1
|
Lubna, Asaf S, Khan I, Jan R, Asif S, Bilal S, Kim KM, Al-Harrasi A. Genetic characterization and phylogenetic analysis of the Nigella sativa (black seed) plastome. Sci Rep 2024; 14:14509. [PMID: 38914674 PMCID: PMC11196742 DOI: 10.1038/s41598-024-65073-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024] Open
Abstract
In this study, the complete plastome sequence of Nigella sativa (black seed), was analyzed for the first time. The plastome spans approximately 154,120 bp, comprising four sections: the Large Single-Copy (LSC) (85,538 bp), the Small Single-Copy (SSC) (17,984 bp), and two Inverted Repeat (IR) regions (25,299 bp). A comparative study of N. sativa's plastome with ten other species from various genera in the Ranunculaceae family reveals substantial structural variations. The contraction of the inverted repeat region in N. sativa influences the boundaries of single-copy regions, resulting in a shorter plastome size than other species. When comparing the plastome of N. sativa with those of its related species, significant divergence is observed, particularly except for N. damascena. Among these, the plastome of A. glaucifolium displays the highest average pairwise sequence divergence (0.2851) with N. sativa, followed by A. raddeana (0.2290) and A. coerulea (0.1222). Furthermore, the study identified 12 distinct hotspot regions characterized by elevated Pi values (> 0.1). These regions include trnH-GUG-psbA, matK-trnQ-UUG, psbK-trnR-UCU, atpF-atpI, rpoB-psbD, ycf3-ndhJ, ndhC-cemA, petA-psaJ, trnN-GUU-ndhF, trnV-GAC-rps12, ycf2-trnI-CAU, and ndhA-ycf1. Approximately, 24 tandem and 48 palindromic and forward repeats were detected in N. sativa plastome. The analysis revealed 32 microsatellites with the majority being mononucleotide repeats. In the N. sativa plastome, phenylalanine had the highest number of codons (1982 codons), while alanine was the least common amino acid with 260 codons. A phylogenetic tree, constructed using protein-coding genes, revealed a distinct monophyletic clade comprising N. sativa and N. damascene, closely aligned with the Cimicifugeae tribe and exhibiting robust support. This plastome provides valuable genetic information for precise species identification, phylogenetic resolution, and evolutionary studies of N. sativa.
Collapse
Affiliation(s)
- Lubna
- Natural and Medical Science Research Center, University of Nizwa, 616, Nizwa, Oman
| | - Sajjad Asaf
- Natural and Medical Science Research Center, University of Nizwa, 616, Nizwa, Oman.
| | - Ibrahim Khan
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Rahmatullah Jan
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Saleem Asif
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Saqib Bilal
- Natural and Medical Science Research Center, University of Nizwa, 616, Nizwa, Oman
| | - Kyung-Min Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Ahmed Al-Harrasi
- Natural and Medical Science Research Center, University of Nizwa, 616, Nizwa, Oman.
| |
Collapse
|
2
|
Li MF, Xiao T, Zhang YH. The complete chloroplast genome of Hedychium flavum Roxb., an ornamental, edible and medicinal plant. Mitochondrial DNA B Resour 2023; 8:1253-1257. [PMID: 38026495 PMCID: PMC10653761 DOI: 10.1080/23802359.2023.2281029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 11/02/2023] [Indexed: 12/01/2023] Open
Abstract
Hedychium flavum Roxb. 1820 is a perennial herb mainly distributed in China, India, Myanmar and Thailand with ornamental, edible and medicinal value. It is extensively cultivated as a source of aromatic essential oils, ornamental plant, food flavorings and vegetables, and folk medicine. In this study, we sequence the complete chloroplast genome of H. flavum by de novo assembly. The assembled genome has a typical quadripartite circular structure with 163,909 bp in length, containing a large single-copy region (LSC, 88,589 bp), a small single-copy region (SSC, 15,762 bp), and two inverted repeat regions (IRs, 29,779 bp). The cp genome contains 133 genes, including 87 protein-coding genes, 38 tRNA genes and 8 rRNA genes. Phylogenetic analysis based on the complete cp genome shows a close affinity of H. flavum and H. neocarneum with 100% bootstrap support. This study will provide useful genetic resource for further phylogenetic analysis of the genus Hedychium and Zingiberaceae.
