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Feng Z, Zheng Y, Jiang Y, Pei J, Huang L. Phylogenetic relationships, selective pressure and molecular markers development of six species in subfamily Polygonoideae based on complete chloroplast genomes. Sci Rep 2024; 14:9783. [PMID: 38684694 PMCID: PMC11059183 DOI: 10.1038/s41598-024-58934-7] [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: 08/08/2023] [Accepted: 04/04/2024] [Indexed: 05/02/2024] Open
Abstract
The subfamily Polygonoideae encompasses a diverse array of medicinal and horticultural plants that hold significant economic value. However, due to the lack of a robust taxonomy based on phylogenetic relationships, the classification within this family is perplexing, and there is also a scarcity of reports on the chloroplast genomes of many plants falling under this classification. In this study, we conducted a comprehensive analysis by sequencing and characterizing the complete chloroplast genomes of six Polygonoideae plants, namely Pteroxygonum denticulatum, Pleuropterus multiflorus, Pleuropterus ciliinervis, Fallopia aubertii, Fallopia dentatoalata, and Fallopia convolvulus. Our findings revealed that these six plants possess chloroplast genomes with a typical quadripartite structure, averaging 162,931 bp in length. Comparative chloroplast analysis, codon usage analysis, and repetitive sequence analysis demonstrated a high level of conservation within the chloroplast genomes of these plants. Furthermore, phylogenetic analysis unveiled a distinct clade occupied by P. denticulatum, while P. ciliinrvis displayed a closer relationship to the three plants belonging to the Fallopia genus. Selective pressure analysis based on maximum likelihood trees showed that a total of 14 protein-coding genes exhibited positive selection, with psbB and ycf1 having the highest number of positive amino acid sites. Additionally, we identified four molecular markers, namely petN-psbM, psal-ycf4, ycf3-trnS-GGA, and trnL-UAG-ccsA, which exhibit high variability and can be utilized for the identification of these six plants.
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Affiliation(s)
- Zhan Feng
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, Sichuan, China
| | - Yan Zheng
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Yuan Jiang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Jin Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, Sichuan, China.
| | - Linfang Huang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
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Liu L, Li H, Li J, Li X, Hu N, Sun J, Zhou W. Chloroplast genomes of Caragana tibetica and Caragana turkestanica: structures and comparative analysis. BMC PLANT BIOLOGY 2024; 24:254. [PMID: 38594633 PMCID: PMC11003120 DOI: 10.1186/s12870-024-04979-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/02/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND The genus Caragana encompasses multiple plant species that possess medicinal and ecological value. However, some species of Caragana are quite similar in morphology, so identifying species in this genus based on their morphological characteristics is considerably complex. In our research, illumina paired-end sequencing was employed to investigate the genetic organization and structure of Caragana tibetica and Caragana turkestanica, including the previously published chloroplast genome sequence of 7 Caragana plants. RESULTS The lengths of C. tibetica and C. turkestanica chloroplast genomes were 128,433 bp and 129,453 bp, respectively. The absence of inverted repeat sequences in these two species categorizes them under the inverted repeat loss clade (IRLC). They encode 110 and 111 genes (4 /4 rRNA genes, 30 /31tRNA genes, and 76 /76 protein-coding genes), respectively. Comparison of the chloroplast genomes of C. tibetica and C. turkestanica with 7 other Caragana species revealed a high overall sequence similarity. However, some divergence was observed between certain intergenic regions (matK-rbcL, psbD-psbM, atpA-psbI, and etc.). Nucleotide diversity (π) analysis revealed the detection of five highly likely variable regions, namely rps2-atpI, accD-psaI-ycf4, cemA-petA, psbN-psbH and rpoA-rps11. Phylogenetic analysis revealed that C. tibetica's sister species is Caragana jubata, whereas C. turkestanica's closest relative is Caragana arborescens. CONCLUSIONS The present study provides worthwhile information about the chloroplast genomes of C. tibetica and C. turkestanica, which aids in the identification and classification of Caragana species.
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Affiliation(s)
- LiE Liu
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China
| | - HongYan Li
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China
| | - JiaXin Li
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China
| | - XinJuan Li
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China
| | - Na Hu
- Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Jing Sun
- Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Wu Zhou
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China.
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Gao Y, Chen Z, Li X, Malik K, Li C. Comparative Analyses of Complete Chloroplast Genomes of Microula sikkimensis and Related Species of Boraginaceae. Genes (Basel) 2024; 15:226. [PMID: 38397215 PMCID: PMC10887780 DOI: 10.3390/genes15020226] [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: 12/23/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
The present study provides a detailed analysis of the chloroplast genome of Microula sikkimensis. The genome consisted of a total of 149,428 bp and four distinct regions, including a large single-copy region (81,329 bp), a small single-copy region (17,261 bp), and an inverted repeat region (25,419 bp). The genome contained 112 genes, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, and some exhibited duplication in the inverted repeat region. The chloroplast genome displayed different GC content across regions, with the inverted repeat region exhibiting the highest. Codon usage analysis and the identification of simple sequence repeats (SSRs) offer valuable genetic markers. Comparative analysis with other Boraginaceae species highlighted conservation and diversity in coding and noncoding regions. Phylogenetic analysis placed M. sikkimensis within the Boraginaceae family, revealing its distinct relationship with specific species.
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Affiliation(s)
- Yunqing Gao
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730000, China; (Y.G.); (K.M.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730000, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
- Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou 730000, China
- Gansu Tech Innovation Centre of Western China Grassland Industry, Lanzhou University, Lanzhou 730000, China
- Centre for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China
| | - Zhenjiang Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730000, China; (Y.G.); (K.M.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730000, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Xiuzhang Li
- Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining 810016, China;
| | - Kamran Malik
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730000, China; (Y.G.); (K.M.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730000, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
- Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou 730000, China
- Gansu Tech Innovation Centre of Western China Grassland Industry, Lanzhou University, Lanzhou 730000, China
- Centre for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China
| | - Chunjie Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730000, China; (Y.G.); (K.M.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730000, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
- Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou 730000, China
- Gansu Tech Innovation Centre of Western China Grassland Industry, Lanzhou University, Lanzhou 730000, China
- Centre for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China
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Javaid N, Ramzan M, Jabeen S, Shah MN, Danish S, Hirad AH. Genomic exploration of Sesuvium sesuvioides: comparative study and phylogenetic analysis within the order Caryophyllales from Cholistan desert, Pakistan. BMC PLANT BIOLOGY 2023; 23:658. [PMID: 38124056 PMCID: PMC10731703 DOI: 10.1186/s12870-023-04670-5] [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: 07/07/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND The Aizoaceae family's Sesuvium sesuvioides (Fenzl) Verdc is a medicinal species of the Cholistan desert, Pakistan. The purpose of this study was to determine the genomic features and phylogenetic position of the Sesuvium genus in the Aizoaceae family. We used the Illumina HiSeq2500 and paired-end sequencing to publish the complete chloroplast sequence of S. sesuvioides. RESULTS The 155,849 bp length cp genome sequence of S. sesuvioides has a 36.8% GC content. The Leucine codon has the greatest codon use (10.6%), 81 simple sequence repetitions of 19 kinds, and 79 oligonucleotide repeats. We investigated the phylogeny of the order Caryophyllales' 27 species from 23 families and 25 distinct genera. The maximum likelihood tree indicated Sesuvium as a monophyletic genus, and sister to Tetragonia. A comparison of S. sesuvioides, with Sesuvium portulacastrum, Mesembryanthemum crystallinum, Mesembryanthemum cordifolium, and Tetragonia tetragonoides was performed using the NCBI platform. In the comparative investigation of genomes, all five genera revealed comparable cp genome structure, gene number and composition. All five species lacked the rps15 gene and the rpl2 intron. In most comparisons with S. sesuvioides, transition substitutions (Ts) were more frequent than transversion substitutions (Tv), producing Ts/Tv ratios larger than one, and the Ka/Ks ratio was lower than one. We determined ten highly polymorphic regions, comprising rpl22, rpl32-trnL-UAG, trnD-GUC-trnY-GUA, trnE-UUC-trnT-GGU, trnK-UUU-rps16, trnM-CAU-atpE, trnH-GUG-psbA, psaJ-rpl33, rps4-trnT-UGU, and trnF-GAA-ndhJ. CONCLUSION The whole S. sesuvioides chloroplast will be examined as a resource for in-depth taxonomic research of the genus when more Sesuvium and Aizoaceae species are sequenced in the future. The chloroplast genomes of the Aizoaceae family are well preserved, with little alterations, indicating the family's monophyletic origin. This study's highly polymorphic regions could be utilized to build realistic and low-cost molecular markers for resolving taxonomic discrepancies, new species identification, and finding evolutionary links among Aizoaceae species. To properly comprehend the evolution of the Aizoaceae family, further species need to be sequenced.
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Affiliation(s)
- Nida Javaid
- Department of Botany, Faculty of Chemical and Biological Sciences, The Islamia University Bahawalpur, Bahawalpur, Punjab, Pakistan
| | - Musarrat Ramzan
- Department of Botany, Faculty of Chemical and Biological Sciences, The Islamia University Bahawalpur, Bahawalpur, Punjab, Pakistan.
| | - Shagufta Jabeen
- Government Associate College for Women Ahmedpur East, Bahawalpur, Punjab, Pakistan
| | - Muhammad Nadeem Shah
- Department of Agriculture, Government College University Lahore, Lahore, Punjab, Pakistan
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, Florida, USA
| | - Subhan Danish
- Department of Soil Science, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, Punjab, Pakistan.
| | - Abdurahman Hajinur Hirad
- Department of Botany and Microbiology, College of Science, King Saud University, P. O. Box.2455, Riyadh, 11451, Saudi Arabia
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Yan M, Dong S, Gong Q, Xu Q, Ge Y. Comparative chloroplast genome analysis of four Polygonatum species insights into DNA barcoding, evolution, and phylogeny. Sci Rep 2023; 13:16495. [PMID: 37779129 PMCID: PMC10543443 DOI: 10.1038/s41598-023-43638-1] [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: 02/28/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023] Open
Abstract
The Polygonatum genus represents a perennial herb with the Liliaceae family, boasting substantial economic and medicinal significance. The majority of Polygonatum plants exhibit notable similarity while lacking distinctive identifying characteristics, thus resulting in the proliferation of adulterated medicinal materials within the market. Within this study, we conducted an in-depth analysis of the complete chloroplast (cp) genomes of four Polygonatum plants and compared them with four closely akin species. The primary objectives were to unveil structural variations, species divergence, and the phylogenetic interrelations among taxa. The cp genomes of the four Polygonatum species were typified by a conventional quadripartite structure, incorporating a large single copy region (LSC), a small single copy region (SSC), and a pair of inverted repeat regions. In total, we annotated a range of 131 to 133 genes, encompassing 84 to 86 protein-coding genes, 38 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes, and 0 to 2 pseudogenes (ycf1, infA). Our comparative analyses unequivocally revealed a remarkable consistency in gene order and GC content within the Polygonatum genus. Furthermore, we predicted a potential 59 to 64 RNA editing sites distributed across 22 protein-coding genes, with the ndhB gene exhibiting the most prominent propensity for RNA editing sites, boasting a tally of 15 sites. Notably, six regions of substantial potential variability were ascertained, characterized by elevated Pi values. Noteworthy, molecular markers for species identification, population genetic scrutiny, and phylogenetic investigations within the genus were identified in the form of the psaJ-rpl33 and trnS + trnT-psaD barcodes. The resultant phylogenetic tree unequivocally depicted the formation of a monophyletic clade comprising species within the evolutionary framework of Liliaceae, demonstrating closer evolutionary affinities with Maianthemum, Dracaeneae, and Asparageae. This comprehensive compendium of findings collectively contributes to the advancement of molecular species identification, elucidation of phylogenetic interrelationships, and the establishment of DNA barcodes tailored to the Polygonatum species.
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Affiliation(s)
- Meixiu Yan
- The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, Zhejiang Province, People's Republic of China
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Shujie Dong
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Qiuyi Gong
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Qin Xu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Yuqing Ge
- The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, Zhejiang Province, People's Republic of China.
