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Yang Q, Xin C, Xiao QS, Lin YT, Li L, Zhao JL. Codon usage bias in chloroplast genes implicate adaptive evolution of four ginger species. FRONTIERS IN PLANT SCIENCE 2023; 14:1304264. [PMID: 38169692 PMCID: PMC10758403 DOI: 10.3389/fpls.2023.1304264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024]
Abstract
Codon usage bias (CUB) refers to different codons exhibiting varying frequencies of usage in the genome. Studying CUB is crucial for understanding genome structure, function, and evolutionary processes. Herein, we investigated the codon usage patterns and influencing factors of protein-coding genes in the chloroplast genomes of four sister genera (monophyletic Roscoea and Cautleya, and monophyletic Pommereschea and Rhynchanthus) from the Zingiberaceae family with contrasting habitats in southwestern China. These genera exhibit distinct habitats, providing a unique opportunity to explore the adaptive evolution of codon usage. We conducted a comprehensive analysis of nucleotide composition and codon usage on protein-coding genes in the chloroplast genomes. The study focused on understanding the relationship between codon usage and environmental adaptation, with a particular emphasis on genes associated with photosynthesis. Nucleotide composition analysis revealed that the overall G/C content of the coding genes was ˂ 48%, indicating an enrichment of A/T bases. Additionally, synonymous and optimal codons were biased toward ending with A/U bases. Natural selection is the primary factor influencing CUB characteristics, particularly photosynthesis-associated genes. We observed differential gene expressions related to light adaptation among sister genera inhabiting different environments. Certain codons were favored under specific conditions, possibly contributing to gene expression regulation in particular environments. This study provides insights into the adaptive evolution of these sister genera by analyzing CUB and offers theoretical assistance for understanding gene expression and regulation. In addition, the data support the relationship between RNA editing and CUB, and the findings shed light on potential research directions for investigating adaptive evolution.
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Affiliation(s)
- Qian Yang
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Cheng Xin
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Qing-Song Xiao
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Ya-Ting Lin
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Li Li
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Jian-Li Zhao
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
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2
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Li J, Li N, Roellig DM, Zhao W, Guo Y, Feng Y, Xiao L. High subtelomeric GC content in the genome of a zoonotic Cryptosporidium species. Microb Genom 2023; 9:mgen001052. [PMID: 37399068 PMCID: PMC10438818 DOI: 10.1099/mgen.0.001052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/24/2023] [Indexed: 07/04/2023] Open
Abstract
Cryptosporidium canis is a zoonotic species causing cryptosporidiosis in humans in addition to its natural hosts dogs and other fur animals. To understand the genetic basis for host adaptation, we sequenced the genomes of C. canis from dogs, minks, and foxes and conducted a comparative genomics analysis. While the genomes of C. canis have similar gene contents and organisations, they (~41.0 %) and C. felis (39.6 %) have GC content much higher than other Cryptosporidium spp. (24.3-32.9 %) sequenced to date. The high GC content is mostly restricted to subtelomeric regions of the eight chromosomes. Most of these GC-balanced genes encode Cryptosporidium-specific proteins that have intrinsically disordered regions and are involved in host-parasite interactions. Natural selection appears to play a more important role in the evolution of codon usage in GC-balanced C. canis, and most of the GC-balanced genes have undergone positive selection. While the identity in whole genome sequences between the mink- and dog-derived isolates is 99.9 % (9365 SNVs), it is only 96.0 % (362 894 SNVs) between them and the fox-derived isolate. In agreement with this, the fox-derived isolate possesses more subtelomeric genes encoding invasion-related protein families. Therefore, the change in subtelomeric GC content appears to be responsible for the more GC-balanced C. canis genomes, and the fox-derived isolate could represent a new Cryptosporidium species.
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Affiliation(s)
- Jiayu Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Na Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Dawn M. Roellig
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Wentao Zhao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Yaqiong Guo
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Yaoyu Feng
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Lihua Xiao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
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3
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Wang ZK, Liu Y, Zheng HY, Tang MQ, Xie SQ. Comparative Analysis of Codon Usage Patterns in Nuclear and Chloroplast Genome of Dalbergia (Fabaceae). Genes (Basel) 2023; 14:genes14051110. [PMID: 37239470 DOI: 10.3390/genes14051110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/04/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
The Dalbergia plants are widely distributed across more than 130 tropical and subtropical countries and have significant economic and medicinal value. Codon usage bias (CUB) is a critical feature for studying gene function and evolution, which can provide a better understanding of biological gene regulation. In this study, we comprehensively analyzed the CUB patterns of the nuclear genome, chloroplast genome, and gene expression, as well as systematic evolution of Dalbergia species. Our results showed that the synonymous and optimal codons in the coding regions of both nuclear and chloroplast genome of Dalbergia preferred ending with A/U at the third codon base. Natural selection was the primary factor affecting the CUB features. Furthermore, in highly expressed genes of Dalbergia odorifera, we found that genes with stronger CUB exhibited higher expression levels, and these highly expressed genes tended to favor the use of G/C-ending codons. In addition, the branching patterns of the protein-coding sequences and the chloroplast genome sequences were very similar in the systematic tree, and different with the cluster from the CUB of the chloroplast genome. This study highlights the CUB patterns and features of Dalbergia species in different genomes, explores the correlation between CUB preferences and gene expression, and further investigates the systematic evolution of Dalbergia, providing new insights into codon biology and the evolution of Dalbergia plants.
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Affiliation(s)
- Zu-Kai Wang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, School of Forestry, Hainan University, Haikou 570228, China
| | - Yi Liu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, School of Forestry, Hainan University, Haikou 570228, China
| | - Hao-Yue Zheng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, School of Forestry, Hainan University, Haikou 570228, China
| | - Min-Qiang Tang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, School of Forestry, Hainan University, Haikou 570228, China
| | - Shang-Qian Xie
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, School of Forestry, Hainan University, Haikou 570228, China
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Pu F, Wang R, Yang X, Hu X, Wang J, Zhang L, Zhao Y, Zhang D, Liu Z, Liu J. Nucleotide and codon usage biases involved in the evolution of African swine fever virus: A comparative genomics analysis. J Basic Microbiol 2023; 63:499-518. [PMID: 36782108 DOI: 10.1002/jobm.202200624] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/05/2023] [Accepted: 01/21/2023] [Indexed: 02/15/2023]
Abstract
Since African swine fever virus (ASFV) replication is closely related to its host's machinery, codon usage of viral genome can be subject to selection pressures. A better understanding of codon usage can give new insights into viral evolution. We implemented information entropy and revealed that the nucleotide usage pattern of ASFV is significantly associated with viral isolation factors (region and time), especially the usages of thymine and cytosine. Despite the domination of adenine and thymine in the viral genome, we found that mutation pressure alters the overall codon usage pattern of ASFV, followed by selective forces from natural selection. Moreover, the nucleotide skew index at the gene level indicates that nucleotide usages influencing synonymous codon bias of ASFV are significantly correlated with viral protein hydropathy. Finally, evolutionary plasticity is proved to contribute to the weakness in synonymous codons with A- or T-end serving as optimal codons of ASFV, suggesting that fine-tuning translation selection plays a role in synonymous codon usages of ASFV for adapting host. Taken together, ASFV is subject to evolutionary dynamics on nucleotide selections and synonymous codon usage, and our detailed analysis offers deeper insights into the genetic characteristics of this newly emerging virus around the world.
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Affiliation(s)
- Feiyang Pu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Rui Wang
- Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA
| | - Xuanye Yang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Xinyan Hu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Jinqian Wang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Lijuan Zhang
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Yongqing Zhao
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Derong Zhang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Zewen Liu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Junlin Liu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
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Li Y, Khandia R, Papadakis M, Alexiou A, Simonov AN, Khan AA. An investigation of codon usage pattern analysis in pancreatitis associated genes. BMC Genom Data 2022; 23:81. [PMID: 36434531 PMCID: PMC9700901 DOI: 10.1186/s12863-022-01089-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 10/10/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Pancreatitis is an inflammatory disorder resulting from the autoactivation of trypsinogen in the pancreas. The genetic basis of the disease is an old phenomenon, and evidence is accumulating for the involvement of synonymous/non-synonymous codon variants in disease initiation and progression. RESULTS The present study envisaged a panel of 26 genes involved in pancreatitis for their codon choices, compositional analysis, relative dinucleotide frequency, nucleotide disproportion, protein physical properties, gene expression, codon bias, and interrelated of all these factors. In this set of genes, gene length was positively correlated with nucleotide skews and codon usage bias. Codon usage of any gene is dependent upon its AT and GC component; however, AGG, CGT, and CGA encoding for Arg, TCG for Ser, GTC for Val, and CCA for Pro were independent of nucleotide compositions. In addition, Codon GTC showed a correlation with protein properties, isoelectric point, instability index, and frequency of basic amino acids. We also investigated the effect of various evolutionary forces in shaping the codon usage choices of genes. CONCLUSIONS This study will enable us to gain insight into the molecular signatures associated with the disease that might help identify more potential genes contributing to enhanced risk for pancreatitis. All the genes associated with pancreatitis are generally associated with physiological function, and mutations causing loss of function, over or under expression leads to an ailment. Therefore, the present study attempts to envisage the molecular signature in a group of genes that lead to pancreatitis in case of malfunction.
