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Ding H, Gao J, Yang J, Zhang S, Han S, Yi R, Ye Y, Kan X. Genome evolution of Buchnera aphidicola (Gammaproteobacteria): Insights into strand compositional asymmetry, codon usage bias, and phylogenetic implications. Int J Biol Macromol 2023; 253:126738. [PMID: 37690648 DOI: 10.1016/j.ijbiomac.2023.126738] [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: 05/02/2023] [Revised: 08/15/2023] [Accepted: 08/25/2023] [Indexed: 09/12/2023]
Abstract
Taxa of Buchnera aphidicola (hereafter "Buchnera") are mutualistic intracellular symbionts of aphids, known for their remarkable biological traits such as genome reduction, strand compositional asymmetry, and symbiont-host coevolution. With the growing availability of genomic data, we performed a comprehensive analysis of 103 genomes of Buchnera strains from 12 host subfamilies, focusing on the genomic characterizations, codon usage patterns, and phylogenetic implications. Our findings revealed consistent features among all genomes, including small genome sizes, low GC contents, and gene losses. We also identified strong strand compositional asymmetries in all strains at the genome level. Further investigation suggested that mutation pressure may have played a crucial role in shaping codon usage of Buchnera. Moreover, the genomic asymmetries were reflected in asymmetric codon usage preferences within chromosomal genes. Notably, the levels of these asymmetries were varied among strains and were significantly influenced by the degrees of genome shrinkages. Lastly, our phylogenetic analyses presented an alternative topology of Aphididae, based on the Buchnera symbionts, providing robust confirmation of the paraphylies of Eriosomatinae, and Macrosiphini. Our objectives are to further understand the strand compositional asymmetry and codon usage bias of Buchnera taxa, and provide new perspectives for phylogenetic studies of Aphididae.
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Affiliation(s)
- Hengwu Ding
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, China
| | - Jinming Gao
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jianke Yang
- School of Basic Medical Sciences, Wannan Medical College, Wuhu 241000, China
| | - Sijia Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Shiyun Han
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Ran Yi
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Yuanxin Ye
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Xianzhao Kan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China.
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Jiang L, Zhang Q, Xiao S, Si F. Deep decoding of codon usage strategies and host adaption preferences of soybean mosaic virus. Int J Biol Macromol 2022; 222:803-817. [PMID: 36167098 DOI: 10.1016/j.ijbiomac.2022.09.179] [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: 08/01/2022] [Revised: 09/13/2022] [Accepted: 09/17/2022] [Indexed: 11/05/2022]
Abstract
Soybean mosaic virus (SMV) has threatened the global yield of Leguminosae crops, but the mechanism of its infection, spread, and evolution remains unknown. A systemic analysis of 107 SMV strains was performed to explore the genome-wide codon usage profile and the various factors influencing the codon usage patterns of SMV, which provides insight into its molecular evolution and elucidates its unknown host adaptation pattern. The overall nucleotide composition and correlation analysis revealed that the preferred synonymous codons mostly end with A/U. Clustering by RSCU value of each strain and phylogenetic tree analysis showed that the SMV isolates studied were divided into four clades, with a low overall extent of codon usage bias (CUB) in SMV. According to the ENC, PR2, neutrality plot, and correspondence analysis, natural selection of geographical diversity may play a critical role in the CUB. Higher adaptability was shown in Glycine with SMV and more pressure was received by clade III. These findings could not only provide valuable information about the overall codon usage pattern of the SMV genome, but could also aid in the clarification of the involved mechanisms that dominate the codon usage patterns and genetic evolution of the SMV genome.
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Affiliation(s)
- Li Jiang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Qiang Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Shimin Xiao
- Shanwei Marine Industry Institute, Shanwei Institute of Technology, Shanwei 516600, China.
| | - Fusheng Si
- Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, China.
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Codon Usage Bias and Cluster Analysis of the MMP-2 and MMP-9 Genes in Seven Mammals. Genet Res (Camb) 2022; 2022:2823356. [PMID: 36118275 PMCID: PMC9467794 DOI: 10.1155/2022/2823356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022] Open
Abstract
Matrix metalloproteinase (MMP)-2 and MMP-9 are a family of Zn2+ and Ca2+-dependent gelatinase MMPs that regulate muscle development and disease treatment, and they are highly conservative during biological evolution. Despite increasing knowledge of MMP genes, their evolutionary mechanism for functional adaption remains unclear. Moreover, analysis of codon usage bias (CUB) is reliable to understand evolutionary associations. However, the distribution of CUB of MMP-2 and MMP-9 genes in mammals has not been revealed clearly. Multiple analytical software was used to study the genetic evolution, phylogeny, and codon usage pattern of these two genes in seven species of mammals. Results showed that the MMP-2 and MMP-9 genes have CUB. By comparing the content of synonymous codon bases amongst seven mammals, we found that MMP-2 and MMP-9 were low-expression genes in mammals with high codon conservation, and their third codon preferred the G/C base. RSCU analysis revealed that these two genes preferred codons encoding delicious amino acids. Analysing what factors influence CUB showed that the third base distributors of these two genes were C/A and C/T, and GC3S had a wide distribution range on the ENC plot reference curve under no selection or mutational pressure. Thus, mutational pressure is an important factor in CUB. This study revealed the usage characteristics of the MMP-2 and MMP-9 gene codons in different mammals and provided basic data for further study towards enhancing meat flavour, treating muscle disease, and optimizing codons.