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Ma N, Yin D, Liu Y, Gao Z, Cao Y, Chen T, Huang Z, Jia Q, Wang D. Succession of endophytic fungi and rhizosphere soil fungi and their correlation with secondary metabolites in Fagopyrum dibotrys. Front Microbiol 2023; 14:1220431. [PMID: 37601353 PMCID: PMC10434241 DOI: 10.3389/fmicb.2023.1220431] [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] [Received: 05/10/2023] [Accepted: 07/07/2023] [Indexed: 08/22/2023] Open
Abstract
Golden buckwheat (Fagopyrum dibotrys, also known as F. acutatum) is a traditional edible herbal medicinal plant with a large number of secondary metabolites and is considered to be a source of therapeutic compounds. Different ecological environments have a significant impact on their compound content and medicinal effects. However, little is known about the interactions between soil physicochemical properties, the rhizosphere, endophytic fungal communities, and secondary metabolites in F. dibotrys. In this study, the rhizosphere soil and endophytic fungal communities of F. dibotrys in five different ecological regions in China were identified based on high-throughput sequencing methods. The correlations between soil physicochemical properties, active components (total saponins, total flavonoids, proanthocyanidin, and epicatechin), and endophytic and rhizosphere soil fungi of F. dibotrys were analyzed. The results showed that soil pH, soil N, OM, and P were significantly correlated with the active components of F. dibotrys. Among them, epicatechin, proanthocyanidin, and total saponins were significantly positively correlated with soil pH, while proanthocyanidin content was significantly positively correlated with STN, SAN, and OM in soil, and total flavone content was significantly positively correlated with P in soil. In soil microbes, Mortierella, Trechispora, Exophiala, Ascomycota_unclassified, Auricularia, Plectosphaerella, Mycena, Fungi_unclassified, Agaricomycetes_unclassified, Coprinellus, and Pseudaleuria were significantly related to key secondary metabolites of F. dibotrys. Diaporthe and Meripilaceae_unclassified were significantly related to key secondary metabolites in the rhizome. This study presents a new opportunity to deeply understand soil-plant-fungal symbioses and secondary metabolites in F. dibotrys, as well as provides a scientific basis for using biological fertilization strategies to improve the quality of F. dibotrys.
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Affiliation(s)
- Nan Ma
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Dengpan Yin
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Ying Liu
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Ziyong Gao
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Yu Cao
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Tongtong Chen
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Ziyi Huang
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Qiaojun Jia
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Dekai Wang
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
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Weng L, Jiang Y, Wang Y, Zhang X, Zhou P, Wu M, Li H, Sun H, Chen S. Chloroplast genome characteristics and phylogeny of the sinodielsia clade (apiaceae: apioideae). BMC PLANT BIOLOGY 2023; 23:284. [PMID: 37246219 DOI: 10.1186/s12870-023-04271-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/07/2023] [Indexed: 05/30/2023]
Abstract
BACKGROUND The Sinodielsia clade of the subfamily Apioideae (Apiacieae) was established in 2008, and it is composed of 37 species from 17 genera. Its circumscription is still poorly delimited and unstable, and interspecific relationships in the clade lack comprehensive analysis. Chloroplast (cp.) genomes provide valuable and informative data sources for evolutionary biology and have been widely used in studies on plant phylogeny. To infer the phylogenetic history of the Sinodielsia clade, we assembled complete cp. genomes of 39 species and then performed phylogenetic analysis based on these cp. genome sequence data combined with 66 published cp. genomes from 16 genera relative to the Sinodielsia clade. RESULTS These 39 newly assembled genomes had a typical quadripartite structure with two inverted repeat regions (IRs: 17,599-31,486 bp) separated by a large single-copy region (LSC: 82,048-94,046 bp) and a small single-copy region (SSC: 16,343-17,917 bp). The phylogenetic analysis showed that 19 species were clustered into the Sinodielsia clade, and they were divided into two subclades. Six mutation hotspot regions were detected from the whole cp. genomes among the Sinodielsia clade, namely, rbcL-accD, ycf4-cemA, petA-psbJ, ycf1-ndhF, ndhF-rpl32 and ycf1, and it was found that ndhF-rpl32 and ycf1 were highly variable in the 105 sampled cp. genomes. CONCLUSION The Sinodielsia clade was subdivided into two subclades relevant to geographical distributions, except for cultivated and introduced species. Six mutation hotspot regions, especially ndhF-rpl32 and ycf1, could be used as potential DNA markers in the identification and phylogenetic analyses of the Sinodielsia clade and Apioideae. Our study provided new insights into the phylogeny of the Sinodielsia clade and valuable information on cp. genome evolution in Apioideae.
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Affiliation(s)
- Long Weng
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Yunhui Jiang
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Yong Wang
- Yunnan Institute of Forest Inventory and Planning, Kunming, 650051, China
| | - Xuemei Zhang
- Yunnan Key Laboratory of Dai and Yi Medicines, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Ping Zhou
- College of Basic Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Mei Wu
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Hongzhe Li
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China.
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Shaotian Chen
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China.
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Carvalho LR, Nunes R, Sobreiro MB, Dias RO, Corvalán LCJ, Braga-Ferreira RS, Targueta CP, Telles MPC. The complete chloroplast genome sequence of Eugenia klotzschiana O. Berg unveils the evolutionary dynamics in plastomes of Myrteae DC. tribe (Myrtaceae). Gene 2023:147488. [PMID: 37196890 DOI: 10.1016/j.gene.2023.147488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/19/2023]
Abstract
Myrteae is the most diversified tribe in the Myrtaceae family and has great ecological and economic importance. Here, we performed the assembly and annotation of the chloroplast genome of Eugenia klotzschiana O. Berg and used this in a comparative analysis with other 13 species from the Myrteae tribe. The E. klotzschiana plastome exhibited a length of 158,977 bp and a very conserved structure and gene composition when compared with other Myrteae genomes. We identified 34 large repetitive sequences and 94 SSR repeats in E. klotzschiana plastome. The trnT-trnL, rpl32-trnL, ndhF-rpl32, psbE-petL, and ycf1 regions were identified as mutational hotspots. A negative selection signal was detected in 74 protein-coding genes while neutral selection was detected in two genes (rps12 and psaI). Furthermore, 222 RNA editing sites were identified in the E. klotzschiana plastome. We also obtained a plastome-based Myrtales phylogenetic tree, including E. klotzschiana for the first time in a molecular phylogeny, recovering its sister relationship for all other Eugenia species. Our results illuminate how evolution shaped the chloroplast genome structure and composition in the Myrteae tribe, especially in the E. klotzschiana plastome.
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Affiliation(s)
- Larissa R Carvalho
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, GO, Brasil
| | - Rhewter Nunes
- Instituto Federal de Goiás - Campus Cidade de Goiás, Goiás, GO, Brasil.
| | - Mariane B Sobreiro
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, GO, Brasil
| | - Renata O Dias
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, GO, Brasil
| | - Leonardo C J Corvalán
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, GO, Brasil
| | | | - Cíntia P Targueta
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, GO, Brasil
| | - Mariana P C Telles
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, GO, Brasil; Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás, Goiânia, GO, Brasil
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9
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Vega M, Quintero-Corrales C, Mastretta-Yanes A, Casas A, López-Hilario V, Wegier A. Multiple domestication events explain the origin of Gossypium hirsutum landraces in Mexico. Ecol Evol 2023; 13:e9838. [PMID: 36911302 PMCID: PMC9994486 DOI: 10.1002/ece3.9838] [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: 05/13/2022] [Revised: 01/21/2023] [Accepted: 01/27/2023] [Indexed: 03/14/2023] Open
Abstract
Several Mesoamerican crops constitute wild-to-domesticated complexes generated by multiple initial domestication events, and continuous gene flow among crop populations and between these populations and their wild relatives. It has been suggested that the domestication of cotton (Gossypium hirsutum) started in the northwest of the Yucatán Peninsula, from where it spread to other regions inside and outside of Mexico. We tested this hypothesis by assembling chloroplast genomes of 23 wild, landraces, and breeding lines (transgene-introgressed and conventional). The phylogenetic analysis showed that the evolutionary history of cotton in Mexico involves multiple events of introgression and genetic divergence. From this, we conclude that Mexican landraces arose from multiple wild populations. Our results also revealed that their structural and functional chloroplast organizations had been preserved. However, genetic diversity decreases as a consequence of domestication, mainly in transgene-introgressed (TI) individuals (π = 0.00020, 0.00001, 0.00016, 0, and 0, of wild, TI-wild, landraces, TI-landraces, and breeding lines, respectively). We identified homologous regions that differentiate wild from domesticated plants and indicate a relationship among the samples. A decrease in genetic diversity associated with transgene introgression in cotton was identified for the first time, and our outcomes are therefore relevant to both biosecurity and agrobiodiversity conservation.
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Affiliation(s)
- Melania Vega
- Genética de la Conservación, Jardín Botánico Instituto de Biología, Universidad Nacional Autónoma de México Ciudad de México Mexico.,Posgrado en Ciencias Biológicas Universidad Nacional Autónoma de México Ciudad de México Mexico
| | - Christian Quintero-Corrales
- Posgrado en Ciencias Biológicas Universidad Nacional Autónoma de México Ciudad de México Mexico.,Departamento de Botánica Instituto de Biología, Universidad Nacional Autónoma de México Ciudad de México Mexico
| | - Alicia Mastretta-Yanes
- Comisión Nacional para el Conocimiento y Uso de la Biodiversidad (CONABIO) Ciudad de México Mexico.,Consejo Nacional de Ciencia y Tecnología (CONACYT) Programa de Investigadores e Investigadoras por México Ciudad de México Mexico
| | - Alejandro Casas
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad Universidad Nacional Autónoma de México Morelia Mexico
| | | | - Ana Wegier
- Genética de la Conservación, Jardín Botánico Instituto de Biología, Universidad Nacional Autónoma de México Ciudad de México Mexico
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10
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Song B, Liu C, Xie D, Xiao Y, Tian R, Li Z, Zhou S, He X. Plastid Phylogenomic Analyses Reveal the Taxonomic Position of Peucedanum franchetii. PLANTS (BASEL, SWITZERLAND) 2022; 12:97. [PMID: 36616226 PMCID: PMC9824613 DOI: 10.3390/plants12010097] [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: 11/28/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Peucedanum franchetii is a famous folk medicinal plant in China. However, the taxonomy of the P. franchetii has not been sufficiently resolved. Due to similar morphological features between P. franchetii and Ligusticopsis members, the World Flora Online (WFO) Plant List suggested that this species transformed into the genus Ligusticopsis and merged with Ligusticopsis likiangensis. However, both species are obviously diverse in leaf shape, bracts, and bracteoles. To check the taxonomic position of P. franchetii, we newly sequenced and assembled the plastome of P. franchetii and compared it with nine other plastomes of the genus Ligusticopsis. Ten plastomes were highly conserved and similar in gene order, codon bias, RNA editing sites, IR borders, and SSRs. Nevertheless, 10 mutation hotspot regions (infA, rps8, matK, ndhF, rps15, psbA-trnH, rps2-rpoC2, psbA-trnK, ycf2-trnL, and ccsA-ndhD) were still detected. In addition, both phylogenetic analyses based on plastome data and ITS sequences robustly supported that P. franchetii was not clustered with members of Peucedanum but nested in Ligusticopsis. P. franchetii was sister to L. likiangensis in the ITS topology but clustered with L. capillacea in the plastome tree. These findings implied that P. franchetii should be transferred to genus Ligusticopsis and not merged with L. likiangensis, but as an independent species, which was further verified by morphological evidences. Therefore, transferring P. franchetii under the genus Ligusticopsis as an independent species was reasonable, and a new combination was presented.
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11
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Chen Q, Chen C, Wang B, Wang Z, Xu W, Huang Y, Sun Q. Complete chloroplast genomes of 11 Sabia samples: Genomic features, comparative analysis, and phylogenetic relationship. FRONTIERS IN PLANT SCIENCE 2022; 13:1052920. [PMID: 36589084 PMCID: PMC9800934 DOI: 10.3389/fpls.2022.1052920] [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: 09/24/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
The genus Sabia is a woody climber belonging to the family Sabiaceae, order Proteales. Several species of this genus have been utilized as medicines for treating diseases, such as rheumatic arthritis, traumatism, hepatitis, etc. However, the lack of molecular data has prevented the accurate identification and refinement of taxonomic relationships in this genus. In this study, chloroplast genomes of 11 samples of the genus Sabia were assembled and analyzed. These chloroplast genomes showed a typical quadripartite structure and ranged in length from 160,956 to 162,209 bp. The structure of the genomes was found to be relatively conserved, with 130 genes annotated, including 85 coding genes, 37 tRNA genes, and eight rRNA genes. A total of 78-98 simple sequence repeats and 52-61 interspersed repeats were detected. Sequence alignment revealed 11 highly variable loci in chloroplast genomes. Among these loci, ndhF-ndhD achieved a remarkably higher resolution than the other regions. In addition, phylogenetic analysis indicated that Sect. Pachydiscus and Sect. Sabia of Sabia did not form two separate monophyletic groups. The divergence time calculated based on the Reltime method indicated that the evolutionary branches of Sabia and Meliosma started to form approximately 85.95 million years ago (Mya), and the species within Sabia began to diverge approximately 7.65 Mya. In conclusion, our study provides a basis for comprehensively exploring the phylogenetic relationships of Sabia. It also provides a methodological basis and data support for establishing a standardized and scientific identification system for this genus.