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Affiliation(s)
- Yuanyang Li
- Third-Grade Pharmacological Laboratory On Chinese Medicine Approved By State Administration of Traditional Chinese Medicine, Medical College of China Three Gorges, Yichang, China ,grid.254148.e0000 0001 0033 6389College of Medical Science, China Three Gorges University, Yichang, China
| | - Rekha Khandia
- grid.411530.20000 0001 0694 3745Department of Biochemistry and Genetics, Barkatullah University, Bhopal, MP 462026 India
| | - Marios Papadakis
- grid.412581.b0000 0000 9024 6397Department of Surgery II, University Hospital Witten-Herdecke, University of Witten-Herdecke, Heusnerstrasse 40, 42283 Wuppertal, Germany
| | - Athanasios Alexiou
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, Australia ,AFNP Med Austria, Vienna, Austria
| | | | - Azmat Ali Khan
- grid.56302.320000 0004 1773 5396Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451 Saudi Arabia
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Xiao G, Zhou J, Huo Z, Wu T, Li Y, Li Y, Wang Y, Wang M. The Shift in Synonymous Codon Usage Reveals Similar Genomic Variation during Domestication of Asian and African Rice. Int J Mol Sci 2022; 23:12860. [PMID: 36361651 PMCID: PMC9656316 DOI: 10.3390/ijms232112860] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 10/29/2023] Open
Abstract
The domestication of wild rice occurred together with genomic variation, including the synonymous nucleotide substitutions that result in synonymous codon usage bias (SCUB). SCUB mirrors the evolutionary specialization of plants, but its characteristics during domestication were not yet addressed. Here, we found cytosine- and guanidine-ending (NNC and NNG) synonymous codons (SCs) were more pronounced than adenosine- and thymine-ending SCs (NNA and NNT) in both wild and cultivated species of Asian and African rice. The ratios of NNC/G to NNA/T codons gradually decreased following the rise in the number of introns, and the preference for NNA/T codons became more obvious in genes with more introns in cultivated rice when compared with those in wild rice. SCUB frequencies were heterogeneous across the exons, with a higher preference for NNA/T in internal exons than in terminal exons. The preference for NNA/T in internal but not terminal exons was more predominant in cultivated rice than in wild rice, with the difference between wild and cultivated rice becoming more remarkable with the rise in exon numbers. The difference in the ratios of codon combinations representing DNA methylation-mediated conversion from cytosine to thymine between wild and cultivated rice coincided with their difference in SCUB frequencies, suggesting that SCUB reveals the possible association between genetic and epigenetic variation during the domestication of rice. Similar patterns of SCUB shift in Asian and African rice indicate that genomic variation occurs in the same non-random manner. SCUB representing non-neutral synonymous mutations can provide insight into the mechanism of genomic variation in domestication and can be used for the genetic dissection of agricultural traits in rice and other crops.
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Affiliation(s)
- Guilian Xiao
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Junzhi Zhou
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Zhiheng Huo
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Tong Wu
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Yingchun Li
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Yajing Li
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Yanxia Wang
- Shijiazhuang Academy of Agriculture and Forestry Sciences, Shijiazhuang 050041, China
| | - Mengcheng Wang
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
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Tian G, Xiao G, Wu T, Zhou J, Xu W, Wang Y, Xia G, Wang M. Alteration of synonymous codon usage bias accompanies polyploidization in wheat. Front Genet 2022; 13:979902. [PMID: 36313462 PMCID: PMC9614214 DOI: 10.3389/fgene.2022.979902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
The diploidization of polyploid genomes is accompanied by genomic variation, including synonymous nucleotide substitutions that may lead to synonymous codon usage bias (SCUB). SCUB can mirror the evolutionary specialization of plants, but its effect on the formation of polyploidies is not well documented. We explored this issue here with hexaploid wheat and its progenitors. Synonymous codons (SCs) ending in either cytosine (NNC) or guanidine (NNG) were more frequent than those ending in either adenosine (NNA) or thymine (NNT), and the preference for NNC/G codons followed the increase in genome ploidy. The ratios between NNC/G and NNA/T codons gradually decreased in genes with more introns, and the difference in these ratios between wheat and its progenitors diminished with increasing ploidy. SCUB frequencies were heterogeneous among exons, and the bias preferred to NNA/T in more internal exons, especially for genes with more exons; while the preference did not appear to associate with ploidy. The SCUB alteration of the progenitors was different during the formation of hexaploid wheat, so that SCUB was the homogeneous among A, B and D subgenomes. DNA methylation-mediated conversion from cytosine to thymine weakened following the increase of genome ploidy, coinciding with the stronger bias for NNC/G SCs in the genome as a function of ploidy, suggesting that SCUB contribute to the epigenetic variation in hexaploid wheat. The patterns in SCUB mirrored the formation of hexaploid wheat, which provides new insight into genome shock-induced genetic variation during polyploidization. SCs representing non-neutral synonymous mutations can be used for genetic dissection and improvement of agricultural traits of wheat and other polyploidies.
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Affiliation(s)
- Geng Tian
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Guilian Xiao
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Tong Wu
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Junzhi Zhou
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Wenjing Xu
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Yanxia Wang
- Shijiazhuang Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Guangmin Xia
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Mengcheng Wang
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
- *Correspondence: Mengcheng Wang,
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Begum NS, Chakraborty S. Influencing elements of codon usage bias in Birnaviridae and its evolutionary analysis. Virus Res 2022; 310:198672. [PMID: 34986367 DOI: 10.1016/j.virusres.2021.198672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/25/2021] [Accepted: 12/30/2021] [Indexed: 11/25/2022]
Abstract
Birnaviridae is a family of double stranded (ds) RNA virus with non-enveloped virions and 2-segmented genomes. These viruses are known to cause diseases in many hosts. Virus of this family has affected the fish and poultry economy in a wide sector. Unevenness in the use of synonymous codons for a particular amino acid in the coding strand of DNA is known as codon usage bias (CUB). Codons that code the same amino acid are used with variable frequency in a variety of life forms. To understand the pattern of CUB in Birnaviridae, we carried out bioinformatics study to understand the properties of coding sequences of proteins. ENC value of Birnaviridae suggested low CUB. Nucleotide analysis revealed high GC content. Parameters such as RSCU values, nucleotide skewness, translational selection, parity plot and neutrality plot were studied to investigate the pattern of codon use and it was clear that both mutational pressure and natural selection contributed to the designing of CUB in Birnaviridae family. The neutrality plot revealed natural selection to dominate the structuring of CUB and hence remained the major CUB determinant in Birnaviridae. Outcome of our study exemplified the pattern of codon use in the Birnaviridae genomes and contributed the basic primary data for fundamental evolutionary research on them.
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Affiliation(s)
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar 788011, Assam, 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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10
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Nair RR, Mohan M, Rudramurthy GR, Vivekanandam R, Satheshkumar PS. Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus. Pathogens 2021; 10:1649. [PMID: 34959603 PMCID: PMC8703355 DOI: 10.3390/pathogens10121649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 11/22/2022] Open
Abstract
Trends associated with codon usage in molluscum contagiosum virus (MCV) and factors governing the evolution of codon usage have not been investigated so far. In this study, attempts were made to decipher the codon usage trends and discover the major evolutionary forces that influence the patterns of codon usage in MCV with special reference to sub-types 1 and 2, MCV-1 and MCV-2, respectively. Three hypotheses were tested: (1) codon usage patterns of MCV-1 and MCV-2 are identical; (2) SCUB (synonymous codon usage bias) patterns of MCV-1 and MCV-2 slightly deviate from that of human host to avoid affecting the fitness of host; and (3) translational selection predominantly shapes the SCUB of MCV-1 and MCV-2. Various codon usage indices viz. relative codon usage value, effective number of codons and codon adaptation index were calculated to infer the nature of codon usage. Correspondence analysis and correlation analysis were performed to assess the relative contribution of silent base contents and significance of codon usage indices in defining bias in codon usage. Among the tested hypotheses, only the second and third hypotheses were accepted.
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Affiliation(s)
- Rahul Raveendran Nair
- Centre for Evolutionary Ecology, Aushmath Biosciences, Vadavalli Post, Coimbatore 641041, India
| | - Manikandan Mohan
- College of Pharmacy, University of Georgia, Athens, GA 30605, USA;
| | | | - Reethu Vivekanandam
- Department of Biotechnology, Bharathiyar University, Coimbatore 641046, 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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12
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Ata G, Wang H, Bai H, Yao X, Tao S. Edging on Mutational Bias, Induced Natural Selection From Host and Natural Reservoirs Predominates Codon Usage Evolution in Hantaan Virus. Front Microbiol 2021; 12:699788. [PMID: 34276633 PMCID: PMC8283416 DOI: 10.3389/fmicb.2021.699788] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 06/07/2021] [Indexed: 12/14/2022] Open
Abstract
The molecular evolutionary dynamics that shape hantaviruses’ evolution are poorly understood even now, besides the contribution of virus-host interaction to their evolution remains an open question. Our study aimed to investigate these two aspects in Hantaan virus (HTNV)—the prototype of hantaviruses and an emerging zoonotic pathogen that infects humans, causing hemorrhagic fever with renal syndrome (HFRS): endemic in Far East Russia, China, and South Korea—via a comprehensive, phylogenetic-dependent codon usage analysis. We found that host- and natural reservoir-induced natural selection is the primary determinant of its biased codon choices, exceeding the mutational bias effect. The phylogenetic analysis of HTNV strains resulted in three distinct clades: South Korean, Russian, and Chinese. An effective number of codon (ENC) analysis showed a slightly biased codon usage in HTNV genomes. Nucleotide composition and RSCU analyses revealed a significant bias toward A/U nucleotides and A/U-ended codons, indicating the potential influence of mutational bias on the codon usage patterns of HTNV. Via ENC-plot, Parity Rule 2 (PR2), and neutrality plot analyses, we would conclude the presence of both mutation pressure and natural selection effect in shaping the codon usage patterns of HTNV; however, natural selection is the dominant factor influencing its codon usage bias. Codon adaptation index (CAI), Relative codon deoptimization index (RCDI), and Similarity Index (SiD) analyses uncovered the intense selection pressure from the host (Human) and natural reservoirs (Striped field mouse and Chinese white-bellied rat) in shaping HTNV biased codon choices. Our study clearly revealed the evolutionary processes in HTNV and the role of virus-host interaction in its evolution. Moreover, it opens the door for a more comprehensive codon usage analysis for all hantaviruses species to determine their molecular evolutionary dynamics and adaptability to several hosts and environments. We believe that our research will help in a better and deep understanding of HTNV evolution that will serve its future basic research and aid live attenuated vaccines design.
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Affiliation(s)
- Galal Ata
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Xianyang, China
| | - Hao Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Xianyang, China
| | - Haoxiang Bai
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Xianyang, China
| | - Xiaoting Yao
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Shiheng Tao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Xianyang, China
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13
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Xu W, Li Y, Li Y, Liu C, Wang Y, Xia G, Wang M. Asymmetric Somatic Hybridization Affects Synonymous Codon Usage Bias in Wheat. Front Genet 2021; 12:682324. [PMID: 34178040 PMCID: PMC8226224 DOI: 10.3389/fgene.2021.682324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/07/2021] [Indexed: 11/24/2022] Open
Abstract
Asymmetric somatic hybridization is an efficient strategy for crop breeding by introducing exogenous chromatin fragments, which leads to whole genomic shock and local chromosomal shock that induces genome-wide genetic variation including indel (insertion and deletion) and nucleotide substitution. Nucleotide substitution causes synonymous codon usage bias (SCUB), an indicator of genomic mutation and natural selection. However, how asymmetric somatic hybridization affects SCUB has not been addressed. Here, we explored this issue by comparing expressed sequence tags of a common wheat cultivar and its asymmetric somatic hybrid line. Asymmetric somatic hybridization affected SCUB and promoted the bias to A- and T-ending synonymous codon (SCs). SCUB frequencies in chromosomes introgressed with exogenous fragments were comparable to those in chromosomes without exogenous fragments, showing that exogenous fragments had no local chromosomal effect. Asymmetric somatic hybridization affected SCUB frequencies in indel-flanking sequences more strongly than in non-flanking sequences, and this stronger effect was present in both chromosomes with and without exogenous fragments. DNA methylation-driven SCUB shift was more pronounced than other SC pairs. SCUB shift was similar among seven groups of allelic chromosomes as well as three sub-genomes. Our work demonstrates that the SCUB shift induced by asymmetric somatic hybridization is attributed to the whole genomic shock, and DNA methylation is a putative force of SCUB shift during asymmetric somatic hybridization. Asymmetric somatic hybridization provides an available method for deepening the nature of SCUB shift and genetic variation induced by genomic shock.
