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Song H, Cao Y, Zhao L, Zhang J, Li S. Review: WRKY transcription factors: Understanding the functional divergence. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 334:111770. [PMID: 37321304 DOI: 10.1016/j.plantsci.2023.111770] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/10/2023] [Accepted: 06/11/2023] [Indexed: 06/17/2023]
Abstract
WRKY transcription factors (TFs) play crucial roles in the growth and development of plants and their response to environmental changes. WRKY TFs have been detected in sequenced plant genomes. The functions and regulatory networks of many WRKY TFs, especially from Arabidopsis thaliana (AtWRKY TFs), have been revealed, and the origin of WRKY TFs in plants is clear. Nonetheless, the relationship between WRKY TFs function and classification is unclear. Furthermore, the functional divergence of homologous WRKY TFs in plants is unclear. In this review, WRKY TFs were explored based on WRKY-related literature published from 1994 to 2022. WRKY TFs were identified in 234 species at the genome and transcriptome levels. The biological functions of ∼ 71 % of AtWRKY TFs were uncovered. Although functional divergence occurred in homologous WRKY TFs, different WRKY TF groups had no preferential function.
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Affiliation(s)
- Hui Song
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China.
| | - Yunpeng Cao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Longgang Zhao
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; High-efficiency Agricultural Technology Industry Research Institute of Saline and Alkaline Land of Dongying, Qingdao Agricultural University, Qingdao 266109, China
| | | | - Shuai Li
- College of Life Science, Qingdao Agricultural University, Qingdao 266109, China.
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Suresh KP, Indrabalan UB, Shreevatsa B, Dharmashekar C, Singh P, Patil SS, Syed A, Elgorban AM, Eswaramoorthy R, Amachawadi RG, Shivamallu C, Kollur SP. Evaluation of codon usage patterns and molecular evolution dynamics in Japanese encephalitis virus: An integrated bioinformatics approach. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 109:105410. [PMID: 36791944 DOI: 10.1016/j.meegid.2023.105410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 01/04/2023] [Accepted: 02/07/2023] [Indexed: 02/16/2023]
Abstract
In the recent survey, Japanese encephalitis (JE) is one of the most common mosquito-borne diseases, accounting for ∼30% of fatalities. The outbreaks of the JE virus (JEV) suggests that exhaustive study is essential for the prevention and management of the disease. The disease mainly spreads in humans and pigs by the vector: mosquito; as this is a major concern, this study had employed various bioinformatics tools to investigate the codon usage bias, evolutionary inference and selection pressure analysis of the Japanese encephalitis virus disease. The results indicated that the JE virus was biased and natural selection was the main factor shaping the codon usage that was determined and confirmed with the Nc, neutrality, PR2 plots and correlation analysis. The evolutionary analysis revealed that the virus had a substitution rate of 1.54 × 10-4 substitution/site/year and the tMRCA was found to be in 1723. The transmission of the virus in the map found transmissions mostly from China and transmitted across Asia and Africa. The selection pressure analysis employed three methods which had 969th codon site as diversifying site and had many purifying sites that shows the virus had evolved rapidly. The inferences from this study would aid people to employ this methodology on various diseases and also perform insilico studies in the field of vaccinology and immunoinformatics.
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Affiliation(s)
| | - Uma Bharathi Indrabalan
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka 560063, India
| | - Bhargav Shreevatsa
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education & Research, Myuru 570015, Karnataka, India.
| | - Chandan Dharmashekar
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education & Research, Myuru 570015, Karnataka, India.
| | - Pranav Singh
- Department of Internal Medicine, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sharanagouda S Patil
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka 560063, India.
| | - Asad Syed
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, Riyadh 11451, Saudi Arabia.
| | - Abdallah M Elgorban
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, Riyadh 11451, Saudi Arabia.
| | - Rajalakshmanan Eswaramoorthy
- Department of Prosthodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai 600 077, Tamilnadu, India.
| | - Raghavendra G Amachawadi
- Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506-5606, USA.
| | - Chandan Shivamallu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education & Research, Myuru 570015, Karnataka, India.
| | - Shiva Prasad Kollur
- School of Physical Sciences, Amrita Vishwa Vidhyapeetham, Mysuru Campus, Mysuru 570 026, Karnataka, India.
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Gonzalez-Sanchez B, Vega-Rodríguez MA, Santander-Jiménez S. A multi-objective butterfly optimization algorithm for protein encoding. Appl Soft Comput 2023. [DOI: 10.1016/j.asoc.2023.110269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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Chen M, Li M, Zhao L, Song H. Deciphering evolutionary dynamics of WRKY genes in Arachis species. BMC Genomics 2023; 24:48. [PMID: 36707767 PMCID: PMC9881300 DOI: 10.1186/s12864-023-09149-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Cultivated peanut (Arachis hypogaea), a progeny of the cross between A. duranensis and A. ipaensis, is an important oil and protein crop from South America. To date, at least six Arachis genomes have been sequenced. WRKY transcription factors (TFs) play crucial roles in plant growth, development, and response to abiotic and biotic stresses. WRKY TFs have been identified in A. duranensis, A. ipaensis, and A. hypogaea cv. Tifrunner; however, variations in their number and evolutionary patterns across various Arachis spp. remain unclear. RESULTS WRKY TFs were identified and compared across different Arachis species, including A. duranensis, A. ipaensis, A. monticola, A. hypogaea cultivars (cv.) Fuhuasheng, A. hypogaea cv. Shitouqi, and A. hypogaea cv. Tifrunner. The results showed that the WRKY TFs underwent dynamic equilibrium between diploid and tetraploid peanut species, characterized by the loss of old WRKY TFs and retention of the new ones. Notably, cultivated peanuts inherited more conserved WRKY orthologs from wild tetraploid peanuts than their wild diploid donors. Analysis of the W-box elements and protein-protein interactions revealed that different domestication processes affected WRKY evolution across cultivated peanut varieties. WRKY TFs of A. hypogaea cv. Fuhuasheng and Shitouqi exhibited a similar domestication process, while those of cv. Tifrunner of the same species underwent a different domestication process based on protein-protein interaction analysis. CONCLUSIONS This study provides new insights into the evolution of WRKY TFs in Arachis spp.
