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Kotari I, Kosiol C, Borges R. The Patterns of Codon Usage between Chordates and Arthropods are Different but Co-evolving with Mutational Biases. Mol Biol Evol 2024; 41:msae080. [PMID: 38667829 PMCID: PMC11108087 DOI: 10.1093/molbev/msae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 03/22/2024] [Accepted: 04/15/2024] [Indexed: 05/22/2024] Open
Abstract
Different frequencies amongst codons that encode the same amino acid (i.e. synonymous codons) have been observed in multiple species. Studies focused on uncovering the forces that drive such codon usage showed that a combined effect of mutational biases and translational selection works to produce different frequencies of synonymous codons. However, only few have been able to measure and distinguish between these forces that may leave similar traces on the coding regions. Here, we have developed a codon model that allows the disentangling of mutation, selection on amino acids and synonymous codons, and GC-biased gene conversion (gBGC) which we employed on an extensive dataset of 415 chordates and 191 arthropods. We found that chordates need 15 more synonymous codon categories than arthropods to explain the empirical codon frequencies, which suggests that the extent of codon usage can vary greatly between animal phyla. Moreover, methylation at CpG sites seems to partially explain these patterns of codon usage in chordates but not in arthropods. Despite the differences between the two phyla, our findings demonstrate that in both, GC-rich codons are disfavored when mutations are GC-biased, and the opposite is true when mutations are AT-biased. This indicates that selection on the genomic coding regions might act primarily to stabilize its GC/AT content on a genome-wide level. Our study shows that the degree of synonymous codon usage varies considerably among animals, but is likely governed by a common underlying dynamic.
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Affiliation(s)
- Ioanna Kotari
- Institut für Populationsgenetik, University of Veterinary Medicine, Veterinärplatz 1, Vienna 1210, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Carolin Kosiol
- Centre for Biological Diversity, School of Biology, University of St Andrews, Fife KY16 9TH, UK
| | - Rui Borges
- Institut für Populationsgenetik, University of Veterinary Medicine, Veterinärplatz 1, Vienna 1210, Austria
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Zhang N, Huang K, Xie P, Deng A, Tang X, Jiang M, Mo P, Yin H, Huang R, Liang J, He F, Liu Y, Hu H, Wang Y. Chloroplast genome analysis and evolutionary insights in the versatile medicinal plant Calendula officinalis L. Sci Rep 2024; 14:9662. [PMID: 38671173 PMCID: PMC11053094 DOI: 10.1038/s41598-024-60455-2] [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: 01/26/2024] [Accepted: 04/23/2024] [Indexed: 04/28/2024] Open
Abstract
Calendula officinalis L.is a versatile medicinal plant with numerous applications in various fields. However, its chloroplast genome structure, features, phylogeny, and patterns of evolution and mutation remain largely unexplored. This study examines the chloroplast genome, phylogeny, codon usage bias, and divergence time of C. officinalis, enhancing our understanding of its evolution and adaptation. The chloroplast genome of C. officinalis is a 150,465 bp circular molecule with a G + C content of 37.75% and comprises 131 genes. Phylogenetic analysis revealed a close relationship between C. officinalis, C. arvensis, and Osteospermum ecklonis. A key finding is the similarity in codon usage bias among these species, which, coupled with the divergence time analysis, supports their close phylogenetic proximity. This similarity in codon preference and divergence times underscores a parallel evolutionary adaptation journey for these species, highlighting the intricate interplay between genetic evolution and environmental adaptation in the Asteraceae family. Moreover unique evolutionary features in C. officinalis, possibly associated with certain genes were identified, laying a foundation for future research into the genetic diversity and medicinal value of C. officinalis.
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Affiliation(s)
- Ningyun Zhang
- Agricultural Products Processing and Food Safety Key Laboratory of Hunan Higher Education, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Kerui Huang
- Agricultural Products Processing and Food Safety Key Laboratory of Hunan Higher Education, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China.
| | - Peng Xie
- Agricultural Products Processing and Food Safety Key Laboratory of Hunan Higher Education, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Aihua Deng
- Agricultural Products Processing and Food Safety Key Laboratory of Hunan Higher Education, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Xuan Tang
- Agricultural Products Processing and Food Safety Key Laboratory of Hunan Higher Education, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Ming Jiang
- Agricultural Products Processing and Food Safety Key Laboratory of Hunan Higher Education, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Ping Mo
- Agricultural Products Processing and Food Safety Key Laboratory of Hunan Higher Education, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Hanbin Yin
- Agricultural Products Processing and Food Safety Key Laboratory of Hunan Higher Education, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Rongjie Huang
- Agricultural Products Processing and Food Safety Key Laboratory of Hunan Higher Education, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Jiale Liang
- Agricultural Products Processing and Food Safety Key Laboratory of Hunan Higher Education, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Fuhao He
- Agricultural Products Processing and Food Safety Key Laboratory of Hunan Higher Education, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Yaping Liu
- Agricultural Products Processing and Food Safety Key Laboratory of Hunan Higher Education, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Haoliang Hu
- Agricultural Products Processing and Food Safety Key Laboratory of Hunan Higher Education, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China.
| | - Yun Wang
- Agricultural Products Processing and Food Safety Key Laboratory of Hunan Higher Education, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China.
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Nkurikiyimfura O, Waheed A, Fang H, Yuan X, Chen L, Wang YP, Lu G, Zhan J, Yang L. Fitness difference between two synonymous mutations of Phytophthora infestans ATP6 gene. BMC Ecol Evol 2024; 24:36. [PMID: 38494489 PMCID: PMC10946160 DOI: 10.1186/s12862-024-02223-4] [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: 12/27/2023] [Accepted: 03/11/2024] [Indexed: 03/19/2024] Open
Abstract
BACKGROUND Sequence variation produced by mutation provides the ultimate source of natural selection for species adaptation. Unlike nonsynonymous mutation, synonymous mutations are generally considered to be selectively neutral but accumulating evidence suggests they also contribute to species adaptation by regulating the flow of genetic information and the development of functional traits. In this study, we analysed sequence characteristics of ATP6, a housekeeping gene from 139 Phytophthora infestans isolates, and compared the fitness components including metabolic rate, temperature sensitivity, aggressiveness, and fungicide tolerance among synonymous mutations. RESULTS We found that the housekeeping gene exhibited low genetic variation and was represented by two major synonymous mutants at similar frequency (0.496 and 0.468, respectively). The two synonymous mutants were generated by a single nucleotide substitution but differed significantly in fitness as well as temperature-mediated spatial distribution and expression. The synonymous mutant ending in AT was more common in cold regions and was more expressed at lower experimental temperature than the synonymous mutant ending in GC and vice versa. CONCLUSION Our results are consistent with the argument that synonymous mutations can modulate the adaptive evolution of species including pathogens and have important implications for sustainable disease management, especially under climate change.
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Affiliation(s)
- Oswald Nkurikiyimfura
- Institute of Plant Virology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Abdul Waheed
- Institute of Plant Virology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Hanmei Fang
- Institute of Plant Virology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Xiaoxian Yuan
- Institute of Plant Virology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Lixia Chen
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Yan-Ping Wang
- College of Chemistry and Life Sciences, Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, Sichuan, 611130, China
| | - Guodong Lu
- Department of Plant Pathology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jiasui Zhan
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden.
| | - Lina Yang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
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Li Y, Hu X, Xiao M, Huang J, Lou Y, Hu F, Fu X, Li Y, He H, Cheng J. An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea. BMC Genom Data 2023; 24:42. [PMID: 37558997 PMCID: PMC10413492 DOI: 10.1186/s12863-023-01143-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/28/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND The chloroplast genome of plants is known for its small size and low mutation and recombination rates, making it a valuable tool in plant phylogeny, molecular evolution, and population genetics studies. Codon usage bias, an important evolutionary feature, provides insights into species evolution, gene function, and the expression of exogenous genes. Coffee, a key crop in the global tropical agricultural economy, trade, and daily life, warrants investigation into its codon usage bias to guide future research, including the selection of efficient heterologous expression systems for coffee genetic transformation. RESULTS Analysis of the codon utilization patterns in the chloroplast genomes of three Coffea species revealed a high degree of similarity among them. All three species exhibited similar base compositions, with high A/T content and low G/C content and a preference for A/T-ending codons. Among the 30 high-frequency codons identified, 96.67% had A/T endings. Fourteen codons were identified as ideal. Multiple mechanisms, including natural selection, were found to influence the codon usage patterns in the three coffee species, as indicated by ENc-GC3s mapping, PR2 analysis, and neutral analysis. Nicotiana tabacum and Saccharomyces cerevisiae have potential value as the heterologous expression host for three species of coffee genes. CONCLUSION This study highlights the remarkable similarity in codon usage patterns among the three coffee genomes, primarily driven by natural selection. Understanding the gene expression characteristics of coffee and elucidating the laws governing its genetic evolution are facilitated by investigating the codon preferences in these species. The findings can enhance the efficacy of exogenous gene expression and serve as a basis for future studies on coffee evolution.
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Affiliation(s)
- Yaqi Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China
| | - Xiang Hu
- Institute of Tropical Eco-Agricultural, Yunnan Academy of Agricultural Sciences, Yuanmou, Yunnan, China
| | - Mingkun Xiao
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China
| | - Jiaxiong Huang
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China
| | - Yuqiang Lou
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China
| | - Faguang Hu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China
| | - Xingfei Fu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China
| | - Yanan Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China
| | - Hongyan He
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China
- Yunnan Academy of Agricultural Engineering, Kunming, Yunnan, China
| | - Jinhuan Cheng
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China.
- Yunnan Academy of Agricultural Engineering, Kunming, Yunnan, China.
