1
|
Yao H, Li T, Ma Z, Wang X, Xu L, Zhang Y, Cai Y, Tang Z. Codon usage pattern of the ancestor of green plants revealed through Rhodophyta. BMC Genomics 2023; 24:538. [PMID: 37697255 PMCID: PMC10496412 DOI: 10.1186/s12864-023-09586-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 08/14/2023] [Indexed: 09/13/2023] Open
Abstract
Rhodophyta are among the closest known relatives of green plants. Studying the codons of their genomes can help us understand the codon usage pattern and characteristics of the ancestor of green plants. By studying the codon usage pattern of all available red algae, it was found that although there are some differences among species, high-bias genes in most red algae prefer codons ending with GC. Correlation analysis, Nc-GC3s plots, parity rule 2 plots, neutrality plot analysis, differential protein region analysis and comparison of the nucleotide content of introns and flanking sequences showed that the bias phenomenon is likely to be influenced by local mutation pressure and natural selection, the latter of which is the dominant factor in terms of translation accuracy and efficiency. It is worth noting that selection on translation accuracy could even be detected in the low-bias genes of individual species. In addition, we identified 15 common optimal codons in seven red algae except for G. sulphuraria for the first time, most of which were found to be complementary and bound to the tRNA genes with the highest copy number. Interestingly, tRNA modification was found for the highly degenerate amino acids of all multicellular red algae and individual unicellular red algae, which indicates that highly biased genes tend to use modified tRNA in translation. Our research not only lays a foundation for exploring the characteristics of codon usage of the red algae as green plant ancestors, but will also facilitate the design and performance of transgenic work in some economic red algae in the future.
Collapse
Affiliation(s)
- Huipeng Yao
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China.
| | - Tingting Li
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Zheng Ma
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Xiyuan Wang
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Lixiao Xu
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Yuxin Zhang
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Yi Cai
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Zizhong Tang
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| |
Collapse
|
2
|
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]
|
3
|
Leonelli L. An in vivo plant platform to assess genes encoding native and synthetic enzymes for carotenoid biosynthesis. Methods Enzymol 2022; 671:489-509. [DOI: 10.1016/bs.mie.2022.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
4
|
Wang H, Ma ZH, Mao J, Chen BH. Genome-wide identification and expression analysis of the EXO70 gene family in grape ( Vitis vinifera L). PeerJ 2021; 9:e11176. [PMID: 33976971 PMCID: PMC8067907 DOI: 10.7717/peerj.11176] [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: 09/11/2020] [Accepted: 03/08/2021] [Indexed: 12/14/2022] Open
Abstract
EXO70 is the pivotal protein subunit of exocyst, which has a very crucial role in enhancing the shielding effect of the cell wall, resisting abiotic and hormonal stresses. This experiment aims to identify family members of the EXO70 gene family in grape and predict the characteristics of this gene family, so as to lay the foundation of further exploring the mechanism of resisting abiotic and hormone stresses of VvEXO70s. Therefore, the Vitis vinifera ‘Red Globe’ tube plantlet were used as materials. Bioinformatics was used to inquire VvEXO70 genes family members, gene structure, system evolution, cis-acting elements, subcellular and chromosomal localization, collinearity, selective pressure, codon bias and tissue expression. All of VvEXO70s had the conserved pfam03081 domain which maybe necessary for interacting with other proteins. Microarray analysis suggested that most genes expressed to varying degrees in tendrils, leaves, seeds, buds, roots and stems. Quantitative Real-Time PCR (qRT-PCR) showed that the expression levels of all genes with 5 mM salicylic acid (SA), 0.1 mM methy jasmonate (MeJA), 20% PEG6000 and 4 °C for 24 h were higher than for 12 h. With 20% PEG6000 treatment about 24 h, the relative expression of VvEXO70-02 was significantly up-regulated and 361 times higher than CK. All genes’ relative expression was higher at 12 h than that at 24 h after treatment with 7 mM hydrogen peroxide (H2O2) and 0.1 mM ethylene (ETH). In conclusion, the expression levels of 14 VvEXO70 genes are distinguishing under these treatments, which play an important role in the regulation of anti-stress signals in grape. All of these test results provide a reference for the future research on the potential function analysis and plant breeding of VvEXO70 genes.
