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Aktürk Dizman Y. Analysis of codon usage bias of exonuclease genes in invertebrate iridescent viruses. Virology 2024; 593:110030. [PMID: 38402641 DOI: 10.1016/j.virol.2024.110030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/04/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024]
Abstract
Invertebrate iridescent viruses (IIVs) are double-stranded DNA viruses that belong to the Iridoviridae family. IIVs result diseases that vary in severity from subclinical to lethal in invertebrate hosts. Codon usage bias (CUB) analysis is a versatile method for comprehending the genetic and evolutionary aspects of species. In this study, we analyzed the CUB in 10 invertebrate iridescent viruses exonuclease genes by calculating and comparing the nucleotide contents, effective number of codons (ENC), codon adaptation index (CAI), relative synonymous codon usage (RSCU), and others. The results revealed that IIVs exonuclease genes are rich in A/T. The ENC analysis displayed a low codon usage bias in IIVs exonuclease genes. ENC-plot, neutrality plot, and parity rule 2 plot demonstrated that besides mutational pressure, other factors like natural selection, dinucleotide content, and aromaticity also contributed to CUB. The findings could enhance our understanding of the evolution of IIVs exonuclease genes.
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Affiliation(s)
- Yeşim Aktürk Dizman
- Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdogan University, 53100, Rize, Türkiye.
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2
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Xiao Y, Huang H, Chen Y, Zheng S, Chen J, Zou Z, Mehmood N, Ullah I, Liao X, Wang J. Insight on genetic features prevalent in five Ipomoea species using comparative codon pattern analysis reveals differences in major codons and reduced GC content at the 5’ end of CDS. Biochem Biophys Res Commun 2023; 657:92-99. [PMID: 37001285 DOI: 10.1016/j.bbrc.2023.03.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/10/2023] [Accepted: 03/10/2023] [Indexed: 03/30/2023]
Abstract
Ipomoea plants possess important commercial, medicinal, and ornamental value. Molecular and morphological studies have confirmed that most species of this genus exhibit similar phenotypes but complex phylogenetic relationships. To date, limited information is available on these evolutionary relationships. In this study, systematic analysis of diverse species from Ipomoea was used to elucidate the relationships in this genus. To this end, we employed the concept of codon usage bias (CUB) to analyze the codon usage bias of five Ipomoea species such as effective number of codons (ENC) and GC content at the third synonym codon position (GC3s). Three types of plots including ENC-GC3s, parity rule 2 (PR2) and neutrality plots were employed to discover the factors determining CUB, and the frequency of hydrogen bonds and nucleotide were calculated to dissect changes in GC content at the 5'-end of the coding sequence. Our results showed little distinctness in CUB among the five species, with a reduction of hydrogen bonds content at the 5'-end (with similar changes in cytosines). In addition, optimal codons of Ipomoea aquatica ended with G or C, different from those of the other four species, which ended in A or T. These results may be useful for exploring the evolutionary relationships among this group, and for understanding the reasons for the variation among Ipomoea species.
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Bansal S, Mallikarjuna MG, Balamurugan A, Nayaka SC, Prakash G. Composition and Codon Usage Pattern Results in Divergence of the Zinc Binuclear Cluster ( Zn(II)2Cys6) Sequences among Ascomycetes Plant Pathogenic Fungi. J Fungi (Basel) 2022; 8:1134. [PMID: 36354901 PMCID: PMC9694491 DOI: 10.3390/jof8111134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/22/2022] [Accepted: 10/23/2022] [Indexed: 07/29/2023] Open
Abstract
Zinc binuclear cluster proteins (ZBC; Zn(II)2Cys6) are unique to the fungi kingdom and associated with a series of functions, viz., the utilization of macromolecules, stress tolerance, and most importantly, host-pathogen interactions by imparting virulence to the pathogen. Codon usage bias (CUB) is the phenomenon of using synonymous codons in a non-uniform fashion during the translation event, which has arisen because of interactions among evolutionary forces. The Zn(II)2Cys6 coding sequences from nine Ascomycetes plant pathogenic species and model system yeast were analysed for compositional and codon usage bias patterns. The clustering analysis diverged the Ascomycetes fungi into two clusters. The nucleotide compositional and relative synonymous codon usage (RSCU) analysis indicated GC biasness toward Ascomycetes fungi compared with the model system S. cerevisiae, which tends to be AT-rich. Further, plant pathogenic Ascomycetes fungi belonging to cluster-2 showed a higher number of GC-rich high-frequency codons than cluster-1 and was exclusively AT-rich in S. cerevisiae. The current investigation also showed the mutual effect of the two evolutionary forces, viz. natural selection and compositional constraints, on the CUB of Zn(II)2Cys6 genes. The perseverance of GC-rich codons of Zn(II)2Cys6 in Ascomycetes could facilitate the invasion process. The findings of the current investigation show the role of CUB and nucleotide composition in the evolutionary divergence of Ascomycetes plant pathogens and paves the way to target specific codons and sequences to modulate host-pathogen interactions through genome editing and functional genomics tools.
