio. Nucleotide diversities analyses provide that cox1 and cox2 in Lucanidae are less diverse than those of Scarabaeoidea. Fifty simple sequence repeats (SSRs) were identified on F. binodulus mitochondrial genome. Comparative analysis of SSRs among five mitochondrial genomes displayed similar trend along with SSR types. Figulus binodulus was sister to all other available family Lucanidae species in the phylogenetic tree.
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Affiliation(s)
- Jungmo Lee
- InfoBoss Inc., Ltd., Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
| | - Jonghyun Park
- InfoBoss Inc., Ltd., Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
| | - Hong Xi
- InfoBoss Inc., Ltd., Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Inc., Ltd., Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
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29
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Yang C, Ma Y, Cheng B, Zhou L, Yu C, Luo L, Pan H, Zhang Q. Molecular Evidence for Hybrid Origin and Phenotypic Variation of Rosa Section Chinenses. Genes (Basel) 2020; 11:genes11090996. [PMID: 32854427 PMCID: PMC7564265 DOI: 10.3390/genes11090996] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/01/2020] [Accepted: 08/18/2020] [Indexed: 11/18/2022] Open
Abstract
Rosa sect. Chinenses (Rosaceae) is an important parent of modern rose that is widely distributed throughout China and plays an important role in breeding and molecular biological research. R. sect. Chinenses has variable morphological traits and mixed germplasm. However, the taxonomic status and genetic background of sect. Chinenses varieties remain unclear. In this study, we collected germplasm resources from sect. Chinenses varieties with different morphological traits. Simple sequence repeat (SSR) markers, chloroplast markers, and single copy nuclear markers were used to explore the genetic background of these germplasm resources. We described the origin of hybridization of rose germplasm resources by combining different molecular markers. The results showed that the flower and hip traits of different species in R. sect. Chinenses were significantly different. The SSR analysis showed that the two wild type varieties have different genetic backgrounds. The double petal varieties of R. sect. Chinenses could be hybrids of two wild type varieties. A phylogenetic analysis showed that the maternal inheritance of sect. Chinenses varieties had two different origins. To some extent, variation in the morphological traits of double petal species of R. sect. Chinenses reflects the influence of cultivation process. This study emphasizes that different genetic markers vary in their characteristics. Therefore, analyzing different genetic markers in could provide an insight into highly heterozygous species.
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Amar MH. ycf1-ndhF genes, the most promising plastid genomic barcode, sheds light on phylogeny at low taxonomic levels in Prunus persica. J Genet Eng Biotechnol 2020; 18:42. [PMID: 32797323 PMCID: PMC7427673 DOI: 10.1186/s43141-020-00057-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/04/2020] [Indexed: 11/10/2022]
Abstract
Background Chloroplast genome sequencing is becoming a valuable process for developing several DNA barcodes. At present, plastid DNA barcode for systematics and evolution in flowering plant rely heavily on the use of non-coding genes. The present study was performed to verify the novelty and suitability of the two hotspot barcode plastid coding gene ycf1 and ndhF, to estimate the rate of molecular evolution in the Prunus genus at low taxonomic levels. Results Here, 25 chloroplast genomes of Prunus genus were selected for sequences annotation to search for the highly variable coding DNA barcode regions. Among them, 5 genera were of our own data, including the ornamental, cultivated, and wild haplotype, while 20 genera have been downloaded from the GenBank database. The results indicated that the two hotspot plastid gene ycf1 and ndhF were the most variable regions within the coding genes in Prunus with an average of 3268 to 3416 bp in length, which have been predicted to have the highest nucleotide diversity, with the overall transition/transversion bias (R = 1.06). The ycf1-ndhF structural domains showed a positive trend evident in structure variation among the 25 specimens tested, due to the variant overlap’s gene annotation and insertion or deletion with a broad trend of the full form of IGS sequence. As a result, the principal component analysis (PCA) and the ML tree data drew an accurate monophyletic annotations cluster in Prunus species, offering unambiguous identification without overlapping groups between peach, almond, and cherry. Conclusion To this end, we put forward the domain of the two-locus ycf1-ndhF genes as the most promising coding plastid DNA barcode in P. persica at low taxonomic levels. We believe that the discovering of further variable loci with high evolutionary rates is extremely useful and potential uses as a DNA barcode in P. persica for further phylogeny study and species identification.