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Affiliation(s)
- Wenjing Xu
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, China
| | - Yingchun Li
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, China
| | - Yajing Li
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, China
| | - Chun Liu
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, China
| | - Yanxia Wang
- Shijiazhuang Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Guangmin Xia
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, China
| | - Mengcheng Wang
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, China
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14
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Wang L, Li Y, Guo Z, Yi Y, Zhang H, Shangguan H, Huang C, Ge J. Genetic changes and evolutionary analysis of canine circovirus. Arch Virol 2021; 166:2235-2247. [PMID: 34104994 DOI: 10.1007/s00705-021-05125-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/15/2021] [Indexed: 11/28/2022]
Abstract
Canine circovirus (canineCV) has been found to be associated with vasculitis, hemorrhage, hemorrhagic enteritis, and diarrhea of canines. CanineCV, like other circoviruses, may also be associated with lymphoid depletion and immunosuppression. This circovirus has been detected worldwide in different countries and species. Recombination and mutation events in the canineCV genome have been described, indicating that the virus is continuing to evolve. However, the origin, codon usage patterns, and host adaptation of canineCV remain to be studied. Here, the coding sequences of 93 canineCV sequences available in the GenBank database were used for analysis. The results showed that canineCV sequences could be classified into five genotypes, as confirmed by phylogenetic and principal component analysis (PCA). Maximum clade credibility (MCC) and maximum-likelihood (ML) trees suggested that canineCV originated from bat circovirus. G/T and A/C nucleotide biases were observed in ORF1 and ORF2, respectively, and a low codon usage bias (CUB) was found in canineCV using an effective number of codon (ENC) analysis. Correlation analysis, ENC plot analysis and neutrality plot analysis indicated that the codon usage pattern was mainly shaped by natural selection. Codon adaptation index (CAI) analysis, relative codon deoptimization index (RCDI) analysis, and similarity index (SiD) analysis revealed a better adaption to Vulpes vulpes than to Canis familiaris. Furthermore, a cross-species transmission hypothesis that canineCV may have evolved from bats (origin analysis) and subsequently adapted to wolves, arctic foxes, dogs, and red foxes, was proposed. This study contributes to our understanding of the factors related to canineCV evolution and host adaption.
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Affiliation(s)
- Lin Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Yifan Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Zhiyuan Guo
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Ying Yi
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Han Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Haikun Shangguan
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Chengshi Huang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Junwei Ge
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China. .,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, 150030, China.
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15
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Bose D, Mukhopadhyay S. The hunt for a yet unknown: Common molecular signature in some genetically monomorphic enterobacteria. J Basic Microbiol 2021; 61:524-546. [PMID: 33991346 DOI: 10.1002/jobm.202000630] [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: 11/24/2020] [Revised: 04/04/2021] [Accepted: 04/22/2021] [Indexed: 11/09/2022]
Abstract
Mark Achtman introduced the term "genetically monomorphic bacteria" (GM bacteria) for some human and plant pathogens. They displayed a great uniformity in terms of their "genetic" properties. This "uniformity" poses a challenge to microbiologists. To address these problems, we used CodonW and IslandViewer 3 as analytical tools and took Escherichia coli, Salmonella, and Shigella strains as a model organisms. We hypothesized that GM bacterium contains a common molecular signature among them. We have found a significant correlation regarding the number of protein-coding genes, predicted highly expressed genes, and the highest length of gene in this regard. On the other hand, the correspondence analysis of pathogenicity-related genes identified by IslandViewer 3 displayed a somewhat unique pattern in GM bacteria. The probable pathogenic genes are clustered into two separate groups, which is a hallmark of some pattern. Similar genes of non-monomorphic pathogenic strain clustered almost similarly, but the clusters are joined together, they are not completely separated. These features, in our considered view, may be considered as codon usages signatures of these bacteria, and E. coli in particular.
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Affiliation(s)
- Debadin Bose
- Department of Botany, Kabi Nazrul College, Murarai, West Bengal, India
| | - Subhasis Mukhopadhyay
- Distributed Information Centre for Bioinformatics, Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Calcutta, West Bengal, India
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16
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Abstract
Recombination increases the local GC-content in genomic regions through GC-biased gene conversion (gBGC). The recent discovery of a large genomic region with extreme GC-content in the fat sand rat Psammomys obesus provides a model to study the effects of gBGC on chromosome evolution. Here, we compare the GC-content and GC-to-AT substitution patterns across protein-coding genes of four gerbil species and two murine rodents (mouse and rat). We find that the known high-GC region is present in all the gerbils, and is characterized by high substitution rates for all mutational categories (AT-to-GC, GC-to-AT, and GC-conservative) both at synonymous and nonsynonymous sites. A higher AT-to-GC than GC-to-AT rate is consistent with the high GC-content. Additionally, we find more than 300 genes outside the known region with outlying values of AT-to-GC synonymous substitution rates in gerbils. Of these, over 30% are organized into at least 17 large clusters observable at the megabase-scale. The unusual GC-skewed substitution pattern suggests the evolution of genomic regions with very high recombination rates in the gerbil lineage, which can lead to a runaway increase in GC-content. Our results imply that rapid evolution of GC-content is possible in mammals, with gerbil species providing a powerful model to study the mechanisms of gBGC.
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Affiliation(s)
- Rodrigo Pracana
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - John F Mulley
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
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17
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Abstract
Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of genetic tools that allow to uncover mechanistic links between genotype and phenotype. Moreover, given its worldwide distribution in diverse habitats and its moderate genome-size, Drosophila has proven very powerful for population genetics inference and was one of the first eukaryotes whose genome was fully sequenced. In this book chapter, we provide a brief historical overview of research in Drosophila and then focus on recent advances during the genomic era. After describing different types and sources of genomic data, we discuss mechanisms of neutral evolution including the demographic history of Drosophila and the effects of recombination and biased gene conversion. Then, we review recent advances in detecting genome-wide signals of selection, such as soft and hard selective sweeps. We further provide a brief introduction to background selection, selection of noncoding DNA and codon usage and focus on the role of structural variants, such as transposable elements and chromosomal inversions, during the adaptive process. Finally, we discuss how genomic data helps to dissect neutral and adaptive evolutionary mechanisms that shape genetic and phenotypic variation in natural populations along environmental gradients. In summary, this book chapter serves as a starting point to Drosophila population genomics and provides an introduction to the system and an overview to data sources, important population genetic concepts and recent advances in the field.
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18
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Abstract
The development of safe and effective vaccines against viruses is central to disease control. With advancements in DNA synthesis technology, the production of synthetic viral genomes has fueled many research efforts that aim to generate attenuated viruses by introducing synonymous mutations. Elucidation of the mechanisms underlying virus attenuation through synonymous mutagenesis is revealing interesting new biology that can be exploited for vaccine development. Here, we review recent advancements in this field of synthetic virology and focus on the molecular mechanisms of attenuation by genetic recoding of viruses. We highlight the action of the zinc finger antiviral protein (ZAP) and RNase L, two proteins involved in the inhibition of viruses enriched for CpG and UpA dinucleotides, that are often the products of virus recoding algorithms. Additionally, we discuss current challenges in the field as well as studies that may illuminate how other host functions, such as translation, are potentially involved in the attenuation of recoded viruses.
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19
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Barbhuiya RI, Uddin A, Chakraborty S. Codon usage pattern and its influencing factors for mitochondrial CO genes among different classes of Arthropoda. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:313-326. [PMID: 32755341 DOI: 10.1080/24701394.2020.1800661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Analysis of codon usage bias (CUB) is very much important in perceiving the knowledge of molecular biology, the discovery of a new gene, designing of transgenes and evolution of gene. In this study, we analyzed compositional features and codon usage of MT-CO (COI, COII and COIII) genes among the classes of Arthropoda to explore the pattern of CUB as no research work was reported yet. Nucleotide composition analysis in CO genes suggested that the genes were AT-rich in all the four classes of Arthropoda. CUB was low in all the classes of Arthropoda for MT-CO genes as revealed from a high effective number of codons (ENC). We also found that the evolutionary forces namely mutation pressure and natural selection were the key influencing factors in CUB among MT-CO genes as revealed by correlation analysis between overall nucleotide composition and nucleotide composition at the 3rd codon position. Correspondence analysis suggested that the pattern of CUB was different among the classes of Arthropoda. Further, it was revealed from the neutrality plot that natural selection had a dominant role while mutation pressure exhibited a minor role in structuring the pattern of codon usage in all the classes of Arthropoda across COI, COII and COIII genes.
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Affiliation(s)
| | - Arif Uddin
- Department of Zoology, M. H. C. M. Science College, Hailakandi, India
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20
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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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21
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Machado HE, Lawrie DS, Petrov DA. Pervasive Strong Selection at the Level of Codon Usage Bias in Drosophila melanogaster. Genetics 2020; 214:511-528. [PMID: 31871131 PMCID: PMC7017021 DOI: 10.1534/genetics.119.302542] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/12/2019] [Indexed: 11/18/2022] Open
Abstract
Codon usage bias (CUB), where certain codons are used more frequently than expected by chance, is a ubiquitous phenomenon and occurs across the tree of life. The dominant paradigm is that the proportion of preferred codons is set by weak selection. While experimental changes in codon usage have at times shown large phenotypic effects in contrast to this paradigm, genome-wide population genetic estimates have supported the weak selection model. Here we use deep genomic population sequencing of two Drosophila melanogaster populations to measure selection on synonymous sites in a way that allowed us to estimate the prevalence of both weak and strong purifying selection. We find that selection in favor of preferred codons ranges from weak (|Nes| ∼ 1) to strong (|Nes| > 10), with strong selection acting on 10-20% of synonymous sites in preferred codons. While previous studies indicated that selection at synonymous sites could be strong, this is the first study to detect and quantify strong selection specifically at the level of CUB. Further, we find that CUB-associated polymorphism accounts for the majority of strong selection on synonymous sites, with secondary contributions of splicing (selection on alternatively spliced genes, splice junctions, and spliceosome-bound sites) and transcription factor binding. Our findings support a new model of CUB and indicate that the functional importance of CUB, as well as synonymous sites in general, have been underestimated.