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Alqahtani T, Khandia R, Puranik N, Alqahtani AM, Chidambaram K, Kamal MA. Codon Usage is Influenced by Compositional Constraints in Genes Associated with Dementia. Front Genet 2022; 13:884348. [PMID: 36017501 PMCID: PMC9395603 DOI: 10.3389/fgene.2022.884348] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/18/2022] [Indexed: 11/28/2022] Open
Abstract
Dementia is a clinical syndrome characterized by progressive cognitive decline, and the symptoms could be gradual, persistent, and progressive. In the present study, we investigated 47 genes that have been linked to dementia. Compositional, selectional, and mutational forces were seen to be involved. Nucleotide components that influenced A- and GC-affected codon usages bias at all three codon positions. The influence of these two compositional constraints on codon usage bias (CUB) was positive for nucleotide A and negative for GC. Nucleotide A also experienced the highest mutational force, and GC-ending codons were preferred over AT-ending codons. A high bias toward GC-ending codons enhances the gene expression level, evidenced by the positive association between CAI- and GC-ending codons. Unusual behavior of the TTG codon showing an inverse relationship with the GC-ending codon and negative influence of gene expression, behavior contrary to all other GC-ending codons, shows an operative selectional force. Furthermore, parity analysis, higher translational selection value, preference of GC-ending codons over AT-ending codons, and association of gene length with gene expression refer to the dominant role of selection pressure with compositional constraint and mutational force-shaping codon usage.
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Affiliation(s)
- Taha Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Nidhi Puranik
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Ali M Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Kumarappan Chidambaram
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Amjad Kamal
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.,King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh.,Enzymoics, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
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Huang X, Jiao Y, Guo J, Wang Y, Chu G, Wang M. Analysis of codon usage patterns in Haloxylon ammodendron based on genomic and transcriptomic data. Gene X 2022; 845:146842. [PMID: 36038027 DOI: 10.1016/j.gene.2022.146842] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/17/2022] [Accepted: 08/23/2022] [Indexed: 11/28/2022] Open
Abstract
Haloxylon ammodendron, a xero-halophytic shrub of Chenopodiaceae, is a dominant species in deserts, which has a strong drought and salt tolerance and plays an important role in sand fixation. However, the codon usage bias (CUB) in H. ammodendron is still unclear at present. In this study, the codon usage patterns of 38,657 coding sequences (CDSs) in the newly released whole-genome sequence data of H. ammodendron and 3,948 CDSs in the previously obtained transcriptome sequencing data were compared and analyzed. The results showed that the CDSs with the total guanineandcytosine(GC)content in the range of 40% ∼ 45% was the most in the genome and transcriptome. Among which, the GC1, GC2, and GC3 contents of genomic CDSs were 50.83%, 40.56%, and 40.23%, respectively, and those of CDSs in the transcriptome were 47.16%, 39.02%, and 39.59%, respectively. Therefore, the bases in H. ammodendron were rich in adenine and thymine, and the overallcodonusage was biasedtoward A- and U-ending codons. The analysis of neutrality plot, effective number of codon (ENC) plot, and parity rule 2 (PR2) bias plot showed that both natural selection and mutation pressure had great influences on the CUB of H. ammodendron, but natural selection was the most important determinant. Besides, gene expression level and the function and protein length of some specific genes also had influences on the codon usage pattern. Finally, a total of 25 common optimal codons were found in the genomic and transcriptomic data, and AU/GC-ending codons ratio was 24:1. It should be noted that the salt-tolerant unigenes had similar codon usage, and the highly expressed genes had higher usage frequency of optimal codons and lower GC content than the lowly expressed genes. In addition, there was no difference in the ENC values of salt-tolerant unigenes in H. ammodendron, and the expression level of the genes had no correlation with CAI. This study will help to elucidate the formation mechanism of H. ammodendron codon usage bias, and make contributions to the identification of new genes and the genetic engineering study on H. ammodendron.