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Affiliation(s)
- Mohamed Hamdy Amar
- Egyptian Deserts Gene Bank, Desert Research Center, B.O.P, Cairo, 11753, Egypt.
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31
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Li C, Zheng Y, Huang P. Molecular markers from the chloroplast genome of rose provide a complementary tool for variety discrimination and profiling. Sci Rep 2020; 10:12188. [PMID: 32699274 PMCID: PMC7376030 DOI: 10.1038/s41598-020-68092-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 06/17/2020] [Indexed: 02/06/2023] Open
Abstract
The rose is one of the most important ornamental woody plants because of its extensive use and high economic value. Herein, we sequenced a complete chloroplast genome of the miniature rose variety Rosa 'Margo Koster' and performed comparative analyses with sequences previously published for other species in the Rosaceae family. The chloroplast genome of Rosa 'Margo Koster', with a size of 157,395 bp, has a circular quadripartite structure typical of angiosperm chloroplast genomes and contains a total of 81 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Conjunction regions in the chloroplast genome of Rosa 'Margo Koster' were verified and manually corrected by Sanger sequencing. Comparative genome analysis showed that the IR contraction and expansion events resulted in rps19 and ycf1 pseudogenes. The phylogenetic analysis within the Rosa genus showed that Rosa 'Margo Koster' is closer to Rosa odorata than to other Rosa species. Additionally, we identified and screened highly divergent sequences and cpSSRs and compared their power to discriminate rose varieties by Sanger sequencing and capillary electrophoresis. The results showed that 15 cpSSRs are polymorphic, but their discriminating power is only moderate among a set of rose varieties. However, more than 150 single nucleotide variations (SNVs) were discovered in the flanking region of cpSSRs, and the results indicated that these SNVs have a higher divergence and stronger power for profiling rose varieties. These findings suggest that nucleotide mutations in the chloroplast genome may be an effective and powerful tool for rose variety discrimination and DNA profiling. These molecular markers in the chloroplast genome sequence of Rosa spp. will facilitate population and phylogenetic studies and other related studies of this species.
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Affiliation(s)
- Changhong Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Silviculture and Tree Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yongqi Zheng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Silviculture and Tree Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Ping Huang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Silviculture and Tree Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
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Yang J, Kang GH, Pak JH, Kim SC. Characterization and Comparison of Two Complete Plastomes of Rosaceae Species ( Potentilla dickinsii var. glabrata and Spiraea insularis) Endemic to Ulleung Island, Korea. Int J Mol Sci 2020; 21:E4933. [PMID: 32668601 PMCID: PMC7404287 DOI: 10.3390/ijms21144933] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/02/2020] [Accepted: 07/10/2020] [Indexed: 01/04/2023] Open
Abstract
Potentilla dickinsii var. glabrata and Spiraea insularis in the family Rosaceae are species endemic to Ulleung Island, Korea, the latter of which is listed as endangered. In this study, we characterized the complete plastomes of these two species and compared these with previously reported plastomes of other Ulleung Island endemic species of Rosaceae (Cotoneaster wilsonii, Prunus takesimensis, Rubus takesimensis, and Sorbus ulleungensis). The highly conserved complete plastomes of P. dickinsii var. glabrata and S. insularis are 158,637 and 155,524 base pairs with GC contents of 37% and 36.9%, respectively. Comparative phylogenomic analysis identified three highly variable intergenic regions (trnT-UGU/trnL-UAA, rpl32/trnL-UAG, and ndhF/rpl32) and one variable genic region (ycf1). Only 14 of the 75 protein-coding genes have been subject to strong purifying selection. Phylogenetic analysis of 23 representative plastomes within the Rosaceae supported the monophyly of Potentilla and the sister relationship between Potentilla and Fragaria and indicated that S. insularis is sister to a clade containing Cotoneaster, Malus, Pyrus, and Sorbus. The plastome resources generated in this study will contribute to elucidating the plastome evolution of insular endemic Rosaceae on Ulleung Island and also in assessing the genetic consequences of anagenetic speciation for various endemic lineages on the island.