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Affiliation(s)
- Shilpi Bansal
- Division of Plant Pathology, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India
| | | | - Alexander Balamurugan
- Division of Plant Pathology, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India
| | - S. Chandra Nayaka
- Department of Studies in Applied Botany and Biotechnology, University of Mysore, Mysore 570005, India
| | - Ganesan Prakash
- Division of Plant Pathology, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India
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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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Tikhomirova TS, Matyunin MA, Lobanov MY, Galzitskaya OV. In-depth analysis of amino acid and nucleotide sequences of Hsp60: how conserved is this protein? Proteins 2021; 90:1119-1141. [PMID: 34964171 DOI: 10.1002/prot.26294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 11/07/2022]
Abstract
Chaperonin Hsp60, as a protein found in all organisms, is of great interest in medicine, since it is present in many tissues and can be used both as a drug and as an object of targeted therapy. Hence, Hsp60 deserves a fundamental comparative analysis to assess its evolutionary characteristics. It was found that the percent identity of Hsp60 amino acid sequences both within and between phyla was not high enough to identify Hsp60s as highly conserved proteins. However, their ATP binding sites are largely conserved. The amino acid composition of Hsp60s remained relatively constant. At the same time, the analysis of the nucleotide sequences showed that GC content in the Hsp60 genes was comparable to or greater than the genomic values, which may indicate a high resistance to mutations due to tight control of the nucleotide composition by DNA repair systems. Natural selection plays a dominant role in the evolution of Hsp60 genes. The degree of mutational pressure affecting the Hsp60 genes is quite low, and its direction does not depend on taxonomy. Interestingly, for the Hsp60 genes from Chordata, Arthropoda, and Proteobacteria the exact direction of mutational pressure could not be determined. However, upon further division into classes, it was found that the direction of the mutational pressure for Hsp60 genes from Fish differs from that for other chordates. The direction of the mutational pressure affects the synonymous codon usage bias. The number of high and low represented codons increases with increasing GC content, which can improve codon usage. Special server has been created for bioinformatics analysis of Hsp60: http://oka.protres.ru:4202/.
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Affiliation(s)
- Tatyana S Tikhomirova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, Russia
| | - Maxim A Matyunin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Michail Yu Lobanov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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Malhotra H, Kumar A. Codon usage signatures in Sabia and Chapare for host adaptation. Bioinformation 2021; 17:891-898. [PMID: 35574503 PMCID: PMC9070627 DOI: 10.6026/97320630017891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/16/2021] [Accepted: 10/16/2021] [Indexed: 11/23/2022] Open
Abstract
Sabia and Chapare viruses in the Arenavirus family cause viral hemorrhagic fever among humans with a fatality rate of 30% with no treatment models. Therefore, it is of interest to document the codon usage, amino acid patterns and associated factors influencing the observed variations in Sabia and Chapare viruses for host adaptation. Multivariate statistical analysis revealed compositional constraint and host selection pressure influencing the viral codon usage patterns. These data suggests the codon usage signatures in Sabia and Chapare viruses for host adaptation in the human host implying its role in the rapid progression of the infection. Dinucleotides UpG and CpA were noted to be over-represented among the Sabia, Chapare viruses and human genomes. Strong restraint from the usage of CpG dinucleotides among viruses is linked with the molecular mimicry of the human immune system. Thus, the data reported from this study help in understanding the mechanism of viral adaptation inside the host genome for further consideration in drug discovery.