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Noor F, Ashfaq UA, Bakar A, Qasim M, Masoud MS, Alshammari A, Alharbi M, Riaz MS. Identification and characterization of codon usage pattern and influencing factors in HFRS-causing hantaviruses. Front Immunol 2023; 14:1131647. [PMID: 37492567 PMCID: PMC10364125 DOI: 10.3389/fimmu.2023.1131647] [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: 12/25/2022] [Accepted: 06/22/2023] [Indexed: 07/27/2023] Open
Abstract
Hemorrhagic fever with renal syndrome (HFRS) is an acute viral zoonosis carried and transmitted by infected rodents through urine, droppings, or saliva. The etiology of HFRS is complex due to the involvement of viral factors and host immune and genetic factors which hinder the development of potential therapeutic solutions for HFRS. Hantaan virus (HTNV), Dobrava-Belgrade virus (DOBV), Seoul virus (SEOV), and Puumala virus (PUUV) are predominantly found in hantaviral species that cause HFRS in patients. Despite ongoing prevention and control efforts, HFRS remains a serious economic burden worldwide. Furthermore, recent studies reported that the hantavirus nucleocapsid protein is a multi-functional protein and plays a major role in the replication cycle of the hantavirus. However, the precise mechanism of the nucleoproteins in viral pathogenesis is not completely understood. In the framework of the current study, various in silico approaches were employed to identify the factors influencing the codon usage pattern of hantaviral nucleoproteins. Based on the relative synonymous codon usage (RSCU) values, a comparative analysis was performed between HFRS-causing hantavirus and their hosts, suggesting that HTNV, DOBV, SEOV, and PUUV, were inclined to evolve their codon usage patterns that were comparable to those of their hosts. The results indicated that most of the overrepresented codons had AU-endings, which revealed that mutational pressure is the major force shaping codon usage patterns. However, the influence of natural selection and geographical factors cannot be ignored on viral codon usage bias. Further analysis also demonstrated that HFRS causing hantaviruses adapted host-specific codon usage patterns to sustain successful replication and transmission chains within hosts. To our knowledge, no study to date reported the factors influencing the codon usage pattern within hantaviral nucleoproteins. Thus, the proposed computational scheme can help in understanding the underlying mechanism of codon usage patterns in HFRS-causing hantaviruses which lend a helping hand in designing effective anti-HFRS treatments in future. This study, although comprehensive, relies on in silico methods and thus necessitates experimental validation for more solid outcomes. Beyond the identified factors influencing viral behavior, there could be other yet undiscovered influences. These potential factors should be targets for further research to improve HFRS therapeutic strategies.
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Affiliation(s)
- Fatima Noor
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Abu Bakar
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Shareef Masoud
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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Shirazi Z, Khakdan F, Rafiei F, Balalami MY, Ranjbar M. Genome-wide identification and expression profile analysis of metal tolerance protein gene family in Eucalyptus grandis under metal stresses. BMC PLANT BIOLOGY 2023; 23:240. [PMID: 37149585 PMCID: PMC10163719 DOI: 10.1186/s12870-023-04240-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/21/2023] [Indexed: 05/08/2023]
Abstract
Metal tolerance proteins (MTPs) as Me2+/H+(K+) antiporters participate in the transport of divalent cations, leading to heavy metal stress resistance and mineral utilization in plants. In the present study, to obtain better knowledge of the biological functions of the MTPs family, 20 potential EgMTPs genes were identified in Eucalyptus grandis and classified into seven groups belonging to three cation diffusion facilitator groups (Mn-CDFs, Zn/Fe-CDFs, and Zn-CDFs) and seven groups. EgMTP-encoded amino acids ranged from 315 to 884, and most of them contained 4-6 recognized transmembrane domains and were clearly prognosticated to localize into the cell vacuole. Almost all EgMTP genes experienced gene duplication events, in which some might be uniformly distributed in the genome. The numbers of cation efflux and the zinc transporter dimerization domain were highest in EgMTP proteins. The promoter regions of EgMTP genes have different cis-regulatory elements, indicating that the transcription rate of EgMTP genes can be a controlled response to different stimuli in multiple pathways. Our findings provide accurate perception on the role of the predicted miRNAs and the presence of SSR marker in the Eucalyptus genome and clarify their functions in metal tolerance regulation and marker-assisted selection, respectively. Gene expression profiling based on previous RNA-seq data indicates a probable function for EgMTP genes during development and responses to biotic stress. Additionally, the upregulation of EgMTP6, EgMTP5, and EgMTP11.1 to excess Cd2+ and Cu2+ exposure might be responsible for metal translocation from roots to leaves.
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Affiliation(s)
- Zahra Shirazi
- Department of Biotechnology Research, Research Institute of Forests and Rangelands, Agricultural Research, Education and Extension Organization (AREEO), National Botanical Garden, Tehran Karaj Freeway, P.O. Box 13185-116, Tehran, Iran.
| | | | - Fariba Rafiei
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Mahdi Yahyazadeh Balalami
- Department of Medicinal Plant Research, Research Institute of Forests and Rangelands, Agricultural Research, Education and Extension Organization (AREEO), National Botanical Garden, Tehran Karaj Freeway, P.O. Box 13185-116, Tehran, Iran
| | - Mojtaba Ranjbar
- Microbial Biotechnology Department, College of Biotechnology, University of Special Modern Technologies, Amol, Iran
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Fiteha YG, Rashed MA, Ali RA, Abd El-Moneim D, Alshanbari FA, Magdy M. Mitogenomic Features and Evolution of the Nile River Dominant Tilapiine Species (Perciformes: Cichlidae). BIOLOGY 2022; 12:biology12010040. [PMID: 36671733 PMCID: PMC9855864 DOI: 10.3390/biology12010040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022]
Abstract
To better understand the diversity and evolution of cichlids, we sequenced, assembled, and annotated the complete mitochondrial genomes of three Nile tilapiine species (Coptodon zillii, Oreochromis niloticus, and Sarotherodon galilaeus) dominating the Nile River waters. Our results showed that the general mitogenomic features were conserved among the Nile tilapiine species. The genome length ranged from 16,436 to 16,631 bp and a total of 37 genes were identified (two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and 1 control region). The ND6 was the only CDS that presented a negative AT skew and a positive GC skew. The most extended repeat sequences were in the D-loop followed by the pseudogenes (trnSGCU). The ND5 showed relatively high substitution rates whereas ATP8 had the lowest substitution rate. The codon usage bias displayed a greater quantity of NNA and NNC at the third position and anti-bias against NNG. The phylogenetic relationship based on the complete mitogenomes and CDS was able to differentiate the three species as previously reported. This study provides new insight into the evolutionary connections between various subfamilies within cichlids while providing new molecular data that can be applied to discriminate between Nile tilapiine species and their populations.
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Affiliation(s)
- Yosur G. Fiteha
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
- Department of Zoology, Faculty of Women for Art, Science and Education, Ain Shams University, Cairo 11566, Egypt
| | - Mohamed A. Rashed
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Ramadan A. Ali
- Department of Zoology, Faculty of Women for Art, Science and Education, Ain Shams University, Cairo 11566, Egypt
| | - Diaa Abd El-Moneim
- Department of Plant Production (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish 45511, Egypt
| | - Fahad A. Alshanbari
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52266, Saudi Arabia
| | - Mahmoud Magdy
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
- Correspondence:
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Borges R, Boussau B, Höhna S, Pereira RJ, Kosiol C. Polymorphism‐aware estimation of species trees and evolutionary forces from genomic sequences with
RevBayes. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Rui Borges
- Institut für Populationsgenetik, Vetmeduni Vienna Wien Austria
| | - Bastien Boussau
- Université de Lyon, Université Claude Bernard Lyon 1 Villeurbanne France
| | - Sebastian Höhna
- GeoBio‐Center, Ludwig‐Maximilians‐Universität München Munich Germany
- Department of Earth and Environmental Sciences, Paleontology & Geobiology Ludwig‐Maximilians‐Universität München Munich Germany
| | - Ricardo J. Pereira
- Division of Evolutionary Biology, Department of Biology II Ludwig‐Maximilians‐Universität München Martinsried Germany
| | - Carolin Kosiol
- Institut für Populationsgenetik, Vetmeduni Vienna Wien Austria
- Centre for Biological Diversity University of St Andrews St Andrews UK
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9
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Sophiarani Y, Chakraborty S. Comparison of compositional constraints: Nuclear genome vs plasmid genome of Pseudomonas syringae pv. tomato DC3000. J Biosci 2022. [DOI: 10.1007/s12038-022-00296-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies. Sci Rep 2022; 12:7028. [PMID: 35487927 PMCID: PMC9054809 DOI: 10.1038/s41598-022-10547-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/21/2022] [Indexed: 11/08/2022] Open
Abstract
Uziflies (Family: Tachinidae) are dipteran endoparasites of sericigenous insects which cause major economic loss in the silk industry globally. Here, we are presenting the first full mitogenome of Blepharipa sp. (Acc: KY644698, 15,080 bp, A + T = 78.41%), a dipteran parasitoid of Muga silkworm (Antheraea assamensis) found in the Indian states of Assam and Meghalaya. This study has confirmed that Blepharipa sp. mitogenome gene content and arrangement is similar to other Tachinidae and Sarcophagidae flies of Oestroidea superfamily, typical of ancestral Diptera. Although, Calliphoridae and Oestridae flies have undergone tRNA translocation and insertion, forming unique intergenic spacers (IGS) and overlapping regions (OL) and a few of them (IGS, OL) have been conserved across Oestroidea flies. The Tachinidae mitogenomes exhibit more AT content and AT biased codons in their protein-coding genes (PCGs) than the Oestroidea counterpart. About 92.07% of all (3722) codons in PCGs of this new species have A/T in their 3rd codon position. The high proportion of AT and repeats in the control region (CR) affects sequence coverage, resulting in a short CR (Blepharipa sp.: 168 bp) and a smaller tachinid mitogenome. Our research unveils those genes with a high AT content had a reduced effective number of codons, leading to high codon usage bias. The neutrality test shows that natural selection has a stronger influence on codon usage bias than directed mutational pressure. This study also reveals that longer PCGs (e.g., nad5, cox1) have a higher codon usage bias than shorter PCGs (e.g., atp8, nad4l). The divergence rates increase nonlinearly as AT content at the 3rd codon position increases and higher rate of synonymous divergence than nonsynonymous divergence causes strong purifying selection. The phylogenetic analysis explains that Blepharipa sp. is well suited in the family of insectivorous tachinid maggots. It's possible that biased codon usage in the Tachinidae family reduces the effective number of codons, and purifying selection retains the core functions in their mitogenome, which could help with efficient metabolism in their endo-parasitic life style and survival strategy.
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Andargie M, Congyi Z. Genome-wide analysis of codon usage in sesame ( Sesamum indicum L.). Heliyon 2022; 8:e08687. [PMID: 35106386 PMCID: PMC8789531 DOI: 10.1016/j.heliyon.2021.e08687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/20/2021] [Accepted: 12/24/2021] [Indexed: 10/28/2022] Open
Abstract
Sesamum indicum is an ancient oil crop grown in tropical and subtropical areas of the world. We have analyzed 23,538 coding sequences (CDS) of S. indicum to understand the factors shaping codon usage in this important oil crop plant. We identified eleven highly preferred codons in S. indicum that have AT-endings. The slope of a neutrality plot was less than one while effective number of codons (ENC) plot showed distribution above and below the standard curve. There is a significant relationship between protein length and relative synonymous codon usage (RSCU) at the primary axis while there is a weak correlation between protein length and Nc values. Correspondence analysis conducted on RSCU values differentiated CDS based on their GC content and their characteristic feature and showed a discrete distribution. Moreover, by determining codon usage, we found out that majority of the lignan biosynthesis related genes showed a weaker codon usage bias. These results provide insights into understanding codon evolution in sesame.