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Affiliation(s)
- Heather E Machado
- Cancer, Ageing, and Somatic Mutation, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - David S Lawrie
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697-3958
| | - Dmitri A Petrov
- Department of Biology, Stanford University, California 94305-5020
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22
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Novoa EM, Jungreis I, Jaillon O, Kellis M. Elucidation of Codon Usage Signatures across the Domains of Life. Mol Biol Evol 2020; 36:2328-2339. [PMID: 31220870 PMCID: PMC6759073 DOI: 10.1093/molbev/msz124] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Because of the degeneracy of the genetic code, multiple codons are translated into the same amino acid. Despite being “synonymous,” these codons are not equally used. Selective pressures are thought to drive the choice among synonymous codons within a genome, while GC content, which is typically attributed to mutational drift, is the major determinant of variation across species. Here, we find that in addition to GC content, interspecies codon usage signatures can also be detected. More specifically, we show that a single amino acid, arginine, is the major contributor to codon usage bias differences across domains of life. We then exploit this finding and show that domain-specific codon bias signatures can be used to classify a given sequence into its corresponding domain of life with high accuracy. We then wondered whether the inclusion of codon usage codon autocorrelation patterns, which reflects the nonrandom distribution of codon occurrences throughout a transcript, might improve the classification performance of our algorithm. However, we find that autocorrelation patterns are not domain-specific, and surprisingly, are unrelated to tRNA reusage, in contrast to previous reports. Instead, our results suggest that codon autocorrelation patterns are a by-product of codon optimality throughout a sequence, where highly expressed genes display autocorrelated “optimal” codons, whereas lowly expressed genes display autocorrelated “nonoptimal” codons.
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Affiliation(s)
- Eva Maria Novoa
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,University of New South Wales Sydney, NSW, Australia
| | - Irwin Jungreis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Olivier Jaillon
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Castellano D, Eyre-Walker A, Munch K. Impact of Mutation Rate and Selection at Linked Sites on DNA Variation across the Genomes of Humans and Other Homininae. Genome Biol Evol 2020; 12:3550-3561. [PMID: 31596481 PMCID: PMC6944223 DOI: 10.1093/gbe/evz215] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2019] [Indexed: 12/23/2022] Open
Abstract
DNA diversity varies across the genome of many species. Variation in diversity across a genome might arise from regional variation in the mutation rate, variation in the intensity and mode of natural selection, and regional variation in the recombination rate. We show that both noncoding and nonsynonymous diversity are positively correlated to a measure of the mutation rate and the recombination rate and negatively correlated to the density of conserved sequences in 50 kb windows across the genomes of humans and nonhuman homininae. Interestingly, we find that although noncoding diversity is equally affected by these three genomic variables, nonsynonymous diversity is mostly dominated by the density of conserved sequences. The positive correlation between diversity and our measure of the mutation rate seems to be largely a direct consequence of regions with higher mutation rates having more diversity. However, the positive correlation with recombination rate and the negative correlation with the density of conserved sequences suggest that selection at linked sites also affect levels of diversity. This is supported by the observation that the ratio of the number of nonsynonymous to noncoding polymorphisms is negatively correlated to a measure of the effective population size across the genome. We show these patterns persist even when we restrict our analysis to GC-conservative mutations, demonstrating that the patterns are not driven by GC biased gene conversion. In conclusion, our comparative analyses describe how recombination rate, gene density, and mutation rate interact to produce the patterns of DNA diversity that we observe along the hominine genomes.
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Affiliation(s)
- David Castellano
- Bioinformatics Research Centre, Aarhus University, Denmark
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, Spain
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, Denmark
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24
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Nucleotide composition affects codon usage toward the 3'-end. PLoS One 2019; 14:e0225633. [PMID: 31800603 PMCID: PMC6892556 DOI: 10.1371/journal.pone.0225633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 11/09/2019] [Indexed: 12/24/2022] Open
Abstract
The 3’-end of the coding sequence in several species is known to show specific codon usage bias. Several factors have been suggested to underlie this phenomenon, including selection against translation efficiency, selection for translation accuracy, and selection against RNA folding. All are supported by some evidence, but there is no general agreement as to which factors are the main determinants. Nor is it known how universal this phenomenon is, and whether the same factors explain it in different species. To answer these questions, we developed a measure that quantifies the codon usage bias at the gene end, and used it to compute this bias for 91 species that span the three domains of life. In addition, we characterized the codons in each species by features that allow discrimination between the different factors. Combining all these data, we were able to show that there is a universal trend to favor AT-rich codons toward the gene end. Moreover, we suggest that this trend is explained by avoidance from forming RNA secondary structures around the stop codon, which may interfere with normal translation termination.
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25
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Classification of Hot and Cold Recombination Regions in Saccharomyces cerevisiae: Comparative Analysis of Two Machine Learning Techniques. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES INDIA SECTION A-PHYSICAL SCIENCES 2019. [DOI: 10.1007/s40010-017-0427-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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26
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Barbhuiya RI, Uddin A, Chakraborty S. Compositional properties and codon usage pattern of mitochondrial ATP gene in different classes of Arthropoda. Genetica 2019; 147:231-248. [PMID: 31152294 DOI: 10.1007/s10709-019-00067-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 05/22/2019] [Indexed: 12/17/2022]
Abstract
Codon usage bias (CUB) is defined as the usage of synonymous codons unequally for an amino acid in a gene transcript. It is influenced by both mutation pressure and natural selection and is a species-specific property. In our current study, we used bioinformatic methods to investigate the coding sequences of mitochondrial adenosine triphosphate gene (MT-ATP) in different classes of arthropoda to know the codon usage pattern of the gene as no work was described earlier. The analysis of compositional properties suggested that the gene is AT rich. The effective number of codons revealed the CUB of both ATP6 and ATP8 gene was moderate. Heat map showed that the codons ending with AT were negatively associated with GC3 while the codons ending with GC were positively associated with GC3 in all the classes of arthropoda. Correspondence study revealed that the pattern of codon usage of ATP6 and ATP8 genes differed across classes. Neutrality plot suggested the codon usage bias of these two genes in phylum arthropoda was influenced by both mutation pressure and natural selection.
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Affiliation(s)
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Science College, Algapur, Hailakandi, Assam, 788150, India
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar, Assam, 788011, India.
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27
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He W, Zhao J, Xing G, Li G, Wang R, Wang Z, Zhang C, Franzo G, Su S, Zhou J. Genetic analysis and evolutionary changes of Porcine circovirus 2. Mol Phylogenet Evol 2019; 139:106520. [PMID: 31152778 DOI: 10.1016/j.ympev.2019.106520] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 05/25/2019] [Accepted: 05/28/2019] [Indexed: 11/26/2022]
Abstract
Porcine circovirus 2 (PCV2) has been increasingly isolated worldwide and represents one of the main causes of economic losses in the swine industry. During evolution, PCV2 has diverged into different genotypes and several recombinant strains have been identified. In this study, we performed thorough genetic, evolutionary and codon usage analyses using 1065 non-recombinant open reading frame 2 (ORF2) sequences from NCBI. Based on ML and Bayesian methods of the ORF2 gene, five main genotypes were defined including, PCV2a, PCV2b, PCV2c, PCV2d and PCV2e. The different genotypes displayed a variable degree of codon usage bias, mainly influenced by natural selection. Moreover, the host adaptation of these PCV2 genotypes to different hosts was analyzed for the first time showing that PCV2 is more adapted to swine than bats. Swine was especially relevant in shaping the PCV2b and PCV2d genomes according the Codon adaptation index (CAI) and Similarity index (SiD). When a broader range of circoviruses was considered, a certain incongruence between the phylogenetic history of these viruses and that of their hosts was observed, suggesting that cross-species transmission has played a major role during circoviruses evolution. Our study provides a new perspective of the evolution of Porcine circoviruses and may serve to aid future research on PCV2 origin and evolution patterns.
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Affiliation(s)
- Wanting He
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jin Zhao
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, 210095 Nanjing, China
| | - Gang Xing
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China
| | - Gairu Li
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, 210095 Nanjing, China
| | - Ruyi Wang
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, 210095 Nanjing, China
| | - Zhixue Wang
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, 210095 Nanjing, China
| | - Cheng Zhang
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, 210095 Nanjing, China
| | - Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16, 35020 Legnaro (PD), Italy
| | - Shuo Su
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, 210095 Nanjing, China.
| | - Jiyong Zhou
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China.
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28
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Liu S, Qiao Z, Wang X, Zeng H, Li Y, Cai N, Chen Y. Analysis of codon usage patterns in "Lonicerae Flos" (Lonicera macranthoides Hand. -Mazz.) based on transcriptome data. Gene 2019; 705:127-132. [PMID: 31028866 DOI: 10.1016/j.gene.2019.04.065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/19/2019] [Accepted: 04/23/2019] [Indexed: 12/22/2022]
Abstract
Lonicera macranthoides Hand. -Mazz. is an important medicinal and economical plant in China, however, the codon usage bias (CUB) in L. macranthoides genes is still unknown. In this study, L. macranthoides transcriptome sequencing has been completed, and codon usage patterns in 36,090 reconstructed genes from the L. macranthoides transcriptome were examined. The mean GC content and GC3 value is 44.9% and 43.1%, respectively, which indicates that nucleotide contents of L. macranthoides genome is somewhat AT rich, and its codon bias pattern tends to use A/T-ending codons. According to neutrality plot, ENC plot, PR2-Bias plot and correspondence analysis, we know that both compositional constraint under selection and mutation could affect the CUB in L. macranthoides, and the mutation is the most determinant factor. Meanwhile, gene expression levels can influence its codon usage pattern. Furthermore, we identified 29 optimal codons and most of them ended with A/U. The study will lay a foundation for future research on gene prediction, genetic engineering and molecular evolution in L. macranthoides.