Collapse
Affiliation(s)
- Mei-Fei Li
- School of Life Science, Yunnan Normal University, Kunming, China
| | - Tao Xiao
- School of Life Science, Yunnan Normal University, Kunming, China
| | - Yong-Hong Zhang
- School of Life Science, Yunnan Normal University, Kunming, China
| |
Collapse
|
3
|
Gao Y, Li S, Yuan G, Fang J, Shen G, Tian Z. Comparison of Biological and Genetic Characteristics between Two Most Common Broad-Leaved Weeds in Paddy Fields: Ammannia arenaria and A. multiflora (Lythraceae). BIOLOGY 2023; 12:936. [PMID: 37508367 PMCID: PMC10375975 DOI: 10.3390/biology12070936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/16/2023] [Accepted: 06/25/2023] [Indexed: 07/30/2023]
Abstract
Ammannia arenaria and A. multifloras, morphologically similar at the seedling stage, are the most common broad-leaved weeds in paddy fields. Our study showed that A. arenaria occupied more space than A. multifloras when competing with rice. However, A. multifloras germination has lower temperature adaptability. No difference in sensitivity to common herbicides between two Ammannia species was observed. Chloroplast (cp) genomes could be conducive to clarify their genetic relationship. The complete cp genome sequences of A. arenaria (158,401 bp) and A. multiflora (157,900 bp) were assembled for the first time. In A. arenaria, there were 91 simple sequence repeats, 115 long repeats, and 86 protein-encoding genes, one, sixteen, and thirty more than those in A. multiflora. Inverted repeats regions expansion and contraction and the phylogenetic tree based on cp genomes demonstrated the closely relationship between the two species. However, in A. arenaria, 20 single nucleotide polymorphisms in the CDS region were detected compared to A. multiflora, which can be used to distinguish the two species. Moreover, there was one unique gene, infA, only in A. arenaria. This study provides reliable molecular resources for future research focusing on the infrageneric taxa identification, phylogenetic resolution, population structure, and biodiversity of Ammannia species.
Collapse
Affiliation(s)
- Yuan Gao
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Shenghui Li
- College of Agriculture, Anshun University, Anshun 561000, China
| | - Guohui Yuan
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Jiapeng Fang
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Guohui Shen
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Zhihui Tian
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| |
Collapse
|
4
|
Yanfei N, Tai S, Chunhua W, Jia D, Fazhong Y. Complete chloroplast genome sequences of the medicinal plant Aconitum transsectum (Ranunculaceae): comparative analysis and phylogenetic relationships. BMC Genomics 2023; 24:90. [PMID: 36855055 PMCID: PMC9976445 DOI: 10.1186/s12864-023-09180-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 02/10/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Aconitum transsectum Diels. (Ranunculaceae) is an important medicinal plant that is widely used in traditional Chinese medicine, but its morphological traits make it difficult to recognize from other Aconitum species. No research has sequenced the chloroplast genome of A.transsectum, despite the fact that phylogenetic analysis based on chloroplast genome sequences provides essential evidence for plant classification. RESULTS In this study, the chloroplast (cp) genome of A. transsectum was sequenced, assembled, and annotated. A. transsectum cp genome is a 155,872 bp tetrameric structure including a large single copy (LSC, 87,671 bp) and a small single copy (SSC, 18,891 bp) section, as well as a pair of inverted repeat sequences (IRa and IRb, 25,894 bp each). 131 genes are encoded by the complete cp genome, comprising 86 protein-coding genes, 37 tRNAs, and 8 rRNAs. The most favored codon in the A. transsectum cp genome is AUG, and 46 repeats and 241 SSRs were also identified. The A. transsectum cp genome is similar in size, gene composition, and IR expansion and contraction to the cp genomes of seven Ranunculaceae species. Phylogenetic analysis of cp genomes of 28 plants from the Ranunculaceae family shows that A. transsectum is most closely related to A. vilmorinianum, A. episcopale, and A. forrestii of Subgen. Aconitum. CONCLUSIONS Overall, this study provides complete cp genome resources for A. transsectum that will be beneficial for identifying potential.
