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Cui X, Liu K, Li E, Zhang Z, Dong W. Chloroplast Genomes Evolution and Phylogenetic Relationships of Caragana species. Int J Mol Sci 2024; 25:6786. [PMID: 38928490 PMCID: PMC11203854 DOI: 10.3390/ijms25126786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 06/18/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
Caragana sensu lato (s.l.) includes approximately 100 species that are mainly distributed in arid and semi-arid regions. Caragana species are ecologically valuable for their roles in windbreaking and sand fixation. However, the taxonomy and phylogenetic relationships of the genus Caragana are still unclear. In this study, we sequenced and assembled the chloroplast genomes of representative species of Caragana and reconstructed robust phylogenetic relationships at the section level. The Caragana chloroplast genome has lost the inverted repeat region and wascategorized in the inverted repeat loss clade (IRLC). The chloroplast genomes of the eight species ranged from 128,458 bp to 135,401 bp and contained 110 unique genes. All the Caragana chloroplast genomes have a highly conserved structure and gene order. The number of long repeats and simple sequence repeats (SSRs) showed significant variation among the eight species, indicating heterogeneous evolution in Caragana. Selective pressure analysis of the genes revealed that most of the protein-coding genes evolved under purifying selection. The phylogenetic analyses indicated that each section forms a clade, except the section Spinosae, which was divided into two clades. This study elucidated the evolution of the chloroplast genome within the widely distributed genus Caragana. The detailed information obtained from this study can serve as a valuable resource for understanding the molecular dynamics and phylogenetic relationships within Caragana.
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Affiliation(s)
| | | | | | - Zhixiang Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (X.C.); (K.L.); (E.L.)
| | - Wenpan Dong
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (X.C.); (K.L.); (E.L.)
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Chen R, Meng S, Wang A, Jiang F, Yuan L, Lei L, Wang H, Fan W. The genomes of seven economic Caesalpinioideae trees provide insights into polyploidization history and secondary metabolite biosynthesis. PLANT COMMUNICATIONS 2024:100944. [PMID: 38733080 DOI: 10.1016/j.xplc.2024.100944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/29/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
The Caesalpinioideae subfamily contains many well-known trees that are important for economic sustainability and human health, but a lack of genomic resources has hindered their breeding and utilization. Here, we present chromosome-level reference genomes for the two food and industrial trees Gleditsia sinensis (921 Mb) and Biancaea sappan (872 Mb), the three shade and ornamental trees Albizia julibrissin (705 Mb), Delonix regia (580 Mb), and Acacia confusa (566 Mb), and the two pioneer and hedgerow trees Leucaena leucocephala (1338 Mb) and Mimosa bimucronata (641 Mb). Phylogenetic inference shows that the mimosoid clade has a much higher evolutionary rate than the other clades of Caesalpinioideae. Macrosynteny comparison suggests that the fusion and breakage of an unstable chromosome are responsible for the difference in basic chromosome number (13 or 14) for Caesalpinioideae. After an ancient whole-genome duplication (WGD) shared by all Caesalpinioideae species (CWGD, ∼72.0 million years ago [MYA]), there were two recent successive WGD events, LWGD-1 (16.2-19.5 MYA) and LWGD-2 (7.1-9.5 MYA), in L. leucocephala. Thereafter, ∼40% gene loss and genome-size contraction have occurred during the diploidization process in L. leucocephala. To investigate secondary metabolites, we identified all gene copies involved in mimosine metabolism in these species and found that the abundance of mimosine biosynthesis genes in L. leucocephala largely explains its high mimosine production. We also identified the set of all potential genes involved in triterpenoid saponin biosynthesis in G. sinensis, which is more complete than that based on previous transcriptome-derived unigenes. Our results and genomic resources will facilitate biological studies of Caesalpinioideae and promote the utilization of valuable secondary metabolites.