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Affiliation(s)
- Mebeaselassie Andargie
- University of Goettingen, Molecular Phytopathology and Mycotoxin Research, Grisebachstrasse 6, 37077 Goettingen, Germany
| | - Zhu Congyi
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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Zhang P, Xu W, Lu X, Wang L. Analysis of codon usage bias of chloroplast genomes in Gynostemma species. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2727-2737. [PMID: 35035132 PMCID: PMC8720125 DOI: 10.1007/s12298-021-01105-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/13/2021] [Accepted: 11/20/2021] [Indexed: 05/05/2023]
Abstract
UNLABELLED Gynostemma plants are important Chinese medicinal material and economic crops. Codon usage analysis is a good way to understand organism evolution and phylogeny. There is no report yet about analysis of codon usage bias of chloroplast genomes in Gynostemma species. In this study, the chloroplast genomes in nine Gynostemma species were analyzed systematically to explore the factors affecting the formation of codon usage bias. The codon usage indicators were analyzed. Multivariate statistical analysis including analysis of neutrality plot, effective number of codons plot, parity rule 2 plot and correspondence were performed. Composition analysis of codons showed that the frequency of GC in chloroplast genes of all nine Gynostemma species was less than 50%, and the protein-coding sequences of chloroplast genes preferred to end with A/T at the third codon position. The chloroplast genes had an overall weak codon usage bias. A total of 29 high frequency codons and 12 optimal codons were identified. These could provide useful information in optimizing and modifying codons thus improving the gene expression of Gynostemma species. The results of multivariate analysis showed that the codon usage patterns were not only affected by single one factor but multiple factors. Mutation pressure, natural selection and base composition might have an influence on the codon usage patterns while natural selection might be the main determinant. The study could provide a reference for organism evolution and phylogeny of Gynostemma species and help to understand the patterns of codons in chloroplast genomes in other plant species. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01105-z.
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Affiliation(s)
- Peipei Zhang
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198 Jiangsu China
| | - Wenbo Xu
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198 Jiangsu China
| | - Xu Lu
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198 Jiangsu China
| | - Long Wang
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198 Jiangsu China
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Wang P, Mao Y, Su Y, Wang J. Comparative analysis of transcriptomic data shows the effects of multiple evolutionary selection processes on codon usage in Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. BMC Genomics 2021; 22:781. [PMID: 34717552 PMCID: PMC8557549 DOI: 10.1186/s12864-021-08106-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 10/19/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Kuruma shrimp, a major commercial shrimp species in the world, has two cryptic or sibling species, Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. Codon usage analysis would contribute to our understanding of the genetic and evolutionary characteristics of the two Marsupenaeus species. In this study, we analyzed codon usage and related indices using coding sequences (CDSs) from RNA-seq data. RESULTS Using CodonW 1.4.2 software, we performed the codon bias analysis of transcriptomes obtained from hepatopancreas tissues, which indicated weak codon bias. Almost all parameters had similar correlations for both species. The gene expression level (FPKM) was negatively correlated with A/T3s. We determined 12 and 14 optimal codons for M. japonicus and M. pulchricaudatus, respectively, and all optimal codons have a C/G-ending. The two Marsupenaeus species had different usage frequencies of codon pairs, which contributed to further analysis of transcriptional differences between them. Orthologous genes that underwent positive selection (ω > 1) had a higher correlation coefficient than that of experienced purifying selection (ω < 1). Parity Rule 2 (PR2) and effective number of codons (ENc) plot analysis showed that the codon usage patterns of both species were influenced by both mutations and selection. Moreover, the average observed ENc value was lower than the expected value for both species, suggesting that factors other than GC may play roles in these phenomena. The results of multispecies clustering based on codon preference were consistent with traditional classification. CONCLUSIONS This study provides a relatively comprehensive understanding of the correlations among codon usage bias, gene expression, and selection pressures of CDSs for M. japonicus and M. pulchricaudatus. The genetic evolution was driven by mutations and selection pressure. Moreover, the results point out new insights into the specificities and evolutionary characteristics of the two Marsupenaeus species.
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Affiliation(s)
- Panpan Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/ Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
- The Jiangsu Provincial Infrastructure for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yong Mao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, China.
| | - Yongquan Su
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Jun Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, Fujian, China
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Mazumder TH, Alqahtani AM, Alqahtani T, Emran TB, A. Aldahish A, Uddin A. Analysis of Codon Usage of Speech Gene FoxP2 among Animals. BIOLOGY 2021; 10:biology10111078. [PMID: 34827071 PMCID: PMC8614651 DOI: 10.3390/biology10111078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/12/2021] [Accepted: 10/16/2021] [Indexed: 12/03/2022]
Abstract
Simple Summary We evaluated codon usage bias in the FoxP2 gene in fishes, birds, reptiles, and mammals. Fishes use C or G—ending codons, while birds, reptiles, and mammals employ T or A—ending codons. Apart from the nucleotide composition, natural selection and mutation pressure might influence the CUB. The ENC observed/ENC expected ratio demonstrated that mutation pressure influences FoxP2 codon usage patterns. Natural selection may have had a key influence in shaping the CUB, although mutation pressure may have played a minor role. FoxP2 gene codon usage is affected by the base composition under mutation bias. Abstract The protein-coding gene FoxP2 (fork head box protein P2) plays a major role in communication and evolutionary changes. The present study carried out a comprehensive codon usage bias analysis in the FoxP2 gene among a diverse group of animals including fishes, birds, reptiles, and mammals. We observed that in the genome of fishes for the FoxP2 gene, codons ending with C or G were most frequently used, while in birds, reptiles, and mammals, codons ending with T or A were most frequently used. A higher ENC value was observed for the FoxP2 gene indicating a lower CUB. Parity role two-bias plots suggested that apart from mutation pressure, other factors such as natural selection might have influenced the CUB. The frequency distribution of the ENC observed and ENC expected ratio revealed that mutation pressure plays a key role in the patterns of codon usage of FoxP2. Besides, correspondence analysis exposed the composition of the nucleobase under mutation bias affects the codon usage of the FoxP2 gene. However, neutrality plots revealed the major role of natural selection over mutation pressure in the CUB of FoxP2. In addition, the codon usage patterns for FoxP2 among the selected genomes suggested that nature has favored nearly all the synonymous codons for encoding the corresponding amino acid. The uniform usage of 12 synonymous codons for FoxP2 was observed among the species of birds. The amino acid usage frequency for FoxP2 revealed that the amino acids Leucine, Glutamine, and Serine were predominant over other amino acids among all the species of fishes, birds, reptiles, and mammals.
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Affiliation(s)
| | - Ali M. Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia; (A.M.A.); (T.A.); (A.A.A.)
| | - Taha Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia; (A.M.A.); (T.A.); (A.A.A.)
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh;
| | - Afaf A. Aldahish
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia; (A.M.A.); (T.A.); (A.A.A.)
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial College, Hailakandi 788150, Assam, India
- Correspondence:
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Cappannini A, Forcelloni S, Giansanti A. Evolutionary pressures and codon bias in low complexity regions of plasmodia. Genetica 2021; 149:217-237. [PMID: 34254217 DOI: 10.1007/s10709-021-00126-6] [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: 09/04/2020] [Accepted: 06/30/2021] [Indexed: 11/25/2022]
Abstract
The biological meaning of low complexity regions in the proteins of Plasmodium species is a topic of discussion in evolutionary biology. There is a debate between selectionists and neutralists, who either attribute or do not attribute an effect of low-complexity regions on the fitness of these parasites, respectively. In this work, we comparatively study 22 Plasmodium species to understand whether their low complexity regions undergo a neutral or, rather, a selective and species-dependent evolution. The focus is on the connection between the codon repertoire of the genetic coding sequences and the occurrence of low complexity regions in the corresponding proteins. The first part of the work concerns the correlation between the length of plasmodial proteins and their propensity at embedding low complexity regions. Relative synonymous codon usage, entropy, and other indicators reveal that the incidence of low complexity regions and their codon bias is species-specific and subject to selective evolutionary pressure. We also observed that protein length, a relaxed selective pressure, and a broad repertoire of codons in proteins, are strongly correlated with the occurrence of low complexity regions. Overall, it seems plausible that the codon bias of low-complexity regions contributes to functional innovation and codon bias enhancement of proteins on which Plasmodium species rest as successful evolutionary parasites.
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Affiliation(s)
- Andrea Cappannini
- Department of Physics, Sapienza, University of Rome, P.le A. Moro 5, 00185, Roma, Italy.
| | - Sergio Forcelloni
- Max Planck Institute of Biochemistry, 82152, Martinsried, Germany.,Department of Chemistry, Technical University of Munich, 85748, Garching, Germany
| | - Andrea Giansanti
- Department of Physics, Sapienza, University of Rome, P.le A. Moro 5, 00185, Roma, Italy.,Istituto Nazionale di Fisica Nucleare, INFN, Roma1 section. 00185, Roma, Italy
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16
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Huo X, Liu S, Li Y, Wei H, Gao J, Yan Y, Zhang G, Liu M. Analysis of synonymous codon usage of transcriptome database in Rheum palmatum. PeerJ 2021; 9:e10450. [PMID: 33505783 PMCID: PMC7789865 DOI: 10.7717/peerj.10450] [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: 06/26/2020] [Accepted: 11/09/2020] [Indexed: 12/21/2022] Open
Abstract
Background Rheum palmatum is an endangered and important medicinal plant in Asian countries, especially in China. However, there is little knowledge about the codon usage bias for R. palmatum CDSs. In this project, codon usage bias was determined based on the R. palmatum 2,626 predicted CDSs from R. palmatum transcriptome. Methods In this study, all codon usage bias parameters and nucleotide compositions were calculated by Python script, Codon W, DNA Star, CUSP of EMBOSS. Results The average GC and GC3 content are 46.57% and 46.6%, respectively, the results suggested that there exists a little more AT than GC in the R. palmatum genes, and the codon bias of R. palmatum genes preferred to end with A/T. We concluded that the codon bias in R. palmatum was affect by nucleotide composition, mutation pressure, natural selection, gene expression levels, and the mutation pressure is the prominent factor. In addition, we figured out 28 optimal codons and most of them ended with A or U. The project here can offer important information for further studies on enhancing the gene expression using codon optimization in heterogeneous expression system, predicting the genetic and evolutionary mechanisms in R. palmatum.