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Affiliation(s)
- Mingwei Chen
- grid.412608.90000 0000 9526 6338Key Laboratory of National Forestry and Grassland Administration On Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, China ,grid.412608.90000 0000 9526 6338Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Meiran Li
- grid.412608.90000 0000 9526 6338Key Laboratory of National Forestry and Grassland Administration On Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, China ,grid.412608.90000 0000 9526 6338Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Longgang Zhao
- grid.412608.90000 0000 9526 6338Key Laboratory of National Forestry and Grassland Administration On Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, China ,grid.412608.90000 0000 9526 6338High-Efficiency Agricultural Technology Industry Research Institute of Saline and Alkaline Land of Dongying, Qingdao Agricultural University, Qingdao, China
| | - Hui Song
- grid.412608.90000 0000 9526 6338Key Laboratory of National Forestry and Grassland Administration On Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, China ,grid.412608.90000 0000 9526 6338Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao, China ,grid.412608.90000 0000 9526 6338High-Efficiency Agricultural Technology Industry Research Institute of Saline and Alkaline Land of Dongying, Qingdao Agricultural University, Qingdao, China
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S GB, Gohil DS, Roy Choudhury S. Genome-wide identification, evolutionary and expression analysis of the cyclin-dependent kinase gene family in peanut. BMC PLANT BIOLOGY 2023; 23:43. [PMID: 36658501 PMCID: PMC9850575 DOI: 10.1186/s12870-023-04045-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Cyclin-dependent kinases (CDKs) are a predominant group of serine/threonine protein kinases that have multi-faceted functions in eukaryotes. The plant CDK members have well-known roles in cell cycle progression, transcriptional regulation, DNA repair, abiotic stress and defense responses, making them promising targets for developing stress adaptable high-yielding crops. There is relatively sparse information available on the CDK family genes of cultivated oilseed crop peanut and its diploid progenitors. RESULTS We have identified 52 putative cyclin-dependent kinases (CDKs) and CDK-like (CDKLs) genes in Arachis hypogaea (cultivated peanut) and total 26 genes in each diploid parent of cultivated peanut (Arachis duranensis and Arachis ipaensis). Both CDK and CDKL genes were classified into eight groups based on their cyclin binding motifs and their phylogenetic relationship with Arabidopsis counterparts. Genes in the same subgroup displayed similar exon-intron structure and conserved motifs. Further, gene duplication analysis suggested that segmental duplication events played major roles in the expansion and evolution of CDK and CDKL genes in cultivated peanuts. Identification of diverse cis-acting response elements in CDK and CDKL genes promoter indicated their potential fundamental roles in multiple biological processes. Various gene expression patterns of CDKs and CDKLs in different peanut tissues suggested their involvement during growth and development. In addition, qRT-PCR analysis demonstrated that most representing CDK and CDKL gene family members were significantly down-regulated under ABA, PEG and mannitol treatments. CONCLUSIONS Genome-wide analysis offers a comprehensive understanding of the classification, evolution, gene structure, and gene expression profiles of CDK and CDKL genes in cultivated peanut and their diploid progenitors. Additionally, it also provides cell cycle regulatory gene resources for further functional characterization to enhance growth, development and abiotic stress tolerance.
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Affiliation(s)
- Gokul Babu S
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, 517507, India
| | - Deependra Singh Gohil
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, 517507, India
| | - Swarup Roy Choudhury
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, 517507, India.
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Hao J, Liang Y, Ping J, Li J, Shi W, Su Y, Wang T. Chloroplast gene expression level is negatively correlated with evolutionary rates and selective pressure while positively with codon usage bias in Ophioglossum vulgatum L. BMC PLANT BIOLOGY 2022; 22:580. [PMID: 36510137 PMCID: PMC9746204 DOI: 10.1186/s12870-022-03960-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 11/24/2022] [Indexed: 05/02/2023]
Abstract
BACKGROUND Characterization of the key factors determining gene expression level has been of significant interest. Previous studies on the relationship among evolutionary rates, codon usage bias, and expression level mostly focused on either nuclear genes or unicellular/multicellular organisms but few in chloroplast (cp) genes. Ophioglossum vulgatum is a unique fern and has important scientific and medicinal values. In this study, we sequenced its cp genome and transcriptome to estimate the evolutionary rates (dN and dS), selective pressure (dN/dS), gene expression level, codon usage bias, and their correlations. RESULTS The correlation coefficients between dN, dS, and dN/dS, and Transcripts Per Million (TPM) average values were -0.278 (P = 0.027 < 0.05), -0.331 (P = 0.008 < 0.05), and -0.311 (P = 0.013 < 0.05), respectively. The codon adaptation index (CAI) and tRNA adaptation index (tAI) were significantly positively correlated with TPM average values (P < 0.05). CONCLUSIONS Our results indicated that when the gene expression level was higher, the evolutionary rates and selective pressure were lower, but the codon usage bias was stronger. We provided evidence from cp gene data which supported the E-R (E stands for gene expression level and R stands for evolutionary rate) anti-correlation.
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Affiliation(s)
- Jing Hao
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yingyi Liang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jingyao Ping
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jinye Li
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Wanxin Shi
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, 518057, China.
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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Lecoy J, Sachin Ranade S, Rosario García-Gil M. Analysis of the ASR and LP3 homologous gene families reveal positive selection acting on LP3-3 gene. Gene 2022; 850:146935. [DOI: 10.1016/j.gene.2022.146935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/20/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022]
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Saha J, Dey S, Pal A. Whole genome sequencing and comparative genomic analyses of Pseudomonas aeruginosa strain isolated from arable soil reveal novel insights into heavy metal resistance and codon biology. Curr Genet 2022; 68:481-503. [PMID: 35763098 DOI: 10.1007/s00294-022-01245-z] [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: 03/28/2022] [Revised: 05/14/2022] [Accepted: 06/06/2022] [Indexed: 11/03/2022]
Abstract
Elevated concentration of non-essential persistent heavy metals and metalloids in the soil is detrimental to essential soil microbes and plants, resulting in diminished diversity and biomass. Thus, isolation, screening, and whole genomic analysis of potent strains of bacteria from arable lands with inherent capabilities of heavy metal resistance and plant growth promotion hold the key for bio remedial applications. This study is an attempt to do the same. In this study, a potent strain of Pseudomonas aeruginosa was isolated from paddy fields, followed by metabolic profiling using FTIR, metal uptake analysis employing ICP-MS, whole genome sequencing and comparative codon usage analysis. ICP-MS study provided insights into a high degree of Cd uptake during the exponential phase of growth under cumulative metal stress to Cd, Zn and Co, which was further corroborated by the detection of cadA gene along with czcCBA operon in the genome upon performing whole-genome sequencing. This potent strain of Pseudomonas aeruginosa also harboured genes, such as copA, chrA, znuA, mgtE, corA, and others conferring resistance against different heavy metals, such as Cd, Zn, Co, Cu, Cr, etc. A comparative codon usage bias analysis at the genomic and genic level, whereby several heavy metal resistant genes were considered in the backdrop of two housekeeping genes among 40 Pseudomonas spp. indicated the presence of a relatively strong codon usage bias in the studied strain. With this work, an effort was made to explore heavy metal-resistant bacteria (isolated from arable soil) and whole genome sequence analysis to get insight into metal resistance for future bio remedial applications.
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Affiliation(s)
- Jayanti Saha
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, West Bengal, 733134, India
| | - Sourav Dey
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, West Bengal, 733134, India
| | - Ayon Pal
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, West Bengal, 733134, India.