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Affiliation(s)
- Rong Chen
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Sihan Meng
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Anqi Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Fan Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Lihua Yuan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Lihong Lei
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Hengchao Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Wei Fan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China.
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Wu J, Zhang J, Guo X, Yu N, Peng D, Xing S. Comprehensive analysis of complete chloroplast genome sequence of Plantago asiatica L. (Plantaginaceae). PLANT SIGNALING & BEHAVIOR 2023; 18:2163345. [PMID: 36592637 PMCID: PMC9809945 DOI: 10.1080/15592324.2022.2163345] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Plantago asiatica L. is a representative individual species of Plantaginaceae, whose high reputation is owed to its edible and medicinal values. However, the phylogeny and genes of the P. asiatica chloroplast have not yet been well described. Here we report the findings of a comprehensive analysis of the P. asiatica chloroplast genome. The P. asiatica chloroplast genome is 164,992 bp, circular, and has a GC content of 37.98%. The circular genome contains 141 genes, including 8 rRNAs, 38 tRNAs, and 95 protein-coding genes. Seventy-two simple sequence repeats are detected. Comparative chloroplast genome analysis of six related species suggests that a higher similarity exists in the coding region than the non-coding region, and differences in the degree of preservation is smaller between P. asiatica and Plantago depressa than among others. Our phylogenetic analysis illustrates P. asiatica has a relatively close relationship with P. depressa, which was also divided into different clades with Plantago ovata and Plantago lagopus in the genus Plantago. This analysis of the P. asiatica chloroplast genome contributes to an improved deeply understanding of the evolutionary relationships among Plantaginaceae.
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Affiliation(s)
- Jing Wu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Jing Zhang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Xiaohu Guo
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Nianjun Yu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, China
- MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, China
| | - Daiyin Peng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, China
- MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, China
| | - Shihai Xing
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, China
- Anhui Province Key Laboratory of Research & Development of Chinese Medicine, Hefei, China
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Caycho E, La Torre R, Orjeda G. Assembly, annotation and analysis of the chloroplast genome of the Algarrobo tree Neltuma pallida (subfamily: Caesalpinioideae). BMC PLANT BIOLOGY 2023; 23:570. [PMID: 37974117 PMCID: PMC10652460 DOI: 10.1186/s12870-023-04581-5] [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: 07/15/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Neltuma pallida is a tree that grows in arid soils in northwestern Peru. As a predominant species of the Equatorial Dry Forest ecoregion, it holds significant economic and ecological value for both people and environment. Despite this, the species is severely threatened and there is a lack of genetic and genomic research, hindering the proposal of evidence-based conservation strategies. RESULTS In this work, we conducted the assembly, annotation, analysis and comparison of the chloroplast genome of a N. pallida specimen with those of related species. The assembled chloroplast genome has a length of 162,381 bp with a typical quadripartite structure (LSC-IRA-SSC-IRB). The calculated GC content was 35.97%. However, this is variable between regions, with a higher GC content observed in the IRs. A total of 132 genes were annotated, of which 19 were duplicates and 22 contained at least one intron in their sequence. A substantial number of repetitive sequences of different types were identified in the assembled genome, predominantly tandem repeats (> 300). In particular, 142 microsatellites (SSR) markers were identified. The phylogenetic reconstruction showed that N. pallida grouped with the other Neltuma species and with Prosopis cineraria. The analysis of sequence divergence between the chloroplast genome sequences of N. pallida, N. juliflora, P. farcta and Strombocarpa tamarugo revealed a high degree of similarity. CONCLUSIONS The N. pallida chloroplast genome was found to be similar to those of closely related species. With a size of 162,831 bp, it had the classical chloroplast quadripartite structure and GC content of 35.97%. Most of the 132 identified genes were protein-coding genes. Additionally, over 800 repetitive sequences were identified, including 142 SSR markers. In the phylogenetic analysis, N. pallida grouped with other Neltuma spp. and P. cineraria. Furthermore, N. pallida chloroplast was highly conserved when compared with genomes of closely related species. These findings can be of great potential for further diversity studies and genetic improvement of N. pallida.