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Affiliation(s)
- Xiaowei Huo
- College of Pharmaceutical Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Sisi Liu
- Hunan Academy of Forestry, Changsha, China
| | - Yimin Li
- College of Pharmacy and Shaanxi Provincial Key Laboratory for Chinese Medicine Basis & New Drugs Research, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Hao Wei
- College of Pharmacy and Shaanxi Provincial Key Laboratory for Chinese Medicine Basis & New Drugs Research, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Jing Gao
- College of Pharmacy and Shaanxi Provincial Key Laboratory for Chinese Medicine Basis & New Drugs Research, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Yonggang Yan
- College of Pharmacy and Shaanxi Provincial Key Laboratory for Chinese Medicine Basis & New Drugs Research, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Gang Zhang
- College of Pharmacy and Shaanxi Provincial Key Laboratory for Chinese Medicine Basis & New Drugs Research, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Mengmeng Liu
- College of Traditional Chinese Medicine, Hebei University, Baoding, China
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Eshkiki EM, Hajiahmadi Z, Abedi A, Kordrostami M, Jacquard C. In Silico Analyses of Autophagy-Related Genes in Rapeseed ( Brassica napus L.) under Different Abiotic Stresses and in Various Tissues. PLANTS 2020; 9:plants9101393. [PMID: 33092180 PMCID: PMC7594038 DOI: 10.3390/plants9101393] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/21/2022]
Abstract
The autophagy-related genes (ATGs) play important roles in plant growth and response to environmental stresses. Brassica napus (B. napus) is among the most important oilseed crops, but ATGs are largely unknown in this species. Therefore, a genome-wide analysis of the B. napus ATG gene family (BnATGs) was performed. One hundred and twenty-seven ATGs were determined due to the B. napus genome, which belongs to 20 main groups. Segmental duplication occurred more than the tandem duplication in BnATGs. Ka/Ks for the most duplicated pair genes were less than one, which indicated that the negative selection occurred to maintain their function during the evolution of B. napus plants. Based on the results, BnATGs are involved in various developmental processes and respond to biotic and abiotic stresses. One hundred and seven miRNA molecules are involved in the post-transcriptional regulation of 41 BnATGs. In general, 127 simple sequence repeat marker (SSR) loci were also detected in BnATGs. Based on the RNA-seq data, the highest expression in root and silique was related to BnVTI12e, while in shoot and seed, it was BnATG8p. The expression patterns of the most BnATGs were significantly up-regulated or down-regulated responding to dehydration, salinity, abscisic acid, and cold. This research provides information that can detect candidate genes for genetic manipulation in B. napus.
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Affiliation(s)
- Elham Mehri Eshkiki
- Department of Agricultural Biotechnology, Payame Noor University (PNU), Tehran P.O. Box 19395-4697, Iran;
| | - Zahra Hajiahmadi
- Department of Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht P.O. Box 41635-1314, Iran; (Z.H.); (A.A.)
| | - Amin Abedi
- Department of Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht P.O. Box 41635-1314, Iran; (Z.H.); (A.A.)
| | - Mojtaba Kordrostami
- Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj P.O. Box 31485498, Iran;
| | - Cédric Jacquard
- Resistance Induction and Bioprotection of Plants Unit (RIBP)—EA4707, SFR Condorcet FR CNRS 3417, University of Reims Champagne-Ardenne, Moulin de la Housse, CEDEX 2, BP 1039, 51687 Reims, France
- Correspondence: ; Tel.: +33-3-26-91-34-36
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18
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Barbhuiya PA, Uddin A, Chakraborty S. Codon usage pattern and evolutionary forces of mitochondrial ND genes among orders of class Amphibia. J Cell Physiol 2020; 236:2850-2868. [PMID: 32960450 DOI: 10.1002/jcp.30050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 08/07/2020] [Accepted: 08/31/2020] [Indexed: 12/18/2022]
Abstract
In this study, we used a bioinformatics approach to analyze the nucleotide composition and pattern of synonymous codon usage in mitochondrial ND genes in three amphibian groups, that is, orders Anura, Caudata, and Gymnophiona to identify the commonality and the differences of codon usage as no research work was reported yet. The high value of the effective number of codons revealed that the codon usage bias (CUB) was low in mitochondrial ND genes among the orders. Nucleotide composition analysis suggested that for each gene, the compositional features differed among Anura, Caudata, and Gymnophiona and the GC content was lower than AT content. Furthermore, a highly significant difference (p < .05) for GC content was found in each gene among the orders. The heat map showed contrasting patterns of codon usage among different ND genes. The regression of GC12 on GC3 suggested a narrow range of GC3 distribution and some points were located in the diagonal, indicating both mutation pressure and natural selection might influence the CUB. Moreover, the slope of the regression line was less than 0.5 in all ND genes among orders, indicating natural selection might have played the dominant role whereas mutation pressure had played a minor role in shaping CUB of ND genes across orders.
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Affiliation(s)
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Hailakandi, Assam, India
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19
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Khodary SM, Anwar AM. Insights into The Codon Usage Bias of 13 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Isolates from Different Geo-locations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.04.01.019463. [PMID: 34013275 PMCID: PMC8132235 DOI: 10.1101/2020.04.01.019463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of Coronavirus disease 2019 (COVID-19) which is an infectious disease that spread throughout the world and was declared as a pandemic by the World Health Organization (WHO). In this study, we performed a genome-wide analysis on the codon usage bias (CUB) of 13 SARS-CoV-2 isolates from different geo-locations (countries) in an attempt to characterize it, unravel the main force shaping its pattern, and understand its adaptation to Homo sapiens . Overall results revealed that, SARS-CoV-2 codon usage is slightly biased similarly to other RNA viruses. Nucleotide and dinucleotide compositions displayed a bias toward A/U content in all codon positions and CpU-ended codons preference, respectively. Eight common putative preferred codons were identified, and all of them were A/U-ended (U-ended: 7, A-ended: 1). In addition, natural selection was found to be the main force structuring the codon usage pattern of SARS-CoV-2. However, mutation pressure and other factors such as compositional constraints and hydrophobicity had an undeniable contribution. Two adaptation indices were utilized and indicated that SARS-CoV-2 is moderately adapted to Homo sapiens compared to other human viruses. The outcome of this study may help in understanding the underlying factors involved in the evolution of SARS-CoV-2 and may aid in vaccine design strategies.
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20
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Majeed A, Kaur H, Bhardwaj P. Selection constraints determine preference for A/U-ending codons in Taxus contorta. Genome 2020; 63:215-224. [PMID: 31986060 DOI: 10.1139/gen-2019-0165] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Unequal utilization of synonymous codons is a well-known phenomenon among living organisms. This phenomenon plays a major role in the enhancement of the accuracy and efficiency of translation. Gymnosperms are rarely paid attention in this aspect. Understanding the degree of and determining the forces influencing codon usage bias (CUB) in Taxus contorta, an endangered Himalayan gymnosperm, will prove useful in interpreting the evolutionary characteristics of this species. Using RNAseq data, 93 790 assembled transcripts were clustered into 32 701 unigenes. Around 13 061 full-length sequences were utilized for the analysis of CUB. Compositional properties showed that GC-content ranged from 28.76% to 65.22%, with an average value of 44.28%, suggesting an AT-rich genome. The mean effective number of codons (ENC) value revealed that CUB is not strong in T. contorta. The preferred codons tended to be A/U ending, whereas the avoided codons tended to be G/C ending. A P2 index of 0.54 and a Mutation Responsive Index (MRI) value of -0.02 in addition to the results revealed by the neutrality, ENC, and parity plots showed that natural selection is a predominating factor governing CUB. Mutational pressure, gene length, hydropathiciy, aromaticity, and nucleotide composition influence CUB weakly.
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Affiliation(s)
- Aasim Majeed
- Molecular Genetics Laboratory, Department of Botany, Central University of Punjab, City Campus, Mansa Road, Bathinda-151001, India.,Molecular Genetics Laboratory, Department of Botany, Central University of Punjab, City Campus, Mansa Road, Bathinda-151001, India
| | - Harpreet Kaur
- Molecular Genetics Laboratory, Department of Botany, Central University of Punjab, City Campus, Mansa Road, Bathinda-151001, India.,Molecular Genetics Laboratory, Department of Botany, Central University of Punjab, City Campus, Mansa Road, Bathinda-151001, India
| | - Pankaj Bhardwaj
- Molecular Genetics Laboratory, Department of Botany, Central University of Punjab, City Campus, Mansa Road, Bathinda-151001, India.,Molecular Genetics Laboratory, Department of Botany, Central University of Punjab, City Campus, Mansa Road, Bathinda-151001, India
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De Mandal S, Mazumder TH, Panda AK, Kumar NS, Jin F. Analysis of synonymous codon usage patterns of HPRT1 gene across twelve mammalian species. Genomics 2020; 112:304-311. [DOI: 10.1016/j.ygeno.2019.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 02/05/2019] [Accepted: 02/14/2019] [Indexed: 01/01/2023]
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Evolutionary Forces and Codon Bias in Different Flavors of Intrinsic Disorder in the Human Proteome. J Mol Evol 2019; 88:164-178. [DOI: 10.1007/s00239-019-09921-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 11/26/2019] [Indexed: 12/22/2022]
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23
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Victor MP, Acharya D, Begum T, Ghosh TC. The optimization of mRNA expression level by its intrinsic properties—Insights from codon usage pattern and structural stability of mRNA. Genomics 2019; 111:1292-1297. [DOI: 10.1016/j.ygeno.2018.08.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/14/2018] [Accepted: 08/24/2018] [Indexed: 11/17/2022]
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Mazumder TH, Uddin A, Chakraborty S. Insights into the nucleotide composition and codon usage pattern of human tumor suppressor genes. Mol Carcinog 2019; 59:15-23. [PMID: 31583785 DOI: 10.1002/mc.23124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 09/05/2019] [Accepted: 09/21/2019] [Indexed: 01/21/2023]
Abstract
Tumor suppressor genes encode different proteins that inhibit the uncontrolled proliferation of cell growth and tumor development. To acquire clues for predicting gene expression level, it is essential to understand the codon usage bias (CUB) of genes to characterize genome which possesses its own compositional characteristics and unique coding sequences. We used bioinformatic tools to analyze the codon usage patterns of 637 human tumor suppressor genes as no work was reported earlier. The mean effective number of codons of these genes was 48, indicating low CUB. Our results exhibited a significant positive correlation among different nucleotide compositions and the codons ending with C base was most frequently used along with the most over-represented codon CTG and GTG codifying leucine and valine amino acid, respectively, in human tumor suppressor genes. The neutrality plot showed a significant positive correlation (Pearson, r = 0. 646; P < .01) suggesting that mutation on GC bias might affect the CUB. However, the linear regression coefficient of GC12 on GC3 in human tumor suppressor genes suggested that natural selection played a major role while mutation pressure played a minor role in the codon usage patterns of tumor suppressor genes in human. Our study would throw light into the factors that affect CUB and the codon usage patterns in the human tumor suppressor genes.
