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Hu X, Li Y, Meng F, Duan Y, Sun M, Yang S, Liu H. Analysis of chloroplast genome characteristics and codon usage bias in 14 species of Annonaceae. Funct Integr Genomics 2024; 24:109. [PMID: 38797780 DOI: 10.1007/s10142-024-01389-w] [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: 03/06/2024] [Revised: 05/18/2024] [Accepted: 05/21/2024] [Indexed: 05/29/2024]
Abstract
For the study of species evolution, chloroplast gene expression, and transformation, the chloroplast genome is an invaluable resource. Codon usage bias (CUB) analysis is a tool that is utilized to improve gene expression and investigate evolutionary connections in genetic transformation. In this study, we analysed chloroplast genome differences, codon usage patterns and the sources of variation on CUB in 14 Annonaceae species using bioinformatics tools. The study showed that there was a significant variation in both gene sizes and numbers between the 14 species, but conservation was still maintained. It's worth noting that there were noticeable differences in the IR/SC sector boundary and the types of SSRs among the 14 species. The mono-nucleotide repeat type was the most common, with A/T repeats being more prevalent than G/C repeats. Among the different types of repeats, forward and palindromic repeats were the most abundant, followed by reverse repeats, and complement repeats were relatively rare. Codon composition analysis revealed that all 14 species had a frequency of GC lower than 50%. Additionally, it was observed that the proteins in-coding sequences of chloroplast genes tend to end with A/T at the third codon position. Among these species, 21 codons exhibited bias (RSCU > 1), and there were 8 high-frequency (HF) codons and 5 optimal codons that were identical across the species. According to the ENC-plot and Neutrality plot analysis, natural selection had less impact on the CUB of A. muricate and A. reticulata. Based on the PR2-plot, it was evident that base G had a higher frequency than C, and T had a higher frequency A. The correspondence analysis (COA) revealed that codon usage patterns different in Annonaceae.
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Affiliation(s)
- Xiang Hu
- Tropical Eco-agriculture Research Institute, Yunnan Academy of Agricultural Sciences, Yuanmou, Yunnan, 651300, China
| | - Yaqi Li
- Tropical and Subtropical Cash Crops Research Institute, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, 678000, China
| | - Fuxuan Meng
- Tropical Eco-agriculture Research Institute, Yunnan Academy of Agricultural Sciences, Yuanmou, Yunnan, 651300, China
| | - Yuanjie Duan
- Tropical Eco-agriculture Research Institute, Yunnan Academy of Agricultural Sciences, Yuanmou, Yunnan, 651300, China
| | - Manying Sun
- Tropical Eco-agriculture Research Institute, Yunnan Academy of Agricultural Sciences, Yuanmou, Yunnan, 651300, China
| | - Shiying Yang
- Tropical Eco-agriculture Research Institute, Yunnan Academy of Agricultural Sciences, Yuanmou, Yunnan, 651300, China
| | - Haigang Liu
- Tropical Eco-agriculture Research Institute, Yunnan Academy of Agricultural Sciences, Yuanmou, Yunnan, 651300, China.
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Eskandari A, Nezhad NG, Leow TC, Rahman MBA, Oslan SN. Essential factors, advanced strategies, challenges, and approaches involved for efficient expression of recombinant proteins in Escherichia coli. Arch Microbiol 2024; 206:152. [PMID: 38472371 DOI: 10.1007/s00203-024-03871-2] [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: 12/10/2023] [Revised: 12/31/2023] [Accepted: 01/25/2024] [Indexed: 03/14/2024]
Abstract
Producing recombinant proteins is a major accomplishment of biotechnology in the past century. Heterologous hosts, either eukaryotic or prokaryotic, are used for the production of these proteins. The utilization of microbial host systems continues to dominate as the most efficient and affordable method for biotherapeutics and food industry productions. Hence, it is crucial to analyze the limitations and advantages of microbial hosts to enhance the efficient production of recombinant proteins on a large scale. E. coli is widely used as a host for the production of recombinant proteins. Researchers have identified certain obstacles with this host, and given the growing demand for recombinant protein production, there is an immediate requirement to enhance this host. The following review discusses the elements contributing to the manifestation of recombinant protein. Subsequently, it sheds light on innovative approaches aimed at improving the expression of recombinant protein. Lastly, it delves into the obstacles and optimization methods associated with translation, mentioning both cis-optimization and trans-optimization, producing soluble recombinant protein, and engineering the metal ion transportation. In this context, a comprehensive description of the distinct features will be provided, and this knowledge could potentially enhance the expression of recombinant proteins in E. coli.