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Affiliation(s)
- Esteban Caycho
- Laboratory of Genomics and Bioinformatics for Biodiversity, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, 15081, Lima, Peru
| | - Renato La Torre
- Laboratory of Genomics and Bioinformatics for Biodiversity, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, 15081, Lima, Peru
| | - Gisella Orjeda
- Laboratory of Genomics and Bioinformatics for Biodiversity, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, 15081, Lima, Peru.
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Shi N, Yang Z, Miao K, Tang L, Zhou N, Xie P, Wen G. Comparative analysis of the medicinal plant Polygonatum kingianum (Asparagaceae) with related verticillate leaf types of the Polygonatum species based on chloroplast genomes. FRONTIERS IN PLANT SCIENCE 2023; 14:1202634. [PMID: 37680362 PMCID: PMC10482041 DOI: 10.3389/fpls.2023.1202634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 07/06/2023] [Indexed: 09/09/2023]
Abstract
Background Polygonatum kingianum has been widely used as a traditional Chinese medicine as well as a healthy food. Because of its highly variable morphology, this medicinal plant is often difficult to distinguish from other related verticillate leaf types of the Polygonatum species. The contaminants in P. kingianum products not only decrease the products' quality but also threaten consumer safety, seriously inhibiting the industrial application of P. kingianum. Methods Nine complete chloroplast (cp) genomes of six verticillate leaf types of the Polygonatum species were de novo assembled and systematically analyzed. Results The total lengths of newly sequenced cp genomes ranged from 155,437 to 155,977 bp, including 86/87 protein-coding, 38 tRNA, and 8 rRNA genes, which all exhibited well-conserved genomic structures and gene orders. The differences in the IR/SC (inverted repeats/single-copy) boundary regions and simple sequence repeats were detected among the verticillate leaf types of the Polygonatum cp genomes. Comparative cp genomes analyses revealed that a higher similarity was conserved in the IR regions than in the SC regions. In addition, 11 divergent hotspot regions were selected, providing potential molecular markers for the identification of the Polygonatum species with verticillate leaf types. Phylogenetic analysis indicated that, as a super barcode, plastids realized a fast and efficient identification that clearly characterized the relationships within the verticillate leaf types of the Polygonatum species. In brief, our results not only enrich the data on the cp genomes of the genus Polygonatum but also provide references for the P. kingianum germplasm resource protection, herbal cultivation, and drug production. Conclusion This study not only accurately identifies P. kingianum species, but also provides valuable information for the development of molecular markers and phylogenetic analyses of the Polygonatum species with verticillate leaf types.
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Affiliation(s)
- Naixing Shi
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Zefen Yang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Ke Miao
- Chinese Academy of Sciences (CAS) Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Lilei Tang
- College of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Nian Zhou
- Chinese Academy of Sciences (CAS) Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Pingxuan Xie
- College of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Guosong Wen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
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Li Z, Huang Z, Wan X, Yu J, Dong H, Zhang J, Zhang C, Wang S. Complete chloroplast genome sequence of Rhododendronmariesii and comparative genomics of related species in the family Ericaeae. COMPARATIVE CYTOGENETICS 2023; 17:163-180. [PMID: 37650109 PMCID: PMC10464601 DOI: 10.3897/compcytogen.17.101427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 07/26/2023] [Indexed: 09/01/2023]
Abstract
Rhododendronmariesii Hemsley et Wilson, 1907, a typical member of the family Ericaeae, possesses valuable medicinal and horticultural properties. In this research, the complete chloroplast (cp) genome of R.mariesii was sequenced and assembled, which proved to be a typical quadripartite structure with the length of 203,480 bp. In particular, the lengths of the large single copy region (LSC), small single copy region (SSC), and inverted repeat regions (IR) were 113,715 bp, 7,953 bp, and 40,918 bp, respectively. Among the 151 unique genes, 98 were protein-coding genes, 8 were tRNA genes, and 45 were rRNA genes. The structural characteristics of the R.mariesiicp genome was similar to other angiosperms. Leucine was the most representative amino acid, while cysteine was the lowest representative. Totally, 30 codons showed obvious codon usage bias, and most were A/U-ending codons. Six highly variable regions were observed, such as trnK-pafI and atpE-rpoB, which could serve as potential markers for future barcoding and phylogenetic research of R.mariesii species. Coding regions were more conserved than non-coding regions. Expansion and contraction in the IR region might be the main length variation in R.mariesii and related Ericaeae species. Maximum-likelihood (ML) phylogenetic analysis revealed that R.mariesii was relatively closed to the R.simsii Planchon, 1853 and R.pulchrum Sweet,1831. This research will supply rich genetic resource for R.mariesii and related species of the Ericaeae.