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Affiliation(s)
- Sisi Liu
- Hunan Academy of Forestry, Changsha 410004, China; Hunan University of Traditional Chinese Medicine, Changsha 410208, China
| | | | | | - Huijie Zeng
- Hunan Academy of Forestry, Changsha 410004, China
| | - Yongxin Li
- Hunan Academy of Forestry, Changsha 410004, China
| | - Neng Cai
- Hunan Academy of Forestry, Changsha 410004, China
| | - Yi Chen
- Hunan Academy of Forestry, Changsha 410004, China
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29
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Li G, Wang H, Wang S, Xing G, Zhang C, Zhang W, Liu J, Zhang J, Su S, Zhou J. Insights into the genetic and host adaptability of emerging porcine circovirus 3. Virulence 2019; 9:1301-1313. [PMID: 29973122 PMCID: PMC6177243 DOI: 10.1080/21505594.2018.1492863] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Porcine circovirus 3 (PCV3) was found to be associated with reproductive disease in pigs, and since its first identification in the United States, it subsequently spread worldwide, especially in China, where it might pose a potential threat to the porcine industry. However, no exhaustive analysis was performed to understand its evolution in the prospect of codon usage pattern. Here, we performed a deep codon usage analysis of PCV3. PCV3 sequences were classified into two clades: PCV3a and PCV3b, confirmed by principal component analysis. Additionally, the degree of codon usage bias of PCV3 was slightly low as inferred from the analysis of the effective number of codons. The codon usage pattern was mainly affected by natural selection, but there was a co-effect of mutation pressure and dinucleotide frequency. Moreover, based on similarity index analysis, codon adaptation index analysis and relative codon deoptimization index analysis, we found that PCV3 might pose a potential risk to public health though with unknow pathogenicity. In conclusion, this work reinforces the systematic understanding of the evolution of PCV3, which was reflected by the codon usage patterns and fitness of this novel emergent virus.
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Affiliation(s)
- Gairu Li
- a MOE Joint International Research Laboratory of Animal Health and Food Safety, Institute of Immunology , Nanjing Agricultural University , Nanjing , China.,b Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine , Nanjing Agricultural University , Nanjing , China
| | - Huijuan Wang
- c Key laboratory of Animal Virology of Ministry of Agriculture , Zhejiang University , Hangzhou , China
| | - Shilei Wang
- a MOE Joint International Research Laboratory of Animal Health and Food Safety, Institute of Immunology , Nanjing Agricultural University , Nanjing , China.,b Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine , Nanjing Agricultural University , Nanjing , China
| | - Gang Xing
- a MOE Joint International Research Laboratory of Animal Health and Food Safety, Institute of Immunology , Nanjing Agricultural University , Nanjing , China.,b Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine , Nanjing Agricultural University , Nanjing , China
| | - Cheng Zhang
- a MOE Joint International Research Laboratory of Animal Health and Food Safety, Institute of Immunology , Nanjing Agricultural University , Nanjing , China.,b Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine , Nanjing Agricultural University , Nanjing , China
| | - Wenyan Zhang
- a MOE Joint International Research Laboratory of Animal Health and Food Safety, Institute of Immunology , Nanjing Agricultural University , Nanjing , China.,b Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine , Nanjing Agricultural University , Nanjing , China
| | - Jie Liu
- a MOE Joint International Research Laboratory of Animal Health and Food Safety, Institute of Immunology , Nanjing Agricultural University , Nanjing , China.,b Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine , Nanjing Agricultural University , Nanjing , China
| | - Junyan Zhang
- a MOE Joint International Research Laboratory of Animal Health and Food Safety, Institute of Immunology , Nanjing Agricultural University , Nanjing , China.,b Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine , Nanjing Agricultural University , Nanjing , China
| | - Shuo Su
- a MOE Joint International Research Laboratory of Animal Health and Food Safety, Institute of Immunology , Nanjing Agricultural University , Nanjing , China.,b Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine , Nanjing Agricultural University , Nanjing , China
| | - Jiyong Zhou
- c Key laboratory of Animal Virology of Ministry of Agriculture , Zhejiang University , Hangzhou , China
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30
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Biswas R, Panja AS, Bandopadhyay R. In Silico Analyses of Burial Codon Bias Among the Species of Dipterocarpaceae Through Molecular and Phylogenetic Data. Evol Bioinform Online 2019; 15:1176934319834888. [PMID: 31223230 PMCID: PMC6563522 DOI: 10.1177/1176934319834888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 02/07/2019] [Indexed: 11/15/2022] Open
Abstract
Introduction: DNA barcode, a molecular marker, is used to distinguish among the closely
related species, and it can be applied across a broad range of taxa to
understand ecology and evolution. MaturaseK gene (matK) and
rubisco bisphosphate carboxylase/oxygenase form I gene
(rbcL) of the chloroplast are highly conserved in a
plant system, which are used as core barcode. This present endeavor entails
the comprehensive examination of the under threat plant species based on
success of discrimination on DNA barcode under selection pressure. Result: The family Dipterocarpaceae comprising of 15 genera is under threat due to
some factors, namely, deforestation, habitat alteration, poor seed, pollen
dispersal, etc. Species of this family was grouped into 6 clusters for
matK and 5 clusters and 2 sub-clusters for
rbcL in the phylogenetic tree by using neighbor-joining
method. Cluster I to cluster VI of matK and cluster I to
cluster V of rbcL genes were analyzed by various codon and
substitution bias tools. Mutational pressure guided the codon bias which was
favored by the avoidance of higher GC content and significant negative
correlation between GC12 and GC3 (in sub-cluster I of cluster I
[0.03 < P], cluster I
[0.00001 < P], and cluster II
[0.01 < P] of rbcL, and cluster IV
[0.013 < P] of matK). After
refining the results, it could be speculated that the lower null expectation
values (R = 0.5 or <0.5) were less divergent from the
evolutionary perspective. Apart from that, the higher null expectation
values (R = >0.85) also showed the same result, which
possibly could be due to the negative impact of very high and low transition
rate than transversion. Conclusion: Through the analysis of inter-generic, inter/intra-specific variation and
phylogenetic data, it was found that both selection and mutation played an
important role in synonymous codon choice in these genes, but they acted
inconsistently on the genes, both matK and
rbcL. In vitro stable proteins of both
matK and rbcL were selected through
natural selection rather than mutational selection. matK
gene had higher individual discrimination and barcode success compared with
rbcL. These discriminatory approaches may describe the
problem related to the extinction of plant species. Hence, it becomes very
imperative to identify and detect the under threat plant species in
advance.
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Affiliation(s)
- Raju Biswas
- UGC-Center of Advanced Study, Department of Botany, The University of Burdwan, Bardhaman, India
| | - Anindya Sundar Panja
- Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, India
| | - Rajib Bandopadhyay
- UGC-Center of Advanced Study, Department of Botany, The University of Burdwan, Bardhaman, India
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31
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Stapley J, Feulner PGD, Johnston SE, Santure AW, Smadja CM. Variation in recombination frequency and distribution across eukaryotes: patterns and processes. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0455. [PMID: 29109219 PMCID: PMC5698618 DOI: 10.1098/rstb.2016.0455] [Citation(s) in RCA: 203] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2017] [Indexed: 01/04/2023] Open
Abstract
Recombination, the exchange of DNA between maternal and paternal chromosomes during meiosis, is an essential feature of sexual reproduction in nearly all multicellular organisms. While the role of recombination in the evolution of sex has received theoretical and empirical attention, less is known about how recombination rate itself evolves and what influence this has on evolutionary processes within sexually reproducing organisms. Here, we explore the patterns of, and processes governing recombination in eukaryotes. We summarize patterns of variation, integrating current knowledge with an analysis of linkage map data in 353 organisms. We then discuss proximate and ultimate processes governing recombination rate variation and consider how these influence evolutionary processes. Genome-wide recombination rates (cM/Mb) can vary more than tenfold across eukaryotes, and there is large variation in the distribution of recombination events across closely related taxa, populations and individuals. We discuss how variation in rate and distribution relates to genome architecture, genetic and epigenetic mechanisms, sex, environmental perturbations and variable selective pressures. There has been great progress in determining the molecular mechanisms governing recombination, and with the continued development of new modelling and empirical approaches, there is now also great opportunity to further our understanding of how and why recombination rate varies.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'.
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Affiliation(s)
- Jessica Stapley
- Centre for Adaptation to a Changing Environment, IBZ, ETH Zürich, 8092 Zürich, Switzerland
| | - Philine G D Feulner
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland.,Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Susan E Johnston
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JY, UK
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Carole M Smadja
- Institut des Sciences de l'Evolution UMR 5554, CNRS, IRD, EPHE, Université de Montpellier, 3095 Montpellier cedex 05, France
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32
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Yang H, Qiu WR, Liu G, Guo FB, Chen W, Chou KC, Lin H. iRSpot-Pse6NC: Identifying recombination spots in Saccharomyces cerevisiae by incorporating hexamer composition into general PseKNC. Int J Biol Sci 2018; 14:883-891. [PMID: 29989083 PMCID: PMC6036749 DOI: 10.7150/ijbs.24616] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 02/04/2018] [Indexed: 02/06/2023] Open
Abstract
Meiotic recombination caused by meiotic double-strand DNA breaks. In some regions the frequency of DNA recombination is relatively higher, while in other regions the frequency is lower: the former is usually called "recombination hotspot", while the latter the "recombination coldspot". Information of the hot and cold spots may provide important clues for understanding the mechanism of genome revolution. Therefore, it is important to accurately predict these spots. In this study, we rebuilt the benchmark dataset by unifying its samples with a same length (131 bp). Based on such a foundation and using SVM (Support Vector Machine) classifier, a new predictor called "iRSpot-Pse6NC" was developed by incorporating the key hexamer features into the general PseKNC (Pseudo K-tuple Nucleotide Composition) via the binomial distribution approach. It has been observed via rigorous cross-validations that the proposed predictor is superior to its counterparts in overall accuracy, stability, sensitivity and specificity. For the convenience of most experimental scientists, the web-server for iRSpot-Pse6NC has been established at http://lin-group.cn/server/iRSpot-Pse6NC, by which users can easily obtain their desired result without the need to go through the detailed mathematical equations involved.