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Affiliation(s)
| | | | | | | | | | - Yuan Huang
- *Correspondence: Yuan Huang, ; Qingwen Sun,
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12
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A Comparative Phylogenetic Analysis on the Chloroplast Genome in Different Reynoutria japonica Populations. Genes (Basel) 2022; 13:genes13111979. [DOI: 10.3390/genes13111979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/21/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022] Open
Abstract
Reynoutria japonica Houtt., a traditional medicine herb of the Polygonaceae family, has been used since ancient times in China due to its various pharmacological effects. Chloroplast genomes are conservative and play an essential role in population diversity analysis. However, there are few studies on the chloroplast genome of R. japonica. In this study, the complete chloroplast genomes of three R. japonica from different regions were performed by next-generation sequencing technology. The results revealed that the lengths of the three chloroplast genomes are between 163,371~163,372 bp, and they have a highly conserved structure with a pair of inverted repeat (IR) regions (31,121 bp), a large single-copy (LSC) region (87,571~87,572 bp), and a small single-copy (SSC) region (13,558 bp). In total, 132 genes were annotated, including 8 rRNA genes, 37 tRNA genes, and 87 protein-coding genes. The phylogenetic analysis strongly revealed that 13 populations of R. japonica form a monophyly, and Fallopia multiflora (Polygonaceae) is its closest species. The two species diverged at ~20.47 million years ago, and R. japonica in China could be further divided into two major groups based on genetic structure analysis. In addition, several potential loci with suitable polymorphism were identified as molecular markers. Our study provides important genetic resources for further development and utilization of R. japonica germplasm, as well as some new insights into the evolutionary characteristics of this medicinal plant.
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13
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Comparative Analyses of Complete Chloroplast Genomes and Karyotypes of Allotetraploid Iris koreana and Its Putative Diploid Parental Species ( Iris Series Chinenses, Iridaceae). Int J Mol Sci 2022; 23:ijms231810929. [PMID: 36142840 PMCID: PMC9504294 DOI: 10.3390/ijms231810929] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/08/2022] [Accepted: 09/15/2022] [Indexed: 12/16/2022] Open
Abstract
The Iris series Chinenses in Korea comprises four species (I. minutoaurea, I. odaesanensis, I. koreana, and I. rossii), and the group includes some endangered species, owing to their high ornamental, economic, and conservation values. Among them, the putative allotetraploid, Iris koreana (2n = 4x = 50), is hypothesized to have originated from the hybridization of the diploids I. minutoaurea (2n = 2x = 22) and I. odaesanensis (2n = 2x = 28) based on morphological characters, chromosome numbers, and genome size additivity. Despite extensive morphological and molecular phylogenetical studies on the genus Iris, little is known about Korean irises in terms of their complete chloroplast (cp) genomes and molecular cytogenetics that involve rDNA loci evolution based on fluorescence in situ hybridization (FISH). This study reports comparative analyses of the karyotypes of the three Iris species (I. koreana, I. odaesanensis, and I. minutoaurea), with an emphasis on the 5S and 35S rDNA loci number and localization using FISH together with the genome size and chromosome number. Moreover, the cp genomes of the same individuals were sequenced and assembled for comparative analysis. The rDNA loci numbers, which were localized consistently at the same position in all species, and the chromosome numbers and genome size values of tetraploid Iris koreana (four 5S and 35S loci; 2n = 50; 1C = 7.35 pg) were additively compared to its putative diploid progenitors, I. minutoaurea (two 5S and 35S loci; 2n = 22; 1C = 3.71 pg) and I. odaesanensis (two 5S and 35S loci; 2n = 28; 1C = 3.68 pg). The chloroplast genomes were 152,259–155,145 bp in length, and exhibited a conserved quadripartite structure. The Iris cp genomes were highly conserved and similar to other Iridaceae cp genomes. Nucleotide diversity analysis indicated that all three species had similar levels of genetic variation, but the cp genomes of I. koreana and I. minutoaurea were more similar to each other than to I. odaesanensis. Positive selection was inferred for psbK and ycf2 genes of the three Iris species. Phylogenetic analyses consistently recovered I. odaesanensis as a sister to a clade containing I. koreana and I. minutoaurea. Although the phylogenetic relationship, rDNA loci number, and localization, together with the genome size and chromosome number of the three species, allowed for the inference of I. minutoaurea as a putative maternal taxon and I. odaesanensis as a paternal taxon, further analyses involving species-specific molecular cytogenetic markers and genomic in situ hybridization are required to interpret the mechanisms involved in the origin of the chromosomal variation in Iris series Chinenses. This study contributes towards the genomic and chromosomal evolution of the genus Iris.
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14
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Peng JY, Zhang XS, Zhang DG, Wang Y, Deng T, Huang XH, Kuang TH, Zhou Q. Newly reported chloroplast genome of Sinosenecio albonervius Y. Liu & Q. E. Yang and comparative analyses with other Sinosenecio species. BMC Genomics 2022; 23:639. [PMID: 36076168 PMCID: PMC9454173 DOI: 10.1186/s12864-022-08872-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/31/2022] [Indexed: 11/10/2022] Open
Abstract
Background Sinosenecio B. Nordenstam (Asteraceae) currently comprises 44 species. To investigate the interspecific relationship, several chloroplast markers, including ndhC-trnV, rpl32-trnL, matK, and rbcL, are used to analyze the phylogeny of Sinosenecio. However, the chloroplast genomes of this genus have not been thoroughly investigated. We sequenced and assembled the Sinosenecio albonervius chloroplast genome for the first time. A detailed comparative analysis was performed in this study using the previously reported chloroplast genomes of three Sinosenecio species. Results The results showed that the chloroplast genomes of four Sinosenecio species exhibit a typical quadripartite structure. There are equal numbers of total genes, protein-coding genes and RNA genes among the annotated genomes. Per genome, 49–56 simple sequence repeats and 99 repeat sequences were identified. Thirty codons were identified as RSCU values greater than 1 in the chloroplast genome of S. albonervius based on 54 protein-coding genes, indicating that they showed biased usage. Among 18 protein-coding genes, 46 potential RNA editing sites were discovered. By comparing these chloroplast genomes' structures, inverted repeat regions and coding regions were more conserved than single-copy and non-coding regions. The junctions among inverted repeat and single-copy regions showed slight difference. Several hot spots of genomic divergence were detected, which can be used as new DNA barcodes for species identification. Phylogenetic analysis of the whole chloroplast genome showed that the four Sinosenecio species have close interspecific relationships. Conclusions The complete chloroplast genome of Sinosenecio albonervius was revealed in this study, which included a comparison of Sinosenecio chloroplast genome structure, variation, and phylogenetic analysis for related species. These will help future research on Sinosenecio taxonomy, identification, origin, and evolution to some extent. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08872-3.
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Affiliation(s)
- Jing-Yi Peng
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, Hunan, China
| | - Xiao-Shuang Zhang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Dai-Gui Zhang
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, Hunan, China.,Key Laboratory of Plant Resources Conservation and Utilization, Jishou University, College of Hunan Province, Jishou, 416000, Hunan, China
| | - Yi Wang
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, Hunan, China
| | - Tao Deng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Xian-Han Huang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Tian-Hui Kuang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Qiang Zhou
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, Hunan, China. .,Key Laboratory of Plant Resources Conservation and Utilization, Jishou University, College of Hunan Province, Jishou, 416000, Hunan, China.
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15
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He M, He Y, Zhang K, Lu X, Zhang X, Gao B, Fan Y, Zhao H, Jha R, Huda MN, Tang Y, Wang J, Yang W, Yan M, Cheng J, Ruan J, Dulloo E, Zhang Z, Georgiev MI, Chapman MA, Zhou M. Comparison of buckwheat genomes reveals the genetic basis of metabolomic divergence and ecotype differentiation. THE NEW PHYTOLOGIST 2022; 235:1927-1943. [PMID: 35701896 DOI: 10.1111/nph.18306] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/22/2022] [Indexed: 05/09/2023]
Abstract
Golden buckwheat (Fagopyrum dibotrys or Fagopyrum cymosum) and Tartary buckwheat (Fagopyrum tataricum) belong to the Polygonaceae and the Fagopyrum genus is rich in flavonoids. Golden buckwheat is a wild relative of Tartary buckwheat, yet golden buckwheat is a traditional Chinese herbal medicine and Tartary buckwheat is a food crop. The genetic basis of adaptive divergence between these two buckwheats is poorly understood. Here, we assembled a high-quality chromosome-level genome of golden buckwheat and found a one-to-one syntenic relationship with the chromosomes of Tartary buckwheat. Two large inversions were identified that differentiate golden buckwheat and Tartary buckwheat. Metabolomic and genetic comparisons of golden buckwheat and Tartary buckwheat indicate an amplified copy number of FdCHI, FdF3H, FdDFR, and FdLAR gene families in golden buckwheat, and a parallel increase in medicinal flavonoid content. Resequencing of 34 wild golden buckwheat accessions across the two morphologically distinct ecotypes identified candidate genes, including FdMYB44 and FdCRF4, putatively involved in flavonoid accumulation and differentiation of plant architecture, respectively. Our comparative genomic study provides abundant genomic resources of genomic divergent variation to improve buckwheat with excellent nutritional and medicinal value.
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Affiliation(s)
- Ming He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuqi He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Kaixuan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Xiang Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Xuemei Zhang
- Annoroad Gene Technology (Beijing) Co. Ltd, Beijing, 100176, China
| | - Bin Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Yu Fan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Hui Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Rintu Jha
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Md Nurul Huda
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Yu Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Junzhen Wang
- Research Station of Alpine Crop, Xichang Institute of Agricultural Sciences, Liangshan, 616150, Sichuan, China
| | - Weifei Yang
- Annoroad Gene Technology (Beijing) Co. Ltd, Beijing, 100176, China
| | - Mingli Yan
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Ehsan Dulloo
- The Alliance of Bioversity International and CIAT, Via di San Domenico, 100153, Rome, Italy
| | - Zongwen Zhang
- The Alliance of Bioversity International and CIAT, Via di San Domenico, 100153, Rome, Italy
| | - Milen I Georgiev
- Group of Plant Cell Biotechnology and Metabolomics, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 4002, Plovdiv, Bulgaria
- Center of Plant Systems Biology and Biotechnology, 4002, Plovdiv, Bulgaria
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
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16
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Comparative Analysis of Complete Chloroplast Genomes of Nine Species of Litsea (Lauraceae): Hypervariable Regions, Positive Selection, and Phylogenetic Relationships. Genes (Basel) 2022; 13:genes13091550. [PMID: 36140718 PMCID: PMC9498446 DOI: 10.3390/genes13091550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022] Open
Abstract
Litsea is a group of evergreen trees or shrubs in the laurel family, Lauraceae. Species of the genus are widely used for a wide range of medicinal and industrial aspects. At present, most studies related to the gene resources of Litsea are restricted to morphological analyses or features of individual genomes, and currently available studies of select molecular markers are insufficient. In this study, we assembled and annotated the complete chloroplast genomes of nine species in Litsea, carried out a series of comparative analyses, and reconstructed phylogenetic relationships within the genus. The genome length ranged from 152,051 to 152,747 bp and a total of 128 genes were identified. High consistency patterns of codon bias, repeats, divergent analysis, single nucleotide polymorphisms (SNP) and insertions and deletions (InDels) were discovered across the genus. Variations in gene length and the presence of the pseudogene ycf1Ψ, resulting from IR contraction and expansion, are reported. The hyper-variable gene rpl16 was identified for its exceptionally high Ka/Ks and Pi values, implying that those frequent mutations occurred as a result of positive selection. Phylogenetic relationships were recovered for the genus based on analyses of full chloroplast genomes and protein-coding genes. Overall, both genome sequences and potential molecular markers provided in this study enrich the available genomic resources for species of Litsea. Valuable genomic resources and divergent analysis are also provided for further research of the evolutionary patterns, molecular markers, and deeper phylogenetic relationships of Litsea.