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Affiliation(s)
- Himani Malhotra
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar Delhi G.T. Road, Phagwara, Punjab, INDIA -144411
| | - Arvind Kumar
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar Delhi G.T. Road, Phagwara, Punjab, INDIA -144411
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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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Gupta S, Singh R. Comparative study of codon usage profiles of Zingiber officinale and its associated fungal pathogens. Mol Genet Genomics 2021; 296:1121-1134. [PMID: 34181071 DOI: 10.1007/s00438-021-01808-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/22/2021] [Indexed: 01/08/2023]
Abstract
Codon usage bias influences the genetic features prevalent in genomes of all the organisms. It also plays a crucial role in establishing the host-pathogen relationship. The present study elucidates the role of codon usage pattern regarding the predilection of fungal pathogens Aspergillus flavus, Aspergillus niger, Fusarium oxysporum and Colletotrichum gloeosporioides towards host plant Zingiber officinale. We found a similar trend of codon usage pattern operative in plant and fungal pathogens. This concurrence might be attributed for the colonization of fungal pathogens in Z. officinale. The transcriptome of both plant and pathogens showed bias towards GC-ending codons. Natural selection and mutational pressure seem to be accountable for shaping the codon usage pattern of host and pathogen. We also identified some distinctive preferred codons in A. flavus, F. oxysporum and Z. officinale that could be regarded as signature codons for the identification of these organisms. Knowledge of favored, avoided and unique codons will help to devise strategies for reducing spice losses due to fungal pathogens.
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Affiliation(s)
- Suruchi Gupta
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, 180001, India
| | - Ravail Singh
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, 180001, India.
- Academy of Scientific and Innovative Research (AcSIR), Jammu, 180001, India.
- DZMB Senckenberg am Meer, Wilhelmshaven, Germany.
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Chakraborty S, Sophiarani Y, Uddin A. Free energy of mRNA positively correlates with GC content in chloroplast transcriptomes of edible legumes. Genomics 2021; 113:2826-2838. [PMID: 34147635 DOI: 10.1016/j.ygeno.2021.06.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 01/01/2021] [Accepted: 06/16/2021] [Indexed: 11/20/2022]
Abstract
In the present study, the results of nucleotide composition analysis showed that the legume chloroplast (cp) transcriptomes were AT rich. From the neutrality plot, we observed that natural selection might have played a major role, while mutation pressure played a minor role in the CUB of cp transcriptomes. Highly significant (p < 0.05) negative correlation was found between mRNA free energy (mFE) and scaled chi-square for entire mRNA in Cicer arietinum and Lens culinaris suggesting that the release of higher energy by entire mRNA molecule might be associated with higher degree of codon usage bias in these two crop plants. Further, highly significant (p < 0.01, p < 0.05) positive correlation of mFE for entire mRNA was found with GC3 and that of mFE for 39 bases with GC, GC1, GC2 and GC3 contents among all the legumes. This indicated that higher GC content might induce the release of more free energy by cp transcriptomes.
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Affiliation(s)
- Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India.
| | | | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi 788150, India
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Dong S, Zhang L, Pang W, Zhang Y, Wang C, Li Z, Ma L, Tang W, Yang G, Song H. Comprehensive analysis of coding sequence architecture features and gene expression in Arachis duranensis. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:213-222. [PMID: 33707864 PMCID: PMC7907404 DOI: 10.1007/s12298-021-00938-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/04/2021] [Accepted: 01/20/2021] [Indexed: 06/09/2023]
Abstract
Coding sequence (CDS) architecture affects gene expression levels in organisms. Codon optimization can increase the gene expression level. Therefore, understanding codon usage patterns has important implications for research on genetic engineering and exogenous gene expression. To date, the codon usage patterns of many model plants have been analyzed. However, the relationship between CDS architecture and gene expression in Arachis duranensis remains poorly understood. According to the results of genome sequencing, A. duranensis has many resistant genes that can be used to improve the cultivated peanut. In this study, bioinformatic approaches were used to estimate A. duranensis CDS architectures, including frequency of the optimal codon (Fop), polypeptide length and GC contents at the first (GC1), second (GC2) and third (GC3) codon positions. In addition, Arachis RNA-seq datasets were downloaded from PeanutBase. The relationships between gene expression and CDS architecture were assessed both under normal growth as well as nematode and drought stress conditions. A total of 26 codons with high frequency were identified, which preferentially ended with A or T in A. duranensis CDSs under the above-mentioned three conditions. A similar CDS architecture was found in differentially expressed genes (DEGs) under nematode and drought stresses. The GC1 content differed between DEGs and non-differentially expressed genes (NDEGs) under both drought and nematode stresses. The expression levels of DEGs were affected by different CDS architectures compared with NDEGs under drought stress. In addition, no correlation was found between differential gene expression and CDS architecture neither under nematode nor under drought stress. These results aid the understanding of gene expression in A. duranensis.
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Affiliation(s)
- Shuwei Dong
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Long Zhang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Wenhui Pang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Yongli Zhang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Chang Wang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Zhenyi Li
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Lichao Ma
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Wei Tang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Guofeng Yang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Hui Song
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
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Xu Q, Chen H, Sun W, Zhu D, Zhang Y, Chen JL, Chen Y. Genome-wide analysis of the synonymous codon usage pattern of Streptococcus suis. Microb Pathog 2021; 150:104732. [PMID: 33429052 DOI: 10.1016/j.micpath.2021.104732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 12/30/2020] [Accepted: 01/03/2021] [Indexed: 01/21/2023]
Abstract
Streptococcus suis (S. suis) is a gram-positive coccus that causes disease in humans and animals. The codon usage pattern of bacteria reveals a range of evolutionary changes that assist them to enhance tolerance to environments. To better understand the genetic features during the evolution of S. suis, we performed codon usage analysis. Nine pathogenic strains of different serotypes and different geographical distribution were analyzed to better understand the differences in their evolutionary process. Nucleotide compositions and relative synonymous codon usage (RSCU) analysis revealed that A/T-ending codons are dominant in S. suis. Neutrality analysis, correspondence analysis and ENC-plot results revealed that natural selection is the predominant element prompting codon usage. Cluster analysis based on RSCU was roughly consistent with the dendrogram rooted genomic BLAST analysis. Comparison of synonymous codon usage pattern between S. suis and susceptible hosts (H. sapiens and S. scrofa) revealed that the codon usage of S. suis is separated from the synonymous codon usage of susceptible hosts. The CAI values implied that S. suis includes a series of predicted highly expressed coding sequences contained in metabolism and transcriptional regulation, revealing the necessity of this pathogen to deal with various environmental conditions. The study of codon usage in S. suis may provide evidence involving the molecular evolution of bacteria and a better understanding of evolutionary relationships between S. suis and its corresponding hosts.