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Affiliation(s)
- Xiang Huang
- College of Agriculture, Shihezi University, Shihezi Xinjiang 832003, P.R. China
| | - Yalin Jiao
- College of Agriculture, Shihezi University, Shihezi Xinjiang 832003, P.R. China
| | - Jiaxing Guo
- College of Agriculture, Shihezi University, Shihezi Xinjiang 832003, P.R. China
| | - Ying Wang
- College of Agriculture, Shihezi University, Shihezi Xinjiang 832003, P.R. China
| | - Guangming Chu
- College of Agriculture, Shihezi University, Shihezi Xinjiang 832003, P.R. China
| | - Mei Wang
- College of Agriculture, Shihezi University, Shihezi Xinjiang 832003, P.R. China.
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Liu SN, Su XY, Chen WQ, Yu JW, Li JR, Jiang P, Cui J, Wang ZQ, Zhang X. Transcriptome profiling of plerocercoid and adult developmental stages of the neglected medical tapeworm Spirometra erinaceieuropaei. Acta Trop 2022; 232:106483. [PMID: 35469749 DOI: 10.1016/j.actatropica.2022.106483] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 11/28/2022]
Abstract
The plerocercoid larvae of the tapeworm Spirometra erinaceieuropaei can parasitize humans and animals and cause serious parasitic zoonosis. However, our knowledge of the developmental process of S. erinaceieuropaei is still inadequate. To better characterize differential and specific genes and pathways associated with parasite development, a comparative transcriptomic analysis of the plerocercoid stage and the adult stage was performed using RNA-seq and de novo analysis. Approximately 13,659 differentially expressed genes (DEGs) were identified in plerocercoids versus adults, of which 6455 DEGs were upregulated and 7204 were downregulated. DEGs involved in parasite immunoevasion were more active in plerocercoid larvae than in adults, while DEGs associated with metabolic activity were upregulated in adults. Gene Ontology (GO) and Kyoto Encyclopedia of Genes (KEGG) analyses revealed that most DEGs involved in protein phosphorylation/dephosphorylation and the Wnt signalling pathway were much more active in plerocercoid larvae. The molecular functions of upregulated unigenes in adults were mainly enriched for metabolic activities. qPCR validated that the expression levels of 10 selected DEGs were consistent with those in RNA-seq, confirming the accuracy of the RNA-seq results. Our results contributed to increasing the knowledge on the S. erinaceieuropaei gene repertoire and expression profile and also provide valuable resources for functional studies on the molecular mechanisms of S. erinaceieuropaei.
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Affiliation(s)
- Shi Nan Liu
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xiao Yi Su
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Wen Qing Chen
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jin Wei Yu
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jing Ru Li
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Peng Jiang
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jing Cui
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Zhong Quan Wang
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xi Zhang
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China.
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Khandia R, Saeed M, Alharbi AM, Ashraf GM, Greig NH, Kamal MA. Codon Usage Bias Correlates With Gene Length in Neurodegeneration Associated Genes. Front Neurosci 2022; 16:895607. [PMID: 35860292 PMCID: PMC9289476 DOI: 10.3389/fnins.2022.895607] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Codon usage analysis is a crucial part of molecular characterization and is used to determine the factors affecting the evolution of a gene. The length of a gene is an important parameter that affects the characteristics of the gene, such as codon usage, compositional parameters, and sometimes, its functions. In the present study, we investigated the association of various parameters related to codon usage with the length of genes. Gene expression is affected by nucleotide disproportion. In sixty genes related to neurodegenerative disorders, the G nucleotide was the most abundant and the T nucleotide was the least. The nucleotide T exhibited a significant association with the length of the gene at both the overall compositional level and the first and second codon positions. Codon usage bias (CUB) of these genes was affected by pyrimidine and keto skews. Gene length was found to be significantly correlated with codon bias in neurodegeneration associated genes. In gene segments with lengths below 1,200 bp and above 2,400 bp, CUB was positively associated with length. Relative synonymous CUB, which is another measure of CUB, showed that codons TTA, GTT, GTC, TCA, GGT, and GGA exhibited a positive association with length, whereas codons GTA, AGC, CGT, CGA, and GGG showed a negative association. GC-ending codons were preferred over AT-ending codons. Overall analysis indicated that the association between CUB and length varies depending on the segment size; however, CUB of 1,200–2,000 bp gene segments appeared not affected by gene length. In synopsis, analysis suggests that length of the genes correlates with various imperative molecular signatures including A/T nucleotide disproportion and codon choices. In the present study we additionally evaluated various molecular features and their correlation with different indices of codon usage, like the Codon Adaptation Index (CAI) and Relative Dynonymous Codon Usage (RSCU) of codons. We also considered the impact of gene fragment size on different molecular features in genes related to neurodegeneration. This analysis will aid our understanding of and in potentially modulating gene expression in cases of defective gene functioning in clinical settings.