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17
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Cay SB, Cinar YU, Kuralay SC, Inal B, Zararsiz G, Ciftci A, Mollman R, Obut O, Eldem V, Bakir Y, Erol O. Genome skimming approach reveals the gene arrangements in the chloroplast genomes of the highly endangered Crocus L. species: Crocus istanbulensis (B.Mathew) Rukšāns. PLoS One 2022; 17:e0269747. [PMID: 35704623 PMCID: PMC9200356 DOI: 10.1371/journal.pone.0269747] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/27/2022] [Indexed: 11/19/2022] Open
Abstract
Crocus istanbulensis (B.Mathew) Rukšāns is one of the most endangered Crocus species in the world and has an extremely limited distribution range in Istanbul. Our recent field work indicates that no more than one hundred individuals remain in the wild. In the present study, we used genome skimming to determine the complete chloroplast (cp) genome sequences of six C. istanbulensis individuals collected from the locus classicus. The cp genome of C. istanbulensis has 151,199 base pairs (bp), with a large single-copy (LSC) (81,197 bp), small single copy (SSC) (17,524 bp) and two inverted repeat (IR) regions of 26,236 bp each. The cp genome contains 132 genes, of which 86 are protein-coding (PCGs), 8 are rRNA and 38 are tRNA genes. Most of the repeats are found in intergenic spacers of Crocus species. Mononucleotide repeats were most abundant, accounting for over 80% of total repeats. The cp genome contained four palindrome repeats and one forward repeat. Comparative analyses among other Iridaceae species identified one inversion in the terminal positions of LSC region and three different gene (psbA, rps3 and rpl22) arrangements in C. istanbulensis that were not reported previously. To measure selective pressure in the exons of chloroplast coding sequences, we performed a sequence analysis of plastome-encoded genes. A total of seven genes (accD, rpoC2, psbK, rps12, ccsA, clpP and ycf2) were detected under positive selection in the cp genome. Alignment-free sequence comparison showed an extremely low sequence diversity across naturally occurring C. istanbulensis specimens. All six sequenced individuals shared the same cp haplotype. In summary, this study will aid further research on the molecular evolution and development of ex situ conservation strategies of C. istanbulensis.
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Affiliation(s)
- Selahattin Baris Cay
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Yusuf Ulas Cinar
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Selim Can Kuralay
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Behcet Inal
- Department of Agricultural Biotechnology, Faculty of Agriculture, University of Siirt, Siirt, Turkey
| | - Gokmen Zararsiz
- Department of Biostatistics, Erciyes University, Kayseri, Turkey
- Drug Application and Research Center (ERFARMA), Erciyes University, Kayseri, Turkey
| | - Almila Ciftci
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Rachel Mollman
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Onur Obut
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Vahap Eldem
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
- * E-mail:
| | - Yakup Bakir
- Department of Plant Bioactive Metabolites, ACTV Biotechnology, Inc., Istanbul, Turkey
| | - Osman Erol
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
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18
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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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Huo Z, Xu W, Guo H, Yang P, Zhang Q, Lu X, Wang L. The complete chloroplast genome of Persicaria perfoliata and comparative analysis with Four Medicinal Plants of Polygonaceae. Genome 2022; 65:377-389. [PMID: 35576612 DOI: 10.1139/gen-2021-0085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Polygonaceae is a large family of medicinal herbs that includes many species used as traditional Chinese medicine, such as Persicaria perfoliate. Here, we sequenced the complete cp genome of P. perfoliata using Illumina sequencing technology with the purpose to provide a method to facilitate accurate identification. After being annotated, the cp genome of P. perfoliata was compared with Fagopyrum tataricum, Persicaria chinensis, Fagopyrum dibotrys and Fallopia multiflora. The complete cp genome of P. perfoliata is 160,730 bp in length, containing a small single copy (SSC) region of 12,927 bp, a large single copy (LSC) region of 85,433 bp and a pair of inverted repeats (IR) regions of 62,370 bp. A total of 131 genes were annotated, including eight rRNA genes, 34 tRNA genes and 84 protein-coding genes. Forty-two simple sequence repeats and fifty-five repeat sequences were identified. Mutational hot spots analyses indicated that five genes (matK, ndhF, ccsA, cemA, rpl20) could be selected as candidates for molecular markers. Moreover, phylogenetic analysis showed that all the Polygonaceae species formed a monophyletic clade, and P. perfoliata showed the closest relationship with P. chinense. The study provides valuable molecular information to accurately identify P. perfoliata and assist in its development and application.
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Affiliation(s)
- Ziting Huo
- China Pharmaceutical University, 56651, Nanjing, China;
| | - Wenbo Xu
- China Pharmaceutical University, 56651, Nanjing, China;
| | - Huijun Guo
- China Pharmaceutical University, 56651, Nanjing, China;
| | - Peng Yang
- China Pharmaceutical University, 56651, Nanjing, China;
| | - Qianwen Zhang
- China Pharmaceutical University, 56651, Nanjing, China;
| | - Xu Lu
- China Pharmaceutical University, 56651, Nanjing, China;
| | - Long Wang
- China Pharmaceutical University, 56651, Nanjing, China;
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20
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Complete Chloroplast Genome of Cnidium monnieri (Apiaceae) and Comparisons with Other Tribe Selineae Species. DIVERSITY 2022. [DOI: 10.3390/d14050323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Cnidium monnieri is an economically important traditional Chinese medicinal plant. In this study, the complete chloroplast (cp) genome of C. monnieri was determined using the Illumina paired-end sequencing, the GetOrganelle de novo assembly strategy, as well as the GeSeq annotation method. Our results showed that the cp genome was 147,371 bp in length with 37.4% GC content and included a large single-copy region (94,361 bp) and a small single-copy region (17,552 bp) separated by a pair of inverted repeat regions (17,729 bp). A total of 129 genes were contained in the cp genome, including 85 protein-coding genes, 36 tRNA genes, and eight rRNA genes. We also investigated codon usage, RNA editing, repeat sequences, simple sequence repeats (SSRs), IR boundaries, and pairwise Ka/Ks ratios. Four hypervariable regions (trnD-trnY-trnE-trnT, ycf2, ndhF-rpl32-trnL, and ycf1) were identified as candidate molecular markers for species authentication. The phylogenetic analyses supported non-monophyly of Cnidium and C. monnieri located in tribe Selineae based on the cp genome sequences and internal transcribed spacer (ITS) sequences. The incongruence of the phylogenetic position of C. monnieri between ITS and cpDNA phylogenies suggested that C. monnieri might have experienced complex evolutions with hybrid and incomplete lineage sorting. All in all, the results presented herein will provide plentiful chloroplast genomic resources for studies of the taxonomy, phylogeny, and species authentication of C. monnieri. Our study is also conducive to elucidating the phylogenetic relationships and taxonomic position of Cnidium.
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Mutinda ES, Mkala EM, Dong X, Yang JX, Waswa EN, Nanjala C, Odago WO, Hu GW, Wang QF. Comparative Genomics, Phylogenetics, Biogeography, and Effects of Climate Change on Toddalia asiatica (L.) Lam. (Rutaceae) from Africa and Asia. PLANTS 2022; 11:231. [DOI: https:/doi.org/10.3390/plants11020231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
In the present study, two samples of Toddalia asiatica species, both collected from Kenya, were sequenced and comparison of their genome structures carried out with T. asiatica species from China, available in the NCBI database. The genome size of both species from Africa was 158, 508 base pairs, which was slightly larger, compared to the reference genome of T. asiatica from Asia (158, 434 bp). The number of genes was 113 for both species from Africa, consisting of 79 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Toddalia asiatica from Asia had 115 genes with 81 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Both species compared displayed high similarity in gene arrangement. The gene number, orientation, and order were highly conserved. The IR/SC boundary structures were the same in all chloroplast genomes. A comparison of pairwise sequences indicated that the three regions (trnH-psbA, rpoB, and ycf1) were more divergent and can be useful in developing effective genetic markers. Phylogenetic analyses of the complete cp genomes and 79 protein-coding genes indicated that the Toddalia species collected from Africa were sister to T. asiatica collected from Asia. Both species formed a sister clade to the Southwest Pacific and East Asian species of Zanthoxylum. These results supported the previous studies of merging the genus Toddalia with Zanthoxylum and taxonomic change of Toddalia asiatica to Zanthoxylum asiaticum, which should also apply for the African species of Toddalia. Biogeographic results demonstrated that the two samples of Toddalia species from Africa diverged from T. asiatica from Asia (3.422 Mya, 95% HPD). These results supported an Asian origin of Toddalia species and later dispersal to Africa and Madagascar. The maxent model analysis showed that Asia would have an expansion of favorable areas for Toddalia species in the future. In Africa, there will be contraction and expansion of the favorable areas for the species. The availability of these cp genomes will provide valuable genetic resources for further population genetics and biogeographic studies of these species. However, more T. asiatica species collected from a wide geographical range are required.
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22
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Mutinda ES, Mkala EM, Dong X, Yang JX, Waswa EN, Nanjala C, Odago WO, Hu GW, Wang QF. Comparative Genomics, Phylogenetics, Biogeography, and Effects of Climate Change on Toddalia asiatica (L.) Lam. (Rutaceae) from Africa and Asia. PLANTS 2022; 11:plants11020231. [PMID: 35050119 PMCID: PMC8781850 DOI: 10.3390/plants11020231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/29/2021] [Accepted: 01/11/2022] [Indexed: 11/16/2022]
Abstract
In the present study, two samples of Toddalia asiatica species, both collected from Kenya, were sequenced and comparison of their genome structures carried out with T. asiatica species from China, available in the NCBI database. The genome size of both species from Africa was 158, 508 base pairs, which was slightly larger, compared to the reference genome of T. asiatica from Asia (158, 434 bp). The number of genes was 113 for both species from Africa, consisting of 79 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Toddalia asiatica from Asia had 115 genes with 81 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Both species compared displayed high similarity in gene arrangement. The gene number, orientation, and order were highly conserved. The IR/SC boundary structures were the same in all chloroplast genomes. A comparison of pairwise sequences indicated that the three regions (trnH-psbA, rpoB, and ycf1) were more divergent and can be useful in developing effective genetic markers. Phylogenetic analyses of the complete cp genomes and 79 protein-coding genes indicated that the Toddalia species collected from Africa were sister to T. asiatica collected from Asia. Both species formed a sister clade to the Southwest Pacific and East Asian species of Zanthoxylum. These results supported the previous studies of merging the genus Toddalia with Zanthoxylum and taxonomic change of Toddalia asiatica to Zanthoxylum asiaticum, which should also apply for the African species of Toddalia. Biogeographic results demonstrated that the two samples of Toddalia species from Africa diverged from T. asiatica from Asia (3.422 Mya, 95% HPD). These results supported an Asian origin of Toddalia species and later dispersal to Africa and Madagascar. The maxent model analysis showed that Asia would have an expansion of favorable areas for Toddalia species in the future. In Africa, there will be contraction and expansion of the favorable areas for the species. The availability of these cp genomes will provide valuable genetic resources for further population genetics and biogeographic studies of these species. However, more T. asiatica species collected from a wide geographical range are required.
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Affiliation(s)
- Elizabeth Syowai Mutinda
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Elijah Mbandi Mkala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- East African Herbarium, National Museums of Kenya, Nairobi 451660-0100, Kenya
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia-Xin Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Emmanuel Nyongesa Waswa
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Consolata Nanjala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wyclif Ochieng Odago
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- East African Herbarium, National Museums of Kenya, Nairobi 451660-0100, Kenya
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence:
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
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Xi J, Lv S, Zhang W, Zhang J, Wang K, Guo H, Hu J, Yang Y, Wang J, Xia G, Fan G, Wang X, Xiao L. Comparative plastomes of Carya species provide new insights into the plastomes evolution and maternal phylogeny of the genus. FRONTIERS IN PLANT SCIENCE 2022; 13:990064. [PMID: 36407576 PMCID: PMC9667483 DOI: 10.3389/fpls.2022.990064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/21/2022] [Indexed: 05/03/2023]
Abstract
Carya, in the Juglandiodeae subfamily, is to a typical temperate-subtropical forest-tree genus for studying the phylogenetic evolution and intercontinental disjunction between eastern Asia (EA) and North America (NA). Species of the genus have high economic values worldwide for their high-quality wood and the rich healthy factors of their nuts. Although previous efforts based on multiple molecular markers or genome-wide SNPs supported the monophyly of Carya and its two EA and NA major subclades, the maternal phylogeny of Carya still need to be comprehensively evaluated. The variation of Carya plastome has never been thoroughly characterized. Here, we novelly present 19 newly generated plastomes of congeneric Carya species, including the recently rediscovered critically endangered C. poilanei. The overall assessment of plastomes revealed highly conservative in the general structures. Our results indicated that remarkable differences in several plastome features are highly consistent with the EA-NA disjunction and showed the relatively diverse matrilineal sources among EA Carya compared to NA Carya. The maternal phylogenies were conducted with different plastome regions and full-length plastome datasets from 30 plastomes, representing 26 species in six genera of Juglandoideae and Myrica rubra (as root). Six out of seven phylogenetic topologies strongly supported the previously reported relationships among genera of Juglandoideae and the two subclades of EA and NA Carya, but displayed significant incongruencies between species within the EA and NA subclades. The phylogenetic tree generated from full-length plastomes demonstrated the optimal topology and revealed significant geographical maternal relationships among Carya species, especially for EA Carya within overlapping distribution areas. The full-length plastome-based phylogenetic topology also strongly supported the taxonomic status of five controversial species as separate species of Carya. Historical and recent introgressive hybridization and plastid captures might contribute to plastome geographic patterns and inconsistencies between topologies built from different datasets, while incomplete lineage sorting could account for the discordance between maternal topology and the previous nuclear genome data-based phylogeny. Our findings highlight full-length plastomes as an ideal tool for exploring maternal relationships among the subclades of Carya, and potentially in other outcrossing perennial woody plants, for resolving plastome phylogenetic relationships.
