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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 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.
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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.
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Ji J, Luo Y, Pei L, Li M, Xiao J, Li W, Wu H, Luo Y, He J, Cheng J, Xie L. Complete Plastid Genomes of Nine Species of Ranunculeae (Ranunculaceae) and Their Phylogenetic Inferences. Genes (Basel) 2023; 14:2140. [PMID: 38136961 PMCID: PMC10742492 DOI: 10.3390/genes14122140] [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: 10/20/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
The tribe Ranunculeae, Ranunculaceae, comprising 19 genera widely distributed all over the world. Although a large number of Sanger sequencing-based molecular phylogenetic studies have been published, very few studies have been performed on using genomic data to infer phylogenetic relationships within Ranunculeae. In this study, the complete plastid genomes of nine species (eleven samples) from Ceratocephala, Halerpestes, and Ranunculus were de novo assembled using a next-generation sequencing method. Previously published plastomes of Oxygraphis and other related genera of the family were downloaded from GenBank for comparative analysis. The complete plastome of each Ranunculeae species has 112 genes in total, including 78 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. The plastome structure of Ranunculeae samples is conserved in gene order and arrangement. There are no inverted repeat (IR) region expansions and only one IR contraction was found in the tested samples. This study also compared plastome sequences across all the samples in gene collinearity, codon usage, RNA editing sites, nucleotide variability, simple sequence repeats, and positive selection sites. Phylogeny of the available Ranunculeae species was inferred by the plastome data using maximum-likelihood and Bayesian inference methods, and data partitioning strategies were tested. The phylogenetic relationships were better resolved compared to previous studies based on Sanger sequencing methods, showing the potential value of the plastome data in inferring the phylogeny of the tribe.
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Affiliation(s)
- Jiaxin Ji
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (J.J.); (Y.L.); (J.X.); (W.L.); (H.W.); (Y.L.); (J.H.)
| | - Yike Luo
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (J.J.); (Y.L.); (J.X.); (W.L.); (H.W.); (Y.L.); (J.H.)
| | - Linying Pei
- College of Agriculture and Forestry, Longdong University, Qingyang 745000, China;
| | - Mingyang Li
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (M.L.); (J.C.)
| | - Jiamin Xiao
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (J.J.); (Y.L.); (J.X.); (W.L.); (H.W.); (Y.L.); (J.H.)
| | - Wenhe Li
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (J.J.); (Y.L.); (J.X.); (W.L.); (H.W.); (Y.L.); (J.H.)
| | - Huanyu Wu
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (J.J.); (Y.L.); (J.X.); (W.L.); (H.W.); (Y.L.); (J.H.)
| | - Yuexin Luo
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (J.J.); (Y.L.); (J.X.); (W.L.); (H.W.); (Y.L.); (J.H.)
| | - Jian He
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (J.J.); (Y.L.); (J.X.); (W.L.); (H.W.); (Y.L.); (J.H.)
| | - Jin Cheng
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (M.L.); (J.C.)
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Lei Xie
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (J.J.); (Y.L.); (J.X.); (W.L.); (H.W.); (Y.L.); (J.H.)
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Qiao X, Wang Z, Sun W, Zhu N, Song M. The complete chloroplast genome of Ranunculus ternatus (Ranunculaceae). Mitochondrial DNA B Resour 2023; 8:1209-1214. [PMID: 38239910 PMCID: PMC10796127 DOI: 10.1080/23802359.2023.2278816] [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: 07/27/2023] [Accepted: 10/29/2023] [Indexed: 01/22/2024] Open
Abstract
Ranunculus ternatus Thunb. 1784 is a plant with important medicinal values. Here we report its chloroplast genome. This chloroplast genome was 156,003 bp in length with a GC content of 37.86%. It is composed of a large single copy (LSC) of 85,397 bp and a small single copy (SSC) of 19,856 bp, which are separated by a pair of inverted repeats (IR) of 25,375 bp each. The chloroplast genome contained 110 unique genes, including 77 protein-coding genes, 4 rRNA genes, and 29 tRNA genes. Phylogenetic analysis indicated that R. ternatus was closely related to R. cassubicifolius. This chloroplast genome not only enriches the genome information of Ranunculus but also will be useful for the evolution study of the family Ranunculaceae.
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Affiliation(s)
- Xinrong Qiao
- College of Pharmaceutical Engineering, Xinyang Agriculture and Forestry University, Xinyang, Henan, China
| | - Zexia Wang
- College of Pharmaceutical Engineering, Xinyang Agriculture and Forestry University, Xinyang, Henan, China
| | - Wei Sun
- College of Pharmaceutical Engineering, Xinyang Agriculture and Forestry University, Xinyang, Henan, China
| | - Nailiang Zhu
- College of Pharmaceutical Engineering, Xinyang Agriculture and Forestry University, Xinyang, Henan, China
| | - Min Song
- College of Pharmaceutical Engineering, Xinyang Agriculture and Forestry University, Xinyang, Henan, China
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