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Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
- *Correspondence: Rekha Khandia, ;
| | - Mohd. Saeed
- Department of Biology, College of Sciences, University of Hail, Hail, Saudi Arabia
| | - Ahmed M. Alharbi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Ghulam Md. Ashraf
- Pre-clinical Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nigel H. Greig
- Drug Design and Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, NIH, Baltimore, MD, United States
| | - Mohammad Amjad Kamal
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
- Enzymoics, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
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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: 6] [Impact Index Per Article: 2.0] [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 GA, Uddin A, Chakraborty S. Analysis of codon usage bias in mitochondrial CO gene among platyhelminthes. Mol Biochem Parasitol 2021; 245:111410. [PMID: 34487743 DOI: 10.1016/j.molbiopara.2021.111410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/19/2021] [Accepted: 08/27/2021] [Indexed: 11/17/2022]
Abstract
The phenomenon of non-uniform usage of the synonymous codons, where some codons are given more preference to others, is known as codon usage bias (CUB). CUB is known to be determined by two major evolutionary forces i.e. mutation pressure and selection. We used various approaches to understand the codon usage pattern in mitochondrial CO (MT-CO) genes involved in complex IV of the respiratory chain (RC) as no work was reported yet. Our present study revealed that CUB was relatively high and the coding sequences were rich in A and T. Correspondence analysis further indicated that A/T compositional properties under mutational pressure might be affecting the codon usage pattern and was different in different classes for MT-CO gene. A highly significant correlation between A% and A3%, T% and T3%, G% and G3%, C% and C3%, GC% and GC3% in all the classes indicated that compositional constraints under mutational pressure and natural selection might affect the CUB. Neutrality plot indicated that both natural selection and mutational bias affected the CUB, where, natural selection played the major role as compared to mutational pressure.
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Affiliation(s)
- Gulshana A Mazumder
- Department of Biotechnology, Assam University, Silchar, 788011, Assam, India
| | - Arif Uddin
- Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, 788150, Assam, India
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar, 788011, Assam, India.
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Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB. Genes (Basel) 2021; 12:genes12081169. [PMID: 34440343 PMCID: PMC8393687 DOI: 10.3390/genes12081169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 12/03/2022] Open
Abstract
Giardia duodenalis, a flagellated parasitic protozoan, the most common cause of parasite-induced diarrheal diseases worldwide. Codon usage bias (CUB) is an important evolutionary character in most species. However, G. duodenalis CUB remains unclear. Thus, this study analyzes codon usage patterns to assess the restriction factors and obtain useful information in shaping G. duodenalis CUB. The neutrality analysis result indicates that G. duodenalis has a wide GC3 distribution, which significantly correlates with GC12. ENC-plot result—suggesting that most genes were close to the expected curve with only a few strayed away points. This indicates that mutational pressure and natural selection played an important role in the development of CUB. The Parity Rule 2 plot (PR2) result demonstrates that the usage of GC and AT was out of proportion. Interestingly, we identified 26 optimal codons in the G. duodenalis genome, ending with G or C. In addition, GC content, gene expression, and protein size also influence G. duodenalis CUB formation. This study systematically analyzes G. duodenalis codon usage pattern and clarifies the mechanisms of G. duodenalis CUB. These results will be very useful to identify new genes, molecular genetic manipulation, and study of G. duodenalis evolution.
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Yang J, Ding H, Kan X. Codon usage patterns and evolution of HSP60 in birds. Int J Biol Macromol 2021; 183:1002-1012. [PMID: 33971236 DOI: 10.1016/j.ijbiomac.2021.05.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 11/27/2022]
Abstract
Heat shock protein 60 (HSP60) is highly conserved from prokaryotic to eukaryotic organisms, acting as molecular chaperone and other vital biological functions. In spite of increasing knowledge of HSP60, its evolutionary mechanism on functional adaption is still far from completely understood. Moreover, analysis of codon usage bias (CUB) is a powerful tool to understand evolutionary association studies. However, so far, as we know, no scientific work on CUB of HSP60 in birds has been reported. In this study, we provide a comprehensive analysis on the codon usage and molecular evolution of HSP60 across birds. The results indicated that HSP60 had a weak codon usage bias with high ENC values (range from 52.66 to 61), low RSCU, and A/T-ending codons were mostly preferred. Meanwhile, it was considered that mutation, natural selection, and genetic drift combined to shape codon usage patterns with different strength proportions among various birds for HSP60. Then, the LRT tests suggested that different lineages of birds might be under similar selective pressures. Besides, the two positive selection sites (151 and 131) were detected and might undergo radical changes. These findings would contribute to understand function diversity and molecular evolution of HSP60 in birds.