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Affiliation(s)
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Hailakandi, Assam, India
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25
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Singh P, Venkatesan A, Padmanabhan P, Gulyas B, Dass J FP. Codon usage of human hepatitis C virus clearance genes in relation to its expression. J Cell Biochem 2019; 121:534-544. [PMID: 31310376 DOI: 10.1002/jcb.29290] [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: 12/18/2018] [Accepted: 03/15/2019] [Indexed: 11/08/2022]
Abstract
Hepatitis C virus (HCV) infection is among the leading causes of hepatocellular carcinoma and liver cirrhosis globally, with a high economic burden. The disease progression is well established, but less is known about the spontaneous HCV infection clearance. This study tries to establish the relationship between codon biasness and expression of HCV clearance candidate genes in normal and HCV infected liver tissues. A total of 112 coding sequences comprising 151 679 codons were subjected to the computation of codon indices, namely relative synonymous codon usage, an effective number of codon (Nc), frequency of optimal codon, codon adaptation index, codon bias index, and base compositions. Codon indices report of GC3s, GC12, hydropathicity, and aromaticity implicates both mutational and translational selection in the candidate gene set. This was further correlated with the differentially expressed genes among the selected genes using BioGPS. A significant correlation is observed between the gene expression of normal liver and cancerous liver tissues with codon bias (Nc). Gene expression is also correlated with relative codon bias values, indicating that CCL5, APOA2, CD28, IFITM1, and TNFSF4 genes have higher expression. These results are quite encouraging in selecting the high responsive genes in HCV clearance. However, there could be additional genes which could also orchestrate the clearance role with the above mentioned first line of defensive genes.
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Affiliation(s)
- Pratichi Singh
- Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Arthi Venkatesan
- Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Parasuraman Padmanabhan
- Centre for Neuroimaging Research at NTU (CeNReN), Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Balazs Gulyas
- Centre for Neuroimaging Research at NTU (CeNReN), Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Febin Prabhu Dass J
- Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
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Payne BL, Alvarez-Ponce D. Codon Usage Differences among Genes Expressed in Different Tissues of Drosophila melanogaster. Genome Biol Evol 2019; 11:1054-1065. [PMID: 30859203 PMCID: PMC6456009 DOI: 10.1093/gbe/evz051] [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] [Accepted: 03/08/2019] [Indexed: 12/22/2022] Open
Abstract
Codon usage patterns are affected by both mutational biases and translational selection. The frequency at which each codon is used in the genome is directly linked to the cellular concentrations of their corresponding tRNAs. Transfer RNA abundances—as well as the abundances of other potentially relevant factors, such as RNA-binding proteins—may vary across different tissues, making it possible that genes expressed in different tissues are subject to different translational selection regimes, and thus differ in their patterns of codon usage. These differences, however, are poorly understood, having been studied only in Arabidopsis, rice and human, with controversial results in human. Drosophila melanogaster is a suitable model organism to study tissue-specific codon adaptation given its large effective population size. Here, we compare 2,046 genes, each expressed specifically in one tissue of D. melanogaster. We show that genes expressed in different tissues exhibit significant differences in their patterns of codon usage, and that these differences are only partially due to differences in GC content, expression levels, or protein lengths. Remarkably, these differences are stronger when analyses are restricted to highly expressed genes. Our results strongly suggest that genes expressed in different tissues are subject to different regimes of translational selection.
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Nath D, Deka H, Uddin A, Chakraborty S. Chronic obstructive pulmonary disease: A crosstalk on nucleotide compositional dynamics and codon usage patterns of the genes involved in disease. J Cell Biochem 2019; 120:7649-7656. [PMID: 30390329 DOI: 10.1002/jcb.28039] [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: 09/18/2018] [Accepted: 10/15/2018] [Indexed: 01/24/2023]
Abstract
Chronic obstructive pulmonary disease (COPD), a lung disease, affects a large number of people worldwide, leading to death. Here, we analyzed the compositional features and trends of codon usage of the genes influencing COPD to understand molecular biology, genetics, and evolutionary relationships of these genes as no work was reported yet. Coding sequences of COPD genes were found to be rich in guanine-cytosine (GC) content. A high value (34-60) of the effective number of codons of the genes indicated low codon usage bias (CUB). Correspondence analysis suggested that the COPD genes were distinct in their codon usage patterns. Relative synonymous codon usage values of codons differed between the more preferred codons and the less-preferred ones. Correlation analysis between overall nucleotides and those at third codon position revealed that mutation pressure might influence the CUB of the genes. The high correlation between GC12 and GC3 signified that directional mutation pressure might have operated at all the three codon positions in COPD genes.
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Affiliation(s)
- Durbba Nath
- Department of Biotechnology, Assam University, Silchar, India
| | - Himangshu Deka
- Department of Biotechnology, Assam University, Silchar, India
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, India
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Liu S, Qiao Z, Wang X, Zeng H, Li Y, Cai N, Chen Y. Analysis of codon usage patterns in "Lonicerae Flos" (Lonicera macranthoides Hand. -Mazz.) based on transcriptome data. Gene 2019; 705:127-132. [PMID: 31028866 DOI: 10.1016/j.gene.2019.04.065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/19/2019] [Accepted: 04/23/2019] [Indexed: 12/22/2022]
Abstract
Lonicera macranthoides Hand. -Mazz. is an important medicinal and economical plant in China, however, the codon usage bias (CUB) in L. macranthoides genes is still unknown. In this study, L. macranthoides transcriptome sequencing has been completed, and codon usage patterns in 36,090 reconstructed genes from the L. macranthoides transcriptome were examined. The mean GC content and GC3 value is 44.9% and 43.1%, respectively, which indicates that nucleotide contents of L. macranthoides genome is somewhat AT rich, and its codon bias pattern tends to use A/T-ending codons. According to neutrality plot, ENC plot, PR2-Bias plot and correspondence analysis, we know that both compositional constraint under selection and mutation could affect the CUB in L. macranthoides, and the mutation is the most determinant factor. Meanwhile, gene expression levels can influence its codon usage pattern. Furthermore, we identified 29 optimal codons and most of them ended with A/U. The study will lay a foundation for future research on gene prediction, genetic engineering and molecular evolution in L. macranthoides.
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Affiliation(s)
- Sisi Liu
- Hunan Academy of Forestry, Changsha 410004, China; Hunan University of Traditional Chinese Medicine, Changsha 410208, China
| | | | | | - Huijie Zeng
- Hunan Academy of Forestry, Changsha 410004, China
| | - Yongxin Li
- Hunan Academy of Forestry, Changsha 410004, China
| | - Neng Cai
- Hunan Academy of Forestry, Changsha 410004, China
| | - Yi Chen
- Hunan Academy of Forestry, Changsha 410004, China
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Biswas R, Panja AS, Bandopadhyay R. In Silico Analyses of Burial Codon Bias Among the Species of Dipterocarpaceae Through Molecular and Phylogenetic Data. Evol Bioinform Online 2019; 15:1176934319834888. [PMID: 31223230 PMCID: PMC6563522 DOI: 10.1177/1176934319834888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 02/07/2019] [Indexed: 11/15/2022] Open
Abstract
Introduction: DNA barcode, a molecular marker, is used to distinguish among the closely
related species, and it can be applied across a broad range of taxa to
understand ecology and evolution. MaturaseK gene (matK) and
rubisco bisphosphate carboxylase/oxygenase form I gene
(rbcL) of the chloroplast are highly conserved in a
plant system, which are used as core barcode. This present endeavor entails
the comprehensive examination of the under threat plant species based on
success of discrimination on DNA barcode under selection pressure. Result: The family Dipterocarpaceae comprising of 15 genera is under threat due to
some factors, namely, deforestation, habitat alteration, poor seed, pollen
dispersal, etc. Species of this family was grouped into 6 clusters for
matK and 5 clusters and 2 sub-clusters for
rbcL in the phylogenetic tree by using neighbor-joining
method. Cluster I to cluster VI of matK and cluster I to
cluster V of rbcL genes were analyzed by various codon and
substitution bias tools. Mutational pressure guided the codon bias which was
favored by the avoidance of higher GC content and significant negative
correlation between GC12 and GC3 (in sub-cluster I of cluster I
[0.03 < P], cluster I
[0.00001 < P], and cluster II
[0.01 < P] of rbcL, and cluster IV
[0.013 < P] of matK). After
refining the results, it could be speculated that the lower null expectation
values (R = 0.5 or <0.5) were less divergent from the
evolutionary perspective. Apart from that, the higher null expectation
values (R = >0.85) also showed the same result, which
possibly could be due to the negative impact of very high and low transition
rate than transversion. Conclusion: Through the analysis of inter-generic, inter/intra-specific variation and
phylogenetic data, it was found that both selection and mutation played an
important role in synonymous codon choice in these genes, but they acted
inconsistently on the genes, both matK and
rbcL. In vitro stable proteins of both
matK and rbcL were selected through
natural selection rather than mutational selection. matK
gene had higher individual discrimination and barcode success compared with
rbcL. These discriminatory approaches may describe the
problem related to the extinction of plant species. Hence, it becomes very
imperative to identify and detect the under threat plant species in
advance.
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Affiliation(s)
- Raju Biswas
- UGC-Center of Advanced Study, Department of Botany, The University of Burdwan, Bardhaman, India
| | - Anindya Sundar Panja
- Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, India
| | - Rajib Bandopadhyay
- UGC-Center of Advanced Study, Department of Botany, The University of Burdwan, Bardhaman, India
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Compositional dynamics and codon usage pattern of BRCA1 gene across nine mammalian species. Genomics 2019; 111:167-176. [DOI: 10.1016/j.ygeno.2018.01.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 12/22/2017] [Accepted: 01/22/2018] [Indexed: 11/19/2022]
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Khan MS, Guan DL, Ma LB, Xie JY, Xu SQ. Analysis of synonymous codon usage pattern of genes in unique non-blood-sucking leech Whitmania pigra. J Cell Biochem 2019; 120:9850-9858. [PMID: 30681200 DOI: 10.1002/jcb.28267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 11/19/2018] [Indexed: 12/17/2022]
Abstract
Whitmania pigra is a unique, fluid-sucking ectoparasite and an anticoagulant medical leech. The codon usage bias (CUB) is the nonuniform usage of synonymous codons in which some codons are more preferred than others. Here, we performed a comprehensive analysis of CUB of genes in W. pigra, analyzing 140 780 transcripts, 59 553 unigenes, and 20 304 qualified coding sequences (CDSs) from the transcriptomic data of W. pigra. The effective number of codons values suggested that the CUB was low in these genes. We recognized profoundly favored codons in W. pigra that have a G/C-ending. Parity rule two-bias plots suggested that both mutation pressure and natural selection might have influenced the CUB. However, neutrality plots revealed that natural selection might have played a major role while mutation pressure might have played a minor role in shaping the CUB. We applied principal component analysis to relative synonymous codon usage values for divided CDSs based on GC content and codon-ending bases. Codon usage in W. pigra had a general inclination toward C-ending codons and natural selection rather than mutation pressure is the dominant force in the genetic evolution of W. pigra. To our knowledge, this is the first study to describe a complete codon usage analysis of W. pigra; this will increase the understanding of CUB and evolution in W. pigra. The analysis of codon usage patterns in W. pigra aids in understanding its evolution and genetic architecture.