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Affiliation(s)
- Hui Yang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Wang-Ren Qiu
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.,Computer Department, Jingdezhen Ceramic Institute, Jingdezhen, 333403, China
| | - Guoqing Liu
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Feng-Biao Guo
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Wei Chen
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.,Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan 063000, China.,Gordon Life Science Institute, Boston, MA 02478, USA
| | - Kuo-Chen Chou
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.,Gordon Life Science Institute, Boston, MA 02478, USA
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.,Gordon Life Science Institute, Boston, MA 02478, USA
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33
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Li G, Wang R, Zhang C, Wang S, He W, Zhang J, Liu J, Cai Y, Zhou J, Su S. Genetic and evolutionary analysis of emerging H3N2 canine influenza virus. Emerg Microbes Infect 2018; 7:73. [PMID: 29691381 PMCID: PMC5915587 DOI: 10.1038/s41426-018-0079-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/19/2018] [Accepted: 03/20/2018] [Indexed: 11/09/2022]
Abstract
The H3N2 canine influenza virus (CIV) originated from an avian species. Since its emergence, it has circulated in multiple states and has caused pandemics among dog populations; however, no comprehensive studies have explored the causes driving these ongoing cases. The study of the codon usage patterns of viruses can reveal the genetic changes required for the viruses to adapt to new hosts and the external environment. Here we performed a thorough genetic, evolutionary, and codon usage analysis. We identified three evolutionary H3N2 CIV clades from a timescaled phylogenetic tree, namely, Origin, China, and Korea/USA, by principal component analysis (PCA). Additionally, we found a low codon usage bias and that mutation pressure, natural selection, and dinucleotide abundance shape the codon usage bias of H3N2 CIVs, with natural selection being more crucial than the others. Moreover, the human codon adaptation index was similar to that of dogs (the natural host) and cats. In addition, the H3N2 CIV similarity index values were higher than those of the avian influenza virus (AIV), suggesting viral adaptation to the host. Therefore, H3N2 CIVs may pose a potential risk to public health in the future, and further epidemiologic, evolutionary, and pathogenetic studies are required.
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Affiliation(s)
- Gairu Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Ruyi Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Cheng Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Shilei Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Wanting He
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Junyan Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jie Liu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yuchen Cai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jiyong Zhou
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Shuo Su
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.
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34
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Im EH, Choi SS. Synonymous Codon Usage Controls Various Molecular Aspects. Genomics Inform 2017; 15:123-127. [PMID: 29307137 PMCID: PMC5769864 DOI: 10.5808/gi.2017.15.4.123] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 09/25/2017] [Indexed: 12/19/2022] Open
Abstract
Synonymous sites are generally considered to be functionally neutral. However, there are recent contradictory findings suggesting that synonymous alleles might have functional roles in various molecular aspects. For instance, a recent study demonstrated that synonymous single nucleotide polymorphisms have a similar effect size as nonsynonymous single nucleotide polymorphisms in human disease association studies. Researchers have recognized synonymous codon usage bias (SCUB) in the genomes of almost all species and have investigated whether SCUB is due to random nucleotide compositional bias or to natural selection of any functional exposure generated by synonymous mutations. One of the most prominent observations on the non-neutrality of synonymous codons is the correlation between SCUB and levels of gene expression, such that highly expressed genes tend to have a higher preference toward so-called optimal codons than lowly expressed genes. In relation, it is known that amounts of cognate tRNAs that bind to optimal codons are significantly higher than the amounts of cognate tRNAs that bind to non-optimal codons in genomes. In the present paper, we review various functions that synonymous codons might have other than regulating expression levels.
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Affiliation(s)
- Eu-Hyun Im
- Division of Biomedical Convergence, College of Biomedical Science, and Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon 24341, Korea
| | - Sun Shim Choi
- Division of Biomedical Convergence, College of Biomedical Science, and Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon 24341, Korea
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35
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Huang X, Xu J, Chen L, Wang Y, Gu X, Peng X, Yang G. Analysis of transcriptome data reveals multifactor constraint on codon usage in Taenia multiceps. BMC Genomics 2017; 18:308. [PMID: 28427327 PMCID: PMC5397707 DOI: 10.1186/s12864-017-3704-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 04/12/2017] [Indexed: 12/04/2022] Open
Abstract
Background Codon usage bias (CUB) is an important evolutionary feature in genomes that has been widely observed in many organisms. However, the synonymous codon usage pattern in the genome of T. multiceps remains to be clarified. In this study, we analyzed the codon usage of T. multiceps based on the transcriptome data to reveal the constraint factors and to gain an improved understanding of the mechanisms that shape synonymous CUB. Results Analysis of a total of 8,620 annotated mRNA sequences from T. multiceps indicated only a weak codon bias, with mean GC and GC3 content values of 49.29% and 51.43%, respectively. Our analysis indicated that nucleotide composition, mutational pressure, natural selection, gene expression level, amino acids with grand average of hydropathicity (GRAVY) and aromaticity (Aromo) and the effective selection of amino-acids all contributed to the codon usage in T. multiceps. Among these factors, natural selection was implicated as the major factor affecting the codon usage variation in T. multiceps. The codon usage of ribosome genes was affected mainly by mutations, while the essential genes were affected mainly by selection. In addition, 21codons were identified as “optimal codons”. Overall, the optimal codons were GC-rich (GC:AU, 41:22), and ended with G or C (except CGU). Furthermore, different degrees of variation in codon usage were found between T. multiceps and Escherichia coli, yeast, Homo sapiens. However, little difference was found between T. multiceps and Taenia pisiformis. Conclusions In this study, the codon usage pattern of T. multiceps was analyzed systematically and factors affected CUB were also identified. This is the first study of codon biology in T. multiceps. Understanding the codon usage pattern in T. multiceps can be helpful for the discovery of new genes, molecular genetic engineering and evolutionary studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3704-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xing Huang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.,Chengdu Agricultural College, Chengdu, 611130, China
| | - Jing Xu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lin Chen
- Meat-processing Application Key Laboratory of Sichuan Province, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, China
| | - Yu Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaobin Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xuerong Peng
- College of Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Guangyou Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
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36
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Choudhury MN, Uddin A, Chakraborty S. Nucleotide composition and codon usage bias of SRY gene. Andrologia 2017; 50. [PMID: 28124482 DOI: 10.1111/and.12787] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2016] [Indexed: 11/27/2022] Open
Abstract
The SRY gene is present within the sex-determining region of the Y chromosome which is responsible for maleness in mammals. The nonuniform usage of synonymous codons in the mRNA transcript for encoding a particular amino acid is the codon usage bias (CUB). Analysis of codon usage pattern is important to understand the genetic and molecular organisation of a gene. It also helps in heterologous gene expression, design of primer and synthetic gene. However, the analysis of codon usage bias of SRY gene was not yet studied. We have used bioinformatic tools to analyse codon usage bias of SRY gene across mammals. Codon bias index (CBI) indicated that the overall extent of codon usage bias was weak. The relative synonymous codon usage (RSCU) analysis suggested that most frequently used codons had an A or C at the third codon position. Compositional constraint played an important role in codon usage pattern as evident from correspondence analysis (CA). Significant correlation among nucleotides constraints indicated that both mutation pressure and natural selection affect the codon usage pattern. Neutrality plot suggested that natural selection might play a major role, while mutation pressure might play a minor role in codon usage pattern in SRY gene in different species of mammals.
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Affiliation(s)
- M N Choudhury
- Department of Biotechnology, Assam University, Silchar, Assam, India
| | - A Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, India
| | - S Chakraborty
- Department of Biotechnology, Assam University, Silchar, Assam, India
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Gorthy S, Narasu L, Gaddameedi A, Sharma HC, Kotla A, Deshpande SP, Are AK. Introgression of Shoot Fly ( Atherigona soccata L. Moench) Resistance QTLs into Elite Post-rainy Season Sorghum Varieties Using Marker Assisted Backcrossing (MABC). FRONTIERS IN PLANT SCIENCE 2017; 8:1494. [PMID: 28919901 PMCID: PMC5585744 DOI: 10.3389/fpls.2017.01494] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/11/2017] [Indexed: 05/19/2023]
Abstract
Shoot fly (Atherigona soccata L. Moench) is a serious pest in sorghum production. Management of shoot fly using insecticides is expensive and environmentally un-safe. Developing host-plant resistance is the best method to manage shoot fly infestation. Number of component traits contribute for imparting shoot fly resistance in sorghum and molecular markers have been reported which were closely linked to QTLs controlling these component traits. In this study, three QTLs associated with shoot fly resistance were introgressed into elite cultivars Parbhani Moti (= SPV1411) and ICSB29004 using marker assisted backcrossing (MABC). Crosses were made between recurrent parents and the QTL donors viz., J2658, J2614, and J2714. The F1s after confirmation for QTL presence were backcrossed to recurrent parents and the resultant lines after two backcrosses were selfed thrice for advancement. The foreground selection was carried out in F1 and BCnF1 generations with 22 polymorphic markers. Forty-three evenly distributed simple sequence repeat markers in the sorghum genome were used in background selection to identify plants with higher recurrent parent genome recovery. By using two backcrosses and four rounds of selfing, six BC2F4 progenies were selected for ICSB29004 × J2658, five BC2F4 progenies were selected for ICSB29004 × J2714 and six BC2F4 progenies were selected for Parbhani Moti × J2614 crosses. Phenotyping of these lines led to the identification of two resistant lines for each QTL region present on chromosome SBI-01, SBI-07 and SBI-10 in ICSB 29004 and Parbhani Moti. All the introgression lines (ILs) showed better shoot fly resistance than the recurrent parents and their agronomic performance was the same or better than the recurrent parents. Further, the ILs had medium plant height, desirable maturity with high yield potential which makes them better candidates for commercialization. In the present study, MABC has successfully improved the shoot fly resistance in sorghum without a yield penalty. This is the first report on the use of MABC for improving shoot fly resistance in post-rainy season sorghum.
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Affiliation(s)
- Sunita Gorthy
- International Crops Research Institute for Semi-Arid TropicsHyderabad, India
- Department of Biotechnology, Jawaharlal Nehru Technological UniversityHyderabad, India
| | - Lakshmi Narasu
- Department of Biotechnology, Jawaharlal Nehru Technological UniversityHyderabad, India
| | - Anil Gaddameedi
- International Crops Research Institute for Semi-Arid TropicsHyderabad, India
| | - Hari C. Sharma
- International Crops Research Institute for Semi-Arid TropicsHyderabad, India
| | - Anuradha Kotla
- International Crops Research Institute for Semi-Arid TropicsHyderabad, India
| | | | - Ashok K. Are
- International Crops Research Institute for Semi-Arid TropicsHyderabad, India
- *Correspondence: Ashok K. Are,
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Hwang HY, Wang J. Effect of mutation mechanisms on variant composition and distribution in Caenorhabditis elegans. PLoS Comput Biol 2017; 13:e1005369. [PMID: 28135268 PMCID: PMC5305269 DOI: 10.1371/journal.pcbi.1005369] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 02/13/2017] [Accepted: 01/17/2017] [Indexed: 01/10/2023] Open
Abstract
Genetic diversity is maintained by continuing generation and removal of variants. While examining over 800,000 DNA variants in wild isolates of Caenorhabditis elegans, we made a discovery that the proportions of variant types are not constant across the C. elegans genome. The variant proportion is defined as the fraction of a specific variant type (e.g. single nucleotide polymorphism (SNP) or indel) within a broader set of variants (e.g. all variants or all non-SNPs). The proportions of most variant types show a correlation with the recombination rate. These correlations can be explained as a result of a concerted action of two mutation mechanisms, which we named Morgan and Sanger mechanisms. The two proposed mechanisms act according to the distinct components of the recombination rate, specifically the genetic and physical distance. Regression analysis was used to explore the characteristics and contributions of the two mutation mechanisms. According to our model, ~20-40% of all mutations in C. elegans wild populations are derived from programmed meiotic double strand breaks, which precede chromosomal crossovers and thus may be the point of origin for the Morgan mechanism. A substantial part of the known correlation between the recombination rate and variant distribution appears to be caused by the mutations generated by the Morgan mechanism. Mathematically integrating the mutation model with background selection model gives a more complete depiction of how the variant landscape is shaped in C. elegans. Similar analysis should be possible in other species by examining the correlation between the recombination rate and variant landscape within the context of our mutation model.