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Abstract
Codon usage bias is the preferential or non-random use of synonymous codons, a ubiquitous phenomenon observed in bacteria, plants and animals. Different species have consistent and characteristic codon biases. Codon bias varies not only with species, family or group within kingdom, but also between the genes within an organism. Codon usage bias has evolved through mutation, natural selection, and genetic drift in various organisms. Genome composition, GC content, expression level and length of genes, position and context of codons in the genes, recombination rates, mRNA folding, and tRNA abundance and interactions are some factors influencing codon bias. The factors shaping codon bias may also be involved in evolution of the universal genetic code. Codon-usage bias is critical factor determining gene expression and cellular function by influencing diverse processes such as RNA processing, protein translation and protein folding. Codon usage bias reflects the origin, mutation patterns and evolution of the species or genes. Investigations of codon bias patterns in genomes can reveal phylogenetic relationships between organisms, horizontal gene transfers, molecular evolution of genes and identify selective forces that drive their evolution. Most important application of codon bias analysis is in the design of transgenes, to increase gene expression levels through codon optimization, for development of transgenic crops. The review gives an overview of deviations of genetic code, factors influencing codon usage or bias, codon usage bias of nuclear and organellar genes, computational methods to determine codon usage and the significance as well as applications of codon usage analysis in biological research, with emphasis on plants.
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Affiliation(s)
| | - Varatharajalu Udayasuriyan
- Department of Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - Vijaipal Bhadana
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, 834010, India
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Wang P, Mao Y, Su Y, Wang J. Comparative analysis of transcriptomic data shows the effects of multiple evolutionary selection processes on codon usage in Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. BMC Genomics 2021; 22:781. [PMID: 34717552 PMCID: PMC8557549 DOI: 10.1186/s12864-021-08106-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 10/19/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Kuruma shrimp, a major commercial shrimp species in the world, has two cryptic or sibling species, Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. Codon usage analysis would contribute to our understanding of the genetic and evolutionary characteristics of the two Marsupenaeus species. In this study, we analyzed codon usage and related indices using coding sequences (CDSs) from RNA-seq data. RESULTS Using CodonW 1.4.2 software, we performed the codon bias analysis of transcriptomes obtained from hepatopancreas tissues, which indicated weak codon bias. Almost all parameters had similar correlations for both species. The gene expression level (FPKM) was negatively correlated with A/T3s. We determined 12 and 14 optimal codons for M. japonicus and M. pulchricaudatus, respectively, and all optimal codons have a C/G-ending. The two Marsupenaeus species had different usage frequencies of codon pairs, which contributed to further analysis of transcriptional differences between them. Orthologous genes that underwent positive selection (ω > 1) had a higher correlation coefficient than that of experienced purifying selection (ω < 1). Parity Rule 2 (PR2) and effective number of codons (ENc) plot analysis showed that the codon usage patterns of both species were influenced by both mutations and selection. Moreover, the average observed ENc value was lower than the expected value for both species, suggesting that factors other than GC may play roles in these phenomena. The results of multispecies clustering based on codon preference were consistent with traditional classification. CONCLUSIONS This study provides a relatively comprehensive understanding of the correlations among codon usage bias, gene expression, and selection pressures of CDSs for M. japonicus and M. pulchricaudatus. The genetic evolution was driven by mutations and selection pressure. Moreover, the results point out new insights into the specificities and evolutionary characteristics of the two Marsupenaeus species.
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Affiliation(s)
- Panpan Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/ Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
- The Jiangsu Provincial Infrastructure for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yong Mao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, China.
| | - Yongquan Su
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Jun Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, Fujian, China
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Latrille T, Lartillot N. Quantifying the impact of changes in effective population size and expression level on the rate of coding sequence evolution. Theor Popul Biol 2021; 142:57-66. [PMID: 34563555 DOI: 10.1016/j.tpb.2021.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 09/08/2021] [Accepted: 09/11/2021] [Indexed: 02/07/2023]
Abstract
Molecular sequences are shaped by selection, where the strength of selection relative to drift is determined by effective population size (Ne). Populations with high Ne are expected to undergo stronger purifying selection, and consequently to show a lower substitution rate for selected mutations relative to the substitution rate for neutral mutations (ω). However, computational models based on biophysics of protein stability have suggested that ω can also be independent of Ne. Together, the response of ω to changes in Ne depends on the specific mapping from sequence to fitness. Importantly, an increase in protein expression level has been found empirically to result in decrease of ω, an observation predicted by theoretical models assuming selection for protein stability. Here, we derive a theoretical approximation for the response of ω to changes in Ne and expression level, under an explicit genotype-phenotype-fitness map. The method is generally valid for additive traits and log-concave fitness functions. We applied these results to protein undergoing selection for their conformational stability and corroborate out findings with simulations under more complex models. We predict a weak response of ω to changes in either Ne or expression level, which are interchangeable. Based on empirical data, we propose that fitness based on the conformational stability may not be a sufficient mechanism to explain the empirically observed variation in ω across species. Other aspects of protein biophysics might be explored, such as protein-protein interactions, which can lead to a stronger response of ω to changes in Ne.
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Affiliation(s)
- T Latrille
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, F-69622 Villeurbanne, France; École Normale Supérieure de Lyon, Université de Lyon, Université Lyon 1, Lyon, France.
| | - N Lartillot
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, F-69622 Villeurbanne, France
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12
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Das JK, Roy S. Comparative analysis of human coronaviruses focusing on nucleotide variability and synonymous codon usage patterns. Genomics 2021; 113:2177-2188. [PMID: 34019999 PMCID: PMC8131179 DOI: 10.1016/j.ygeno.2021.05.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 05/09/2021] [Accepted: 05/14/2021] [Indexed: 01/04/2023]
Abstract
The prevailing COVID-19 pandemic has drawn the attention of the scientific community to study the evolutionary origin of Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2). This study is a comprehensive quantitative analysis of the protein-coding sequences of seven human coronaviruses (HCoVs) to decipher the nucleotide sequence variability and codon usage patterns. It is essential to understand the survival ability of the viruses, their adaptation to hosts, and their evolution. The current analysis revealed a high abundance of the relative dinucleotide (odds ratio), GC and CT pairs in the first and last two codon positions, respectively, as well as a low abundance of the CG pair in the last two positions of the codon, which might be related to the evolution of the viruses. A remarkable level of variability of GC content in the third position of the codon among the seven coronaviruses was observed. Codons with high RSCU values are primarily from the aliphatic and hydroxyl amino acid groups, and codons with low RSCU values belong to the aliphatic, cyclic, positively charged, and sulfur-containing amino acid groups. In order to elucidate the evolutionary processes of the seven coronaviruses, a phylogenetic tree (dendrogram) was constructed based on the RSCU scores of the codons. The severe and mild categories CoVs were positioned in different clades. A comparative phylogenetic study with other coronaviruses depicted that SARS-CoV-2 is close to the CoV isolated from pangolins (Manis javanica, Pangolin-CoV) and cats (Felis catus, SARS(r)-CoV). Further analysis of the effective number of codon (ENC) usage bias showed a relatively higher bias for SARS-CoV and MERS-CoV compared to SARS-CoV-2. The ENC plot against GC3 suggested that the mutational bias might have a role in determining the codon usage variation among candidate viruses. A codon adaptability study on a few human host parasites (from different kingdoms), including CoVs, showed a diverse adaptability pattern. SARS-CoV-2 and SARS-CoV exhibit relatively lower but similar codon adaptability compared to MERS-CoV.