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Affiliation(s)
- Jianwei Xi
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Saibin Lv
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Weiping Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Jingbo Zhang
- Department of Biological Sciences, St. John’s University - Queens, NY, United States
- *Correspondence: Lihong Xiao, ; Jingbo Zhang,
| | - Ketao Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Haobing Guo
- The Beijing Genomics Institute (BGI) -Qingdao, The Beijing Genomics Institute (BGI)-Shenzhen, Qingdao, China
| | - Jie Hu
- The Beijing Genomics Institute (BGI) -Qingdao, The Beijing Genomics Institute (BGI)-Shenzhen, Qingdao, China
| | - Yang Yang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Jianhua Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Guohua Xia
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Guangyi Fan
- The Beijing Genomics Institute (BGI) -Qingdao, The Beijing Genomics Institute (BGI)-Shenzhen, Qingdao, China
| | - Xinwang Wang
- Pecan Breeding and Genetics, Southern Plains Agricultural Research Center, USDA-ARS, College Station, TX, United States
| | - Lihong Xiao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- *Correspondence: Lihong Xiao, ; Jingbo Zhang,
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Cui G, Wang C, Wei X, Wang H, Wang X, Zhu X, Li J, Yang H, Duan H. Complete chloroplast genome of Hordeum brevisubulatum: Genome organization, synonymous codon usage, phylogenetic relationships, and comparative structure analysis. PLoS One 2021; 16:e0261196. [PMID: 34898618 PMCID: PMC8668134 DOI: 10.1371/journal.pone.0261196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 11/28/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Hordeum brevisubulatum, known as fine perennial forage, is used for soil salinity improvement in northern China. Chloroplast (cp) genome is an ideal model for assessing its genome evolution and the phylogenetic relationships. We de novo sequenced and analyzed the cp genome of H. brevisubulatum, providing a fundamental reference for further studies in genetics and molecular breeding. RESULTS The cp genome of H. brevisubulatum was 137,155 bp in length with a typical quadripartite structure. A total of 130 functional genes were annotated and the gene of accD was lost in the process of evolution. Among all the annotated genes, 16 different genes harbored introns and the genes of ycf3 and rps12 contained two introns. Parity rule 2 (PR2) plot analysis showed that majority of genes had a bias toward T over A in the coding strand in all five Hordeum species, and a slight G over C in the other four Hordeum species except for H. bogdanil. Additionally, 52 dispersed repeat sequences and 182 simple sequence repeats were identified. Moreover, some unique SSRs of each species could be used as molecular markers for further study. Compared to the other four Hordeum species, H. brevisubulatum was most closely related to H. bogdanii and its cp genome was relatively conserved. Moreover, inverted repeat regions (IRa and IRb) were less divergent than other parts and coding regions were relatively conserved compared to non-coding regions. Main divergence was presented at the SSC/IR border. CONCLUSIONS This research comprehensively describes the architecture of the H. brevisubulatum cp genome and improves our understanding of its cp biology and genetic diversity, which will facilitate biological discoveries and cp genome engineering.
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Affiliation(s)
- Guangxin Cui
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Chunmei Wang
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Xiaoxing Wei
- Academy of Animal and Veterinary Sciences, Qinghai University, Xining, Qinghai, China
| | - Hongbo Wang
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Laboratory of Quality & Safety Risk Assessment for Livestock Products, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
| | - Xiaoli Wang
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Xinqiang Zhu
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - JinHua Li
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Hongshan Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- * E-mail: (HY); (HD)
| | - Huirong Duan
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- * E-mail: (HY); (HD)
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Dong S, Ying Z, Yu S, Wang Q, Liao G, Ge Y, Cheng R. Complete chloroplast genome of Stephania tetrandra (Menispermaceae) from Zhejiang Province: insights into molecular structures, comparative genome analysis, mutational hotspots and phylogenetic relationships. BMC Genomics 2021; 22:880. [PMID: 34872502 PMCID: PMC8647421 DOI: 10.1186/s12864-021-08193-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 11/16/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The Stephania tetrandra S. Moore (S. tetrandra) is a medicinal plant belonging to the family Menispermaceae that has high medicinal value and is well worth doing further exploration. The wild resources of S. tetrandra were widely distributed in tropical and subtropical regions of China, generating potential genetic diversity and unique population structures. The geographical origin of S. tetrandra is an important factor influencing its quality and price in the market. In addition, the species relationship within Stephania genus still remains uncertain due to high morphological similarity and low support values of molecular analysis approach. The complete chloroplast (cp) genome data has become a promising strategy to determine geographical origin and understand species evolution for closely related plant species. Herein, we sequenced the complete cp genome of S. tetrandra from Zhejiang Province and conducted a comparative analysis within Stephania plants to reveal the structural variations, informative markers and phylogenetic relationship of Stephania species. RESULTS The cp genome of S. tetrandra voucher ZJ was 157,725 bp, consisting of a large single copy region (89,468 bp), a small single copy region (19,685 bp) and a pair of inverted repeat regions (24,286 bp each). A total of 134 genes were identified in the cp genome of S. tetrandra, including 87 protein-coding genes, 8 rRNA genes, 37 tRNA genes and 2 pseudogene copies (ycf1 and rps19). The gene order and GC content were highly consistent in the Stephania species according to the comparative analysis results, with the highest RSCU value in arginine (1.79) and lowest RSCU value in serine of S. tetrandra, respectively. A total of 90 SSRs have been identified in the cp genome of S. tetrandra, where repeats that consisting of A or T bases were much higher than that of G or C bases. In addition, 92 potential RNA editing sites were identified in 25 protein-coding genes, with the most predicted RNA editing sites in ndhB gene. The variations on length and expansion extent to the junction of ycf1 gene were observed between S. tetrandra vouchers from different regions, indicating potential markers for further geographical origin discrimination. Moreover, the values of transition to transversion ratio (Ts/Tv) in the Stephania species were significantly higher than 1 using Pericampylus glaucus as reference. Comparative analysis of the Stephania cp genomes revealed 5 highly variable regions, including 3 intergenic regions (trnH-psbA, trnD-trnY, trnP) and two protein coding genes (rps16 and ndhA). The identified mutational hotspots of Stephania plants exhibited multiple SNP sites and Gaps, as well as different Ka/Ks ratio values. In addition, five pairs of specific primers targeting the divergence regions were accordingly designed, which could be utilized as potential molecular markers for species identification, population genetic and phylogenetic analysis in Stephania species. Phylogenetic tree analysis based on the conserved chloroplast protein coding genes indicated a sister relationship between S. tetrandra and the monophyletic group of S. japonica and S. kwangsiensis with high support values, suggesting a close genetic relationship within Stephania plants. However, two S. tetrandra vouches from different regions failed to cluster into one clade, confirming the occurrences of genetic diversities and requiring further investigation for geographical tracing strategy. CONCLUSIONS Overall, we provided comprehensive and detailed information on the complete chloroplast genome and identified nucleotide diversity hotspots of Stephania species. The obtained genetic resource of S. tetrandra from Zhejiang Province would facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of Stephania plants.
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Affiliation(s)
- Shujie Dong
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Zhiqi Ying
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Shuisheng Yu
- The Administration Bureau of Zhejiang Jiulongshan National Nature Reserve, Suichang, Zhejiang Province, People's Republic of China
| | - Qirui Wang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Guanghui Liao
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Yuqing Ge
- The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, Zhejiang Province, People's Republic of China.
| | - Rubin Cheng
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China.
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Zhang LL, He Y, Sheng F, Hu YF, Song Y, Li W, Chen J, Zhang J, Zou L. Towards a better understanding of Fagopyrum dibotrys: a systematic review. Chin Med 2021; 16:89. [PMID: 34530893 PMCID: PMC8447528 DOI: 10.1186/s13020-021-00498-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 08/30/2021] [Indexed: 01/12/2023] Open
Abstract
Fagopyrum dibotrys (F. dibotrys) (D.Don) H.Hara is a well-known edible herbal medicine in Asian countries. It has been widely used for the treatment of lung diseases, swelling, etc., and is also an important part of many Chinese medicine prescriptions. At present, more than 100 compounds have been isolated and identified from F. dibotrys, and these compounds can be primarily divided into flavonoids, phenols, terpenes, steroids, and fatty acids. Flavonoids and phenolic compounds are considered to be the main active ingredients of F. dibotrys. Previous pharmacological studies have shown that F. dibotrys possesses anti-inflammatory, anti-cancer, anti-oxidant, anti-bacterial, and anti-diabetic activities. Additional studies on functional genes have led to a better understanding of the metabolic pathways and regulatory factors related with the flavonoid active ingredients in F. dibotrys. In this paper, we systemically reviewed the research advances on the phytochemistry and pharmacology of F. dibotrys, as well as the functional genes related to the synthesis of active ingredients, aiming to promote the development and utilization of F. dibotrys.
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Affiliation(s)
- Le-Le Zhang
- School of Basic Medical Sciences, Chengdu University, Chengdu, China
| | - Yan He
- School of Basic Medical Sciences, Chengdu University, Chengdu, China
| | - Feiya Sheng
- School of Basic Medical Sciences, Chengdu University, Chengdu, China.
| | - Ying-Fan Hu
- School of Basic Medical Sciences, Chengdu University, Chengdu, China
| | - Yu Song
- Key Laboratory of Coarse Cereal Processing of Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu, China
| | - Wei Li
- School of Basic Medical Sciences, Chengdu University, Chengdu, China
| | - Jiarong Chen
- Affiliated Hospital of Chengdu University, Chengdu, China
| | - Jinming Zhang
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing of Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu, China.
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Complete Chloroplast Genome Sequence and Comparative and Phylogenetic Analyses of the Cultivated Cyperus esculentus. DIVERSITY 2021. [DOI: 10.3390/d13090405] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Cyperus esculentus produces large amounts of oil as one of the main oil storage reserves in underground tubers, making this crop species not only a promising resource for edible oil and biofuel in food and chemical industry, but also a model system for studying oil accumulation in non-seed tissues. In this study, we determined the chloroplast genome sequence of the cultivated C. esculentus (var. sativus Boeckeler). The results showed that the complete chloroplast genome of C. esculentus was 186,255 bp in size, and possessed a typical quadripartite structure containing one large single copy (100,940 bp) region, one small single copy (10,439 bp) region, and a pair of inverted repeat regions of 37,438 bp in size. Sequence analyses indicated that the chloroplast genome encodes 141 genes, including 93 protein-coding genes, 40 transfer RNA genes, and 8 ribosomal RNA genes. We also identified 396 simple-sequence repeats and 49 long repeats, including 15 forward repeats and 34 palindromes within the chloroplast genome of C. esculentus. Most of these repeats were distributed in the noncoding regions. Whole chloroplast genome comparison with those of the other four Cyperus species indicated that both the large single copy and inverted repeat regions were more divergent than the small single copy region, with the highest variation found in the inverted repeat regions. In the phylogenetic trees based on the complete chloroplast genomes of 13 species, all five Cyperus species within the Cyperaceae formed a clade, and C. esculentus was evolutionarily more related to C. rotundus than to the other three Cyperus species. In summary, the chloroplast genome sequence of the cultivated C. esculentus provides a valuable genomic resource for species identification, evolution, and comparative genomic research on this crop species and other Cyperus species in the Cyperaceae family.