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Affiliation(s)
- Muhammad Salabat Khan
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, People's Republic of China
| | - De-Long Guan
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, People's Republic of China
| | - Li-Bin Ma
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, People's Republic of China
| | - Juan-Ying Xie
- School of Computer Science, Shaanxi Normal University, Xi'an, Shaanxi, People's Republic of China
| | - Sheng-Quan Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, People's Republic of China
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Maldonado LL, Stegmayer G, Milone DH, Oliveira G, Rosenzvit M, Kamenetzky L. Whole genome analysis of codon usage in Echinococcus. Mol Biochem Parasitol 2018; 225:54-66. [DOI: 10.1016/j.molbiopara.2018.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 07/20/2018] [Accepted: 08/01/2018] [Indexed: 01/15/2023]
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Zhang X, Zhou T, Yang J, Sun J, Ju M, Zhao Y, Zhao G. Comparative Analyses of Chloroplast Genomes of Cucurbitaceae Species: Lights into Selective Pressures and Phylogenetic Relationships. Molecules 2018; 23:E2165. [PMID: 30154353 PMCID: PMC6225112 DOI: 10.3390/molecules23092165] [Citation(s) in RCA: 11] [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: 07/18/2018] [Revised: 08/21/2018] [Accepted: 08/24/2018] [Indexed: 01/20/2023] Open
Abstract
Cucurbitaceae is the fourth most important economic plant family with creeping herbaceous species mainly distributed in tropical and subtropical regions. Here, we described and compared the complete chloroplast genome sequences of ten representative species from Cucurbitaceae. The lengths of the ten complete chloroplast genomes ranged from 155,293 bp (C. sativus) to 158,844 bp (M. charantia), and they shared the most common genomic features. 618 repeats of three categories and 813 microsatellites were found. Sequence divergence analysis showed that the coding and IR regions were highly conserved. Three protein-coding genes (accD, clpP, and matK) were under selection and their coding proteins often have functions in chloroplast protein synthesis, gene transcription, energy transformation, and plant development. An unconventional translation initiation codon of psbL gene was found and provided evidence for RNA editing. Applying BI and ML methods, phylogenetic analysis strongly supported the position of Gomphogyne, Hemsleya, and Gynostemma as the relatively original lineage in Cucurbitaceae. This study suggested that the complete chloroplast genome sequences were useful for phylogenetic studies. It would also determine potential molecular markers and candidate DNA barcodes for coming studies and enrich the valuable complete chloroplast genome resources of Cucurbitaceae.
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Affiliation(s)
- Xiao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China.
| | - Jia Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Jingjing Sun
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Miaomiao Ju
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Yuemei Zhao
- College of Biopharmaceutical and Food Engineering, Shangluo University, Shangluo 726000, China.
| | - Guifang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China.
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Guan DL, Ma LB, Khan MS, Zhang XX, Xu SQ, Xie JY. Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints. BMC Genomics 2018; 19:542. [PMID: 30016953 PMCID: PMC6050667 DOI: 10.1186/s12864-018-4937-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 07/10/2018] [Indexed: 02/07/2023] Open
Abstract
Background Hirudinaria manillensis is an ephemeral, blood-sucking ectoparasite, possessing anticoagulant capacities with potential medical applications. Analysis of codon usage patterns would contribute to our understanding of the evolutionary mechanisms and genetic architecture of H. manillensis, which in turn would provide insight into the characteristics of other leeches. We analysed codon usage and related indices using 18,000 coding sequences (CDSs) retrieved from H. manillensis RNA-Seq data. Results We identified four highly preferred codons in H. manillensis that have G/C-endings. Points generated in an effective number of codons (ENC) plot distributed below the standard curve and the slope of a neutrality plot was less than 1. Highly expressed CDSs had lower ENC content and higher GC content than weakly expressed CDSs. Principal component analysis conducted on relative synonymous codon usage (RSCU) values divided CDSs according to GC content and divided codons according to ending bases. Moreover, by determining codon usage, we found that the majority of blood-diet related genes have undergone less adaptive evolution in H. manillensis, except for those with homologous sequences in the host species. Conclusions Codon usage in H. manillensis had an overall preference toward C-endings and indicated that codon usage patterns are mediated by differential expression, GC content, and biological function. Although mutation pressure effects were also notable, the majority of genetic evolution in H. manillensis was driven by natural selection. Electronic supplementary material The online version of this article (10.1186/s12864-018-4937-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- De-Long Guan
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China
| | - Li-Bin Ma
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China
| | - Muhammad Salabat Khan
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China
| | - Xiu-Xiu Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China
| | - Sheng-Quan Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China.
| | - Juan-Ying Xie
- School of Computer Science, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China.
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Yang Y, Zhu J, Feng L, Zhou T, Bai G, Yang J, Zhao G. Plastid Genome Comparative and Phylogenetic Analyses of the Key Genera in Fagaceae: Highlighting the Effect of Codon Composition Bias in Phylogenetic Inference. FRONTIERS IN PLANT SCIENCE 2018; 9:82. [PMID: 29449857 PMCID: PMC5800003 DOI: 10.3389/fpls.2018.00082] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/15/2018] [Indexed: 05/10/2023]
Abstract
Fagaceae is one of the largest and economically important taxa within Fagales. Considering the incongruence among inferences from plastid and nuclear genes in the previous Fagaceae phylogeny studies, we assess the performance of plastid phylogenomics in this complex family. We sequenced and assembled four complete plastid genomes (Fagus engleriana, Quercus spinosa, Quercus aquifolioides, and Quercus glauca) using reference-guided assembly approach. All of the other 12 published plastid genomes in Fagaceae were retrieved for genomic analyses (including repeats, sequence divergence and codon usage) and phylogenetic inference. The genomic analyses reveal that plastid genomes in Fagaceae are conserved. Comparing the phylogenetic relationships of the key genera in Fagaceae inferred from different codon positions and gene function datasets, we found that the first two codon sites dataset recovered nearly all relationships and received high support. Thus, the result suggested that codon composition bias had great influence on Fagaceae phylogenetic inference. Our study not only provides basic understanding of Fagaceae plastid genomes, but also illuminates the effectiveness of plastid phylogenomics in resolving relationships of this intractable family.
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Affiliation(s)
- Yanci Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China
| | - Juan Zhu
- Middle School of Xi'an Electronic Science and Technology, Xi'an, China
| | - Li Feng
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Guoqing Bai
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Xi'an, China
| | - Jia Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China
| | - Guifang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China
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Paul P, Malakar AK, Chakraborty S. Compositional bias coupled with selection and mutation pressure drives codon usage in Brassica campestris genes. Food Sci Biotechnol 2017; 27:725-733. [PMID: 30263798 DOI: 10.1007/s10068-017-0285-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 11/28/2017] [Accepted: 12/03/2017] [Indexed: 11/25/2022] Open
Abstract
The plant Brassica campestris includes the vegetables turnip and Chinese cabbage, important plants of economic importance. Here, we have analysed the codon usage bias of B. campestris for 116 protein coding genes. Neutrality analysis showed that B. campestris had a wide range of GC3s, and a significant correlation was observed between GC12 and GC3. Nc versus GC3s plot showed a few genes on or proximate to the expected curve, but the majority of points were found to be scattered distantly from the expected curve. Correspondence analysis on codon usage revealed that the position preference of codons on multidimensional space totally depends on the presence of A and T at synonymous third codon position. These results altogether suggest that composition bias along with selection (major) and mutation pressure (minor) affects the codon usage pattern of the protein coding genes in Brassica campestris.
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Affiliation(s)
- Prosenjit Paul
- Department of Biotechnology, Assam University, Silchar, Assam 788011 India
| | - Arup Kumar Malakar
- Department of Biotechnology, Assam University, Silchar, Assam 788011 India
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Codon usage and amino acid usage influence genes expression level. Genetica 2017; 146:53-63. [DOI: 10.1007/s10709-017-9996-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 10/09/2017] [Indexed: 11/30/2022]
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Analysis of codon usage patterns in Ginkgo biloba reveals codon usage tendency from A/U-ending to G/C-ending. Sci Rep 2016; 6:35927. [PMID: 27808241 PMCID: PMC5093902 DOI: 10.1038/srep35927] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 10/07/2016] [Indexed: 11/08/2022] Open
Abstract
As one of the most ancient tree species, the codon usage pattern analysis of Ginkgo biloba is a useful way to understand its evolutionary and genetic mechanisms. Several studies have been conducted on angiosperms, but seldom on gymnosperms. Based on RNA-Seq data of the G. biloba transcriptome, amount to 17,579 unigenes longer than 300 bp were selected and analyzed from 68,547 candidates. The codon usage pattern tended towards more frequently use of A/U-ending codons, which showed an obvious gradient progressing from gymnosperms to dicots to monocots. Meanwhile, analysis of high/low-expression unigenes revealed that high-expression unigenes tended to use G/C-ending codons together with more codon usage bias. Variation of unigenes with different functions suggested that unigenes involving in environment adaptation use G/C-ending codons more frequently with more usage bias, and these results were consistent with the conclusion that the formation of G. biloba codon usage bias was dominated by natural selection.
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Genome-Wide Analysis of Codon Usage Bias in Epichloë festucae. Int J Mol Sci 2016; 17:ijms17071138. [PMID: 27428961 PMCID: PMC4964511 DOI: 10.3390/ijms17071138] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/24/2016] [Accepted: 07/08/2016] [Indexed: 11/17/2022] Open
Abstract
Analysis of codon usage data has both practical and theoretical applications in understanding the basics of molecular biology. Differences in codon usage patterns among genes reflect variations in local base compositional biases and the intensity of natural selection. Recently, there have been several reports related to codon usage in fungi, but little is known about codon usage bias in Epichloë endophytes. The present study aimed to assess codon usage patterns and biases in 4870 sequences from Epichloë festucae, which may be helpful in revealing the constraint factors such as mutation or selection pressure and improving the bioreactor on the cloning, expression, and characterization of some special genes. The GC content with 56.41% is higher than the AT content (43.59%) in E. festucae. The results of neutrality and effective number of codons plot analyses showed that both mutational bias and natural selection play roles in shaping codon usage in this species. We found that gene length is strongly correlated with codon usage and may contribute to the codon usage patterns observed in genes. Nucleotide composition and gene expression levels also shape codon usage bias in E. festucae. E. festucae exhibits codon usage bias based on the relative synonymous codon usage (RSCU) values of 61 sense codons, with 25 codons showing an RSCU larger than 1. In addition, we identified 27 optimal codons that end in a G or C.