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Affiliation(s)
- Jayanta Kumar Das
- Department of Pediatrics, Johns Hopkins University School of Medicine, MD, USA.
| | - Swarup Roy
- Network Reconstruction & Analysis (NetRA) Lab, Department of Computer Applications, Sikkim University, Gangtok, India.
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Das JK, Chakraborty S, Roy S. A scheme for inferring viral-host associations based on codon usage patterns identifies the most affected signaling pathways during COVID-19. J Biomed Inform 2021; 118:103801. [PMID: 33965637 PMCID: PMC8102073 DOI: 10.1016/j.jbi.2021.103801] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 05/02/2021] [Accepted: 05/03/2021] [Indexed: 12/16/2022]
Abstract
Understanding the molecular mechanism of COVID-19 pathogenesis helps in the rapid therapeutic target identification. Usually, viral protein targets host proteins in an organized fashion. The expression of any viral gene depends mostly on the host translational machinery. Recent studies report the great significance of codon usage biases in establishing host-viral protein–protein interactions (PPI). Exploring the codon usage patterns between a pair of co-evolved host and viral proteins may present novel insight into the host-viral protein interactomes during disease pathogenesis. Leveraging the similarity in codon usage patterns, we propose a computational scheme to recreate the host-viral protein–protein interaction network. We use host proteins from seventeen (17) essential signaling pathways for our current work towards understanding the possible targeting mechanism of SARS-CoV-2 proteins. We infer both negatively and positively interacting edges in the network. Further, extensive analysis is performed to understand the host PPI network topologically and the attacking behavior of the viral proteins. Our study reveals that viral proteins mostly utilize codons, rare in the targeted host proteins (negatively correlated interaction). Among them, non-structural proteins, NSP3 and structural protein, Spike (S), are the most influential proteins in interacting with multiple host proteins. While ranking the most affected pathways, MAPK pathways observe to be the worst affected during the SARS-CoV-2 infection. Several proteins participating in multiple pathways are highly central in host PPI and mostly targeted by multiple viral proteins. We observe many potential targets (host proteins) from the affected pathways associated with the various drug molecules, including Arsenic trioxide, Dexamethasone, Hydroxychloroquine, Ritonavir, and Interferon beta, which are either under clinical trial or in use during COVID-19.
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Affiliation(s)
- Jayanta Kumar Das
- Department of Pediatrics, Johns Hopkins University, School of Medicine, MD, USA
| | | | - Swarup Roy
- Network Reconstruction & Analysis (NetRA) Lab, Department of Computer Applications, Sikkim University, Gangtok, India.
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14
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Zhang H, Xie J, Wang W, Wang J. Comparison of Brassica Genomes reveals asymmetrical gene retention between functional groups of genes in recurrent polyploidizations. PLANT MOLECULAR BIOLOGY 2021; 106:193-206. [PMID: 33742369 DOI: 10.1007/s11103-021-01137-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
We provided a study on homeologous gene evolution of homeologous genes by comparing Brassica genomes. Polyploidy has played fundamental roles during the evolution of plants. Following polyploidization, many duplicated genes are diversified or lost in a process termed diploidization. Understanding the retention and diversification of homeologs after polyploidization will help elucidate the process of diploidization. Here, we investigated the evolution of homeologous genes in Brassica genomes and observed similarly asymmetrical gene retention among different functional groups and consistent retention after recurrent polyploidizations. In the comparative analysis of Brassica diploid genomes, we found that preferentially retained genes show different patterns on sequence and expression divergence: genes with the function of 'biosynthetic process' and 'transport' were under much stronger purifying selection, while transcriptional regulatory genes diverged much faster than other genes. Duplicate pairs of the former two functional groups show conserved high expression patterns, while most of transcriptional regulatory genes are simultaneously lowly expressed. Furthermore, homeologs in diploids and allotetraploids showed similar loss and retention patterns: duplicates in progenitor genomes were more likely to be retained and accumulated fewer substitutions. However, transcriptional regulation is also enriched in the genes that do not have any non-synonymous mutations in the Brassica allotetraploids, indicating that some of these genes were under strong purifying selection. Overall, our study provided insight into the evolution of homeologs genes during diploidization process.
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Affiliation(s)
- Haorui Zhang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Jiandan Xie
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Wenliang Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Jianbo Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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15
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Dong S, Zhang L, Pang W, Zhang Y, Wang C, Li Z, Ma L, Tang W, Yang G, Song H. Comprehensive analysis of coding sequence architecture features and gene expression in Arachis duranensis. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:213-222. [PMID: 33707864 PMCID: PMC7907404 DOI: 10.1007/s12298-021-00938-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/04/2021] [Accepted: 01/20/2021] [Indexed: 06/09/2023]
Abstract
Coding sequence (CDS) architecture affects gene expression levels in organisms. Codon optimization can increase the gene expression level. Therefore, understanding codon usage patterns has important implications for research on genetic engineering and exogenous gene expression. To date, the codon usage patterns of many model plants have been analyzed. However, the relationship between CDS architecture and gene expression in Arachis duranensis remains poorly understood. According to the results of genome sequencing, A. duranensis has many resistant genes that can be used to improve the cultivated peanut. In this study, bioinformatic approaches were used to estimate A. duranensis CDS architectures, including frequency of the optimal codon (Fop), polypeptide length and GC contents at the first (GC1), second (GC2) and third (GC3) codon positions. In addition, Arachis RNA-seq datasets were downloaded from PeanutBase. The relationships between gene expression and CDS architecture were assessed both under normal growth as well as nematode and drought stress conditions. A total of 26 codons with high frequency were identified, which preferentially ended with A or T in A. duranensis CDSs under the above-mentioned three conditions. A similar CDS architecture was found in differentially expressed genes (DEGs) under nematode and drought stresses. The GC1 content differed between DEGs and non-differentially expressed genes (NDEGs) under both drought and nematode stresses. The expression levels of DEGs were affected by different CDS architectures compared with NDEGs under drought stress. In addition, no correlation was found between differential gene expression and CDS architecture neither under nematode nor under drought stress. These results aid the understanding of gene expression in A. duranensis.