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Affiliation(s)
- Quanming Xu
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hong Chen
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wen Sun
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dewen Zhu
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongyi Zhang
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ji-Long Chen
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ye Chen
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Comprehensive profiling of codon usage signatures and codon context variations in the genus Ustilago. World J Microbiol Biotechnol 2019; 35:118. [DOI: 10.1007/s11274-019-2693-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 07/07/2019] [Indexed: 02/02/2023]
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13
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Roy A, van Staden J. Insights into the riddles of codon usage patterns and codon context signatures in fungal genus
Puccinia
, a persistent threat to global agriculture. J Cell Biochem 2019; 120:19555-19566. [DOI: 10.1002/jcb.29263] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 06/06/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Ayan Roy
- Research Centre for Plant Growth and Development School of Life Sciences, University of KwaZulu‐Natal Pietermaritzburg South Africa
| | - Johannes van Staden
- Research Centre for Plant Growth and Development School of Life Sciences, University of KwaZulu‐Natal Pietermaritzburg South Africa
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Mazumder GA, Uddin A, Chakraborty S. Preference of A/T ending codons in mitochondrial ATP6 gene under phylum Platyhelminthes. Mol Biochem Parasitol 2018; 225:15-26. [DOI: 10.1016/j.molbiopara.2018.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 08/17/2018] [Accepted: 08/22/2018] [Indexed: 11/27/2022]
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15
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Paul P, Malakar AK, Chakraborty S. Codon usage vis-a-vis start and stop codon context analysis of three dicot species. J Genet 2018; 97:97-107. [PMID: 29666329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
To understand the variation in genomic composition and its effect on codon usage, we performed the comparative analysis of codon usage and nucleotide usage in the genes of three dicots, Glycine max, Arabidopsis thaliana and Medicago truncatula. The dicot genes were found to be A/T rich and have predominantly A-ending and/or T-ending codons. GC3s directly mimic theusage pattern of global GC content. Relative synonymous codon usage analysis suggests that the high usage frequency of A/T over G/C mononucleotide containing codons in AT-rich dicot genome is due to compositional constraint as a factor of codon usage bias. Odds ratio analysis identified the dinucleotides TpG, TpC, GpA, CpA and CpT as over-represented, where, CpG and TpA as under-represented dinucleotides. The results of (NcExp-NcObs)/NcExp plot suggests that selection pressure other than mutation played a significant role in influencing the pattern of codon usage in these dicots. PR2 analysis revealed the significant role of selection pressure on codon usage. Analysis of varience on codon usage at start and stop site showed variation in codon selection in these sites. This study provides evidence that the dicot genes were subjected to compositional selection pressure.
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Affiliation(s)
- Prosenjit Paul
- Department of Biotechnology, Assam University, Silchar 788 011, India.
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Paul P, Malakar AK, Chakraborty S. Codon usage vis-a-vis start and stop codon context analysis of three dicot species. J Genet 2018. [DOI: 10.1007/s12041-018-0892-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Wang P, Su L, Gao H, Jiang X, Wu X, Li Y, Zhang Q, Wang Y, Ren F. Genome-Wide Characterization of bHLH Genes in Grape and Analysis of their Potential Relevance to Abiotic Stress Tolerance and Secondary Metabolite Biosynthesis. FRONTIERS IN PLANT SCIENCE 2018; 9:64. [PMID: 29449854 PMCID: PMC5799661 DOI: 10.3389/fpls.2018.00064] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 01/12/2018] [Indexed: 05/17/2023]
Abstract
Basic helix-loop-helix (bHLH) transcription factors are involved in many abiotic stress responses as well as flavonol and anthocyanin biosynthesis. In grapes (Vitis vinifera L.), flavonols including anthocyanins and condensed tannins are most abundant in the skins of the berries. Flavonols are important phytochemicals for viticulture and enology, but grape bHLH genes have rarely been examined. We identified 94 grape bHLH genes in a genome-wide analysis and performed Nr and GO function analyses for these genes. Phylogenetic analyses placed the genes into 15 clades, with some remaining orphans. 41 duplicate gene pairs were found in the grape bHLH gene family, and all of these duplicate gene pairs underwent purifying selection. Nine triplicate gene groups were found in the grape bHLH gene family and all of these triplicate gene groups underwent purifying selection. Twenty-two grape bHLH genes could be induced by PEG treatment and 17 grape bHLH genes could be induced by cold stress treatment including a homologous form of MYC2, VvbHLH007. Based on the GO or Nr function annotations, we found three other genes that are potentially related to anthocyanin or flavonol biosynthesis: VvbHLH003, VvbHLH007, and VvbHLH010. We also performed a cis-acting regulatory element analysis on some genes involved in flavonoid or anthocyanin biosynthesis and our results showed that most of these gene promoters contained G-box or E-box elements that could be recognized by bHLH family members.