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Affiliation(s)
- JiYoung Yang
- Research Institute for Dok-do and Ulleung-do Island, Department of Biology, School of Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, Gyeongsangbuk-do 41566, Korea;
| | - Gi-Ho Kang
- Baekdudaegan National Arboretum, 1501 Chunyang-ro, Chungyang-myeon, Bonghwa-gun, Gyeongsangbuk-do 36209, Korea;
| | - Jae-Hong Pak
- Research Institute for Dok-do and Ulleung-do Island, Department of Biology, School of Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, Gyeongsangbuk-do 41566, Korea;
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon, Gyeonggi-do 16419, Korea
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Teshome GE, Mekbib Y, Hu G, Li ZZ, Chen J. Comparative analyses of 32 complete plastomes of Tef ( Eragrostis tef ) accessions from Ethiopia: phylogenetic relationships and mutational hotspots. PeerJ 2020; 8:e9314. [PMID: 32596045 PMCID: PMC7307559 DOI: 10.7717/peerj.9314] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 05/17/2020] [Indexed: 12/31/2022] Open
Abstract
Eragrostis tef is an important cereal crop in Ethiopia with excellent storage properties, high–quality food, and the unique ability to thrive in extreme environmental conditions. However, the application of advanced molecular tools for breeding and conservation of these species is extremely limited. Therefore, developing chloroplast genome resources and high-resolution molecular markers are valuable to E. tef population and biogeographic studies. In the current study, we assembled and compared the complete plastomes of 32 E. tef accessions. The size of the plastomes ranged from 134,349 to 134,437 bp with similar GC content (∼38.3%). Genomes annotations revealed 112 individual genes, including 77 protein-coding, 31 tRNA, and 4 rRNA genes. Comparison of E. tef plastomes revealed a low degree of intraspecific sequence variations and no structural differentiations. Furthermore, we found 34 polymorphic sites (13 cpSSRs, 12 InDels, and 9 SNPs) that can be used as valuable DNA barcodes. Among them, the majority (88%) of the polymorphic sites were identified in the noncoding genomic regions. Nonsynonymous (ka) and synonymous (ks) substitution analysis showed that all PCGs were under purifying selection (ka/ks <1). The phylogenetic analyses of the whole plastomes and polymorphic region sequences were able to distinguish the accession from the southern population, indicating its potential to be used as a super-barcode. In conclusion, the newly generated plastomes and polymorphic markers developed here could be a useful genomic resource in molecular breeding, population genetics and the biogeographical study of E. tef.
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Affiliation(s)
- Girma Eshetu Teshome
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, Hubei, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yeshitila Mekbib
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, Hubei, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guangwan Hu
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Zhi-Zhong Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jinming Chen
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China
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Liu F, Movahedi A, Yang W, Xu L, Xie J, Zhang Y. The complete chloroplast genome and characteristics analysis of Callistemon rigidus R.Br. Mol Biol Rep 2020; 47:5013-5024. [PMID: 32515001 DOI: 10.1007/s11033-020-05567-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/29/2020] [Indexed: 10/24/2022]
Abstract
Callistemon rigidus R.Br. one of the traditional Chinese medicinal plants, is acrid-flavored and mild-natured, with the prominent effects reducing swelling, resolving phlegm, and dispelling rheumatism. Clinically, it has been commonly used to treat cold, cough and asthma, pain and swelling from impact injuries, eczema, rheumatic arthralgia. The chloroplast genome study on Callistemon rigidus R.Br. is a few seen. This study demonstrates the data collected from the assembly and annotation of the chloroplast (cp) genome of Callistemon rigidus R.Br., followed by furthers comparative analysis with the cp genomes of closely related species. C. rigidus R.Br. showed a cp genome in the size of 158, 961 bp long with 36.78% GC content, among which a pair of inverted repeats (IRs) of 26, 671 bp separated a large single-copy (LSC) region of 87, 162 bp and a small single-copy (SSC) region of 18, 457 bp. Altogether 131 genes were hosted, including 37 transfer RNAs, 8 ribosomal RNAs, and 86 protein-coding genes. 284 simple sequence repeats (SSRs) were also marked out. A comparative analysis of the genome structure and the sequence data of closely related species unveiled the conserved gene order in the IR and LSC/SSC regions, a quite constructive finding for future phylogenetic research. Overall, this study providing C. rigidus R.Br. genomic resources could positively contribute to the evolutionary study and the phylogenetic reconstruction of Myrtaceae.