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Affiliation(s)
- Azadeh Eskandari
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Biochemistry, FacultyofBiotechnologyand BiomolecularSciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Nima Ghahremani Nezhad
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Enzyme Technology and X-Ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | | | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
- Department of Biochemistry, FacultyofBiotechnologyand BiomolecularSciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
- Enzyme Technology and X-Ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
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Huo Y, Cheng M, Tang M, Zhang M, Yang X, Zheng Y, Zhao T, He P, Yu J. GhCTSF1, a short PPR protein with a conserved role in chloroplast development and photosynthesis, participates in intron splicing of rpoC1 and ycf3-2 transcripts in cotton. PLANT COMMUNICATIONS 2024:100858. [PMID: 38444162 DOI: 10.1016/j.xplc.2024.100858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 03/07/2024]
Abstract
Cotton is one of the most important textile fibers worldwide. As crucial agronomic traits, leaves play an essential role in the growth, disease resistance, fiber quality, and yield of cotton plants. Pentatricopeptide repeat (PPR) proteins are a large family of nuclear-encoded proteins involved in organellar or nuclear RNA metabolism. Using a virus-induced gene silencing assay, we found that cotton plants displayed variegated yellow leaf phenotypes with decreased chlorophyll content when expression of the PPR gene GhCTSF1 was silenced. GhCTSF1 encodes a chloroplast-localized protein that contains only two PPR motifs. Disruption of GhCTSF1 substantially reduces the splicing efficiency of rpoC1 intron 1 and ycf3 intron 2. Loss of function of the GhCTSF1 ortholog EMB1417 causes splicing defects in rpoC1 and ycf3-2, leading to impaired chloroplast structure and decreased photosynthetic rates in Arabidopsis. We also found that GhCTSF1 interacts with two splicing factors, GhCRS2 and GhWTF1. Defects in GhCRS2 and GhWTF1 severely affect intron splicing of rpoC1 and ycf3-2 in cotton, leading to defects in chloroplast development and a reduction in photosynthesis. Our results suggest that GhCTSF1 is specifically required for splicing rpoC1 and ycf3-2 in cooperation with GhCRS2 and GhWTF1.