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Affiliation(s)
- Ho-Yon Hwang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, United States of America
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, United States of America
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Evolution of codon usage in Zika virus genomes is host and vector specific. Emerg Microbes Infect 2016; 5:e107. [PMID: 27729643 PMCID: PMC5117728 DOI: 10.1038/emi.2016.106] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/21/2016] [Accepted: 08/25/2016] [Indexed: 12/12/2022]
Abstract
The codon usage patterns of viruses reflect the evolutionary changes that allow them to optimize their survival and adapt their fitness to the external environment and, most importantly, their hosts. Here we report the genotype-specific codon usage patterns of Zika virus (ZIKV) strains from the current and previous outbreaks. Several genotype-specific and common codon usage traits were noted in the ZIKV coding sequences, indicating their independent evolutionary origins from a common ancestor. The overall influence of natural selection was more profound than that of mutation pressure, acting on a specific set of viral genes in the Asian-genotype ZIKV strains from the recent outbreak. An interplay between codon adaptation and deoptimization may have allowed the virus to adapt to multiple host and vectors and is reported for the first time in ZIKV genomes. Combining our codon analysis with geographical data on Aedes populations in the Americas suggested that ZIKV has evolved host- and vector-specific codon usage patterns to maintain successful replication and transmission chains within multiple hosts and vectors.
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Choi JY, Aquadro CF. Recent and Long-Term Selection Across Synonymous Sites in Drosophila ananassae. J Mol Evol 2016; 83:50-60. [PMID: 27481397 DOI: 10.1007/s00239-016-9753-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 07/23/2016] [Indexed: 11/28/2022]
Abstract
In Drosophila, many studies have examined the short- or long-term evolution occurring across synonymous sites. Few, however, have examined both the recent and long-term evolution to gain a complete view of this selection. Here we have analyzed Drosophila ananassae DNA polymorphism and divergence data using several different methods, and have identified evidence of positive selection favoring preferred codons in both recent and long-term evolutionary time scale. Further in D. ananassae, the strength of selection for preferred codons was stronger on the X chromosome compared to the autosomes. We show that this stronger selection is not due to higher gene expression of X-linked genes. Analysis of the selectively neutral introns indicated that the X chromosome also had a preference for GC over AT nucleotides, potentially from GC-biased gene conversions (gcBGCs) that can also affect the base composition of synonymous sites. Thus selection for preferred codons and gcBGC both seem to be partially responsible for shaping the D. ananassae synonymous site evolution.
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Affiliation(s)
- Jae Young Choi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, USA.
| | - Charles F Aquadro
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, USA
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Dwivedi AK, Chouhan U. Comparative study of artificial neural network for classification of hot and cold recombination regions in Saccharomyces cerevisiae. Neural Comput Appl 2016. [DOI: 10.1007/s00521-016-2466-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Genome-Wide Analysis of Codon Usage Bias in Epichloë festucae. Int J Mol Sci 2016; 17:ijms17071138. [PMID: 27428961 PMCID: PMC4964511 DOI: 10.3390/ijms17071138] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/24/2016] [Accepted: 07/08/2016] [Indexed: 11/17/2022] Open
Abstract
Analysis of codon usage data has both practical and theoretical applications in understanding the basics of molecular biology. Differences in codon usage patterns among genes reflect variations in local base compositional biases and the intensity of natural selection. Recently, there have been several reports related to codon usage in fungi, but little is known about codon usage bias in Epichloë endophytes. The present study aimed to assess codon usage patterns and biases in 4870 sequences from Epichloë festucae, which may be helpful in revealing the constraint factors such as mutation or selection pressure and improving the bioreactor on the cloning, expression, and characterization of some special genes. The GC content with 56.41% is higher than the AT content (43.59%) in E. festucae. The results of neutrality and effective number of codons plot analyses showed that both mutational bias and natural selection play roles in shaping codon usage in this species. We found that gene length is strongly correlated with codon usage and may contribute to the codon usage patterns observed in genes. Nucleotide composition and gene expression levels also shape codon usage bias in E. festucae. E. festucae exhibits codon usage bias based on the relative synonymous codon usage (RSCU) values of 61 sense codons, with 25 codons showing an RSCU larger than 1. In addition, we identified 27 optimal codons that end in a G or C.
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Stevison LS, Woerner AE, Kidd JM, Kelley JL, Veeramah KR, McManus KF, Bustamante CD, Hammer MF, Wall JD. The Time Scale of Recombination Rate Evolution in Great Apes. Mol Biol Evol 2016; 33:928-45. [PMID: 26671457 PMCID: PMC5870646 DOI: 10.1093/molbev/msv331] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequence data from 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez J, et al. 2013. Great ape genetic diversity and population history. Nature 499:471-475). We also identified species-specific recombination hotspots in each group using a modified LDhot framework, which greatly improves statistical power to detect hotspots at varying strengths. We show that fewer hotspots are shared among chimpanzee subspecies than within human populations, further narrowing the time scale of complete hotspot turnover. Further, using species-specific PRDM9 sequences to predict potential binding sites (PBS), we show higher predicted PRDM9 binding in recombination hotspots as compared to matched cold spot regions in multiple great ape species, including at least one chimpanzee subspecies. We found that correlations between broad-scale recombination rates decline more rapidly than nucleotide divergence between species. We also compared the skew of recombination rates at centromeres and telomeres between species and show a skew from chromosome means extending as far as 10-15 Mb from chromosome ends. Further, we examined broad-scale recombination rate changes near a translocation in gorillas and found minimal differences as compared to other great ape species perhaps because the coordinates relative to the chromosome ends were unaffected. Finally, on the basis of multiple linear regression analysis, we found that various correlates of recombination rate persist throughout the African great apes including repeats, diversity, and divergence. Our study is the first to analyze within- and between-species genome-wide recombination rate variation in several close relatives.
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Affiliation(s)
- Laurie S Stevison
- Institute for Human Genetics, University of California San Francisco Department of Biological Sciences, Auburn University
| | - August E Woerner
- Arizona Research Laboratories, Division of Biotechnology, University of Arizona Department of Genetics, University of Arizona
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan Department of Computational Medicine & Bioinformatics, University of Michigan
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University Department of Genetics, Stanford University
| | - Krishna R Veeramah
- Arizona Research Laboratories, Division of Biotechnology, University of Arizona Department of Ecology and Evolution, Stony Brook University
| | - Kimberly F McManus
- Department of Biology, Stanford University Department of Biomedical Informatics, Stanford University
| | | | - Michael F Hammer
- Arizona Research Laboratories, Division of Biotechnology, University of Arizona Department of Ecology and Evolutionary Biology, University of Arizona Department of Anthropology, University of Arizona
| | - Jeffrey D Wall
- Institute for Human Genetics, University of California San Francisco Department of Epidemiology & Biostatistics, University of California San Francisco
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Sundararajan A, Dukowic-Schulze S, Kwicklis M, Engstrom K, Garcia N, Oviedo OJ, Ramaraj T, Gonzales MD, He Y, Wang M, Sun Q, Pillardy J, Kianian SF, Pawlowski WP, Chen C, Mudge J. Gene Evolutionary Trajectories and GC Patterns Driven by Recombination in Zea mays. FRONTIERS IN PLANT SCIENCE 2016; 7:1433. [PMID: 27713757 PMCID: PMC5031598 DOI: 10.3389/fpls.2016.01433] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/08/2016] [Indexed: 05/20/2023]
Abstract
Recombination occurring during meiosis is critical for creating genetic variation and plays an essential role in plant evolution. In addition to creating novel gene combinations, recombination can affect genome structure through altering GC patterns. In maize (Zea mays) and other grasses, another intriguing GC pattern exists. Maize genes show a bimodal GC content distribution that has been attributed to nucleotide bias in the third, or wobble, position of the codon. Recombination may be an underlying driving force given that recombination sites are often associated with high GC content. Here we explore the relationship between recombination and genomic GC patterns by comparing GC gene content at each of the three codon positions (GC1, GC2, and GC3, collectively termed GCx) to instances of a variable GC-rich motif that underlies double strand break (DSB) hotspots and to meiocyte-specific gene expression. Surprisingly, GCx bimodality in maize cannot be fully explained by the codon wobble hypothesis. High GCx genes show a strong overlap with the DSB hotspot motif, possibly providing a mechanism for the high evolutionary rates seen in these genes. On the other hand, genes that are turned on in meiosis (early prophase I) are biased against both high GCx genes and genes with the DSB hotspot motif, possibly allowing important meiotic genes to avoid DSBs. Our data suggests a strong link between the GC-rich motif underlying DSB hotspots and high GCx genes.
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Affiliation(s)
| | | | | | | | - Nathan Garcia
- National Center for Genome Resources, Santa FeNM, USA
| | | | | | | | - Yan He
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, IthacaNY, USA
| | - Minghui Wang
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, IthacaNY, USA
- Biotechnology Resource Center Bioinformatics Facility, Cornell University, IthacaNY, USA
| | - Qi Sun
- Biotechnology Resource Center Bioinformatics Facility, Cornell University, IthacaNY, USA
| | - Jaroslaw Pillardy
- Biotechnology Resource Center Bioinformatics Facility, Cornell University, IthacaNY, USA
| | - Shahryar F. Kianian
- Cereal Disease Laboratory, United States Department of Agriculture – Agricultural Research Service, St. PaulMN, USA
| | - Wojciech P. Pawlowski
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, IthacaNY, USA
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, St. PaulMN, USA
| | - Joann Mudge
- National Center for Genome Resources, Santa FeNM, USA
- *Correspondence: Joann Mudge,
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Yang X, Ma X, Luo X, Ling H, Zhang X, Cai X. Codon Usage Bias and Determining Forces in Taenia solium Genome. THE KOREAN JOURNAL OF PARASITOLOGY 2015; 53:689-97. [PMID: 26797435 PMCID: PMC4725240 DOI: 10.3347/kjp.2015.53.6.689] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 08/10/2015] [Accepted: 10/06/2015] [Indexed: 11/23/2022]
Abstract
The tapeworm Taenia solium is an important human zoonotic parasite that causes great economic loss and also endangers public health. At present, an effective vaccine that will prevent infection and chemotherapy without any side effect remains to be developed. In this study, codon usage patterns in the T. solium genome were examined through 8,484 protein-coding genes. Neutrality analysis showed that T. solium had a narrow GC distribution, and a significant correlation was observed between GC12 and GC3. Examination of an NC (ENC vs GC3s)-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENC (the effective number of codons) values were detected below the expected curve, suggesting that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally. We also identified 26 optimal codons in the T. solium genome, all of which ended with either a G or C residue. These optimal codons in the T. solium genome are likely consistent with tRNAs that are highly expressed in the cell, suggesting that mutational and translational selection forces are probably driving factors of codon usage bias in the T. solium genome.