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Sundararajan A, Dukowic-Schulze S, Kwicklis M, Engstrom K, Garcia N, Oviedo OJ, Ramaraj T, Gonzales MD, He Y, Wang M, Sun Q, Pillardy J, Kianian SF, Pawlowski WP, Chen C, Mudge J. Gene Evolutionary Trajectories and GC Patterns Driven by Recombination in Zea mays. FRONTIERS IN PLANT SCIENCE 2016; 7:1433. [PMID: 27713757 PMCID: PMC5031598 DOI: 10.3389/fpls.2016.01433] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/08/2016] [Indexed: 05/20/2023]
Abstract
Recombination occurring during meiosis is critical for creating genetic variation and plays an essential role in plant evolution. In addition to creating novel gene combinations, recombination can affect genome structure through altering GC patterns. In maize (Zea mays) and other grasses, another intriguing GC pattern exists. Maize genes show a bimodal GC content distribution that has been attributed to nucleotide bias in the third, or wobble, position of the codon. Recombination may be an underlying driving force given that recombination sites are often associated with high GC content. Here we explore the relationship between recombination and genomic GC patterns by comparing GC gene content at each of the three codon positions (GC1, GC2, and GC3, collectively termed GCx) to instances of a variable GC-rich motif that underlies double strand break (DSB) hotspots and to meiocyte-specific gene expression. Surprisingly, GCx bimodality in maize cannot be fully explained by the codon wobble hypothesis. High GCx genes show a strong overlap with the DSB hotspot motif, possibly providing a mechanism for the high evolutionary rates seen in these genes. On the other hand, genes that are turned on in meiosis (early prophase I) are biased against both high GCx genes and genes with the DSB hotspot motif, possibly allowing important meiotic genes to avoid DSBs. Our data suggests a strong link between the GC-rich motif underlying DSB hotspots and high GCx genes.
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Affiliation(s)
| | | | | | | | - Nathan Garcia
- National Center for Genome Resources, Santa FeNM, USA
| | | | | | | | - Yan He
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, IthacaNY, USA
| | - Minghui Wang
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, IthacaNY, USA
- Biotechnology Resource Center Bioinformatics Facility, Cornell University, IthacaNY, USA
| | - Qi Sun
- Biotechnology Resource Center Bioinformatics Facility, Cornell University, IthacaNY, USA
| | - Jaroslaw Pillardy
- Biotechnology Resource Center Bioinformatics Facility, Cornell University, IthacaNY, USA
| | - Shahryar F. Kianian
- Cereal Disease Laboratory, United States Department of Agriculture – Agricultural Research Service, St. PaulMN, USA
| | - Wojciech P. Pawlowski
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, IthacaNY, USA
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, St. PaulMN, USA
| | - Joann Mudge
- National Center for Genome Resources, Santa FeNM, USA
- *Correspondence: Joann Mudge,
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Gerdol M, De Moro G, Venier P, Pallavicini A. Analysis of synonymous codon usage patterns in sixty-four different bivalve species. PeerJ 2015; 3:e1520. [PMID: 26713259 PMCID: PMC4690358 DOI: 10.7717/peerj.1520] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 11/28/2015] [Indexed: 12/21/2022] Open
Abstract
Synonymous codon usage bias (CUB) is a defined as the non-random usage of codons encoding the same amino acid across different genomes. This phenomenon is common to all organisms and the real weight of the many factors involved in its shaping still remains to be fully determined. So far, relatively little attention has been put in the analysis of CUB in bivalve mollusks due to the limited genomic data available. Taking advantage of the massive sequence data generated from next generation sequencing projects, we explored codon preferences in 64 different species pertaining to the six major evolutionary lineages in Bivalvia. We detected remarkable differences across species, which are only partially dependent on phylogeny. While the intensity of CUB is mild in most organisms, a heterogeneous group of species (including Arcida and Mytilida, among the others) display higher bias and a strong preference for AT-ending codons. We show that the relative strength and direction of mutational bias, selection for translational efficiency and for translational accuracy contribute to the establishment of synonymous codon usage in bivalves. Although many aspects underlying bivalve CUB still remain obscure, we provide for the first time an overview of this phenomenon in this large, commercially and environmentally important, class of marine invertebrates.
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Affiliation(s)
- Marco Gerdol
- Department of Life Sciences, University of Trieste , Trieste , Italy
| | - Gianluca De Moro
- Department of Life Sciences, University of Trieste , Trieste , Italy
| | - Paola Venier
- Department of Biology, University of Padova , Padova , Italy
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Abstract
Amino acids typically are encoded by multiple synonymous codons that are not used with the same frequency. Codon usage bias has drawn considerable attention, and several explanations have been offered, including variation in GC-content between species. Focusing on a simple parameter—combined GC proportion of all the synonymous codons for a particular amino acid, termed GCsyn—we try to deepen our understanding of the relationship between GC-content and amino acid/codon usage in more details. We analyzed 65 widely distributed representative species and found a close association between GCsyn, GC-content, and amino acids usage. The overall usages of the four amino acids with the greatest GCsyn and the five amino acids with the lowest GCsyn both vary with the regional GC-content, whereas the usage of the remaining 11 amino acids with intermediate GCsyn is less variable. More interesting, we discovered that codon usage frequencies are nearly constant in regions with similar GC-content. We further quantified the effects of regional GC-content variation (low to high) on amino acid usage and found that GC-content determines the usage variation of amino acids, especially those with extremely high GCsyn, which accounts for 76.7% of the changed GC-content for those regions. Our results suggest that GCsyn correlates with GC-content and has impact on codon/amino acid usage. These findings suggest a novel approach to understanding the role of codon and amino acid usage in shaping genomic architecture and evolutionary patterns of organisms.
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Xiang H, Zhang R, Butler RR, Liu T, Zhang L, Pombert JF, Zhou Z. Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes. PLoS One 2015; 10:e0129223. [PMID: 26057384 PMCID: PMC4461291 DOI: 10.1371/journal.pone.0129223] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/06/2015] [Indexed: 12/29/2022] Open
Abstract
The sub-3 Mbp genomes from microsporidian species of the Encephalitozoon genus are the smallest known among eukaryotes and paragons of genomic reduction and compaction in parasites. However, their diminutive stature is not characteristic of all Microsporidia, whose genome sizes vary by an order of magnitude. This large variability suggests that different evolutionary forces are applied on the group as a whole. In this study, we have compared the codon usage bias (CUB) between eight taxonomically distinct microsporidian genomes: Encephalitozoon intestinalis, Encephalitozoon cuniculi, Spraguea lophii, Trachipleistophora hominis, Enterocytozoon bieneusi, Nematocida parisii, Nosema bombycis and Nosema ceranae. While the CUB was found to be weak in all eight Microsporidia, nearly all (98%) of the optimal codons in S. lophii, T. hominis, E. bieneusi, N. parisii, N. bombycis and N. ceranae are fond of A/U in third position whereas most (64.6%) optimal codons in the Encephalitozoon species E. intestinalis and E. cuniculi are biased towards G/C. Although nucleotide composition biases are likely the main factor driving the CUB in Microsporidia according to correlation analyses, directed mutational pressure also likely affects the CUB as suggested by ENc-plots, correspondence and neutrality analyses. Overall, the Encephalitozoon genomes were found to be markedly different from the other microsporidians and, despite being the first sequenced representatives of this lineage, are uncharacteristic of the group as a whole. The disparities observed cannot be attributed solely to differences in host specificity and we hypothesize that other forces are at play in the lineage leading to Encephalitozoon species.
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Affiliation(s)
- Heng Xiang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
- * E-mail: (HX); (ZYZ)
| | - Ruizhi Zhang
- Biotechnology Research Center, Southwest University, Chongqing 400715, China
| | - Robert R. Butler
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, Illinois, United States of America
| | - Tie Liu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
| | - Li Zhang
- Department of Math and Information, China West Normal University, Nanchong, Sichuan 637000, China
| | - Jean-François Pombert
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, Illinois, United States of America
| | - Zeyang Zhou
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
- * E-mail: (HX); (ZYZ)
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Yang X, Luo X, Cai X. Analysis of codon usage pattern in Taenia saginata based on a transcriptome dataset. Parasit Vectors 2014; 7:527. [PMID: 25440955 PMCID: PMC4268816 DOI: 10.1186/s13071-014-0527-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 11/06/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Codon usage bias is an important evolutionary feature in a genome and has been widely documented in many genomes. Analysis of codon usage bias has significance for mRNA translation, design of transgenes, new gene discovery, and studies of molecular biology and evolution, etc. However, the information about synonymous codon usage pattern of T. saginata genome remains unclear. T. saginata is a food-borne zoonotic cestode which infects approximataely 50 million humans worldwide, and causes significant health problems to the host and considerable socio-economic losses as a consequence. In this study, synonymous codon usage in T. saginata were examined. METHODS Total RNA was isolated from T. saginata cysticerci and 91,487 unigenes were generated using Illumina sequencing technology. After filtering, the final sequence collection containing 11,399 CDSs was used for our analysis. RESULTS Neutrality analysis showed that the T. saginata had a wide GC3 distribution and a significant correlation was observed between GC12 and GC3. NC-plot showed most of genes on or close to the expected curve, but only a few points with low-ENC values were below it, suggesting that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally. We also identified twenty-three optimal codons in the T. saginata genome, all of which were ended with a G or C residue. These results suggest that mutational and selection forces are probably driving factors of codon usage bias in T. saginata genome. Meanwhile, other factors such as protein length, gene expression, GC content of genes, the hydropathicity of each protein also influence codon usage. CONCLUSIONS Here, we systematically analyzed the codon usage pattern and identified factors shaping in codon usage bias in T. saginata. Currently, no complete nuclear genome is available for codon usage analysis at the genome level in T. saginata. This is the first report to investigate codon biology in T. sagninata. Such information does not only bring about a new perspective for understanding the mechanisms of biased usage of synonymous codons but also provide useful clues for molecular genetic engineering and evolutionary studies.
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Affiliation(s)
- Xing Yang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, PR China. .,College of Veterinary Medicine, Jilin University, Changchun, 130000, PR China.
| | - Xuenong Luo
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, PR China.
| | - Xuepeng Cai
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, PR China. .,College of Veterinary Medicine, Jilin University, Changchun, 130000, PR China.