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Affiliation(s)
- Yuzhu Huo
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Mengxue Cheng
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Meiju Tang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Meng Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Xiaofan Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Yating Zheng
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Tong Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Peng He
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
| | - Jianing Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
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Xiao F, Zhao Y, Wang X, Jian X. Characterization of the chloroplast genome of Gleditsia species and comparative analysis. Sci Rep 2024; 14:4262. [PMID: 38383559 PMCID: PMC10881578 DOI: 10.1038/s41598-024-54608-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 02/14/2024] [Indexed: 02/23/2024] Open
Abstract
The genus Gleditsia has significant medicinal and economic value, but information about the chloroplast genomic characteristics of Gleditsia species has been limited. Using the Illumina sequencing, we assembled and annotated the whole chloroplast genomes of seven Gleditsia species (Gleditsia sinensis, Gleditsia japonica var. delavayi (G. delavayi), G. fera, G. japonica, G. microphylla, Fructus Gleditsiae Abnormalis (Zhū Yá Zào), G. microphylla mutant). The assembled genomes revealed that Gleditsia species have a typical circular tetrad structure, with genome sizes ranging from 162,746 to 170,907 bp. Comparative genomic analysis showed that most (65.8-75.8%) of the abundant simple sequence repeats in Gleditsia and Gymnocladus species were located in the large single copy region. The Gleditsia chloroplast genome prefer T/A-ending codons and avoid C/G-ending codons, positive selection was acting on the rpoA, rpl20, atpB, ndhA and ycf4 genes, most of the chloroplast genes of Gleditsia species underwent purifying selection. Expansion and contraction of the inverted repeat (IR)/single copy (SC) region showed similar patterns within the Gleditsia genus. Polymorphism analysis revealed that coding regions were more conserved than non-coding regions, and the IR region was more conserved than the SC region. Mutational hotspots were mostly found in intergenic regions such as "rps16-trnQ", "trnT-trnL", "ndhG-ndhI", and "rpl32-trnL" in Gleditsia. Phylogenetic analysis showed that G. fera is most closely related to G. sinensis,G. japonica and G. delavayi are relatively closely related. Zhū Yá Zào can be considered a bud mutation of the G. sinensis. The albino phenotype of G. microphylla mutant is not caused by variations in the chloroplast genome, and that the occurrence of the albino phenotype may be due to mutations in chloroplast-related genes involved in splicing or localization functions. This study will help us enhance our exploration of the genetic evolution and geographical origins of the Gleditsia genus.
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Affiliation(s)
- Feng Xiao
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Yang Zhao
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China.
| | - Xiurong Wang
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Xueyan Jian
- College of Continuing Education, Yanbian University, Yanji, 133002, Jilin, China
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Mahapatra K, Mukherjee A, Suyal S, Dar MA, Bhagavatula L, Datta S. Regulation of chloroplast biogenesis, development, and signaling by endogenous and exogenous cues. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:167-183. [PMID: 38623168 PMCID: PMC11016055 DOI: 10.1007/s12298-024-01427-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 02/07/2024] [Accepted: 02/27/2024] [Indexed: 04/17/2024]
Abstract
Chloroplasts are one of the defining features in most plants, primarily known for their unique property to carry out photosynthesis. Besides this, chloroplasts are also associated with hormone and metabolite productions. For this, biogenesis and development of chloroplast are required to be synchronized with the seedling growth to corroborate the maximum rate of photosynthesis following the emergence of seedlings. Chloroplast biogenesis and development are dependent on the signaling to and from the chloroplast, which are in turn regulated by several endogenous and exogenous cues. Light and hormones play a crucial role in chloroplast maturation and development. Chloroplast signaling involves a coordinated two-way connection between the chloroplast and nucleus, termed retrograde and anterograde signaling, respectively. Anterograde and retrograde signaling are involved in regulation at the transcriptional level and downstream modifications and are modulated by several metabolic and external cues. The communication between chloroplast and nucleus is essential for plants to develop strategies to cope with various stresses including high light or high heat. In this review, we have summarized several aspects of chloroplast development and its regulation through the interplay of various external and internal factors. We have also discussed the involvement of chloroplasts as sensors of various external environment stress factors including high light and temperature, and communicate via a series of retrograde signals to the nucleus, thus playing an essential role in plants' abiotic stress response.