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Affiliation(s)
- Xing Yang
- College of Veterinary Medicine, Jilin University, Changchun, 130000, P. R. China ; State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, P. R. China
| | - Xusheng Ma
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, P. R. China
| | - Xuenong Luo
- College of Veterinary Medicine, Jilin University, Changchun, 130000, P. R. China
| | - Houjun Ling
- College of Veterinary Medicine, Jilin University, Changchun, 130000, P. R. China
| | - Xichen Zhang
- College of Veterinary Medicine, Jilin University, Changchun, 130000, P. R. China
| | - Xuepeng Cai
- College of Veterinary Medicine, Jilin University, Changchun, 130000, P. R. China.,State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, P. R. China
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Yahara K, Didelot X, Jolley KA, Kobayashi I, Maiden MCJ, Sheppard SK, Falush D. The Landscape of Realized Homologous Recombination in Pathogenic Bacteria. Mol Biol Evol 2015; 33:456-71. [PMID: 26516092 PMCID: PMC4866539 DOI: 10.1093/molbev/msv237] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Recombination enhances the adaptive potential of organisms by allowing genetic variants to be tested on multiple genomic backgrounds. Its distribution in the genome can provide insight into the evolutionary forces that underlie traits, such as the emergence of pathogenicity. Here, we examined landscapes of realized homologous recombination of 500 genomes from ten bacterial species and found all species have “hot” regions with elevated rates relative to the genome average. We examined the size, gene content, and chromosomal features associated with these regions and the correlations between closely related species. The recombination landscape is variable and evolves rapidly. For example in Salmonella, only short regions of around 1 kb in length are hot whereas in the closely related species Escherichia coli, some hot regions exceed 100 kb, spanning many genes. Only Streptococcus pyogenes shows evidence for the positive correlation between GC content and recombination that has been reported for several eukaryotes. Genes with function related to the cell surface/membrane are often found in recombination hot regions but E. coli is the only species where genes annotated as “virulence associated” are consistently hotter. There is also evidence that some genes with “housekeeping” functions tend to be overrepresented in cold regions. For example, ribosomal proteins showed low recombination in all of the species. Among specific genes, transferrin-binding proteins are recombination hot in all three of the species in which they were found, and are subject to interspecies recombination.
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Affiliation(s)
- Koji Yahara
- Biostatistics Center, Kurume University, Kurume, Fukuoka, Japan College of Medicine, Institute of Life Science, Swansea University, Swansea, United Kingdom
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Keith A Jolley
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Ichizo Kobayashi
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | | | - Samuel K Sheppard
- College of Medicine, Institute of Life Science, Swansea University, Swansea, United Kingdom Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Daniel Falush
- College of Medicine, Institute of Life Science, Swansea University, Swansea, United Kingdom Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
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Mugal CF, Weber CC, Ellegren H. GC-biased gene conversion links the recombination landscape and demography to genomic base composition. Bioessays 2015; 37:1317-26. [DOI: 10.1002/bies.201500058] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Carina F. Mugal
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Claudia C. Weber
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
- Department of Biology; Center for Computational Genetics and Genomics; Temple University; Philadelphia PA USA
| | - Hans Ellegren
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
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The relationship of recombination rate, genome structure, and patterns of molecular evolution across angiosperms. BMC Evol Biol 2015; 15:194. [PMID: 26377000 PMCID: PMC4574184 DOI: 10.1186/s12862-015-0473-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 09/01/2015] [Indexed: 12/31/2022] Open
Abstract
Background Although homologous recombination affects the efficacy of selection in populations, the pattern of recombination rate evolution and its effects on genome evolution across plants are largely unknown. Recombination can reduce genome size by enabling the removal of LTR retrotransposons, alter codon usage by GC biased gene conversion, contribute to complex histories of gene duplication and loss through tandem duplication, and enhance purifying selection on genes. Therefore, variation in recombination rate across species may explain some of the variation in genomic architecture as well as rates of molecular evolution. We used phylogenetic comparative methods to investigate the evolution of global meiotic recombination rate in angiosperms and its effects on genome architecture and selection at the molecular level using genetic maps and genome sequences from thirty angiosperm species. Results Recombination rate is negatively correlated with genome size, which is likely caused by the removal of LTR retrotransposons. After correcting recombination rates for euchromatin content, we also found an association between global recombination rate and average gene family size. This suggests a role for recombination in the preservation of duplicate genes or expansion of gene families. An analysis of the correlation between the ratio of nonsynonymous to synonymous substitution rates (dN/dS) and recombination rate in 3748 genes indicates that higher recombination rates are associated with an increased efficacy of purifying selection, suggesting that global recombination rates affect variation in rates of molecular evolution across distantly related angiosperm species, not just between populations. We also identified shifts in dN/dS for recombination proteins that are associated with shifts in global recombination rate across our sample of angiosperms. Conclusions Although our analyses only reveal correlations, not mechanisms, and do not include potential covariates of recombination rate, like effective population size, they suggest that global recombination rates may play an important role in shaping the macroevolutionary patterns of gene and genome evolution in plants. Interspecific recombination rate variation is tightly correlated with genome size as well as variation in overall LTR retrotransposon abundances. Recombination may shape gene-to-gene variation in dN/dS between species, which might impact the overall gene duplication and loss rates. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0473-3) contains supplementary material, which is available to authorized users.
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Nasrullah I, Butt AM, Tahir S, Idrees M, Tong Y. Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Marburg virus evolution. BMC Evol Biol 2015; 15:174. [PMID: 26306510 PMCID: PMC4550055 DOI: 10.1186/s12862-015-0456-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 08/17/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The Marburg virus (MARV) has a negative-sense single-stranded RNA genome, belongs to the family Filoviridae, and is responsible for several outbreaks of highly fatal hemorrhagic fever. Codon usage patterns of viruses reflect a series of evolutionary changes that enable viruses to shape their survival rates and fitness toward the external environment and, most importantly, their hosts. To understand the evolution of MARV at the codon level, we report a comprehensive analysis of synonymous codon usage patterns in MARV genomes. Multiple codon analysis approaches and statistical methods were performed to determine overall codon usage patterns, biases in codon usage, and influence of various factors, including mutation pressure, natural selection, and its two hosts, Homo sapiens and Rousettus aegyptiacus. RESULTS Nucleotide composition and relative synonymous codon usage (RSCU) analysis revealed that MARV shows mutation bias and prefers U- and A-ended codons to code amino acids. Effective number of codons analysis indicated that overall codon usage among MARV genomes is slightly biased. The Parity Rule 2 plot analysis showed that GC and AU nucleotides were not used proportionally which accounts for the presence of natural selection. Codon usage patterns of MARV were also found to be influenced by its hosts. This indicates that MARV have evolved codon usage patterns that are specific to both of its hosts. Moreover, selection pressure from R. aegyptiacus on the MARV RSCU patterns was found to be dominant compared with that from H. sapiens. Overall, mutation pressure was found to be the most important and dominant force that shapes codon usage patterns in MARV. CONCLUSIONS To our knowledge, this is the first detailed codon usage analysis of MARV and extends our understanding of the mechanisms that contribute to codon usage and evolution of MARV.
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Affiliation(s)
- Izza Nasrullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Azeem M Butt
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, 53700, Pakistan.
| | - Shifa Tahir
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, Nouzilly, F-37380, France. .,CNRS, UMR7247, F-37380, Nouzilly, France. .,Université François Rabelais de Tours, Tours, F-37380, France.
| | - Muhammad Idrees
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, 53700, Pakistan.
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China.
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Baeza M, Alcaíno J, Barahona S, Sepúlveda D, Cifuentes V. Codon usage and codon context bias in Xanthophyllomyces dendrorhous. BMC Genomics 2015; 16:293. [PMID: 25887493 PMCID: PMC4404019 DOI: 10.1186/s12864-015-1493-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 03/27/2015] [Indexed: 01/11/2023] Open
Abstract
Background Synonymous codons are used differentially in organisms from the three domains of life, a phenomenon referred to as codon usage bias. In addition, codon pair bias, particularly in the 3’ codon context, has also been described in several organisms and is associated with the accuracy and rate of translation. An improved understanding of both types of bias is important for the optimization of heterologous protein expression, particularly in biotechnologically important organisms, such as the yeast Xanthophyllomyces dendrorhous, a promising bioresource for the carotenoid astaxanthin. Using genomic and transcriptomic data, the codon usage and codon context biases of X. dendrorhous open reading frames (ORFs) were analyzed to determine their expression levels, GC% and sequence lengths. X. dendrorhous totiviral ORFs were also included in these analyses. Results A total of 1,695 X. dendrorhous ORFs were identified through comparison with sequences in multiple databases, and the intron-exon structures of these sequences were determined. Although there were important expression variations among the ORFs under the studied conditions (different phases of growth and available carbon sources), most of these sequences were highly expressed under at least one of the analyzed conditions. Independent of the culture conditions, the highly expressed genes showed a strong bias in both codon usage and the 3’ context, with a minor association with the GC% and no relationship to the sequence length. The codon usage and codon-pair bias of the totiviral ORFs were highly variable with no similarities to the host ORFs. Conclusions There is a direct relation between the level of gene expression and codon usage and 3′ context bias in X. dendrorhous, which is more evident for ORFs that are expressed at the highest levels under the studied conditions. However, there is no direct relation between the totiviral ORF biases and the host ORFs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1493-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marcelo Baeza
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile.
| | - Jennifer Alcaíno
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile.
| | - Salvador Barahona
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile.
| | - Dionisia Sepúlveda
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile.
| | - Víctor Cifuentes
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile.
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