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Affiliation(s)
- Fenxiang Liu
- School of Business and Trade, Nanjing Institute of Industry Technology, Nanjing, 210023, China
| | - Ali Movahedi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.
| | - Wenguo Yang
- Department of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| | - Lei Xu
- Genepioneer Biotechnologies Inc., Nanjing, 210023, China
| | - Jigang Xie
- School of Business and Trade, Nanjing Institute of Industry Technology, Nanjing, 210023, China
| | - Yu Zhang
- School of Business and Trade, Nanjing Institute of Industry Technology, Nanjing, 210023, China
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Heo KI, Park J, Xi H, Min J. The complete chloroplast genome of Agrimonia pilosa Ledeb. isolated in Korea (Rosaceae): investigation of intraspecific variations on its chloroplast genomes. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2264-2266. [PMID: 33367001 PMCID: PMC7510681 DOI: 10.1080/23802359.2020.1772144] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 05/16/2020] [Indexed: 10/26/2022]
Abstract
The complete chloroplast genome of Agrimonia pilosa Ledeb. isolated in Korea is 155,125 bp long (GC ratio is 36.9%) and has four subregions: 84,458 bp of large single copy (34.9%) and 18,737 bp of small single copy (30.4%) regions are separated by 25,965 bp of inverted repeat (42.6%) regions including 129 genes (84 protein-coding genes, eight rRNAs, and 37 tRNAs). 258 SNPs and 542 INDELs were identified as intraspecific variations against the partial genome (KY419942). Phylogenetic trees show that our chloroplast genome was clustered with the previous A. pilosa chloroplast genome.
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Affiliation(s)
- Kyeong-In Heo
- InfoBoss Inc., Seoul, Republic of Korea.,InfoBoss Research Center, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Inc., Seoul, Republic of Korea.,InfoBoss Research Center, Seoul, Republic of Korea
| | - Hong Xi
- InfoBoss Inc., Seoul, Republic of Korea.,InfoBoss Research Center, Seoul, Republic of Korea
| | - Juhyeon Min
- InfoBoss Inc., Seoul, Republic of Korea.,InfoBoss Research Center, Seoul, Republic of Korea
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Shi C, Han K, Li L, Seim I, Lee SMY, Xu X, Yang H, Fan G, Liu X. Complete Chloroplast Genomes of 14 Mangroves: Phylogenetic and Comparative Genomic Analyses. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8731857. [PMID: 32462024 PMCID: PMC7225854 DOI: 10.1155/2020/8731857] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/20/2020] [Accepted: 04/02/2020] [Indexed: 11/17/2022]
Abstract
Mangroves are a group of plant species that occupy the coastal intertidal zone and are major components of this ecologically important ecosystem. Mangroves belong to about twenty diverse families. Here, we sequenced and assembled chloroplast genomes of 14 mangrove species from eight families spanning five rosid orders and one asterid order: Fabales (Pongamia pinnata), Lamiales (Avicennia marina), Malpighiales (Excoecaria agallocha, Bruguiera sexangula, Kandelia obovata, Rhizophora stylosa, and Ceriops tagal), Malvales (Hibiscus tiliaceus, Heritiera littoralis, and Thespesia populnea), Myrtales (Laguncularia racemosa, Sonneratia ovata, and Pemphis acidula), and Sapindales (Xylocarpus moluccensis). These chloroplast genomes range from 149 kb to 168 kb in length. A conserved structure of two inverted repeats (IRa and IRb, ~25.8 kb), one large single-copy region (LSC, ~89.0 kb), and one short single-copy region (SSC, ~18.9 kb) as well as ~130 genes (85 protein-coding, 37 tRNAs, and 8 rRNAs) was observed. We found the lowest divergence in the IR regions among the four regions. We also identified simple sequence repeats (SSRs), which were found to be variable in numbers. Most chloroplast genes are highly conserved, with only four genes under positive selection or relaxed pressure. Combined with publicly available chloroplast genomes, we carried out phylogenetic analysis and confirmed the previously reported phylogeny within rosids, including the positioning of obscure families in Malpighiales. Our study reports 14 mangrove chloroplast genomes and illustrates their genome features and evolution.