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Affiliation(s)
- Kalyan Mahapatra
- Plant Cell and Developmental Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh 462066 India
| | - Arpan Mukherjee
- Plant Cell and Developmental Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh 462066 India
| | - Shikha Suyal
- Plant Cell and Developmental Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh 462066 India
| | - Mansoor Ali Dar
- Plant Cell and Developmental Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh 462066 India
| | | | - Sourav Datta
- Plant Cell and Developmental Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh 462066 India
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Zheng S, Yang L, Zheng H, Wu J, Zhou Z, Tian J. Identification of Hub Genes and Physiological Effects of Overexpressing the Photosynthesis-Related Gene Soly720 in Tomato under High-CO 2 Conditions. Int J Mol Sci 2024; 25:757. [PMID: 38255831 PMCID: PMC10815203 DOI: 10.3390/ijms25020757] [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: 11/23/2023] [Revised: 12/23/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
Changes in the atmospheric CO2 concentration influence plant growth and development by affecting the morphological structure and photosynthetic performance. Despite evidence for the macro-effects of elevated CO2 concentrations on plant morphology and yield in tomato, the gene regulatory network and key genes related to cross-regulation have not been reported. To identify the hub genes and metabolic pathways involved in the response of tomato to CO2 enrichment, weighted gene co-expression network analysis was conducted using gene expression profiles obtained by RNA sequencing. The role of the photosynthesis-related gene Soly720 (Solyc01g007720) in CO2-enriched tomato plants was explored. Tomato plants responded to CO2 enrichment primarily through RNA-related pathways and the metabolism of amino acids, fatty acids, and carbohydrates. The hub genes in co-expression networks were associated with plant growth and development, including cellular components and photosynthesis. Compared to wild-type plants, transgenic plants overexpressing the Soly720 gene exhibited 13.4%, 5.5%, 8.9%, and 4.1% increases in plant height, stem diameter, leaf length, and leaf width, respectively, under high-CO2 conditions. The morphological improvements in transgenic plants were accompanied by enhancement of photosynthetic performance in terms of chlorophyll contents, photosynthetic characteristics, and key enzyme activities. This study elucidates the response network of tomato to CO2 enrichment and demonstrates the regulatory role of Soly720 in photosynthesis under high-CO2 conditions.
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Affiliation(s)
| | | | | | | | | | - Jieyun Tian
- Horticulture College, Shanxi Agricultural University, Jinzhong 030801, China; (S.Z.); (L.Y.); (H.Z.); (J.W.); (Z.Z.)
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Xu Y, Wu Z, Shen W, Zhou H, Li H, He X, Li R, Qin B. Disruption of the rice ALS1 localized in chloroplast causes seedling-lethal albino phenotype. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111925. [PMID: 37981085 DOI: 10.1016/j.plantsci.2023.111925] [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: 09/27/2023] [Revised: 11/03/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023]
Abstract
Chloroplasts are the organelles responsible for photosynthesis and regulate normal plant growth. Although translation elongation factors play important roles in chloroplast development, functional studies of chloroplast translation elongation factors in higher plants remain very sparse. Here, we obtained a rice mutant exhibiting seedling-lethal albino phenotype and named it albino and lethal seedling 1 (als1). Consistently, low content of photosynthetic pigments, malformed chloroplasts and defective photosynthesis were observed in als1 mutant leaves. Map-based cloning experiment showed that als1 mutant had a T base insertion in Os02g0595700, causing a frame shift and premature stop codon. ALS1 encoded a GTP-binding protein EF-Tu, which acts as a translation elongation factor in chloroplast protein translation. ALS1 was found to be expressed throughout plant with highest expression level in young leaves. Moreover, ALS1 was located in chloroplast, whereas the truncated als1 could not normally be located in chloroplast. Additionally, the ALS1 mutation significantly influenced the expression of downstream genes, such as genes relevant to chlorophyll biosynthesis, photosynthesis as well as chloroplast development. These results show that ALS1 acts as a key regulator of chloroplast development and plant growth.
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Affiliation(s)
- Yibo Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Agricultural College, Guangxi University, Nanning 530005, China
| | - Zishuai Wu
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Wei Shen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Agricultural College, Guangxi University, Nanning 530005, China
| | - Haiyu Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Agricultural College, Guangxi University, Nanning 530005, China
| | - Hu Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Xinhua He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Agricultural College, Guangxi University, Nanning 530005, China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Agricultural College, Guangxi University, Nanning 530005, China
| | - Baoxiang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Agricultural College, Guangxi University, Nanning 530005, China.