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Genome-wide analysis of codon usage bias patterns in an enterotoxigenic Escherichia coli F18 strain. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0519-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Chen Y, Xu Q, Tan C, Li X, Chi X, Cai B, Yu Z, Ma Y, Chen JL. Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Senecavirus A evolution. Microb Pathog 2017; 112:313-319. [PMID: 28943149 PMCID: PMC7172466 DOI: 10.1016/j.micpath.2017.09.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 09/16/2017] [Accepted: 09/18/2017] [Indexed: 11/24/2022]
Abstract
Senecavirus A (SVA) infection was recently confirmed in pigs in Brazil, United States of America and Canada. To better understand the molecular characteristics of isolated SVA genomes, we first reported genome-wide comprehensive analyses of codon usage and various factors that have contribute to the molecular evolution in SVA. The effective number of codons (ENC) ranged from 54.51 to 55.54 with an average of 54.87 ± 0.285, which reveals a relatively stable nucleotide composition. We found that codon usage bias of the SVA was low. Mutational pressure acted as an increasingly dominant factor for the evolution of the virus compared with the natural selection. Notably, codon usage bias was also affected by the geographic distribution and isolated time. The first systemic analysis on the codon usage bias of the SVA provides important information for the understanding of the evolution of the SVA and has fundamental and theoretical benefits.
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Affiliation(s)
- Ye Chen
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Quanming Xu
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chen Tan
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinxin Li
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaojuan Chi
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Binxiang Cai
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ziding Yu
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanmei Ma
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Ji-Long Chen
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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Yi S, Li Y, Wang W. Selection shapes the patterns of codon usage in three closely related species of genus Misgurnus. Genomics 2017; 110:134-142. [PMID: 28911975 DOI: 10.1016/j.ygeno.2017.09.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/29/2017] [Accepted: 09/07/2017] [Indexed: 11/17/2022]
Abstract
Neutrality plots revealed that selection probably dominates codon bias, whereas mutation plays only a minor role, in shaping the codon bias in three loaches, Misgurnus anguillicaudatus, M. mohoity, and M. bipartitus. These three species also clearly showed similar tendencies in the preferential usage of codons. Nineteen, nine, and 14 preferred codon pairs and 179, 182, and 173 avoided codon pairs were also detected in M. anguillicaudatus, M. bipartitus, and M. mohoity, respectively, and the most frequently avoided type of cP3-cA1 dinucleotide in these species was nnUAnn. The expression-linked patterns of codon usage revealed that higher expression was associated with higher GC3, lower ENC, and a smaller proportion of amino acids with high size/complexity (S/C) scores in these three species. These results elucidate selectively driven codon bias in Misgurnus species, and reveal the potential importance of expression-mediated selection in shaping the genome evolution of fish.
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Affiliation(s)
- Shaokui Yi
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanhe Li
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Weimin Wang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
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Song H, Liu J, Song Q, Zhang Q, Tian P, Nan Z. Comprehensive Analysis of Codon Usage Bias in Seven Epichloë Species and Their Peramine-Coding Genes. Front Microbiol 2017; 8:1419. [PMID: 28798739 PMCID: PMC5529348 DOI: 10.3389/fmicb.2017.01419] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 07/13/2017] [Indexed: 11/22/2022] Open
Abstract
Codon usage bias plays an important role in shaping genomes and genes in unicellular species and multicellular species. Here, we first analyzed codon usage bias in seven Epichloë species and their peramine-coding genes. Our results showed that both natural selection and mutation pressure played a role in forming codon usage bias in seven Epichloë species. All seven Epichloë species contained a peramine-coding gene cluster. Interestingly, codon usage bias of peramine-coding genes were not affected by natural selection or mutation pressure. There were 13 codons more frequently found in Epichloë genome sequences, peramine-coding gene clusters and orthologous peramine-coding genes, all of which had a bias to end with a C nucleotide. In the seven genomes analyzed, codon usage was biased in highly expressed coding sequences (CDSs) with shorter length and higher GC content. Genes in the peramine-coding gene cluster had higher GC content at the third nucleotide position of the codon, and highly expressed genes had higher GC content at the second position. In orthologous peramine-coding CDSs, high expression level was not significantly correlated with CDS length and GC content. Analysis of selection pressure identified that the genes orthologous to peramine genes were under purifying selection. There were no differences in codon usage bias and selection pressure between peramine product genes and non-functional peramine product genes. Our results provide insights into understanding codon evolution in Epichloë species.