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Affiliation(s)
- Jianke Yang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China; School of Preclinical Medicine, Wannan Medical College, Wuhu, Anhui, China
| | - Hengwu Ding
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China; Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu, Anhui, China
| | - Xianzhao Kan
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China; Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu, Anhui, China.
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13
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Gupta S, Paul K, Roy A. Codon usage signatures in the genus Cryptococcus: A complex interplay of gene expression, translational selection and compositional bias. Genomics 2020; 113:821-830. [PMID: 33096254 DOI: 10.1016/j.ygeno.2020.10.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/16/2020] [Accepted: 10/05/2020] [Indexed: 11/30/2022]
Abstract
The fungal genus Cryptococcus comprises of several diverse species. The pathogens forming Cryptococcus neoformans/ Cryptococcus gatti species complex are of immense clinical significance owing to the high frequency of infections and deaths globally. Three closely related non-pathogenic species namely, Cryptococcus amylolentus, Cryptococcus wingfieldii and Cryptococcus depauperatus are the non-pathogenic ancestral species from which pathogenic lineages have diverged. In the current study, a comprehensive analysis of factors influencing the codon and amino acid usage bias in six pathogenic and three non-pathogenic species was performed. Our results revealed that though compositional bias played a crucial role, translational selection and gene expression were the key determinants of codon usage variations. Analysis of relative dinucleotide abundance and codon context signatures revealed strict avoidance of TpA dinucleotide across genomes. Multivariate statistical analysis based on codon usage data resulted in discrete clustering of pathogens and non-pathogens which correlated with previous reports on their phylogenetic distribution.
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Affiliation(s)
- Shelly Gupta
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Punjab 144411, India.
| | - Karan Paul
- Department of Biochemistry, DAV University, Jalandhar, Punjab 144001, India
| | - Ayan Roy
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Punjab 144411, India.
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14
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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: 4] [Impact Index Per Article: 1.0] [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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15
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Mazumder GA, Uddin A, Chakraborty S. Analysis of codon usage pattern of mitochondrial ND genes in Platyhelminthes. Mol Biochem Parasitol 2020; 238:111294. [PMID: 32592756 DOI: 10.1016/j.molbiopara.2020.111294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/18/2020] [Accepted: 06/20/2020] [Indexed: 01/24/2023]
Abstract
Codon usage bias (CUB) is the nonrandom usage of synonymous codons in which some codons are more preferred to others.CUB can be determined by mutation pressure and selection. Various approaches have been used to understand the pattern of CUB in the mitochondrial ND (MT-ND or ND) genes involved in complex I of respiratory chain in five different classes of Platyhelminthes as no work was reported yet. The present study revealed that the CUB varies across MT-ND genes and the coding sequences showed the richness of A and T. Correspondence analysis implied the effect of mutational pressure and also the pattern of codon usage was different in different classes of platyhelminthes for MT-ND genes. Highly significant correlation was observed between overall nucleotide composition and its 3rd codon position in most of the homogeneous nucleotides such as A% and A3%, T% and T3%, G% and G3%, C% and C3%, GC% and GC3% and also some significant correlations observed among heterogeneous nucleotides in all the five classes for MT-ND genes suggested the role of mutational pressure as well as natural selection in affecting the CUB. Neutrality plot suggested that the contributions of natural selection and mutational pressure varied across different classes of platyhelminthes and also differed in different MT-ND genes.
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Affiliation(s)
| | - Arif Uddin
- Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, 788150 Assam, India
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar, 788011 Assam, India.