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Affiliation(s)
- Chengcheng Shi
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 101408, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Kai Han
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Liangwei Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Inge Seim
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing 210046, China
- Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Woolloongabba 4102, Australia
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Xun Xu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Huanming Yang
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 101408, China
- BGI-Shenzhen, Shenzhen 518083, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
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Li H, Guo Q, Li Q, Yang L. Long-reads reveal that Rhododendron delavayi plastid genome contains extensive repeat sequences, and recombination exists among plastid genomes of photosynthetic Ericaceae. PeerJ 2020; 8:e9048. [PMID: 32351791 PMCID: PMC7183307 DOI: 10.7717/peerj.9048] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/02/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Rhododendron delavayi Franch. var. delavayi is a wild ornamental plant species in Guizhou Province, China. The lack of its plastid genome information seriously hinders the further application and conservation of the valuable resource. METHODS The complete plastid genome of R. delavayi was assembled from long sequence reads. The genome was then characterized, and compared with those of other photosynthetic Ericaceae species. RESULTS The plastid genome of R. delavayi has a typical quadripartite structure, and a length of 202,169 bp. It contains a large number of repeat sequences and shows preference for codon usage. The comparative analysis revealed the irregular recombination of gene sets, including rearrangement and inversion, in the large single copy region. The extreme expansion of the inverted repeat region shortened the small single copy, and expanded the full length of the genome. In addition, consistent with traditional taxonomy, R. delavayi with nine other species of the same family were clustered into Ericaceae based on the homologous protein-coding sequences of the plastid genomes. Thus, the long-read assembly of the plastid genome of R. delavayi would provide basic information for the further study of the evolution, genetic diversity, and conservation of R. delavayi and its relatives.
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Affiliation(s)
- Huie Li
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Qiqiang Guo
- Institute for Forest Resources & Environment of Guizhou, Guizhou University, Guiyang, Guizhou, China
| | - Qian Li
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Lan Yang
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
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Yin X, Liao B, Guo S, Liang C, Pei J, Xu J, Chen S. The chloroplasts genomic analyses of Rosa laevigata, R. rugosa and R. canina. Chin Med 2020; 15:18. [PMID: 32082412 PMCID: PMC7020376 DOI: 10.1186/s13020-020-0298-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/05/2020] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Many species of the genus Rosa have been used as ornamental plants and traditional medicines. However, industrial development of roses is hampered due to highly divergent characteristics. METHODS We analyzed the chloroplast (cp) genomes of Rosa laevigata, R. rugosa and R. canina, including the repeat sequences, inverted-repeat (IR) contractions and expansions, and mutation sites. RESULTS The size of the cp genome of R. laevigata, R. rugosa and R. canina was between 156 333 bp and 156 533 bp, and contained 113 genes (30 tRNA genes, 4 rRNA genes and 79 protein-coding genes). The regions with a higher degree of variation were screened out (trnH-GUU, trnS-GCU, trnG-GCC, psbA-trnH, trnC-GCA,petN, trnT-GGU, psbD, petA, psbJ, ndhF, rpl32,psaC and ndhE). Such higher-resolution loci lay the foundation of barcode-based identification of cp genomes in Rosa genus. A phylogenetic tree of the genus Rosa was reconstructed using the full sequences of the cp genome. These results were largely in accordance with the current taxonomic status of Rosa. CONCLUSIONS Our data: (i) reveal that cp genomes can be used for the identification and classification of Rosa species; (ii) can aid studies on molecular identification, genetic transformation, expression of secondary metabolic pathways and resistant proteins; (iii) can lay a theoretical foundation for the discovery of disease-resistance genes and cultivation of Rosa species.