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Affiliation(s)
- Shuwei Dong
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Long Zhang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Wenhui Pang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Yongli Zhang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Chang Wang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Zhenyi Li
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Lichao Ma
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Wei Tang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Guofeng Yang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Hui Song
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
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16
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Shi T, Rahmani RS, Gugger PF, Wang M, Li H, Zhang Y, Li Z, Wang Q, Van de Peer Y, Marchal K, Chen J. Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants. Mol Biol Evol 2020; 37:2394-2413. [PMID: 32343808 PMCID: PMC7403625 DOI: 10.1093/molbev/msaa105] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
For most sequenced flowering plants, multiple whole-genome duplications (WGDs) are found. Duplicated genes following WGD often have different fates that can quickly disappear again, be retained for long(er) periods, or subsequently undergo small-scale duplications. However, how different expression, epigenetic regulation, and functional constraints are associated with these different gene fates following a WGD still requires further investigation due to successive WGDs in angiosperms complicating the gene trajectories. In this study, we investigate lotus (Nelumbo nucifera), an angiosperm with a single WGD during the K-pg boundary. Based on improved intraspecific-synteny identification by a chromosome-level assembly, transcriptome, and bisulfite sequencing, we explore not only the fundamental distinctions in genomic features, expression, and methylation patterns of genes with different fates after a WGD but also the factors that shape post-WGD expression divergence and expression bias between duplicates. We found that after a WGD genes that returned to single copies show the highest levels and breadth of expression, gene body methylation, and intron numbers, whereas the long-retained duplicates exhibit the highest degrees of protein-protein interactions and protein lengths and the lowest methylation in gene flanking regions. For those long-retained duplicate pairs, the degree of expression divergence correlates with their sequence divergence, degree in protein-protein interactions, and expression level, whereas their biases in expression level reflecting subgenome dominance are associated with the bias of subgenome fractionation. Overall, our study on the paleopolyploid nature of lotus highlights the impact of different functional constraints on gene fate and duplicate divergence following a single WGD in plant.
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Affiliation(s)
- Tao Shi
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Razgar Seyed Rahmani
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Paul F Gugger
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD
| | - Muhua Wang
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hui Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yue Zhang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhizhong Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qingfeng Wang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Centre for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Information Technology, IDLab, IMEC, Ghent University, Ghent, Belgium
| | - Jinming Chen
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
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17
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Chen Z, Zhao J, Qiao J, Li W, Li J, Xu R, Wang H, Liu Z, Xing B, Wendel JF, Grover CE. Comparative analysis of codon usage between Gossypium hirsutum and G. barbadense mitochondrial genomes. Mitochondrial DNA B Resour 2020; 5:2500-2506. [PMID: 33457843 PMCID: PMC7782173 DOI: 10.1080/23802359.2020.1780969] [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] [Indexed: 11/06/2022] Open
Abstract
Gossypium hirsutum and G. barbadense mitochondrial genomes were analyzed to understand the factors shaping codon usage. While most analyses of codon usage suggest minimal to no bias, nucleotide composition, specifically GC content, was significantly correlated with codon usage. In general, both mitochondrial genomes favor codons that end in A or U, with a secondary preference for pyrimidine rich codons. These observations are similar to previous reports of codon usage in cotton nuclear genomes, possibly suggestive of a general bias spanning genomic compartment. Although evidence for codon usage bias is weak for most genes, we identified six genes (i.e. atp8, atp9, sdh3, sdh4, mttB and rpl2) with significant nonrandom codon usage. In general, we find multiple factors that influence cotton mitochondrial genome codon usage, which may include selection in a subset of genes.
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Affiliation(s)
- Zhiwen Chen
- Institute of Carbon Materials Science, Shanxi Datong University, Datong, China
| | - Jianguo Zhao
- Institute of Carbon Materials Science, Shanxi Datong University, Datong, China.,College of Chemistry and Environment Engineering, Shanxi Datong University, Datong, China
| | - Jun Qiao
- College of Chemistry and Environment Engineering, Shanxi Datong University, Datong, China
| | - Weijia Li
- Institute of Carbon Materials Science, Shanxi Datong University, Datong, China
| | - Jingwei Li
- Institute of Carbon Materials Science, Shanxi Datong University, Datong, China
| | - Ran Xu
- College of Chemistry and Environment Engineering, Shanxi Datong University, Datong, China
| | - Haiyan Wang
- College of Chemistry and Environment Engineering, Shanxi Datong University, Datong, China
| | - Zehui Liu
- College of Chemistry and Environment Engineering, Shanxi Datong University, Datong, China
| | - Baoyan Xing
- Institute of Carbon Materials Science, Shanxi Datong University, Datong, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Corrinne E Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
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18
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Singh R, Sophiarani Y. A report on DNA sequence determinants in gene expression. Bioinformation 2020; 16:422-431. [PMID: 32831525 PMCID: PMC7434957 DOI: 10.6026/97320630016422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 11/26/2022] Open
Abstract
The biased usage of nucleotides in coding sequence and its correlation with gene expression has been observed in several studies. A complex set of interactions between genes and
other components of the expression system determine the amount of proteins produced from coding sequences. It is known that the elongation rate of polypeptide chain is affected by
both codon usage bias and specific amino acid compositional constraints. Therefore, it is of interest to review local DNA-sequence elements and other positional as well as
combinatorial constraints that play significant role in gene expression.
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Affiliation(s)
- Ravail Singh
- Indian Institute of Integrative Medicine, CSIR, Canal Road, Jammu-180001
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19
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Saha J, Saha BK, Pal Sarkar M, Roy V, Mandal P, Pal A. Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes. Front Microbiol 2019; 10:2896. [PMID: 31921071 PMCID: PMC6928123 DOI: 10.3389/fmicb.2019.02896] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/02/2019] [Indexed: 01/02/2023] Open
Abstract
Soil is a diversified and complex ecological niche, home to a myriad of microorganisms particularly bacteria. The physico-chemical complexities of soil results in a plethora of physiological variations to exist within the different types of soil dwelling bacteria, giving rise to a wide variation in genome structure and complexity. This serves as an attractive proposition to analyze and compare the genome of a large number soil bacteria to comprehend their genome complexity and evolution. In this study a combination of codon usage and molecular phylogenetics of the whole genome and key housekeeping genes like infB (translation initiation factor 2), trpB (tryptophan synthase, beta subunit), atpD (ATP synthase, beta subunit), and rpoB (RNA polymerase, beta subunit) of 92 soil bacterial species spread across the entire eubacterial domain and residing in different soil types was performed. The results indicated the direct relationship of genome size with codon bias and coding frequency in the studied bacteria. The codon usage profile demonstrated by the gene trpB was found to be relatively different from the rest of the housekeeping genes with a large number of bacteria having a greater percentage of genes with Nc values less than the Nc of trpB. The results from the overall codon usage bias profile also depicted that the codon usage bias in the key housekeeping genes of soil bacteria was majorly due to selectional pressure and not mutation. The analysis of hydrophobicity of the gene product encoded by the rpoB coding sequences demonstrated tight clustering across all the soil bacteria suggesting conservation of protein structure for maintenance of form and function. The phylogenetic affinities inferred using 16S rRNA gene and the housekeeping genes demonstrated conflicting signals with trpB gene being the noisiest one. The housekeeping gene atpD was found to depict the least amount of evolutionary change in the soil bacteria considered in this study except in two Clostridium species. The phylogenetic and codon usage analysis of the soil bacteria consistently demonstrated the relatedness of Azotobacter chroococcum with different species of the genus Pseudomonas.