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Affiliation(s)
- Hui Song
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhou, China
| | - Jing Liu
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhou, China
| | - Qiuyan Song
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhou, China
| | - Qingping Zhang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhou, China
| | - Pei Tian
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhou, China
| | - Zhibiao Nan
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhou, China
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Sadhasivam A, Vetrivel U. Genome-wide codon usage profiling of ocular infective Chlamydia trachomatis serovars and drug target identification. J Biomol Struct Dyn 2017. [PMID: 28627970 DOI: 10.1080/07391102.2017.1343685] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Chlamydia trachomatis (C.t) is a Gram-negative obligate intracellular bacteria and is a major causative of infectious blindness and sexually transmitted diseases. Among the varied serovars of this organism, A, B and C are reported as prominent ocular pathogens. Genomic studies of these strains shall aid in deciphering potential drug targets and genomic influence on pathogenesis. Hence, in this study we performed deep statistical profiling of codon usage in these serovars. The overall base composition analysis reveals that these serovars are over biased to AU than GC. Similarly, relative synonymous codon usage also showed preference towards A/U ending codons. Parity Rule 2 analysis inferred unequal distribution of AT and GC, indicative of other unknown factors acting along with mutational pressure to influence codon usage bias (CUB). Moreover, absolute quantification of CUB also revealed lower bias across these serovars. The effect of natural selection on CUB was also confirmed by neutrality plot, reinforcing natural selection under mutational pressure turned to be a pivotal role in shaping the CUB in the strains studied. Correspondence analysis (COA) clarified that, C.t C/TW-3 to show a unique trend in codon usage variation. Host influence analysis on shaping the codon usage pattern also inferred some speculative relativity. In a nutshell, our finding suggests that mutational pressure is the dominating factor in shaping CUB in the strains studied, followed by natural selection. We also propose potential drug targets based on cumulative analysis of strand bias, CUB and human non-homologue screening.
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Affiliation(s)
- Anupriya Sadhasivam
- a Centre for Bioinformatics , Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Sankara Nethralaya , Chennai 600 006 , Tamil Nadu , India
| | - Umashankar Vetrivel
- a Centre for Bioinformatics , Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Sankara Nethralaya , Chennai 600 006 , Tamil Nadu , India
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Li J, Gu F, Wu R, Yang J, Zhang KQ. Phylogenomic evolutionary surveys of subtilase superfamily genes in fungi. Sci Rep 2017; 7:45456. [PMID: 28358043 PMCID: PMC5371821 DOI: 10.1038/srep45456] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 02/28/2017] [Indexed: 01/10/2023] Open
Abstract
Subtilases belong to a superfamily of serine proteases which are ubiquitous in fungi and are suspected to have developed distinct functional properties to help fungi adapt to different ecological niches. In this study, we conducted a large-scale phylogenomic survey of subtilase protease genes in 83 whole genome sequenced fungal species in order to identify the evolutionary patterns and subsequent functional divergences of different subtilase families among the main lineages of the fungal kingdom. Our comparative genomic analyses of the subtilase superfamily indicated that extensive gene duplications, losses and functional diversifications have occurred in fungi, and that the four families of subtilase enzymes in fungi, including proteinase K-like, Pyrolisin, kexin and S53, have distinct evolutionary histories which may have facilitated the adaptation of fungi to a broad array of life strategies. Our study provides new insights into the evolution of the subtilase superfamily in fungi and expands our understanding of the evolution of fungi with different lifestyles.
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Affiliation(s)
- Juan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P.R. China
| | - Fei Gu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P.R. China
| | - Runian Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P.R. China
| | - JinKui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P.R. China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P.R. China
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