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Affiliation(s)
- Xianmei Yin
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611130 China
| | - Baosheng Liao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institution of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Shuai Guo
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institution of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Conglian Liang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355 China
| | - Jin Pei
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611130 China
| | - Jiang Xu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institution of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institution of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
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Li P, Lou G, Cai X, Zhang B, Cheng Y, Wang H. Comparison of the complete plastomes and the phylogenetic analysis of Paulownia species. Sci Rep 2020; 10:2225. [PMID: 32042041 PMCID: PMC7010769 DOI: 10.1038/s41598-020-59204-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 12/30/2019] [Indexed: 11/08/2022] Open
Abstract
Paulownia species are important ecological, economic and ornamental species, but their phylogenetic relationship remains unclear, which seriously affects the development and utilization of these important resources. The complete chloroplast genomes of six Paulownia species were assembled by next-generation sequencing data. By adding two known Paulownia chloroplast genomes to these six assembled genomes, we performed the comparative analysis and phylogenetic tree reconstruction of Paulownia. The results indicated that the chloroplast genomes of Paulownia species ranged in size from 154,107 to 154,694 bp. These chloroplast genomes contained 117 unique functional genes, including 80 protein-coding genes, four rRNA genes, and 33 tRNA genes. Twelve hotspot regions, five protein-coding genes and seven noncoding regions, were identified in the chloroplast genomes that showed high levels of sequence variation. Additionally, positive selection was observed in three genes, rps2, rbcL and ndhG. The maximum likelihood (ML) and Bayesian (BI) analysis strongly supported the monophyletic origin of Paulownia species, which clustered into two major clades: One clade included P. coreana, P. tomentosa and P. kawakamii, while the other clade comprised the 5 other species including P. fargesii and P. australis. This study provides useful genetic information for phylogenetic reconstruction, taxonomic discrepancies, and studying species evolution and phylogeography in Paulownia.
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Affiliation(s)
- Pingping Li
- College of Life Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Gongli Lou
- College of plant protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaoran Cai
- College of plant protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Bin Zhang
- College of plant protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yueqin Cheng
- College of plant protection, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Hongwei Wang
- College of Life Science, Henan Agricultural University, Zhengzhou, 450002, China.
- College of plant protection, Henan Agricultural University, Zhengzhou, 450002, China.
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Asaf S, Khan A, Khan AL, Al-Harrasi A, Al-Rawahi A. Complete Chloroplast Genomes of Vachellia nilotica and Senegalia senegal: Comparative Genomics and Phylogenomic Placement in a New Generic System. PLoS One 2019; 14:e0225469. [PMID: 31765416 PMCID: PMC6876885 DOI: 10.1371/journal.pone.0225469] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 11/05/2019] [Indexed: 12/15/2022] Open
Abstract
Vachellia and Senegalia are the most important genera in the subfamily Mimosoideae (Fabaceae). Recently, species from both genera were separated from the long-characterized Acacia due to their macro-morphological characteristics. However, this morpho-taxonomic differentiation struggles to discriminate some species, for example, Vachellia nilotica and Senegalia senegal. Therefore, sequencing the chloroplast (cp) genomes of these species and determining their phylogenetic placement via conserved genes may help to validate the taxonomy. Hence, we sequenced the cp genomes of V. nilotica and S. senegal, and the results showed that the sizes of the genomes are 165.3 and 162.7 kb, respectively. The cp genomes of both species comprised large single-copy regions (93,849~91,791 bp) and pairs of inverted repeats (IR; 26,093~26,008 bp). The total numbers of genes found in the V. nilotica and S. senegal cp genomes were 135 and 132, respectively. Approximately 123:130 repeats and 290:281 simple sequence repeats were found in the S. senegal and V. nilotica cp genomes, respectively. Genomic characterization was undertaken by comparing these genomes with those of 17 species belonging to related genera in Fabaceae. A phylogenetic analysis of the whole genome dataset and 56 shared genes was undertaken by generating cladograms with the same topologies and placing both species in a new generic system. These results support the likelihood of identifying segregate genera from Acacia with phylogenomic disposition of both V. nilotica and S. senegal in the subfamily Mimosoideae. The current study is the first to obtain complete genomic information on both species and may help to elucidate the genome architecture of these species and evaluate the genetic diversity among species.