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16
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Barbhuiya PA, Uddin A, Chakraborty S. Analysis of compositional properties and codon usage bias of mitochondrial CYB gene in anura, urodela and gymnophiona. Gene 2020; 751:144762. [PMID: 32407767 DOI: 10.1016/j.gene.2020.144762] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/24/2020] [Accepted: 05/08/2020] [Indexed: 01/17/2023]
Abstract
We delineated the pattern of synonymous codon usage bias (CUB) and its determinants in mitochondrial CYB gene of respiratory chain across different amphibian groups namely orders anura, urodela and gymnophiona. We observed that CUB was low in CYB gene of amphibia. The gymnophionans had comparatively high bias followed by urodeles and anurans. The codons namely TCA, CCA, CAA, CGA, TGA, AAA and ACA were over-represented in all three orders. The codons such as GCC and TCC were over-represented in anura whereas in urodela, the over-represented codons were TTA, CTA, ATA, GTA, GAA, GGA and GCA. In gymnophiona, GCC, TTA, CTA, ATA, GTA, GAA and GGA codons were over-represented. The regression analysis between effective number of codons (ENC) and nucleobase at the 3rd position revealed that nucleobase A and C influenced CUB positively in order anura, while in urodela and gymnophiona, nucleobase A and T influenced the CUB positively. Mutation pressure and natural selection mutually illustrate the CUB of CYB gene (complex III gene) of amphibia as elucidated by correlation analysis between 3rd nucleotide in a codon and overall nucleotide content of the gene. However, neutrality plot showed that natural selection was the dominant evolutionary factor of CUB.
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Affiliation(s)
- Parvin A Barbhuiya
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakand 788150, Assam, India
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India.
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17
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Begum Y, Mondal SK. Comprehensive study of the genes involved in chlorophyll synthesis and degradation pathways in some monocot and dicot plant species. J Biomol Struct Dyn 2020; 39:2387-2414. [PMID: 32292132 DOI: 10.1080/07391102.2020.1748717] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chlorophyll (Chl) biosynthesis is one of the most important cellular processes essential for plant photosynthesis. Chl degradation pathway is also important catabolic process occurs during leaf senescence, fruit ripening and under biotic or abiotic stress conditions. Here we have systematically investigated the molecular evolution, gene structure, compositional analysis along with ENc plot, correspondence analysis and codon usage bias of the proteins and encoded genes involved in Chl metabolism from monocots and dicots. The gene and species specific phylogenetic trees using amino acid sequences showed clear clustering formation of the selected species based on monocots and dicots but not supported by 18S rRNA. Nucleotide composition of the encoding genes showed that average GC%, GC1%, GC2% and GC3% were higher in monocots. RSCU analysis depicts that genes from monocots for both pathways and genes for synthesis pathway from dicots only biased to G/C-ending synonymous codons but in degradation pathway most optimal codons (except UUG) in dicots biased to A/U-ending synonymous codons. We found strong evidence of episodic diversifying selection at several amino acid sites in all genes investigated. Conserved domain and gene structures were observed for the genes with varying lengths of introns and exons, involved in Chl metabolism along with some intronless genes within synthesis pathway. ENc and correspondence analyses suggested the mutational or selection constraint on the genes to shape the codon usage. These comprehensive studies may be helpful in further research in molecular phylogenetics and genomics and to better understand the evolutionary dynamics of Chl metabolic pathway.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yasmin Begum
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, West Bengal, India.,Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-II), University of Calcutta, Kolkata, West Bengal, India
| | - Sunil Kanti Mondal
- Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India
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18
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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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19
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Feng JM, Jiang CQ, Sun ZY, Hua CJ, Wen JF, Miao W, Xiong J. Single-cell transcriptome sequencing of rumen ciliates provides insight into their molecular adaptations to the anaerobic and carbohydrate-rich rumen microenvironment. Mol Phylogenet Evol 2019; 143:106687. [PMID: 31740334 DOI: 10.1016/j.ympev.2019.106687] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 11/11/2019] [Accepted: 11/13/2019] [Indexed: 01/26/2023]
Abstract
Rumen ciliates are a specialized group of ciliates exclusively found in the anaerobic, carbohydrate-rich rumen microenvironment. However, the molecular and mechanistic basis of the physiological and behavioral adaptation of ciliates to the rumen microenvironment is undefined. We used single-cell transcriptome sequencing to explore the adaptive evolution of three rumen ciliates: two entodiniomorphids, Entodinium furca and Diplodinium dentatum; and one vestibuliferid, Isotricha intestinalis. We found that all three species are members of monophyletic orders within the class Litostomatea, with E. furca and D. dentatum in Entodiniomorphida and I. intestinalis in Vestibuliferida. The two entodiniomorphids might use H2-producing mitochondria and the vestibuliferid might use anaerobic mitochondria to survive under strictly anaerobic conditions. Moreover, carbohydrate-active enzyme (CAZyme) genes were identified in all three species, including cellulases, hemicellulases, and pectinases. The evidence that all three species have acquired prokaryote-derived genes by horizontal gene transfer (HGT) to digest plant biomass includes a significant enrichment of gene ontology categories such as cell wall macromolecule catabolic process and carbohydrate catabolic process and the identification of genes in common between CAZyme and HGT groups. These findings suggest that HGT might be an important mechanism in the adaptive evolution of ciliates to the rumen microenvironment.