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Babbitt GA, Alawad MA, Schulze KV, Hudson AO. Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid. Nucleic Acids Res 2014; 42:10915-26. [PMID: 25200075 PMCID: PMC4176184 DOI: 10.1093/nar/gku811] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
While mRNA stability has been demonstrated to control rates of translation, generating both global and local synonymous codon biases in many unicellular organisms, this explanation cannot adequately explain why codon bias strongly tracks neighboring intergene GC content; suggesting that structural dynamics of DNA might also influence codon choice. Because minor groove width is highly governed by 3-base periodicity in GC, the existence of triplet-based codons might imply a functional role for the optimization of local DNA molecular dynamics via GC content at synonymous sites (≈GC3). We confirm a strong association between GC3-related intrinsic DNA flexibility and codon bias across 24 different prokaryotic multiple whole-genome alignments. We develop a novel test of natural selection targeting synonymous sites and demonstrate that GC3-related DNA backbone dynamics have been subject to moderate selective pressure, perhaps contributing to our observation that many genes possess extreme DNA backbone dynamics for their given protein space. This dual function of codons may impose universal functional constraints affecting the evolution of synonymous and non-synonymous sites. We propose that synonymous sites may have evolved as an 'accessory' during an early expansion of a primordial genetic code, allowing for multiplexed protein coding and structural dynamic information within the same molecular context.
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Affiliation(s)
- Gregory A Babbitt
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA 14623
| | - Mohammed A Alawad
- B. Thomas Golisano College of Computing and Information Sciences, Rochester Institute of Technology, Rochester NY, USA 14623
| | - Katharina V Schulze
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX, USA 77030
| | - André O Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA 14623
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Yuan J, Yang M, Ren J, Fu B, Jiang F, Zhang X. Analysis of genomic characters reveals that four distinct gene clusters are correlated with different functions in Burkholderia cenocepacia AU 1054. Appl Microbiol Biotechnol 2013; 98:361-72. [PMID: 24305740 DOI: 10.1007/s00253-013-5415-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 11/11/2013] [Accepted: 11/11/2013] [Indexed: 11/30/2022]
Abstract
Possessing three circular chromosomes is a distinct genomic characteristic of Burkholderia cenocepacia AU 1054, a clinically important pathogen in cystic fibrosis. In this study, base composition, codon usage and functional role category were analyzed in the B. cenocepacia AU 1054 genome. Although no bias in the base and codon usage was detected between any two chromosomes, function differences did exist in the genes of each chromosome. Similar base composition and differential functional role categories indicated that genes on these three chromosomes were relatively stable and that a proper division of labor was established. Based on variations in the base or codon usage, four small gene clusters were observed in all of the genes. Multivariate analysis revealed that protein hydrophobicity played a predominant role in shaping base usage bias, while horizontal gene transfer and the gene expression level were the two most important factors that affected the codon usage bias. Interestingly, we also found that these gene clusters were correlated with different biological functions: (i) 45 pyrimidine-leading-codon preferred genes were predominantly involved in regulatory function; (ii) most drug resistance-related genes involved in 826 genes that coding for hydrophobic proteins; (iii) most of the 111 horizontal transfer genes were responsible for genomic plasticity; and (iv) 73 highly expressed genes (predicted by their codon adaptation index values) showed environmental adaptation to cystic fibrosis. Our results showed that genes with base or codon usage bias were affected by mutational pressure and natural selection, and their functions could contribute to drug assistance and transmissible activity in B. cenocepacia.
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Affiliation(s)
- Jianbo Yuan
- Institute of Oceanology, Chinese Academy of Sciences, No. 7, Nanhai Road, Qingdao, 266071, China
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Rashmi M, Swati D. Comparative Genomics of Trypanosomatid Pathogens using Codon Usage Bias. Bioinformation 2013; 9:912-8. [PMID: 24307769 PMCID: PMC3842577 DOI: 10.6026/97320630009912] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 10/19/2013] [Indexed: 11/25/2022] Open
Abstract
UNLABELLED It is well known that an amino acid can be encoded by more than one codon, called synonymous codons. The preferential use of one particular codon for coding an amino acid is referred to as codon usage bias (CUB). A quantitative analytical method, CUB and a related tool, Codon Adaptative Index have been applied to comparatively study whole genomes of a few pathogenic Trypanosomatid species. This quantitative attempt is of direct help in the comparison of qualitative features like mutational and translational selection. Pathogens of the Leishmania and Trypanosoma genus cause debilitating disease and suffering in human beings and animals. Of these, whole genome sequences are available for only five species. The complete coding sequences (CDS), highly expressed, essential and low expressed genes have all been studied for their CUB signature. The codon usage bias of essential genes and highly expressed genes show distribution similar to codon usage bias of all CDSs in Trypanosomatids. Translational selection is the dominant force selecting the preferred codon, and selection due to mutation is negligible. In contrast to an earlier study done on these pathogens, it is found in this work that CUB and CAI may be used to distinguish the Trypanosomatid genomes at the sub-genus level. Further, CUB may effectively be used as a signature of the species differentiation by using Principal Component Analysis (PCA). ABBREVIATIONS CUB - Codon Usage Bias, CAI - Codon Adaptative Index, CDS - Coding sequences, t-RNA - Transfer RNA, PCA - Principal Component Analysis.
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Affiliation(s)
- Mayank Rashmi
- Department of Bioinformatics, MMV, Banaras Hindu University, Varanasi-221005, India
| | - D Swati
- Department of Bioinformatics, MMV, Banaras Hindu University, Varanasi-221005, India
- Department of Physics, MMV, Banaras Hindu University, Varanasi 221005, India
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Pal A, Mukhopadhyay S, Bothra AK. Statistical analysis of pentose phosphate pathway genes from eubacteria and eukarya reveals translational selection as a major force in shaping codon usage pattern. Bioinformation 2013; 9:349-56. [PMID: 23750079 PMCID: PMC3669787 DOI: 10.6026/97320630009349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 03/27/2013] [Indexed: 11/23/2022] Open
Abstract
Comparative analysis of metabolic pathways among widely diverse species provides an excellent opportunity to extract information about the functional relation of organisms and pentose phosphate pathway exemplifies one such pathway. A comparative codon usage analysis of the pentose phosphate pathway genes of a diverse group of organisms representing different niches and the related factors affecting codon usage with special reference to the major forces influencing codon usage patterns was carried out. It was observed that organism specific codon usage bias percolates into vital metabolic pathway genes irrespective of their near universality. A clear distinction in the codon usage pattern of gram positive and gram negative bacteria, which is a major classification criterion for bacteria, in terms of pentose phosphate pathway was an important observation of this study. The codon utilization scheme in all the organisms indicates the presence of translation selection as a major force in shaping codon usage. Another key observation was the segregation of the H. sapiens genes as a separate cluster by correspondence analysis, which is primarily attributed to the different codon usage pattern in this genus along with its longer gene lengths. We have also analyzed the amino acid distribution comparison of transketolase protein primary structures among all the organisms and found that there is a certain degree of predictability in the composition profile except in A. fumigatus and H. sapiens, where few exceptions are prominent. In A. fumigatus, a human pathogen responsible for invasive aspergillosis, a significantly different codon usage pattern, which finally translated into its amino acid composition model portraying a unique profile in a key pentose phosphate pathway enzyme transketolase was observed.
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Affiliation(s)
- Ayon Pal
- Department of Botany, Raiganj College (University College) P.O.- Raiganj, Dist.- Uttar Dinajpur, PIN-733134, West Bengal, India
| | - Subhasis Mukhopadhyay
- Bioinformatics Centre, Department of Biophysics, Molecular Biology and Bioinformatics University of Calcutta, 92 APC Road, Kolkata-700009, West Bengal, India
| | - Asim Kumar Bothra
- Cheminformatics Bioinformatics Lab, Department of Chemistry, Raiganj College (University College) P.O.- Raiganj, Dist.- Uttar Dinajpur, PIN-733134, West Bengal, India
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Piovesan A, Vitale L, Pelleri MC, Strippoli P. Universal tight correlation of codon bias and pool of RNA codons (codonome): The genome is optimized to allow any distribution of gene expression values in the transcriptome from bacteria to humans. Genomics 2013; 101:282-9. [PMID: 23466472 DOI: 10.1016/j.ygeno.2013.02.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 02/18/2013] [Accepted: 02/21/2013] [Indexed: 10/27/2022]
Abstract
Codon bias is the phenomenon in which distinct synonymous codons are used with different frequencies. We define here the "codonome value" as the total number of codons present across all the expressed mRNAs in a given biological condition. We have developed the "CODONOME" software, which calculates the codon bias and, following integration with a gene expression profile, estimates the actual frequency of each codon at the transcriptome level (codonome bias) of a given tissue. Systematic analysis across different human tissues and multiple species shows a surprisingly tight correlation between the codon bias and the codonome bias. An aneuploidy and cancer condition such as that of Down Syndrome-related acute megakaryoblastic leukemia (DS-AMKL), does not appear to alter this relationship. The law of correlation between codon bias and codonome emerges as a property of the distribution and range of the number, sequence and expression level of the genes in a genome.
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Affiliation(s)
- Allison Piovesan
- Department of Experimental, Diagnostic and Specialty Medicine, Activity of Histology, Embryology and Applied Biology, University of Bologna, via Belmeloro 8, 40126 Bologna (BO), Italy.
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Ahmad T, Sablok G, Tatarinova TV, Xu Q, Deng XX, Guo WW. Evaluation of codon biology in citrus and Poncirus trifoliata based on genomic features and frame corrected expressed sequence tags. DNA Res 2013; 20:135-50. [PMID: 23315666 PMCID: PMC3628444 DOI: 10.1093/dnares/dss039] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Citrus, as one of the globally important fruit trees, has been an object of interest for understanding genetics and evolutionary process in fruit crops. Meta-analyses of 19 Citrus species, including 4 globally and economically important Citrus sinensis, Citrus clementina, Citrus reticulata, and 1 Citrus relative Poncirus trifoliata, were performed. We observed that codons ending with A- or T- at the wobble position were preferred in contrast to C- or G- ending codons, indicating a close association with AT richness of Citrus species and P. trifoliata. The present study postulates a large repertoire of a set of optimal codons for the Citrus genus and P. trifoliata and demonstrates that GCT and GGT are evolutionary conserved optimal codons. Our observation suggested that mutational bias is the dominating force in shaping the codon usage bias (CUB) in Citrus and P. trifoliata. Correspondence analysis (COA) revealed that the principal axis [axis 1; COA/relative synonymous codon usage (RSCU)] contributes only a minor portion (∼10.96%) of the recorded variance. In all analysed species, except P. trifoliata, Gravy and aromaticity played minor roles in resolving CUB. Compositional constraints were found to be strongly associated with the amino acid signatures in Citrus species and P. trifoliata. Our present analysis postulates compositional constraints in Citrus species and P. trifoliata and plausible role of the stress with GC3 and coevolution pattern of amino acid.
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Affiliation(s)
- Touqeer Ahmad
- Key Laboratory of Horticultural Plant Biology MOE, Huazhong Agricultural University, Wuhan 430070, China
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