Collapse
Affiliation(s)
- Niu Yanfei
- grid.412720.20000 0004 1761 2943Key Laboratory for Forest Resources Conservation and Utilization, Southwest Mountains of China, Southwest Forestry University, Kunming, 650224 China ,grid.506261.60000 0001 0706 7839Yunnan Institute of Materia Medica, Kunming, 650111 China ,Yunnan Baiyao Group Chinese Medicinal Resources Division, Kunming, 650500 China
| | - Su Tai
- grid.506261.60000 0001 0706 7839Yunnan Institute of Materia Medica, Kunming, 650111 China
| | - Wu Chunhua
- Key Laboratory of State Forestry and Grassland Administration On Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Kunming, 650224, China. .,College of Chemical Engineering, Southwest Forestry University, Kunming, 650224, China.
| | - Deng Jia
- grid.412720.20000 0004 1761 2943Key Laboratory for Forest Resources Conservation and Utilization, Southwest Mountains of China, Southwest Forestry University, Kunming, 650224 China
| | - Yang Fazhong
- grid.412720.20000 0004 1761 2943Key Laboratory for Forest Resources Conservation and Utilization, Southwest Mountains of China, Southwest Forestry University, Kunming, 650224 China ,Key Laboratory of State Forestry and Grassland Administration On Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Kunming, 650224 China
| |
Collapse
|
5
|
Saikia J, Washmin N, Borah T, Sarmah P, Konwar P, Siga A, Haldar S, Banik D. Physicochemical properties, chemical composition and sensory attributes of Alpinia nigra (Gaertn.) B.L. Burtt rhizome: an underutilized spice source. Eur Food Res Technol 2023. [DOI: 10.1007/s00217-023-04200-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
6
|
Fang H, Dai G, Liao B, Zhou P, Liu Y. Application of chloroplast genome in the identification of Phyllanthus urinaria and its common adulterants. FRONTIERS IN PLANT SCIENCE 2023; 13:1099856. [PMID: 36684764 PMCID: PMC9853280 DOI: 10.3389/fpls.2022.1099856] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/13/2022] [Indexed: 06/03/2023]
Abstract
BACKGROUND Phyllanthus urinaria L. is extensively used as ethnopharmacological material in China. In the local marketplace, this medicine can be accidentally contaminated, deliberately substituted, or mixed with other related species. The contaminants in herbal products are a threat to consumer safety. Due to the scarcity of genetic information on Phyllanthus plants, more molecular markers are needed to avoid misidentification. METHODS In this study, the complete chloroplast genome of nine species of the genus Phyllanthus was de novo assembled and characterized. RESULTS This study revealed that all of these species exhibited a conserved quadripartite structure, which includes a large single copy (LSC) region and small single copy (SSC) region, and two copies of inverted repeat regions (IRa and IRb), which separate the LSC and SSC regions. And the genome structure, codon usage, and repeat sequences were highly conserved and showed similarities among the nine species. Three highly variable regions (trnS-GCU-trnG-UCC, trnT-UGU-trnL-UAA, and petA-psbJ) might be helpful as potential molecular markers for identifying P. urinaria and its contaminants. In addition, the molecular clock analysis results showed that the divergence time of the genus Phyllanthus might occur at ~ 48.72 Ma. CONCLUSION This study provides valuable information for further species identification, evolution, and phylogenetic research of Phyllanthus.