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Zhao J, Chen H, Li G, Jumaturti MA, Yao X, Hu Y. Phylogenetics Study to Compare Chloroplast Genomes in Four Magnoliaceae Species. Curr Issues Mol Biol 2023; 45:9234-9251. [PMID: 37998755 PMCID: PMC10670740 DOI: 10.3390/cimb45110578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/07/2023] [Accepted: 11/12/2023] [Indexed: 11/25/2023] Open
Abstract
Magnoliaceae, a family of perennial woody plants, contains several endangered species whose taxonomic status remains ambiguous. The study of chloroplast genome information can help in the protection of Magnoliaceae plants and confirmation of their phylogenetic relationships. In this study, the chloroplast genomes were sequenced, assembled, and annotated in Woonyoungia septentrionalis and three Michelia species (Michelia champaca, Michelia figo, and Michelia macclurei). Comparative analyses of genomic characteristics, repetitive sequences, and sequence differences were performed among the four Magnoliaceae plants, and phylogenetic relationships were constructed with twenty different magnolia species. The length of the chloroplast genomes varied among the four studied species ranging from 159,838 bp (Woonyoungia septentrionalis) to 160,127 bp (Michelia macclurei). Four distinct hotspot regions were identified based on nucleotide polymorphism analysis. They were petA-psbJ, psbJ-psbE, ndhD-ndhE, and rps15-ycf1. These gene fragments may be developed and utilized as new molecular marker primers. By using Liriodendron tulipifera and Liriodendron chinense as outgroups reference, a phylogenetic tree of the four Magnoliaceae species and eighteen other Magnoliaceae species was constructed with the method of Shared Coding Sequences (CDS). Results showed that the endangered species, W. septentrionalis, is relatively genetically distinct from the other three species, indicating the different phylogenetic processes among Magnoliaceae plants. Therefore, further genetic information is required to determine the relationships within Magnoliaceae. Overall, complete chloroplast genome sequences for four Magnoliaceae species reported in this paper have shed more light on phylogenetic relationships within the botanical group.
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Affiliation(s)
- Jianyun Zhao
- Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning 530004, China; (J.Z.); (G.L.); (M.A.J.); (X.Y.)
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning 530004, China
| | - Hu Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China;
| | - Gaiping Li
- Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning 530004, China; (J.Z.); (G.L.); (M.A.J.); (X.Y.)
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning 530004, China
| | - Maimaiti Aisha Jumaturti
- Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning 530004, China; (J.Z.); (G.L.); (M.A.J.); (X.Y.)
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning 530004, China
| | - Xiaomin Yao
- Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning 530004, China; (J.Z.); (G.L.); (M.A.J.); (X.Y.)
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning 530004, China
| | - Ying Hu
- Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning 530004, China; (J.Z.); (G.L.); (M.A.J.); (X.Y.)
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning 530004, China
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He H, Wang T, Tang C, Cao Z, Pu X, Li Y, Li X. Complete Chloroplast Genomes of Saussurea katochaete, Saussurea superba, and Saussurea stella: Genome Structures and Comparative and Phylogenetic Analyses. Genes (Basel) 2023; 14:2002. [PMID: 38002945 PMCID: PMC10670953 DOI: 10.3390/genes14112002] [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: 09/19/2023] [Revised: 10/21/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
Saussurea plants are widely distributed in Asia and Europe; however, their complex phylogenetic relationships have led to many difficulties in phylogenetic studies and interspecific identification. In this study, we assembled, annotated, and analyzed the chloroplast genomes of three Saussurea plants: Saussurea katochaete, Saussurea superba, and Saussurea stella. The results showed that the full-length sequences of the three Saussurea plants were 152,561 bp, 151,452 bp, and 152,293 bp, respectively, which represent the typical quadripartite structure, and the genomes were relatively conserved. The gene annotation results showed that the chloroplast genomes of S. katochaete, S. superba, and S. stella were annotated with 128, 124, and 127 unique genes, respectively, which included 83, 80, and 83 protein-coding genes (PCGs), respectively, 37, 36, and 36 tRNA genes, respectively, and 8 rRNA genes. Moreover, 46, 45, and 43 SSR loci, respectively, and nine highly variable regions (rpl32-trnL-UAG, rpl32, ndhF-rpl32, ycf1, trnC-GCA-petN, trnC-GCA, rpcL, psbE-petL, and rpl16-trnG-UUG) were identified and could be used as potential molecular markers for population identification and phylogenetic study of Saussurea plants. Phylogenetic analyses strongly support the sisterhood of S. katochaete with S. superba and S. stella, and are all clustered with S. depsagensis, S. inversa, S. medusa, and S. gossipihora, of which S. gossipiphora is most closely related. Additionally, the phylogenetic results indicate a high frequency of differentiation among different species of Saussurea plants, and many different species or genera are morphologically very different from each other, which may be related to certain genetic material in the chloroplasts. This study provides an important reference for the identification of Saussurea plants and studies their evolution and phylogenetics.