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Affiliation(s)
- Jin-Mei Feng
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan 430056, China
| | - Chuan-Qi Jiang
- Shenzhen Institute of Guangdong Ocean University, Shenzhen 518120, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen 518120, China; Shenzhen Dapeng New District Science and Technology Innovation Service Center, Shenzhen 518119, China; Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zong-Yi Sun
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Cong-Jie Hua
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan 430056, China
| | - Jian-Fan Wen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; State Key Laboratory of Freshwater Ecology and Biotechnology of China, Wuhan 430072, China; CAS Center for Excellence in Animal Evolution and Genetics, Kunming 650223, China.
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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20
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Lamolle G, Fontenla S, Rijo G, Tort JF, Smircich P. Compositional Analysis of Flatworm Genomes Shows Strong Codon Usage Biases Across All Classes. Front Genet 2019; 10:771. [PMID: 31543897 PMCID: PMC6739440 DOI: 10.3389/fgene.2019.00771] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/22/2019] [Indexed: 11/13/2022] Open
Abstract
In the present work, we performed a comparative genome-wide analysis of 22 species representative of the main clades and lifestyles of the phylum Platyhelminthes. We selected a set of 700 orthologous genes conserved in all species, measuring changes in GC content, codon, and amino acid usage in orthologous positions. Values of 3rd codon position GC spanned over a wide range, allowing to discriminate two distinctive clusters within freshwater turbellarians, Cestodes and Trematodes respectively. Furthermore, a hierarchical clustering of codon usage data differs remarkably from the phylogenetic tree. Additionally, we detected a synonymous codon usage bias that was more dramatic in extreme GC-poor or GC-rich genomes, i.e., GC-poor Schistosomes preferred to use AT-rich terminated synonymous codons, while GC-rich M. lignano showed the opposite behavior. Interestingly, these biases impacted the amino acidic usage, with preferred amino acids encoded by codons following the GC content trend. These are associated with non-synonymous substitutions at orthologous positions. The detailed analysis of the synonymous and non-synonymous changes provides evidence for a two-hit mechanism where both mutation and selection forces drive the diverse coding strategies of flatworms.
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Affiliation(s)
- Guillermo Lamolle
- Departamento de Genética, Facultad de Medicina, Universidad de la Republica, UDELAR, Montevideo, Uruguay
| | - Santiago Fontenla
- Departamento de Genética, Facultad de Medicina, Universidad de la Republica, UDELAR, Montevideo, Uruguay
| | - Gastón Rijo
- Departamento de Genética, Facultad de Medicina, Universidad de la Republica, UDELAR, Montevideo, Uruguay
| | - Jose F Tort
- Departamento de Genética, Facultad de Medicina, Universidad de la Republica, UDELAR, Montevideo, Uruguay
| | - Pablo Smircich
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, IIBCE, MEC, Montevideo, Uruguay.,Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la Republica, UDELAR, Montevideo, Uruguay
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21
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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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22
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Liu Y, Yang Y, Xu J, Dong X, Gu X, Xie Y, Lai W, Jing B, Peng X, Yang G. Expression and serodiagnostic potential of antigen B and thioredoxin peroxidase from Taenia multiceps. Vet Parasitol 2019; 272:58-63. [PMID: 31395206 DOI: 10.1016/j.vetpar.2019.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/08/2019] [Accepted: 07/11/2019] [Indexed: 10/26/2022]
Abstract
Coenurosis is a serious parasitic disease of herbivorous animals caused by the metacestode of Taenia multiceps (Coenurus cerebralis). Accordingly, a significant amount of research is currently dedicated to the development of appropriate antigens for use in rapid and accurate coenurosis diagnosis kits. In the present study, antigen B (AgB) and thioredoxin peroxidase (TPx) from T. multiceps were cloned and expressed using a prokaryotic system, molecular characterization of Tm-AgB was determined by bioinformatical analyses. The serological diagnostic potentials of rTm-AgB and rTm-TPx were evaluated by indirect ELISA and compared with those of previously reported rTm-AnxB2, rTm-HSP70, and rTm-GST. The results showed that Tm-AgB is a specific lipoprotein of cestodes with good thermal stability. The ELISA assay showed that rTm-AgB exhibited a sensitivity of 95.8% and a specificity of 87.5%, indicating its strong potential for serological diagnosis of T. multiceps.
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Affiliation(s)
- Yuchen Liu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, China.
| | - Yingdong Yang
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua 617000, China.
| | - Jing Xu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, China.
| | - Xiaowei Dong
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, China.
| | - Xiaobin Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, China.