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Park I, Song JH, Yang S, Chae S, Moon BC. Plastid Phylogenomic Data Offers Novel Insights Into the Taxonomic Status of the Trichosanthes kirilowii Complex (Cucurbitaceae) in South Korea. FRONTIERS IN PLANT SCIENCE 2021; 12:559511. [PMID: 34386020 PMCID: PMC8353159 DOI: 10.3389/fpls.2021.559511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
Trichosanthes is a genus in Cucurbitaceae comprising 90-100 species. Trichosanthes species are valuable as herbaceous medicinal ingredients. The fruits, seeds, and roots of species such as T. kirilowii and T. rosthornii are used in Korean traditional herbal medicines. T. rosthornii is only found in China, whereas in South Korea two varieties, T. kirilowii var. kirilowii and T. kirilowii var. japonica, are distributed. T. kirilowii var. kirilowii and T. kirilowii var. japonica have different fruit and leaf shapes but are recognized as belonging to the same species. Furthermore, although its members have herbal medicine applications, genomic information of the genus is still limited. The broad goals of this study were (i) to evaluate the taxonomy of Trichosanthes using plastid phylogenomic data and (ii) provide molecular markers specific for T. kirilowii var. kirilowii and T. kirilowii var. japonica, as these have differences in their pharmacological effectiveness and thus should not be confused and adulterated. Comparison of five Trichosanthes plastid genomes revealed locally divergent regions, mainly within intergenic spacer regions (trnT-UGU-trnL-UAA: marker name Tri, rrn4.5-rrn5: TRr, trnE-UUC-trnT-GGU: TRtt). Using these three markers as DNA-barcodes for important herbal medicine species in Trichosanthes, the identity of Trichosanthes material in commercial medicinal products in South Korea could be successfully determined. Phylogenetic analysis of the five Trichosanthes species revealed that the species are clustered within tribe Sicyoeae. T. kirilowii var. kirilowii and T. rosthornii formed a clade with T. kirilowii var. japonica as their sister group. As T. kirilowii in its current circumscription is paraphyletic and as the two varieties can be readily distinguished morphologically (e.g., in leaf shape), T. kirilowii var. japonica should be treated (again) as an independent species, T. japonica.
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Affiliation(s)
- Inkyu Park
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, South Korea
| | - Jun-Ho Song
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, South Korea
| | - Sungyu Yang
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, South Korea
| | - Sungwook Chae
- Herbal Medicine Research Division, Korea Institute of Oriental Medicine, Daejeon, South Korea
| | - Byeong Cheol Moon
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, South Korea
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Scobeyeva VA, Artyushin IV, Krinitsina AA, Nikitin PA, Antipin MI, Kuptsov SV, Belenikin MS, Omelchenko DO, Logacheva MD, Konorov EA, Samoilov AE, Speranskaya AS. Gene Loss, Pseudogenization in Plastomes of Genus Allium ( Amaryllidaceae), and Putative Selection for Adaptation to Environmental Conditions. Front Genet 2021; 12:674783. [PMID: 34306019 PMCID: PMC8296844 DOI: 10.3389/fgene.2021.674783] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/15/2021] [Indexed: 01/07/2023] Open
Abstract
Amaryllidaceae is a large family with more than 1,600 species, belonging to 75 genera. The largest genus—Allium—is vast, comprising about a thousand species. Allium species (as well as other members of the Amaryllidaceae) are widespread and diversified, they are adapted to a wide range of habitats from shady forests to open habitats like meadows, steppes, and deserts. The genes present in chloroplast genomes (plastomes) play fundamental roles for the photosynthetic plants. Plastome traits could thus be associated with geophysical abiotic characteristics of habitats. Most chloroplast genes are highly conserved and are used as phylogenetic markers for many families of vascular plants. Nevertheless, some studies revealed signatures of positive selection in chloroplast genes of many plant families including Amaryllidaceae. We have sequenced plastomes of the following nine Allium (tribe Allieae of Allioideae) species: A. zebdanense, A. moly, A. victorialis, A. macleanii, A. nutans, A. obliquum, A. schoenoprasum, A. pskemense, A. platyspathum, A. fistulosum, A. semenovii, and Nothoscordum bivalve (tribe Leucocoryneae of Allioideae). We compared our data with previously published plastomes and provided our interpretation of Allium plastome genes’ annotations because we found some noteworthy inconsistencies with annotations previously reported. For Allium species we estimated the integral evolutionary rate, counted SNPs and indels per nucleotide position as well as compared pseudogenization events in species of three main phylogenetic lines of genus Allium to estimate whether they are potentially important for plant physiology or just follow the phylogenetic pattern. During examination of the 38 species of Allium and the 11 of other Amaryllidaceae species we found that rps16, rps2, infA, ccsA genes have lost their functionality multiple times in different species (regularly evolutionary events), while the pseudogenization of other genes was stochastic events. We found that the “normal” or “pseudo” state of rps16, rps2, infA, ccsA genes correlates well with the evolutionary line of genus the species belongs to. The positive selection in various NADH dehydrogenase (ndh) genes as well as in matK, accD, and some others were found. Taking into account known mechanisms of coping with excessive light by cyclic electron transport, we can hypothesize that adaptive evolution in genes, coding subunits of NADH-plastoquinone oxidoreductase could be driven by abiotic factors of alpine habitats, especially by intensive light and UV radiation.
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Affiliation(s)
- Victoria A Scobeyeva
- Department of Evolution, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Department of Molecular and Biological Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ilya V Artyushin
- Department of Vertebrate Zoology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anastasiya A Krinitsina
- Department of Higher Plants, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Pavel A Nikitin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Maxim I Antipin
- Botanical Garden, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergei V Kuptsov
- Botanical Garden, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maxim S Belenikin
- Department of Molecular and Biological Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Denis O Omelchenko
- Laboratory of Plant Genomics, Institute for Information Transmission Problems, Moscow, Russia
| | - Maria D Logacheva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Evgenii A Konorov
- Laboratory of Animal Genetics, Vavilov Institute of General Genetics, Russian Academy of Science (RAS), Moscow, Russia
| | - Andrey E Samoilov
- Group of Genomics and Postgenomic Technologies, Central Research Institute of Epidemiology, Moscow, Russia
| | - Anna S Speranskaya
- Department of Higher Plants, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Group of Genomics and Postgenomic Technologies, Central Research Institute of Epidemiology, Moscow, Russia
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Wanga VO, Dong X, Oulo MA, Mkala EM, Yang JX, Onjalalaina GE, Gichua MK, Kirika PM, Gituru RW, Hu GW, Wang QF. Complete Chloroplast Genomes of Acanthochlamys bracteata (China) and Xerophyta (Africa) (Velloziaceae): Comparative Genomics and Phylogenomic Placement. FRONTIERS IN PLANT SCIENCE 2021; 12:691833. [PMID: 34194461 PMCID: PMC8238049 DOI: 10.3389/fpls.2021.691833] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/19/2021] [Indexed: 05/15/2023]
Abstract
Acanthochlamys P.C. Kao is a Chinese endemic monotypic genus, whereas Xerophyta Juss. is a genus endemic to Africa mainland, Arabian Peninsula and Madagascar with ca.70 species. In this recent study, the complete chloroplast genome of Acanthochlamys bracteata was sequenced and its genome structure compared with two African Xerophyta species (Xerophyta spekei and Xerophyta viscosa) present in the NCBI database. The genomes showed a quadripartite structure with their sizes ranging from 153,843 bp to 155,498 bp, having large single-copy (LSC) and small single-copy (SSC) regions divided by a pair of inverted repeats (IR regions). The total number of genes found in A. bracteata, X. spekei and X. viscosa cp genomes are 129, 130, and 132, respectively. About 50, 29, 28 palindromic, forward and reverse repeats and 90, 59, 53 simple sequence repeats (SSRs) were found in the A. bracteata, X. spekei, and X. viscosa cp genome, respectively. Nucleotide diversity analysis in all species was 0.03501, Ka/Ks ratio average score was calculated to be 0.26, and intergeneric K2P value within the Order Pandanales was averaged to be 0.0831. Genomic characterization was undertaken by comparing the genomes of the three species of Velloziaceae and it revealed that the coding regions were more conserved than the non-coding regions. However, key variations were noted mostly at the junctions of IRs/SSC regions. Phylogenetic analysis suggests that A. bracteata species has a closer genetic relationship to the genus Xerophyta. The present study reveals the complete chloroplast genome of A. bracteata and gives a genomic comparative analysis with the African species of Xerophyta. Thus, can be useful in developing DNA markers for use in the study of genetic variabilities and evolutionary studies in Velloziaceae.
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Affiliation(s)
- Vincent Okelo Wanga
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Millicent Akinyi Oulo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Elijah Mbandi Mkala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Jia-Xin Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Guy Eric Onjalalaina
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Moses Kirega Gichua
- Botany Department, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | | | - Robert Wahiti Gituru
- Botany Department, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
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Huang R, Xie X, Li F, Tian E, Chao Z. Chloroplast genomes of two Mediterranean Bupleurum species and the phylogenetic relationship inferred from combined analysis with East Asian species. PLANTA 2021; 253:81. [PMID: 33765202 DOI: 10.1007/s00425-021-03602-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
The chloroplast genomes of Mediterranean Bupleurum species are reported for the first time. Phylogenetic analysis supports the species as a basal clade of Bupleurum with divergence time at 35.40 Ma. Bupleurum is one of the most species-rich genus with high medicinal value in Apiaceae. Although infrageneric classifications of Bupleurum have been the subject of numerous studies, it still remains controversial. Chloroplast genome information will prove essential in advancing our understanding on phylogenetic study. Here we report cp genomes of two woody Bupleurum species (Bupleurum gibraltaricum and B. fruticosum) endemic to Mediterranean. The complete cp genomes of the two species were 157,303 and 157,391 bp in size, respectively. They encoded 114 unique genes including 30 tRNA genes, 4 rRNA genes and 80 protein coding genes. Genome structure, distributions of SDRs and SSRs, gene content exhibited similarities among Bupleurum species. High variable hotspots were detected in eight intergenic spacers and four genes. Most of genes were under purifying selection with two exceptions: atpF and clpP. The phylogenetic analysis based on 80 coding genes revealed that the genus was divided into 2 distinct clades corresponding to the 2 subgenera (subg. Penninervia, subg. Bupleurum) with divergence time at the end of collision of India with Eurasia. Most species diversified mainly during the later period of uplift of Qinghai-Tibetan Plateau. The cp genomes of the two Bupleurum species can be significant complementary to insights into the cp genome characteristics of this genus. The comparative chloroplast genomes and phylogenetic analysis advances our understanding of the evolution of cp genomes and phylogeny in Bupleurum.
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Affiliation(s)
- Rong Huang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Xuena Xie
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Fang Li
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Enwei Tian
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Zhi Chao
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China.
- Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou, 510515, China.
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Yang W, Zou J, Yu Y, Long W, Li S. Repeats in mitochondrial and chloroplast genomes characterize the ecotypes of the Oryza. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:7. [PMID: 37309528 PMCID: PMC10236085 DOI: 10.1007/s11032-020-01198-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/28/2020] [Indexed: 06/14/2023]
Abstract
Mitochondria and chloroplast are very important organelles for organism, participating in basic life activity. Their genomes contain many repeats which can lead to a variation of genome structure. Oryza is an important genus for human beings' nutrition. Several mitochondrial and chloroplast genomes of Oryza have been sequenced, which help us to insight the distribution and evolution of the repeats in Oryza species. In this paper, we compared six mitochondrial and 13 chloroplast genomes of Oryza and found that the structures of mitochondrial genomes were more diverse than chloroplast genomes. Since repeats can change the structure of the genome, resulting in the structural diversity of the genome, we analyzed all repeats and found 31 repeats in mitochondrial and 13 repeats in chloroplast genomes. Further, we developed 21 pairs of MRS molecular markers and 12 pairs of CRS molecular markers based on mitochondrial repeats and chloroplast repeats, respectively. These molecular markers can be used to detect the repeat-mediated recombination in Oryza mitochondrial and chloroplast genomes by PCR or fluorescence quantification. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-020-01198-6.
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Affiliation(s)
- Weilong Yang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072 China
| | - Jianing Zou
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072 China
| | - Yajie Yu
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072 China
| | - Weixiong Long
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072 China
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072 China
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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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Alzahrani DA, Yaradua SS, Albokhari EJ, Abba A. Complete chloroplast genome sequence of Barleria prionitis, comparative chloroplast genomics and phylogenetic relationships among Acanthoideae. BMC Genomics 2020; 21:393. [PMID: 32532210 PMCID: PMC7291470 DOI: 10.1186/s12864-020-06798-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 05/27/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The plastome of medicinal and endangered species in Kingdom of Saudi Arabia, Barleria prionitis was sequenced. The plastome was compared with that of seven Acanthoideae species in order to describe the plastome, spot the microsatellite, assess the dissimilarities within the sampled plastomes and to infer their phylogenetic relationships. RESULTS The plastome of B. prionitis was 152,217 bp in length with Guanine-Cytosine and Adenine-Thymine content of 38.3 and 61.7% respectively. It is circular and quadripartite in structure and constitute of a large single copy (LSC, 83, 772 bp), small single copy (SSC, 17, 803 bp) and a pair of inverted repeat (IRa and IRb 25, 321 bp each). 131 genes were identified in the plastome out of which 113 are unique and 18 were repeated in IR region. The genome consists of 4 rRNA, 30 tRNA and 80 protein-coding genes. The analysis of long repeat showed all types of repeats were present in the plastome and palindromic has the highest frequency. A total number of 98 SSR were also identified of which mostly were mononucleotide Adenine-Thymine and are located at the non coding regions. Comparative genomic analysis among the plastomes revealed that the pair of the inverted repeat is more conserved than the single copy region. In addition high variation is observed in the intergenic spacer region than the coding region. The genes, ycf1and ndhF and are located at the border junction of the small single copy region and IRb region of all the plastome. The analysis of sequence divergence in the protein coding genes indicates that the following genes undergo positive selection (atpF, petD, psbZ, rpl20, petB, rpl16, rps16, rpoC, rps7, rpl32 and ycf3). Phylogenetic analysis indicated sister relationship between Ruellieae and Justcieae. In addition, Barleria, Justicia and Ruellia are paraphyletic, suggesting that Justiceae, Ruellieae, Andrographideae and Barlerieae should be treated as tribes. CONCLUSIONS This study sequenced and assembled the first plastome of the taxon Barleria and reported the basics resources for evolutionary studies of B. prionitis and tools for phylogenetic relationship studies within the core Acanthaceae.