Collapse
Affiliation(s)
- Han Wang
- Department of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Zong-Huan Ma
- Department of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Juan Mao
- Department of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Bai-Hong Chen
- Department of Horticulture, Gansu Agricultural University, Lanzhou, China
| |
Collapse
|
5
|
Duan H, Zhang Q, Wang C, Li F, Tian F, Lu Y, Hu Y, Yang H, Cui G. Analysis of codon usage patterns of the chloroplast genome in Delphinium grandiflorum L. reveals a preference for AT-ending codons as a result of major selection constraints. PeerJ 2021; 9:e10787. [PMID: 33552742 PMCID: PMC7819120 DOI: 10.7717/peerj.10787] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/24/2020] [Indexed: 01/28/2023] Open
Abstract
Background Codon usage bias analysis is a suitable strategy for identifying the principal evolutionary driving forces in different organisms. Delphinium grandiflorum L. is a perennial herb with high economic value and typical biological characteristics. Evolutionary analysis of D. grandiflorum can provide a rich resource of genetic information for developing hybridization resources of the genus Delphinium. Methods Synonymous codon usage (SCU) and related indices of 51 coding sequences from the D. grandiflorum chloroplast (cp) genome were calculated using Codon W, Cups of EMBOSS, SPSS and Microsoft Excel. Multivariate statistical analysis combined by principal component analysis (PCA), correspondence analysis (COA), PR2-plot mapping analysis and ENC plot analysis was then conducted to explore the factors affecting the usage of synonymous codons. Results The SCU bias of D. grandiflorum was weak and codons preferred A/T ending. A SCU imbalance between A/T and G/C at the third base position was revealed by PR2-plot mapping analysis. A total of eight codons were identified as the optimal codons. The PCA and COA results indicated that base composition (GC content, GC3 content) and gene expression were important for SCU bias. A majority of genes were distributed below the expected curve from the ENC plot analysis and up the standard curve by neutrality plot analysis. Our results showed that with the exception of notable mutation pressure effects, the majority of genetic evolution in the D. grandiflorum cp genome might be driven by natural selection. Discussions Our results provide a theoretical foundation for elucidating the genetic architecture and mechanisms of D. grandiflorum, and contribute to enriching D. grandiflorum genetic resources.
Collapse
Affiliation(s)
- Huirong Duan
- Chinese Academy of Agricultural Sciences Lanzhou Institute of Husbandry and Pharmaceutical Science, Lanzhou, China
| | - Qian Zhang
- Chinese Academy of Agricultural Sciences Lanzhou Institute of Husbandry and Pharmaceutical Science, Lanzhou, China
| | - Chunmei Wang
- Chinese Academy of Agricultural Sciences Lanzhou Institute of Husbandry and Pharmaceutical Science, Lanzhou, China
| | - Fang Li
- Institute of Grassland Science, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Fuping Tian
- Chinese Academy of Agricultural Sciences Lanzhou Institute of Husbandry and Pharmaceutical Science, Lanzhou, China
| | - Yuan Lu
- Chinese Academy of Agricultural Sciences Lanzhou Institute of Husbandry and Pharmaceutical Science, Lanzhou, China
| | - Yu Hu
- Chinese Academy of Agricultural Sciences Lanzhou Institute of Husbandry and Pharmaceutical Science, Lanzhou, China
| | - Hongshan Yang
- Chinese Academy of Agricultural Sciences Lanzhou Institute of Husbandry and Pharmaceutical Science, Lanzhou, China
| | - Guangxin Cui
- Chinese Academy of Agricultural Sciences Lanzhou Institute of Husbandry and Pharmaceutical Science, Lanzhou, China
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Shen Z, Gan Z, Zhang F, Yi X, Zhang J, Wan X. Analysis of codon usage patterns in citrus based on coding sequence data. BMC Genomics 2020; 21:234. [PMID: 33327935 PMCID: PMC7739459 DOI: 10.1186/s12864-020-6641-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 03/03/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Codon usage is an important determinant of gene expression levels that can help us understand codon biology, evolution and mRNA translation of species. The majority of previous codon usage studies have focused on single species analysis, although few studies have focused on the species within the same genus. In this study, we proposed a multispecies codon usage analysis workflow to reveal the genetic features and correlation in citrus. RESULTS Our codon usage analysis workflow was based on the GC content, GC plot, and relative synonymous codon usage value of each codon in 8 citrus species. This approach allows for the comparison of codon usage bias of different citrus species. Next, we performed cluster analysis and obtained an overview of the relationship in citrus. However, traditional methods cannot conduct quantitative analysis of the correlation. To further estimate the correlation among the citrus species, we used the frequency profile to construct feature vectors of each species. The Pearson correlation coefficient was used to quantitatively analyze the distance among the citrus species. This result was consistent with the cluster analysis. CONCLUSIONS Our findings showed that the citrus species are conserved at the genetic level and demonstrated the existing genetic evolutionary relationship in citrus. This work provides new insights into codon biology and the evolution of citrus and other plant species.