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Affiliation(s)
- Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Arif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, Bodo, Norway
| | - Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
- * E-mail: (ALK); (AAH)
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
- * E-mail: (ALK); (AAH)
| | - Ahmed Al-Rawahi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
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41
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Yang J, Takayama K, Pak JH, Kim SC. Comparison of the Whole-Plastome Sequence between the Bonin Islands Endemic Rubus boninensis and Its Close Relative, Rubus trifidus (Rosaceae), in the Southern Korean Peninsula. Genes (Basel) 2019; 10:E774. [PMID: 31581648 PMCID: PMC6826710 DOI: 10.3390/genes10100774] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/19/2019] [Accepted: 09/27/2019] [Indexed: 12/03/2022] Open
Abstract
Rubus boninensis is a rare endemic species found on the Bonin Islands with a very restricted distribution. It is morphologically most closely related to Rubus trifidus, occurring widely in the southern Korean peninsula and Japan. This species pair provides a good example of anagenetic speciation on an oceanic island in the northwestern Pacific Ocean-R. trifidus as a continental progenitor and R. boninensis as an insular derivative species. In this study, we firstly characterized the complete plastome of R. boninensis and R. trifidus and compared this species pair to another anagenetically derived species pair (R. takesimensis-R. crataegifolius). The complete plastome of R. trifidus was 155,823 base pairs (bp) long, slightly longer (16 bp) than that of R. boninensis (155,807 bp). No structural or content rearrangements were found between the species pair. Eleven hotspot regions, including trnH/psbA, were identified between R. trifidus and R. boninensis. Phylogenetic analysis of 19 representative plastomes within the family Rosaceae suggested sister relationships between R. trifidus and R. boninensis, and between R. crataegifolius and R. takesimensis. The plastome resources generated by the present study will help elucidate plastome evolution and resolve phylogenetic relationships within highly complex and reticulated lineages of the genus Rubus.
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Affiliation(s)
- JiYoung Yang
- Department of Biology, Research Institute for Dok-do and Ulleung-do Island, School of Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, Gyeongsangbuk-do 41566, Korea.
| | - Koji Takayama
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Jae-Hong Pak
- Department of Biology, Research Institute for Dok-do and Ulleung-do Island, School of Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, Gyeongsangbuk-do 41566, Korea.
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon, Gyeonggi-do 16419, Korea.
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Ge Y, Dong X, Wu B, Wang N, Chen D, Chen H, Zou M, Xu Z, Tan L, Zhan R. Evolutionary analysis of six chloroplast genomes from three Persea americana ecological races: Insights into sequence divergences and phylogenetic relationships. PLoS One 2019; 14:e0221827. [PMID: 31532782 PMCID: PMC6750585 DOI: 10.1371/journal.pone.0221827] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 08/15/2019] [Indexed: 11/19/2022] Open
Abstract
Chloroplasts significantly influence species phylogenies because of their maternal inheritance and the moderate evolutionary rate of their genomes. Avocado, which is a member of the family Lauraceae, has received considerable attention from botanists, likely because of its position as a basal angiosperm. However, there is relatively little avocado genomic information currently available. In this study, six complete avocado chloroplast genomes from three ecological races were assembled to examine the sequence diversity among the three avocado ecological races. A comparative genomic analysis revealed that 515 simple sequence repeat loci and 176 repeats belonging to four other types were polymorphic across the six chloroplast genomes. Three highly variable regions (trnC-GCA-petN, petN-psbM, and petA-psbJ) were identified as highly informative markers. A phylogenetic analysis based on 79 common protein-coding genes indicated that the six examined avocado accessions from three ecological races form a monophyletic clade. The other three genera belonging to the Persea group clustered to form a sister clade with a high bootstrap value. These chloroplast genomes provide important genetic information for future attempts at identifying avocado races and for the related biological research.