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Affiliation(s)
- Zhiliang Li
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei Province, ChinaHuanggang Normal UniversityHuanggangChina
| | - Zhiwei Huang
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei Province, ChinaHuanggang Normal UniversityHuanggangChina
| | - Xuchun Wan
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei Province, ChinaHuanggang Normal UniversityHuanggangChina
| | - Jiaojun Yu
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei Province, ChinaHuanggang Normal UniversityHuanggangChina
| | - Hongjin Dong
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei Province, ChinaHuanggang Normal UniversityHuanggangChina
| | - Jialiang Zhang
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei Province, ChinaHuanggang Normal UniversityHuanggangChina
| | - Chunyu Zhang
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei Province, ChinaHuanggang Normal UniversityHuanggangChina
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, ChinaHuazhong Agricultural UniversityWuhanChina
| | - Shuzhen Wang
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei Province, ChinaHuanggang Normal UniversityHuanggangChina
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Pu T, Zhao ZN, Yu X. The complete chloroplast genome of Crataegus scabrifolia (Franch.) Rehd (Rosaceae), a medicinal and edible plant in Southwest China. Mitochondrial DNA B Resour 2023; 8:81-85. [PMID: 36643811 PMCID: PMC9833407 DOI: 10.1080/23802359.2022.2160668] [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] [Indexed: 01/11/2023] Open
Abstract
Crataegus scabrifolia (Franch.) Rehd is a medicinal and edible plant in Southwest China. The chloroplast genome of C. scabrifolia was analyzed by high-throughput sequencing technology, and its genetic relationship to related species was discussed. The chloroplast genome is 159,637 bp long, with two inverted repeat (IR) regions (26,384 bp each) that separate a large single-copy (LSC) region (87,730 bp) and a small single-copy (SSC) region (19,139 bp). A total of 127 genes were annotated, including 83 protein-coding genes, 8 rRNA genes, and 36 tRNA genes. The phylogenetic tree shows that C. hupehensis is closely related to C. scabrifolia with strong bootstrap support.