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, China.
| | - Weimin Lai
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, China.
| | - Bo Jing
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, China.
| | - Xuerong Peng
- Department of Chemistry, College of Life and Basic Science, Sichuan Agricultural University, Wenjiang 611130, China.
| | - Guangyou Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, China.
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23
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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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24
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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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25
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Liu Y, Guo C, Dong X, Gu X, Xie Y, Lai W, Peng X, Yang G. Molecular characterisation and expression analysis of two heat-shock proteins in Taenia multiceps. Parasit Vectors 2019; 12:93. [PMID: 30867020 PMCID: PMC6417115 DOI: 10.1186/s13071-019-3352-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/26/2019] [Indexed: 01/06/2023] Open
Abstract
Background Taenia multiceps is a harmful tapeworm and its larval form (coenurus cerebralis) is the causative agent of coenurosis, a disease affecting the health of herbivores, resulting in great economic loss to animal husbandry. Heat-shock proteins (HSPs), expressed in all prokaryotes and eukaryotes, act as molecular chaperones and can affect pathogenicity. Methods Herein, cDNAs of T. multiceps genes Tm-HSP60 and Tm-p36 were cloned and molecularly characterised by bioinformatics analyses. The immunogenicity and immunoreactivity of recombinant rTm-HSP60 and rTm-p36 proteins were investigated by immunoblotting and indirect ELISA was established to evaluate their serodiagnostic potential. Tissue localisation and transcriptional level at different life stages of T. multiceps were determined by immunohistochemical and quantitative real-time PCR analyses. Result The 533 residue rTm-HSP60 and the 314 residue rTm-p36 proteins share typical highly conserved features of HSPs. Tm-p36 shares structural characteristics with metazoan small HSPs, with two N-terminal α-crystallin domains. Compared with Tm-p36, Tm-HSP60 displayed stronger immunogenicity, and the indirect ELISA based on rTm-HSP60 exhibited a sensitivity of 83.3% and a specificity of 87.5%, while rTm-p36 was not suitable to develop indirect ELISA. Tm-HSP60 was widely distributed in all stages of T. multiceps, albeit at relatively low levels, while Tm-p36 was specifically distributed in the protoscolex and oncosphere. Conclusions The sequence, structural and functional analyses of these two HSPs indicates that they may play important roles in the life-cycle of T. multiceps as molecular chaperones. Tm-HSP60 displayed stronger immunogenicity compare to Tm-p36, and has the potential for antibody detection. Tm-p36 was strongly associated with the activation of oncospheres and has potential interest for vaccination. Electronic supplementary material The online version of this article (10.1186/s13071-019-3352-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuchen Liu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, China
| | - Cheng Guo
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, China
| | - Xiaowei Dong
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, China
| | - Xiaobin Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, China
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, China
| | - Weimin Lai
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, China
| | - Xuerong Peng
- Department of Chemistry, College of Life and Basic Science, Sichuan Agricultural University, Wenjiang, 611130, China
| | - Guangyou Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, China.
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26
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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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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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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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Development of a direct PCR assay to detect Taenia multiceps eggs isolated from dog feces. Vet Parasitol 2017; 251:7-11. [PMID: 29426480 DOI: 10.1016/j.vetpar.2017.12.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 01/08/2023]
Abstract
Taenia multiceps is a tapeworm that leads to the death of livestock, resulting in major economic losses worldwide. The adult stage of this parasite invades the small intestine of dogs and other canids. In the present study, we developed a direct PCR assay to detect T. multiceps eggs isolated from dog feces to help curb further outbreaks. The genomic DNA was rapidly released using a lysis buffer and the PCR reaction was developed to amplify a 433-bp fragment of the T. multiceps mitochondrial gene encoding NADH dehydrogenase subunit 5 (nad5) from eggs isolated from dog feces. The procedure could be completed within 3 h, including flotation. The sensitivity of the assay was determined by detecting DNA from defined numbers of eggs, and the specificity was determined by detecting DNA from other intestinal tapeworm and roundworm species that commonly infect dogs. In addition, 14 taeniid-positive fecal samples determined by the flotation technique were collected and further evaluated by the regular PCR and our direct PCR. The results showed that the direct PCR developed herein was sensitive enough to detect the DNA from as few as 10 T. multiceps eggs and that no cross-reactions with other tapeworm and roundworm were observed, suggesting its high sensitivity and specificity for T. multiceps detection. Moreover, 14 taeniid-positive samples were screened by the regular PCR and direct PCR, with detection rates of 78.6% and 85.7%, respectively. In conclusion, the direct PCR assay developed in the present study has high sensitivity and specificity to identify T. multiceps eggs isolated from dog feces and therefore could represent an invaluable tool to identify T. multiceps outbreaks and would contribute to future clinical applications.
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