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Affiliation(s)
- Jayanti Saha
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Barnan K. Saha
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Monalisha Pal Sarkar
- Mycology & Plant Pathology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Vivek Roy
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Parimal Mandal
- Mycology & Plant Pathology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Ayon Pal
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
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20
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Pal A, Saha BK, Saha J. Comparative in silico analysis of ftsZ gene from different bacteria reveals the preference for core set of codons in coding sequence structuring and secondary structural elements determination. PLoS One 2019; 14:e0219231. [PMID: 31841523 PMCID: PMC6913975 DOI: 10.1371/journal.pone.0219231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/28/2019] [Indexed: 11/19/2022] Open
Abstract
The deluge of sequence information in the recent times provide us with an excellent opportunity to compare organisms on a large genomic scale. In this study we have tried to decipher the variation in the gene organization and structuring of a vital bacterial gene called ftsZ which codes for an integral component of the bacterial cell division, the FtsZ protein. FtsZ is homologous to tubulin protein and has been found to be ubiquitous in eubacteria. FtsZ is showing increasing promise as a target for antibacterial drug discovery. Our study of ftsZ protein from 143 different bacterial species spanning a wider range of morphological and physiological type demonstrates that the ftsZ gene of about ninety three percent of the organisms show relatively biased codon usage profile and significant GC deviation from their genomic GC content. Comparative codon usage analysis of ftsZ and a core housekeeping gene rpoB demonstrated that codon usage pattern of ftsZ CDS is shaped by natural selection to a large extent and mimics that of a housekeeping gene. We have also detected a tendency among the different organisms to utilize a core set of codons in structuring the ftsZ coding sequence. We observed that the compositional frequency of the amino acid serine in the FtsZ protein appears to be a indicator of the bacterial lifestyle. Our meticulous analysis of the ftsZ gene linked with the corresponding FtsZ protein show that there is a bias towards the use of specific synonymous codons particularly in the helix and strand regions of the multi-domain FtsZ protein. Overall our findings suggest that in an indispensable and vital protein such as FtsZ, there is an inherent tendency to maintain form for optimized performance in spite of the extrinsic variability in coding features.
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Affiliation(s)
- Ayon Pal
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, West Bengal, India
| | - Barnan Kumar Saha
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, West Bengal, India
| | - Jayanti Saha
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, West Bengal, India
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Song H, Guo Z, Hu X, Qian L, Miao F, Zhang X, Chen J. Evolutionary balance between LRR domain loss and young NBS-LRR genes production governs disease resistance in Arachis hypogaea cv. Tifrunner. BMC Genomics 2019; 20:844. [PMID: 31722670 PMCID: PMC6852974 DOI: 10.1186/s12864-019-6212-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 10/22/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Cultivated peanut (Arachis hypogaea L.) is an important oil and protein crop, but it has low disease resistance; therefore, it is important to reveal the number, sequence features, function, and evolution of genes that confer resistance. Nucleotide-binding site-leucine-rich repeats (NBS-LRRs) are resistance genes that are involved in response to various pathogens. RESULTS We identified 713 full-length NBS-LRRs in A. hypogaea cv. Tifrunner. Genetic exchange events occurred on NBS-LRRs in A. hypogaea cv. Tifrunner, which were detected in the same subgenomes and also found in different subgenomes. Relaxed selection acted on NBS-LRR proteins and LRR domains in A. hypogaea cv. Tifrunner. Using quantitative trait loci (QTL), we found that NBS-LRRs were involved in response to late leaf spot, tomato spotted wilt virus, and bacterial wilt in A. duranensis (2 NBS-LRRs), A. ipaensis (39 NBS-LRRs), and A. hypogaea cv. Tifrunner (113 NBS-LRRs). In A. hypogaea cv. Tifrunner, 113 NBS-LRRs were classified as 75 young and 38 old NBS-LRRs, indicating that young NBS-LRRs were involved in response to disease after tetraploidization. However, compared to A. duranensis and A. ipaensis, fewer LRR domains were found in A. hypogaea cv. Tifrunner NBS-LRR proteins, partly explaining the lower disease resistance of the cultivated peanut. CONCLUSIONS Although relaxed selection acted on NBS-LRR proteins and LRR domains, LRR domains were preferentially lost in A. hypogaea cv. Tifrunner compared to A. duranensis and A. ipaensis. The QTL results suggested that young NBS-LRRs were important for resistance against diseases in A. hypogaea cv. Tifrunner. Our results provid insight into the greater susceptibility of A. hypogaea cv. Tifrunner to disease compared to A. duranensis and A. ipaensis.
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Affiliation(s)
- Hui Song
- Grassland Agri-husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China.
| | - Zhonglong Guo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Xiaohui Hu
- Shandong Peanut Research Institute, Qingdao, China
| | - Lang Qian
- Dalian Academy of Agricultural Sciences, Dalian, China
| | - Fuhong Miao
- Grassland Agri-husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Xiaojun Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Jing Chen
- Shandong Peanut Research Institute, Qingdao, China.
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22
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Cao Y, Jiang L, Wang L, Cai Y. Evolutionary Rate Heterogeneity and Functional Divergence of Orthologous Genes in Pyrus. Biomolecules 2019; 9:biom9090490. [PMID: 31527450 PMCID: PMC6770726 DOI: 10.3390/biom9090490] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 09/09/2019] [Accepted: 09/12/2019] [Indexed: 11/21/2022] Open
Abstract
Negatively selected genes (NSGs) and positively selected genes (PSGs) are the two types of most nuclear protein-coding genes in organisms. However, the evolutionary rates and characteristics of different types of genes have been rarely understood. In the present study, we investigate the rates of synonymous substitution (Ks) and the rates of non-synonymous substitution (Ka) by comparing the orthologous genes of two sequenced Pyrus species, Pyrus bretschneideri and Pyrus communis. Subsequently, we compared the evolutionary rates, gene structures, and expression profiles during different fruit development between PSGs and NSGs. Compared with the NSGs, the PSGs have fewer exons, shorter gene length, lower synonymous substitution rates and have higher evolutionary rates. Remarkably, gene expression patterns between two Pyrus species fruit indicated functional divergence for most of the orthologous genes derived from a common ancestor, and subfunctionalization for some of them. Overall, the present study shows that PSGs differs from NSGs not only under environmental selective pressure (Ka/Ks), but also in their structural, functional, and evolutionary properties. Additionally, our resulting data provides important insights for the evolution and highlights the diversification of orthologous genes in two Pyrus species.
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Affiliation(s)
- Yunpeng Cao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China.
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Lan Jiang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China.
| | - Lihu Wang
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan 056038, China.