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Affiliation(s)
- Tian Pu
- School of Forestry, Southwest Forestry University, Kunming, China
| | - Zhen-Ning Zhao
- School of Forestry, Southwest Forestry University, Kunming, China
| | - Xiao Yu
- School of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, China,CONTACT Xiao Yu School of Landscape Architecture, Southwest Forestry University, 300 Bailong temple, Qingyun Street, Kunming, 650224China
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Cai H, Gu X, Li Y, Ren Y, Yan S, Yang M. Cold Resistance of Euonymus japonicus Beihaidao Leaves and Its Chloroplast Genome Structure and Comparison with Celastraceae Species. PLANTS 2022; 11:plants11192449. [PMID: 36235317 PMCID: PMC9573587 DOI: 10.3390/plants11192449] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/08/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022]
Abstract
Euonymus japonicus Beihaidao is one of the most economically important ornamental species of the Euonymus genus. There are approximately 97 genera and 1194 species of plants worldwide in this family (Celastraceae). Using E. japonicus Beihaidao, we conducted a preliminary study of the cold resistance of this species, evaluated its performance during winter, assembled and annotated its chloroplast genome, and performed a series of analyses to investigate its gene structure GC content, sequence alignment, and nucleic acid diversity. Our objectives were to understand the evolutionary relationships of the genus and to identify positive selection genes that may be related to adaptations to environmental change. The results indicated that E. japonicus Beihaidao leaves have certain cold resistance and can maintain their viability during wintering. Moreover, the chloroplast genome of E. japonicus Beihaidao is a typical double-linked ring tetrad structure, which is similar to that of the other four Euonymus species, E. hamiltonianus, E. phellomanus, E. schensianus, and E. szechuanensis, in terms of gene structure, gene species, gene number, and GC content. Compared to other Celastraceae species, the variation in the chloroplast genome sequence was lower, and the gene structure was more stable. The phylogenetic relationships of 37 species inferred that members of the Euonymus genus do not form a clade and that E. japonicus Beihaidao is closely related to E. japonicus and E. fortunei. A total of 11 functional positive selected genes were identified, which may have played an important role in the process of Celastraceae species adapting to environmental changes. Our study provides important genetic information to support further investigations into the phylogenetic development and adaptive evolution of Celastraceae species.
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Affiliation(s)
- Hongyu Cai
- Forest Department, College of Forestry, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Xiaozheng Gu
- Forest Department, College of Forestry, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Yongtan Li
- Forest Department, College of Forestry, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Yachao Ren
- Forest Department, College of Forestry, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Shufang Yan
- Hebei Academy of Forestry and Grassland Science, Shijiazhuang 050050, China
| | - Minsheng Yang
- Forest Department, College of Forestry, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
- Correspondence: ; Tel.: +86-0312-752-8715
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Han S, Wang R, Hong X, Wu C, Zhang S, Kan X. Plastomes of Bletilla (Orchidaceae) and Phylogenetic Implications. Int J Mol Sci 2022; 23:ijms231710151. [PMID: 36077549 PMCID: PMC9456473 DOI: 10.3390/ijms231710151] [Citation(s) in RCA: 6] [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: 07/30/2022] [Revised: 08/22/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
The genus Bletilla is a small genus of only five species distributed across Asia, including B. chartacea, B. foliosa, B. formosana, B. ochracea and B. striata, which is of great medicinal importance. Furthermore, this genus is a member of the key tribe Arethuseae (Orchidaceae), harboring an extremely complicated taxonomic history. Recently, the monophyletic status of Bletilla has been challenged, and the phylogenetic relationships within this genus are still unclear. The plastome, which is rich in both sequence and structural variation, has emerged as a powerful tool for understanding plant evolution. Along with four new plastomes, this work is committed to exploring plastomic markers to elucidate the phylogeny of Bletilla. Our results reveal considerable plastomic differences between B. sinensis and the other three taxa in many aspects. Most importantly, the specific features of the IR junction patterns, novel pttRNA structures and codon aversion motifs can serve as useful molecular markers for Bletilla phylogeny. Moreover, based on maximum likelihood and Bayesian inference methods, our phylogenetic analyses based on two datasets of Arethuseae strongly imply that Bletilla is non-monophyletic. Accordingly, our findings from this study provide novel potential markers for species identification, and shed light on the evolution of Bletilla and Arethuseae.
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Affiliation(s)
- Shiyun Han
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu 241000, China
| | - Rongbin Wang
- Institute of Chinese Medicine Resources, Anhui College of Traditional Chinese Medicine, Wuhu 241002, China
- Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Xin Hong
- Anhui Provincial Engineering Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
| | - Cuilian Wu
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu 241000, China
- Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Sijia Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu 241000, China
- Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Xianzhao Kan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu 241000, China
- Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Correspondence: ; Tel.: +86-139-5537-2268
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