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Affiliation(s)
- Dhafer A Alzahrani
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Samaila S Yaradua
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia. .,Department of Biology, Umaru Musa Yaradua University, Centre for Biodiversity and Conservation, Katsina, Nigeria.
| | - Enas J Albokhari
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Biological Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Abidina Abba
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Zhou T, Zhu H, Wang J, Xu Y, Xu F, Wang X. Complete chloroplast genome sequence determination of Rheum species and comparative chloroplast genomics for the members of Rumiceae. PLANT CELL REPORTS 2020; 39:811-824. [PMID: 32221666 DOI: 10.1007/s00299-020-02532-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/13/2020] [Indexed: 05/10/2023]
Abstract
Complete plastomes of Rheum species facilitated to clarify the phylogeny of Polygonaceae, and comparative chloroplast genomics contributed to develop genetic markers for the authentication of Rheum species. Rheum (Polygonaceae) is widely distributed throughout the temperate and subtropical areas of Asian interior. Rheum species are usually perennial herbs, and half of them are endemic to China with important medicinal properties. On account of similar morphological characteristics, species delimitation of Rheum still remains unclear. Chloroplast genomes of eight Rheum species, Rumex crispus and Oxyria digyna were characterized. Based on the comparison of genome structure of these species and the two published Rheum species, it is shown that plastome sequences of these species are relatively conserved with the same gene order, and three Sect. Palmata species remarkably showed high sequence similarities. Some hotspots could be used to discriminate the Rheum species, and 17 plastid genes were subject to positive selection. The phylogenetic analyses indicated that all the Polygonaceae species were clustered in the same group and showed that Rheum species, except for Rheum wittrockii, formed a monophyletic group with high maximum parsimony/maximum likelihood bootstrap support values and Bayesian posterior probabilities. The molecular dating based on plastomes indicated that the divergences within Polygonaceae species were dated to the Upper Cretaceous period [73.86-77.99 million years ago (Ma)]. The divergence of Sect. Palmata species was estimated to have occurred around 1.60 Ma, indicating that its diversification was affected by the repeated climatic fluctuation in the Quaternary.
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Affiliation(s)
- Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
- Key Laboratory of Qiyao Resources and Anti-Tumor Activities, Shaanxi Administration of Traditional Chinese Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Honghong Zhu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jian Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yucan Xu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Fusheng Xu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Xumei Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
- Key Laboratory of Qiyao Resources and Anti-Tumor Activities, Shaanxi Administration of Traditional Chinese Medicine, Xi'an Jiaotong University, Xi'an, 710061, China.
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Logacheva MD, Schelkunov MI, Fesenko AN, Kasianov AS, Penin AA. Mitochondrial Genome of Fagopyrum esculentum and the Genetic Diversity of Extranuclear Genomes in Buckwheat. PLANTS (BASEL, SWITZERLAND) 2020; 9:E618. [PMID: 32408719 PMCID: PMC7285332 DOI: 10.3390/plants9050618] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/08/2020] [Accepted: 05/09/2020] [Indexed: 12/27/2022]
Abstract
Fagopyrum esculentum (common buckwheat) is an important agricultural non-cereal grain plant. Despite extensive genetic studies, the information on its mitochondrial genome is still lacking. Using long reads generated by single-molecule real-time technology coupled with circular consensus sequencing (CCS) protocol, we assembled the buckwheat mitochondrial genome and detected that its prevalent form consists of 10 circular chromosomes with a total length of 404 Kb. In order to confirm the presence of a multipartite structure, we developed a new targeted assembly tool capable of processing long reads. The mitogenome contains all genes typical for plant mitochondrial genomes and long inserts of plastid origin (~6.4% of the total mitogenome length). Using this new information, we characterized the genetic diversity of mitochondrial and plastid genomes in 11 buckwheat cultivars compared with the ancestral subspecies, F. esculentum ssp. ancestrale. We found it to be surprisingly low within cultivars: Only three to six variations in the mitogenome and one to two in the plastid genome. In contrast, the divergence with F. esculentum ssp. ancestrale is much higher: 220 positions differ in the mitochondrial genome and 159 in the plastid genome. The SNPs in the plastid genome are enriched in non-synonymous substitutions, in particular in the genes involved in photosynthesis: psbA, psbC, and psbH. This presumably reflects the selection for the increased photosynthesis efficiency as a part of the buckwheat breeding program.
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Affiliation(s)
- Maria D. Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (M.I.S.); (A.S.K.); (A.A.P.)
- Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | - Mikhail I. Schelkunov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (M.I.S.); (A.S.K.); (A.A.P.)
- Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | - Aleksey N. Fesenko
- Federal Scientific Center of Legumes and Groat Crops, 302502 Orel, Russia;
| | - Artem S. Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (M.I.S.); (A.S.K.); (A.A.P.)
| | - Aleksey A. Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (M.I.S.); (A.S.K.); (A.A.P.)
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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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Kahraman K, Lucas SJ. Comparison of different annotation tools for characterization of the complete chloroplast genome of Corylus avellana cv Tombul. BMC Genomics 2019; 20:874. [PMID: 31747873 PMCID: PMC6865063 DOI: 10.1186/s12864-019-6253-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/31/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several bioinformatics tools have been designed for assembly and annotation of chloroplast (cp) genomes, making it difficult to decide which is most useful and applicable to a specific case. The increasing number of plant genomes provide an opportunity to accurately obtain cp genomes from whole genome shotgun (WGS) sequences. Due to the limited genetic information available for European hazelnut (Corylus avellana L.) and as part of a genome sequencing project, we analyzed the complete chloroplast genome of the cultivar 'Tombul' with multiple annotation tools. RESULTS Three different annotation strategies were tested, and the complete cp genome of C. avellana cv Tombul was constructed, which was 161,667 bp in length, and had a typical quadripartite structure. A large single copy (LSC) region of 90,198 bp and a small single copy (SSC) region of 18,733 bp were separated by a pair of inverted repeat (IR) regions of 26,368 bp. In total, 125 predicted functional genes were annotated, including 76 protein-coding, 25 tRNA, and 4 rRNA unique genes. Comparative genomics indicated that the cp genome sequences were relatively highly conserved in species belonging to the same order. However, there were still some variations, especially in intergenic regions, that could be used as molecular markers for analyses of phylogeny and plant identification. Simple sequence repeat (SSR) analysis showed that there were 83 SSRs in the cp genome of cv Tombul. Phylogenetic analysis suggested that C. avellana cv Tombul had a close affinity to the sister group of C. fargesii and C. chinensis, and then a closer evolutionary relationship with Betulaceae family than other species of Fagales. CONCLUSION In this study, the complete cp genome of Corylus avellana cv Tombul, the most widely cultivated variety in Turkey, was obtained and annotated, and additionally phylogenetic relationships were predicted among Fagales species. Our results suggest a very accurate assembly of chloroplast genome from next generation whole genome shotgun (WGS) sequences. Enhancement of taxon sampling in Corylus species provide genomic insights into phylogenetic analyses. The nucleotide sequences of cv Tombul cp genomes can provide comprehensive genetic insight into the evolution of genus Corylus.
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Affiliation(s)
- Kadriye Kahraman
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Sabanci University, 34956, Istanbul, Turkey
| | - Stuart James Lucas
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Sabanci University, 34956, Istanbul, Turkey.
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Lee SR, Kim K, Lee BY, Lim CE. Complete chloroplast genomes of all six Hosta species occurring in Korea: molecular structures, comparative, and phylogenetic analyses. BMC Genomics 2019; 20:833. [PMID: 31706273 PMCID: PMC6842461 DOI: 10.1186/s12864-019-6215-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/22/2019] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The genus Hosta is a group of economically appreciated perennial herbs consisting of approximately 25 species that is endemic to eastern Asia. Due to considerable morphological variability, the genus has been well recognized as a group with taxonomic problems. Chloroplast is a cytoplasmic organelle with its own genome, which is the most commonly used for phylogenetic and genetic diversity analyses for land plants. To understand the genomic architecture of Hosta chloroplasts and examine the level of nucleotide and size variation, we newly sequenced four (H. clausa, H. jonesii, H. minor, and H. venusta) and analyzed six Hosta species (including the four, H. capitata and H. yingeri) distributed throughout South Korea. RESULTS The average size of complete chloroplast genomes for the Hosta taxa was 156,642 bp with a maximum size difference of ~ 300 bp. The overall gene content and organization across the six Hosta were nearly identical with a few exceptions. There was a single tRNA gene deletion in H. jonesii and four genes were pseudogenized in three taxa (H. capitata, H. minor, and H. jonesii). We did not find major structural variation, but there were a minor expansion and contractions in IR region for three species (H. capitata, H. minor, and H. venusta). Sequence variations were higher in non-coding regions than in coding regions. Four genic and intergenic regions including two coding genes (psbA and ndhD) exhibited the largest sequence divergence showing potential as phylogenetic markers. We found compositional codon usage bias toward A/T at the third position. The Hosta plastomes had a comparable number of dispersed and tandem repeats (simple sequence repeats) to the ones identified in other angiosperm taxa. The phylogeny of 20 Agavoideae (Asparagaceae) taxa including the six Hosta species inferred from complete plastome data showed well resolved monophyletic clades for closely related taxa with high node supports. CONCLUSIONS Our study provides detailed information on the chloroplast genome of the Hosta taxa. We identified nucleotide diversity hotspots and characterized types of repeats, which can be used for developing molecular markers applicable in various research area.
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Affiliation(s)
- Soo-Rang Lee
- Department of Biological Science, Texas Tech University, Lubbock, TX USA
| | - Kyeonghee Kim
- National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689 South Korea
| | - Byoung-Yoon Lee
- National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689 South Korea
| | - Chae Eun Lim
- National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689 South Korea
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Yaradua SS, Alzahrani DA, Albokhary EJ, Abba A, Bello A. Complete Chloroplast Genome Sequence of Justicia flava: Genome Comparative Analysis and Phylogenetic Relationships among Acanthaceae. BIOMED RESEARCH INTERNATIONAL 2019; 2019:4370258. [PMID: 31467890 PMCID: PMC6699374 DOI: 10.1155/2019/4370258] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/26/2019] [Indexed: 01/08/2023]
Abstract
The complete chloroplast genome of J. flava, an endangered medicinal plant in Saudi Arabia, was sequenced and compared with cp genome of three Acanthaceae species to characterize the cp genome, identify SSRs, and also detect variation among the cp genomes of the sampled Acanthaceae. NOVOPlasty was used to assemble the complete chloroplast genome from the whole genome data. The cp genome of J. flava was 150, 888bp in length with GC content of 38.2%, and has a quadripartite structure; the genome harbors one pair of inverted repeat (IRa and IRb 25, 500bp each) separated by large single copy (LSC, 82, 995 bp) and small single copy (SSC, 16, 893 bp). There are 132 genes in the genome, which includes 80 protein coding genes, 30 tRNA, and 4 rRNA; 113 are unique while the remaining 19 are duplicated in IR regions. The repeat analysis indicates that the genome contained all types of repeats with palindromic occurring more frequently; the analysis also identified total number of 98 simple sequence repeats (SSR) of which majority are mononucleotides A/T and are found in the intergenic spacer. The comparative analysis with other cp genomes sampled indicated that the inverted repeat regions are conserved than the single copy regions and the noncoding regions show high rate of variation than the coding region. All the genomes have ndhF and ycf1 genes in the border junction of IRb and SSC. Sequence divergence analysis of the protein coding genes showed that seven genes (petB, atpF, psaI, rpl32, rpl16, ycf1, and clpP) are under positive selection. The phylogenetic analysis revealed that Justiceae is sister to Ruellieae. This study reported the first cp genome of the largest genus in Acanthaceae and provided resources for studying genetic diversity of J. flava as well as resolving phylogenetic relationships within the core Acanthaceae.