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
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23
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Naini R, Pavankumar P, Prabhakar S, Kancha RK, Rao KV, Reddy VD. Evolvement of nutraceutical onion plants engineered for resveratrol biosynthetic pathway. PLANT CELL REPORTS 2019; 38:1127-1137. [PMID: 31154513 DOI: 10.1007/s00299-019-02432-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 06/09/2023]
Abstract
Genetically engineered onion expressing codon-optimized VvSTS1 gene accumulated stilbenes and extended life span in yeast and can serve as potential nutraceutical. Resveratrol (RV) is a natural polyphenolic compound found in certain plant species including grapes. RV is well known for its nutraceutical properties and to assuage several disease conditions. Onion is the second most consumed vegetable worldwide and contains large quantities of precursor molecules, malonyl-CoA and para-coumaroyl-CoA that are needed for RV biosynthesis. The present study reports the development of nutraceutical onion by engineering RV biosynthetic pathway. A codon-optimized grapevine synthetic stilbene synthase gene (VvSTS1) was synthesized using native grapevine sequence. Six-week-old healthy yellowish compact nodular calli were co-cultivated with Agrobacterium tumefaciens harbouring pCAMBIA1300-hpt II-CaMV35S-VvSTS1-nos. PCR analysis revealed the presence of VvSTS1 and hpt II genes in putative transgenics. Southern blot analysis confirmed the integration of VvSTS1 gene and independent nature of transformants. LC-ESI-HRMS analysis revealed the accumulation of variable quantities of RV (24.98-50.18 µg/g FW) and its glycosylated form polydatin (33.6-67.15 µg/g FW) in both leaves and bulbs, respectively, indicating the successful engineering of RV biosynthetic pathway into onion. The transgenic onion bulb extracts extended the life span in haploid yeast. The transgenic onion accumulating RV and polydatin, developed for the first of its kind, may serve as a potential nutraceutical resource.
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Affiliation(s)
- Raju Naini
- Centre for Plant Molecular Biology (CPMB), Osmania University, Hyderabad, Telangana, 500007, India
| | - P Pavankumar
- Centre for Mass Spectrometry, CSIR-Indian Institute of Chemical Technology, Hyderabad, Telangana, 500007, India
- Acadamy of Scientific and Innovative Research, CSIR-IICT, Hyderabad, India
| | - S Prabhakar
- Centre for Mass Spectrometry, CSIR-Indian Institute of Chemical Technology, Hyderabad, Telangana, 500007, India
- Acadamy of Scientific and Innovative Research, CSIR-IICT, Hyderabad, India
| | - Rama Krishna Kancha
- Centre for Plant Molecular Biology (CPMB), Osmania University, Hyderabad, Telangana, 500007, India
| | | | - Vudem Dashavantha Reddy
- Centre for Plant Molecular Biology (CPMB), Osmania University, Hyderabad, Telangana, 500007, India.
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Genetic evolution and codon usage analysis of NKX-2.5 gene governing heart development in some mammals. Genomics 2019; 112:1319-1329. [PMID: 31377427 DOI: 10.1016/j.ygeno.2019.07.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/26/2019] [Accepted: 07/31/2019] [Indexed: 11/21/2022]
Abstract
NKX-2.5 gene is responsible for cardiac development and its targeted disruption apprehends cardiac development at the linear heart tube stage. Bioinformatic analysis was employed to investigate the codon usage pattern and dN/dS of mammalian NKX-2.5 gene. The relative synonymous codon usage analysis revealed variation in codon usage and two synonymous codons namely ATA (Ile) and GTA (Val) were absent in NKX-2.5 gene across selected mammalian species suggesting that these two codons were possibly selected against during evolution. Parity rule 2 analysis of two and four fold amino acids showed CT bias whereas six-fold amino acids revealed GA bias. Neutrality analysis suggests that selection played a prominent role while mutation had a minor role. The dN/dS analysis suggests synonymous substitution played a significant role and it negatively correlated with p-distance of the gene. Purifying natural selection played a dominant role in the genetic evolution of NKX-2.5 gene in mammals.
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Song H, Sun J, Yang G. The characteristic of Arachis duranensis-specific genes and their potential function. Gene 2019; 705:60-66. [PMID: 31009681 DOI: 10.1016/j.gene.2019.04.052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/12/2019] [Accepted: 04/18/2019] [Indexed: 11/17/2022]
Abstract
Arachis species produce flowers aerially, and then grow into the ground, where they develop into fruits; a feature that is unique to Arachis species. We hypothesized that Arachis species evolved genes specifically involved in the control of aerial flowers and the formation of underground fruits. Arachis duranensis is more resistant to biotic and abiotic stressors. Here, we compared different legume species and identified Arachis duranensis-specific genes. We analyzed gene expression patterns, base substitution patterns and sequence features between genes that are conserved across legume plants and A. duranensis-specific genes. Furthermore, we tested the role of A. duranensis-specific genes during seed development, response to nematode Meloidogyne arenaria infection and drought stress. We found that A. duranensis-specific genes had characteristics of young genes. The gene expression level and breadth were lower in the A. duranensis-specific genes compared to conserved genes. The A. duranensis-specific genes had higher codon usage bias than conserved genes, and the polypeptide length and GC content at the three codon sites were lower compared to conserved genes. Of the A. duranensis-specific genes, single-copy and duplicated genes had different features. The RNA-seq result showed A. duranensis-specific genes were involved in seed development, as well as response to nematode infection and drought stress. In addition, we detected asymmetric functions in A. duranensis-specific duplicated genes in response to nematode infection and drought stress.
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Affiliation(s)
- Hui Song
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, China.
| | - Juan Sun
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, China
| | - Guofeng Yang
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, China.
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Song H, Sun J, Yang G. Old and young duplicate genes reveal different responses to environmental changes in Arachis duranensis. Mol Genet Genomics 2019; 294:1199-1209. [PMID: 31076861 DOI: 10.1007/s00438-019-01574-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/03/2019] [Indexed: 11/24/2022]
Abstract
Old and young duplicate genes have been reported in some organisms. However, little is known about the properties of old and young duplicate genes in Arachis. Here, we have identified old and young duplicate genes in Arachis duranensis, and analyzed the evolution, gene complexity, gene expression pattern, and functional divergence between old and young duplicate genes. Our results showed different evolutionary, gene complexity and gene expression patterns, as well as differing correlations between old and young duplicate genes. Gene ontology results showed that old duplicate genes play a crucial role in lipid and amino acid biosynthesis and the oxidation-reduction process and that young duplicate genes are preferentially involved in photosynthesis and response to biotic stimulus. Transcriptome data sets revealed that most old and young duplicate genes had asymmetric function, and only a few duplicate genes exhibited symmetric function under drought and nematode stress. We found that old duplicate genes are preferentially involved in lipid and amino acid metabolism and response to abiotic stress, while young duplicate genes are likely to participate in photosynthesis and response to biotic stress. This work provides a better understanding of the evolution and functional divergence of old and young duplicate genes in A. duranensis.