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Affiliation(s)
- Hui He
- Qinghai Academy of Animal and Veterinary Science, Xining 810016, China; (H.H.); (T.W.); (C.T.); (Z.C.); (X.P.)
| | - Tao Wang
- Qinghai Academy of Animal and Veterinary Science, Xining 810016, China; (H.H.); (T.W.); (C.T.); (Z.C.); (X.P.)
| | - Chuyu Tang
- Qinghai Academy of Animal and Veterinary Science, Xining 810016, China; (H.H.); (T.W.); (C.T.); (Z.C.); (X.P.)
| | - Zhengfei Cao
- Qinghai Academy of Animal and Veterinary Science, Xining 810016, China; (H.H.); (T.W.); (C.T.); (Z.C.); (X.P.)
| | - Xiaojian Pu
- Qinghai Academy of Animal and Veterinary Science, Xining 810016, China; (H.H.); (T.W.); (C.T.); (Z.C.); (X.P.)
| | - Yuling Li
- Qinghai Academy of Animal and Veterinary Science, Xining 810016, China; (H.H.); (T.W.); (C.T.); (Z.C.); (X.P.)
| | - Xiuzhang Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Sciences, Qinghai University, Xining 810016, China
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Bulle M, Sheri V, Aileni M, Zhang B. Chloroplast Genome Engineering: A Plausible Approach to Combat Chili Thrips and Other Agronomic Insect Pests of Crops. PLANTS (BASEL, SWITZERLAND) 2023; 12:3448. [PMID: 37836188 PMCID: PMC10574609 DOI: 10.3390/plants12193448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023]
Abstract
The world population's growing demand for food is expected to increase dramatically by 2050. The agronomic productivity for food is severely affected due to biotic and abiotic constraints. At a global level, insect pests alone account for ~20% loss in crop yield every year. Deployment of noxious chemical pesticides to control insect pests always has a threatening effect on human health and environmental sustainability. Consequently, this necessitates for the establishment of innovative, environmentally friendly, cost-effective, and alternative means to mitigate insect pest management strategies. According to a recent study, using chloroplasts engineered with double-strand RNA (dsRNA) is novel successful combinatorial strategy deployed to effectively control the most vexing pest, the western flower thrips (WFT: Frankliniella occidentalis). Such biotechnological avenues allowed us to recapitulate the recent progress of research methods, such as RNAi, CRISPR/Cas, mini chromosomes, and RNA-binding proteins with plastid engineering for a plausible approach to effectively mitigate agronomic insect pests. We further discussed the significance of the maternal inheritance of the chloroplast, which is the major advantage of chloroplast genome engineering.
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Affiliation(s)
- Mallesham Bulle
- Agri Biotech Foundation, Agricultural University Campus, Rajendranagar, Hyderabad 500030, India
| | - Vijay Sheri
- Department of Biology, East Carolina University, Greenville, NC 27858, USA;
| | - Mahender Aileni
- Department of Biotechnology, Telangana University, Dichpally, Nizamabad 503322, India;
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA;
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