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Affiliation(s)
- Samaila S. Yaradua
- Department of Biology, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre for Biodiversity and Conservation, Department of Biology, Umaru Musa Yaradua University, Katsina, Nigeria
| | | | - Enas J. Albokhary
- Department of Biology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abidina Abba
- Department of Biology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abubakar Bello
- Centre for Biodiversity and Conservation, Department of Biology, Umaru Musa Yaradua University, Katsina, Nigeria
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Xu F, He L, Gao S, Su Y, Li F, Xu L. Comparative Analysis of two Sugarcane Ancestors Saccharum officinarum and S. spontaneum based on Complete Chloroplast Genome Sequences and Photosynthetic Ability in Cold Stress. Int J Mol Sci 2019; 20:E3828. [PMID: 31387284 PMCID: PMC6696253 DOI: 10.3390/ijms20153828] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 08/02/2019] [Accepted: 08/02/2019] [Indexed: 01/11/2023] Open
Abstract
Polyploid Saccharum with complex genomes hindered the progress of sugarcane improvement, while their chloroplast genomes are much smaller and simpler. Chloroplast (cp), the vital organelle, is the site of plant photosynthesis, which also evolves other functions, such as tolerance to environmental stresses. In this study, the cp genome of two sugarcane ancestors Saccharum officinarum and S. spontaneum were sequenced, and genome comparative analysis between these two species was carried out, together with the photosynthetic ability. The length is 141,187 bp for S. officinarum and that is 7 bp longer than S. spontaneum, with the same GC content (38.44%) and annotated gene number (134), 13 with introns among them. There is a typical tetrad structure, including LSC, SSC, IRb and IRa. Of them, LSC and IRa/IRb are 18 bp longer and 6 bp shorter than those in S. spontaneum (83,047 bp and 22,795 bp), respectively, while the size of SSC is same (12,544 bp). Five genes exhibit contraction and expansion at the IR junctions, but only one gene ndhF with 29 bp expansion at the border of IRb/SSC. Nucleotide diversity (Pi) based on sliding window analysis showed that the single copy and noncoding regions were more divergent than IR- and coding regions, and the variant hotspots trnG-trnM, psbM-petN, trnR-rps14, ndhC-trnV and petA-psbJ in the LSC and trnL-ccsA in the SSC regions were detected, and petA-psbJ with the highest divergent value of 0.01500. Genetic distances of 65 protein genes vary from 0.00000 to 0.00288 between two species, and the selective pressure on them indicated that only petB was subjected to positive selection, while more genes including rpoC2, rps3, ccsA, ndhA, ndhA, psbI, atpH and psaC were subjected to purifying or very strong purifying selection. There are larger number of codons in S. spontaneum than that in S. officinarum, while both species have obvious codon preference and the codons with highest-(AUG) and lowest frequency (AUA) are same. Whilst, the most abundant amino acid is leucine in both S. officinarum and S. spontaneum, with number of 2175 (10.88% of total) and 2228 (10.90% of total) codons, respectively, and the lowest number is cysteine, with only 221 (1.105%) and 224 (1.096%), respectively. Protein collinearity analysis showed the high collinearity though several divergences were present in cp genomes, and identification of simple sequence repeats (SSRs) were included in this study. In addition, in order to compare cold tolerance and explore the expanding function of this environmental stress, the chlorophyll relative content (SPAD) and chlorophyll fluorescence Fv/Fm were measured. The significantly higher SPAD were observed in S. spontaneum than those in S. officinarum, no matter what the control conditions, exposure to low temperature or during recovery, and so was for Fv/Fm under exposure to low temperature, together with higher level of SPAD in S. spontaneum in each measurement. Aforementioned results suggest much stronger photosynthetic ability and cold tolerance in S. spontaneum. Our findings build a foundation to investigate the biological mechanism of two sugarcane ancestor chloroplasts and retrieve reliable molecular resources for phylogenetic and evolutionary studies, and will be conducive to genetic improvement of photosynthetic ability and cold resistance in modern sugarcane.
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Affiliation(s)
- Fu Xu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lilian He
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Shiwu Gao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Fusheng Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China.
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Gao B, Yuan L, Tang T, Hou J, Pan K, Wei N. The complete chloroplast genome sequence of Alpinia oxyphylla Miq. and comparison analysis within the Zingiberaceae family. PLoS One 2019; 14:e0218817. [PMID: 31233551 PMCID: PMC6590956 DOI: 10.1371/journal.pone.0218817] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/10/2019] [Indexed: 11/18/2022] Open
Abstract
Alpinia oxyphylla Miq. (A. oxyphylla) is an important edible and traditional herbal medicine. In this study, the complete chloroplast genome of A. oxyphylla was sequenced, analysed, and compared to five species in the Zingiberaceae family. The size of the A. oxyphylla chloroplast genome was 161351 bp, which consisted of a large single-copy (LSC, 87248 bp) and small single-copy (SSC, 16175 bp) region separated by a pair of inverted repeats (IRa and IRb, 28964 bp each). The genome encoded 132 unique genes, including 87 protein-coding genes, 37 tRNAs and four rRNAs. The GC content of the genome was 36.17%. A total of 53 simple sequence repeats (SSRs) and 80 long repeats were identified in the A. oxyphylla chloroplast genome. The chloroplast genome of A. oxyphylla shared the highest sequence similarity of >90% with the chloroplast genome of A. zerumbet, and six chloroplast genomes in the Zingiberaceae family were compared by using CGView Comparison Tool (CCT). According to the phylogenetic tree, the Zingiberaceae family is divided into two categories, which coincide with the classification of the characteristics of sun-like and shade-like in plants. Our results reveal the phototrophic component of NADH-dehydrogenase (ndhB and ndhC), photosystem II (psbZ) and ATP synthase (atpE, atpF) exhibit adaptive evolution under different environments, and the strength of light is an important trigger for the adaptations at the chloroplast level.
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Affiliation(s)
- Bingmiao Gao
- Hainan Provincial Key Laboratory of R&D on Tropical Herbs, Hainan Medical University, Haikou, China
- School of Pharmacy, Hainan Medical University, Haikou, China
| | - Lin Yuan
- School of Pharmacy, Hainan Medical University, Haikou, China
| | - Tianle Tang
- Environmental Science, School of Tropical and Laboratory Medicine, Hainan Medical University, Haikou, China
| | - Jie Hou
- School of Pharmacy, Hainan Medical University, Haikou, China
| | - Kun Pan
- School of Pharmacy, Hainan Medical University, Haikou, China
| | - Na Wei
- Hainan Provincial Key Laboratory of R&D on Tropical Herbs, Hainan Medical University, Haikou, China
- School of Pharmacy, Hainan Medical University, Haikou, China
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Zhou T, Ruhsam M, Wang J, Zhu H, Li W, Zhang X, Xu Y, Xu F, Wang X. The Complete Chloroplast Genome of Euphrasia regelii, Pseudogenization of ndh Genes and the Phylogenetic Relationships Within Orobanchaceae. Front Genet 2019; 10:444. [PMID: 31156705 PMCID: PMC6528182 DOI: 10.3389/fgene.2019.00444] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/29/2019] [Indexed: 12/31/2022] Open
Abstract
Euphrasia (Orobanchaceae) is a genus which is widely distributed in temperate regions of the southern and northern hemisphere. The taxonomy of Euphrasia is still controversial due to the similarity of morphological characters and a lack of genomic resources. Here, we present the first complete chloroplast (cp) genome of this taxonomically challenging genus. The cp genome of Euphrasia regelii consists of 153,026 bp, including a large single-copy region (83,893 bp), a small single-copy region (15,801 bp) and two inverted repeats (26,666 bp). There are 105 unique genes, including 71 protein-coding genes, 30 tRNA and 4 rRNA genes. Although the structure and gene order is comparable to the one in other angiosperm cp genomes, genes encoding the NAD(P)H dehydrogenase complex are widely pseudogenized due to mutations resulting in frameshifts, and stop codon positions. We detected 36 dispersed repeats, 7 tandem repeats and 65 simple sequence repeat loci in the E. regelii plastome. Comparative analyses indicated that the cp genome of E. regelii is more conserved compared to other hemiparasitic taxa in the Pedicularideae and Buchnereae. No structural rearrangements or loss of genes were detected. Our analyses suggested that three genes (clpP, ycf2 and rps14) were under positive selection and other genes under purifying selection. Phylogenetic analysis of monophyletic Orobanchaceae based on 45 plastomes indicated a close relationship between E. regelii and Neobartsia inaequalis. In addition, autotrophic lineages occupied the earliest diverging branches in our phylogeny, suggesting that autotrophy is the ancestral trait in this parasitic family.
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Affiliation(s)
- Tao Zhou
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
| | - Jian Wang
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Honghong Zhu
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Wenli Li
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Xiao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), School of Life Sciences, Northwest University, Xi’an, China
| | - Yucan Xu
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Fusheng Xu
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Xumei Wang
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
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44
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Nazish M, Zafar M, Ahmad M, Sultana S, Ullah R, Alqahtani AS, Ullah F, Ahmad S, Ashfaq S, Ullah F. Palyno-morphological investigations of halophytic taxa of Amaranthaceae through SEM from Salt range of Northern Punjab, Pakistan. Microsc Res Tech 2019; 82:304-316. [PMID: 30614130 DOI: 10.1002/jemt.23173] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 09/22/2018] [Accepted: 10/22/2018] [Indexed: 11/09/2022]
Abstract
The pollen morphology of 11 salt tolerant plant species of family Amaranthaceae from the salt range of Northern Punjab, Pakistan has been studied. The palyno-morphological characters were examined using light and scanning electron microscope. The examined all salt tolerant species have a slight difference in size but have similarity in shape, pore ornamentation, and polarity. The observed morphological characters of pollen grains were pollen symmetry, size, shape, pore ornamentation, pore size, number of pores, exine thickness, polar and equatorial diameter and, P/E ratio. Apolar type of pollens has been observed in all species. Shape of pollens was spheroidal. Exine sculpturing of pollen grains was scabrate (six spp), microechinate (four spp), and microechinate-scabrate (one spp). Different pori numbers were observed in different species. The pantoporate aperturate and sunken pore ornamentation have been reported in all species. A pollen taxonomic key was developed using examined morphological characters for the accurate identification of halophytic taxa. The high fertility and low sterility of pollens confirmed that the selected halophytes are well-established in the salt region. The findings highlight the taxonomic significance of pollen morphology in correct identification and differentiation of salt tolerant plant species.
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Affiliation(s)
- Moona Nazish
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Zafar
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Mushtaq Ahmad
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shazia Sultana
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Riaz Ullah
- Medicinal, Aromatic & Poisonous Plants Research Center MAPPRC, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia.,Department of Chemistry, Government College Ara Khel FR Kohat KPK, Kohat, Pakistan
| | - Ali S Alqahtani
- Medicinal, Aromatic & Poisonous Plants Research Center MAPPRC, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia.,Department of Pharmacognosy, College of Pharmacy, King Saud University, PO box 2457, 10 Riyadh 11451, Saudi Arabia
| | - Farhat Ullah
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shafiq Ahmad
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shomaila Ashfaq
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fazal Ullah
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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45
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Mo Q, Fu A, Lin Z, Wang W, Gong L, Li W. Expression and purification of antimicrobial peptide AP2 using SUMO fusion partner technology inEscherichia coli. Lett Appl Microbiol 2018; 67:606-613. [DOI: 10.1111/lam.13079] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Q. Mo
- Key Laboratory of Animal Molecular Nutrition of Education of Ministry; College of Animal Sciences, Zhejiang University; Hangzhou China
- College of Biosystems Engineering and Food Science, Zhejiang University; Hangzhou China
| | - A. Fu
- Key Laboratory of Animal Molecular Nutrition of Education of Ministry; College of Animal Sciences, Zhejiang University; Hangzhou China
- Institute of Biology, Westlake Institute for Advanced Study; Westlake University; Hangzhou Zhejiang Province China
| | - Z. Lin
- Key Laboratory of Animal Molecular Nutrition of Education of Ministry; College of Animal Sciences, Zhejiang University; Hangzhou China
| | - W. Wang
- Linyi Institute for Food and Drug Control; Linyi Shandong China
| | - L. Gong
- Key Laboratory of Animal Molecular Nutrition of Education of Ministry; College of Animal Sciences, Zhejiang University; Hangzhou China
| | - W. Li
- Key Laboratory of Animal Molecular Nutrition of Education of Ministry; College of Animal Sciences, Zhejiang University; Hangzhou China
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