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Affiliation(s)
- Hui Song
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, China.
| | - Juan Sun
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, China
| | - Guofeng Yang
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, China.
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Mizuno N, Yasui Y. Gene flow signature in the S-allele region of cultivated buckwheat. BMC PLANT BIOLOGY 2019; 19:125. [PMID: 30943914 PMCID: PMC6448236 DOI: 10.1186/s12870-019-1730-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 03/19/2019] [Indexed: 05/17/2023]
Abstract
BACKGROUND Buckwheat (Fagopyrum esculentum Moench.) is an annual crop that originated in southern China. The nutritious seeds are used in cooking much like cereal grains. Buckwheat is an outcrossing species with heteromorphic self-incompatibility due to its dimorphic (i.e., short- and long-styled) flowers and intra-morph infertility. The floral morphology and intra-morph incompatibility are both determined by a single S locus. Plants with short-styled flowers are heterozygous (S/s) and plants with long-styled flowers are homozygous recessive (s/s) at this locus, and the S/S genotype is not found. Recently, we built a draft genome assembly of buckwheat and identified the 5.4-Mb-long S-allele region harbored by short-styled plants. In this study, the first report on the genome-wide diversity of buckwheat, we used a genotyping-by-sequencing (GBS) dataset to evaluate the genome-wide nucleotide diversity within cultivated buckwheat landraces worldwide. We also investigated the utility of the S-allele region for phylogenetic analysis of buckwheat. RESULTS Buckwheat showed high nucleotide diversity (0.0065), comparable to that of other outcrossing plants, based on a genome-wide simple nucleotide polymorphism (SNP) analysis. Phylogenetic analyses based on genome-wide SNPs showed that cultivated buckwheat comprises two groups, Asian and European, and revealed lower nucleotide diversity in the European group (0.0055) and low differentiation between the Asian and European groups. The nucleotide diversity (0.0039) estimated from SNPs in the S-allele region is lower than that in genome-wide SNPs. Phylogenetic analysis based on this region detected three diverged groups, S-1, S-2, and S-3. CONCLUSION The SNPs detected using the GBS dataset were effective for elucidating the evolutionary history of buckwheat, and led to the following conclusions: (1) the low nucleotide diversity of the entire genome in the European group and low differentiation between the Asian and European groups suggested genetic bottlenecks associated with dispersion from Asia to Europe, and/or recent intensified cultivation and selection in Europe; and (2) the high diversification in the S-allele region was indicative of gene flows from wild to cultivated buckwheat, suggesting that cultivated buckwheat may have multiple origins.
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Affiliation(s)
- Nobuyuki Mizuno
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Yasuo Yasui
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
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Song H, Sun J, Yang G. Comparative analysis of selection mode reveals different evolutionary rate and expression pattern in Arachis duranensis and Arachis ipaënsis duplicated genes. PLANT MOLECULAR BIOLOGY 2018; 98:349-361. [PMID: 30298428 DOI: 10.1007/s11103-018-0784-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 09/28/2018] [Indexed: 06/08/2023]
Abstract
Our results reveal that Ks is a determining factor affecting selective pressure and different evolution and expression patterns are detected between PSGs and NSGs in wild Arachis duplicates. Selective pressure, including purifying (negative) and positive selection, can be detected in organisms. However, studies on comparative evolutionary rates, gene expression patterns and gene features between negatively selected genes (NSGs) and positively selected genes (PSGs) are lagging in paralogs of plants. Arachis duranensis and Arachis ipaënsis are ancestors of the cultivated peanut, an important oil and protein crop. Here, we carried out a series of systematic analyses, comparing NSG and PSG in paralogs, using genome sequences and transcriptome datasets in A. duranensis and A. ipaënsis. We found that synonymous substitution rate (Ks) is a determining factor affecting selective pressure in A. duranensis and A. ipaënsis duplicated genes. Lower expression level, lower gene expression breadth, higher codon bias and shorter polypeptide length were found in PSGs and not in NSGs. The correlation analyses showed that gene expression breadth was positively correlated with polypeptide length and GC content at the first codon site (GC1) in PSGs and NSGs, respectively. There was a negative correlation between expression level and polypeptide length in PSGs. In NSGs, the Ks was positively correlated with expression level, gene expression breadth, GC1, and GC content at the third codon site (GC3), but selective pressure was negatively correlated with expression level, gene expression breadth, polypeptide length, GC1, and GC3 content. The function of most duplicated gene pairs was divergent under drought and nematode stress. Taken together, our results show that different evolution and expression patterns occur between PSGs and NSGs in paralogs of two wild Arachis species.
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Affiliation(s)
- Hui Song
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, 700# Changcheng Road, Qingdao, China.
| | - Juan Sun
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, 700# Changcheng Road, Qingdao, China
| | - Guofeng Yang
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, 700# Changcheng Road, Qingdao, China.
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Song H, Sun W, Yang G, Sun J. WRKY transcription factors in legumes. BMC PLANT BIOLOGY 2018; 18:243. [PMID: 30332991 PMCID: PMC6192229 DOI: 10.1186/s12870-018-1467-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/03/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND WRKY transcription factors, so named because of the WRKYGQK heptapeptide at the N-terminal end, are widely distributed in plants and play an important role in physiological changes and response to biotic and abiotic stressors. Many previous studies have focused on the evolution of WRKY transcription factors in a given plant; however, little is known about WRKY evolution in legumes. The gene expression pattern of duplicated WRKY transcription factors remains unclear. RESULTS We first identified the WRKY proteins in 12 legumes. We found that the WRKYGQK heptapeptide tended to mutate into WRKYGKK. The Q site in WRKYGQK preferentially mutated, while W, K, and Y were conserved. The phylogenetic tree shows that the WRKY proteins in legumes have multiple origins, especially group IIc. For example, WRKY64 from Lupinus angustifolius (LaWRKY64) contains three WRKY domains, of which the first two clustered together in the N-terminal WRKY domain of the group I WRKY protein, and the third WRKY domain grouped in the C-terminal WRKY domain of the group I WRKY protein. Orthologous WRKY genes have a faster evolutionary rate and are subject to constrained selective pressure, unlike paralogous WRKY genes. Different gene features were observed between duplicated WRKY genes and singleton WRKY genes. Duplicated Glycine max WRKY genes with similar gene features have gene expression divergence. CONCLUSIONS We analyzed the WRKY number and type in 12 legumes, concluding that the WRKY proteins have multiple origins. A novel WRKY protein, LaWRKY64, was found in L. angustifolius. The first two WRKY domains of LaWRKY64 have the same origin. The orthologous and paralogous WRKY proteins have different evolutionary rates. Duplicated WRKY genes have gene expression divergence under normal growth conditions in G. max. These results provide insight into understanding WRKY evolution and expression.
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Affiliation(s)
- Hui Song
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, 266109 China
| | - Weihong Sun
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, 266109 China
| | - Guofeng Yang
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, 266109 China
| | - Juan Sun
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, 266109 China
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