Collapse
Affiliation(s)
| | | | | | - Ping Zhou
- *Correspondence: Yinglin Liu, ; Ping Zhou,
| | | |
Collapse
|
7
|
Gao Y, Shen G, Yuan G, Tian Z. Comparative Analysis of Whole Chloroplast Genomes of Three Common Species of Echinochloa (Gramineae) in Paddy Fields. Int J Mol Sci 2022; 23:ijms232213864. [PMID: 36430336 PMCID: PMC9698722 DOI: 10.3390/ijms232213864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/30/2022] [Accepted: 11/06/2022] [Indexed: 11/12/2022] Open
Abstract
Echinochloa crus-galli var. crus-galli, E. crus-galli var. zelayensis, and E. glabrescens, morphologically similar at the seedling stage, are the most pernicious barnyard grass species in paddy fields worldwide. Chloroplast (cp) genomes could be conducive to their identification. In this study, we assembled the complete cp genome sequences of Echinochloa crus-galli var. crus-galli (139,856 bp), E. crus-galli var. zelayensis (139,874 bp), and E. glabrescens (139,874 bp), which exhibited a typical circular tetramerous structure, large and small single-copy regions, and a pair of inverted repeats. In Echinochloa crus-galli var. crus-galli, there were 136 simple sequence (SSRs) and 62 long (LRs) repeats, and in the other two species, 139 SSRs and 68 LRs. Each cp genome contains 92 protein-encoding genes. In Echinochloa crus-galli var. crus-galli and E. glabrescens, 321 and 1 single-nucleotide polymorphisms were detected compared to Echinochloa crus-galli var. zelayensis. IR expansion and contraction revealed small differences between the three species. The phylogenetic tree based on cp genomes demonstrated the phylogenetic relationship between ten barnyard grass species and other common Gramineae plants, showing new genetic relationships of the genus Echinochloa. This study provides valuable information on cp genomes, useful for identifying and classifying the genus Echinochloa and studying its phylogenetic relationships and evolution.
Collapse
|
8
|
Gong L, Ding X, Guan W, Zhang D, Zhang J, Bai J, Xu W, Huang J, Qiu X, Zheng X, Zhang D, Li S, Huang Z, Su H. Comparative chloroplast genome analyses of Amomum: insights into evolutionary history and species identification. BMC PLANT BIOLOGY 2022; 22:520. [PMID: 36352400 PMCID: PMC9644571 DOI: 10.1186/s12870-022-03898-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Species in genus Amomum always have important medicinal and economic values. Classification of Amomum using morphological characters has long been a challenge because they exhibit high similarity. The main goals of this study were to mine genetic markers from cp genomes for Amomum species identification and discover their evolutionary history through comparative analysis. RESULTS Three species Amomum villosum, Amomum maximum and Amomum longipetiolatum were sequenced and annotated for the complete chloroplast (cp) genomes, and the cp genomes of A. longipetiolatum and A. maximum were the first reported. Three cp genomes exhibited typical quadripartite structures with 163,269-163,591 bp in length. Each genome encodes 130 functional genes including 79 protein-coding, 26 tRNAs and 3 rRNAs genes. 113-152 SSRs and 99 long repeats were identified in the three cp genomes. By designing specific primers, we amplified the highly variable loci and the mined genetic marker ccsA exhibited a relatively high species identification resolution in Amomum. The nonsynonymous and synonymous substitution ratios (Ka/Ks) in Amomum and Alpinia showed that most genes were subjected to a purifying selection. Phylogenetic analysis revealed the evolutionary relationships of Amomum and Alpinia species and proved that Amomum is paraphyletic. In addition, the sequenced sample of A. villosum was found to be a hybrid, becoming the first report of natural hybridization of this genus. Meanwhile, the high-throughput sequencing-based ITS2 analysis was proved to be an efficient tool for interspecific hybrid identification and with the help of the chloroplast genome, the hybrid parents can be also be determined. CONCLUSION The comparative analysis and mined genetic markers of cp genomes were conducive to species identification and evolutionary relationships of Amomum.
Collapse
Affiliation(s)
- Lu Gong
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Xiaoxia Ding
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Wan Guan
- Luqiao Hospital, Taizhou Enze Medical Center (Group), Taizhou, Zhejiang, China
| | - Danchun Zhang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
| | - Jing Zhang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Junqi Bai
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Wen Xu
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Juan Huang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Xiaohui Qiu
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Xiasheng Zheng
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Danyan Zhang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Shijie Li
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Zhihai Huang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China.
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China.
| | - He Su
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China.
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China.
| |
Collapse
|