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Affiliation(s)
- Yu Ge
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xiangshu Dong
- College of Agriculture, Yunnan University, Yunnan, China
| | - Bin Wu
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Nan Wang
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Di Chen
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Haihong Chen
- College of Agriculture, Guangxi Vocational and Technical College, Nanning, China
| | - Minghong Zou
- South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Zining Xu
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Lin Tan
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Rulin Zhan
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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Shahzadi I, Abdullah, Mehmood F, Ali Z, Ahmed I, Mirza B. Chloroplast genome sequences of Artemisia maritima and Artemisia absinthium: Comparative analyses, mutational hotspots in genus Artemisia and phylogeny in family Asteraceae. Genomics 2019; 112:1454-1463. [PMID: 31450007 DOI: 10.1016/j.ygeno.2019.08.016] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/16/2019] [Accepted: 08/21/2019] [Indexed: 12/14/2022]
Abstract
Artemisia L. is a complex genus of medicinal importance. Publicly available chloroplast genomes of few Artemisia species are insufficient to resolve taxonomic discrepancies at species level. We report chloroplast genome sequences of two further Artemisia species: A. maritima (151,061 bp) and A. absinthium (151,193 bp). Both genomes possess typical quadripartite structure comprising of a large single copy, a small single copy and a pair of long inverted repeats. The two genomes exhibited high similarities in genome sizes, gene synteny, GC content, synonymous and non-synonymous substitutions, codon usage, amino acids frequencies, RNA editing sites, microsatellites, and oligonucleotide repeats. Transition to transversion ratio was <1. Maximum likelihood tree showed Artemisia a monophyletic genus, sister to genus Chrysanthemum. We also identified 20 highly polymorphic regions including rpoC2-rps2, trnR-UCU-trnG-UCC, rps18-rpl20, and trnL-UAG-rpl32 that could be used to develop authentic and cost-effective markers to resolve taxonomic discrepancies and infer phylogenetic relationships among Artemisia species.
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Affiliation(s)
- Iram Shahzadi
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Abdullah
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Furrukh Mehmood
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Zain Ali
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, Pakistan
| | - Bushra Mirza
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan.
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Comparison of Four Complete Chloroplast Genomes of Medicinal and Ornamental Meconopsis Species: Genome Organization and Species Discrimination. Sci Rep 2019; 9:10567. [PMID: 31332227 PMCID: PMC6646306 DOI: 10.1038/s41598-019-47008-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/08/2019] [Indexed: 11/26/2022] Open
Abstract
High-throughput sequencing of chloroplast genomes has been used to gain insight into the evolutionary relationships of plant species. In this study, we sequenced the complete chloroplast genomes of four species in the Meconopsis genus: M. racemosa, M. integrifolia (Maxim.) Franch, M. horridula and M. punicea. These plants grow in the wild and are recognized as having important medicinal and ornamental applications. The sequencing results showed that the size of the Meconopsis chloroplast genome ranges from 151864 to 153816 bp. A total of 127 genes comprising 90 protein-coding genes, 37 tRNA genes and 8 rRNA genes were observed in all four chloroplast genomes. Comparative analysis of the four chloroplast genomes revealed five hotspot regions (matK, rpoC2, petA, ndhF, and ycf1), which could potentially be used as unique molecular markers for species identification. In addition, the ycf1 gene may also be used as an effective molecular marker to distinguish Papaveraceae and determine the evolutionary relationships among plant species in the Papaveraceae family. Futhermore, these four genomes can provide valuable genetic information for other related studies.
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Kim Y, Heo KI, Nam S, Xi H, Lee S, Park J. The complete chloroplast genome of candidate new species from Rosa rugosa in Korea (Rosaceae). Mitochondrial DNA B Resour 2019; 4:2433-2435. [PMID: 33365574 PMCID: PMC7687460 DOI: 10.1080/23802359.2019.1637296] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 06/22/2019] [Indexed: 11/22/2022] Open
Abstract
Complete chloroplast genome of candidate new species from Rosa rugosa, named as Rosa angusta, is 156,989 bp long and has four subregions: 86,227 bp of large single copy (LSC) and 18,816 bp of small single copy (SSC) regions are separated by 25,793 bp of inverted repeat (IR) regions including 130 genes (85 protein-coding genes, eight rRNAs, and 37 tRNAs). The overall GC content of this chloroplast genome is 37.2% and in the LSC, SSC, and IR regions are 35.2%, 31.1%, and 42.8%, respectively. Phylogenetic trees show that R. angusta is close to R. rugosa with enough number of sequence variations.
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Affiliation(s)
- Yongsung Kim
- InfoBoss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Kyeong-In Heo
- InfoBoss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Suhwan Nam
- Baekdudaegan National Arboretum, Gyeongsangbuk-do, Republic of Korea
| | - Hong Xi
- InfoBoss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Sangtae Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
| | - Jongsun Park
- InfoBoss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
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