Collapse
Affiliation(s)
- Zenan Shen
- High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100000, China
| | - Zhimeng Gan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fa Zhang
- High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100000, China
| | - Xinyao Yi
- Department of Computer Science and Engineering, University of South Carolina, Colombia, 29201, USA
| | - Jinzhi Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaohua Wan
- High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China. .,University of Chinese Academy of Sciences, Beijing, 100000, China.
| |
Collapse
|
8
|
Mycobacterium lepromatosis genome exhibits unusually high CpG dinucleotide content and selection is key force in shaping codon usage. INFECTION GENETICS AND EVOLUTION 2020; 84:104399. [PMID: 32512206 DOI: 10.1016/j.meegid.2020.104399] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 05/30/2020] [Accepted: 06/03/2020] [Indexed: 01/06/2023]
Abstract
Mycobacterium lepromatosis was identified as a causative agent for leprosy in the year 2008 in the United States and later more cases were identified in Canada, Singapore, Brazil, and Myanmar. It is known to cause diffuse lepromatosis leprosy among humans. Since it is invasive, the mortality rates are higher in comparison to the M. leprae. At genomic level, there exists 90.9% similarity between M. lepromatosis and M. leprae. Codon usage analysis based on analyses of 228 coding sequences (CDSs) of M. lepromatosis, revealed that the genome is GC rich. Among the total 16 dinucleotides, CpG dinucleotide possesses the highest dinucleotide frequency in M. lepromatosis, that is strikingly an unobvious observation since higher CpG is associated with higher proinflammatory cytokine production and NF-κB activation that eventually leads to high pathogenicity. To evade immune response, CpG content is generally less in pathogens. The unusually high CpG content can be explained by the fact that the nucleotide composition of M. lepromatosis is CG rich. Various forces interplay to shape codon usage pattern of any organism including selection; mutation, nucleotide composition as well as GC biased gene conversion. To understand the interplay between various forces; neutrality, parity, Nc-GC3 (Effective number of codons-GC content at 3rd position of the codon), aromaticity (AROMO) and the general average hydropathicity score (GRAVY) analyses have been carried out. The analyses revealed that selection force is the major contributory force. Along with the selection; mutation, nucleotide composition as well as GC biased gene conversion also play role in shaping codon usage bias in M. lepromatosis. This is the first report on the codon usage in M. lepromatosis.
Collapse
|
9
|
|
10
|
Lee JS, Goh CJ, Park D, Hahn Y. Identification of a novel plant RNA virus species of the genus Amalgavirus in the family Amalgaviridae from chia (Salvia hispanica). Genes Genomics 2019; 41:10.1007/s13258-019-00782-1. [PMID: 30649686 DOI: 10.1007/s13258-019-00782-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/03/2019] [Indexed: 01/30/2023]
Abstract
BACKGROUND Chia (Salvia hispanica) is a flowering plant in the family Lamiaceae, which produces seeds that are a rich source of various nutritional compounds. OBJECTIVE To identify a novel RNA virus potentially associated with chia. METHODS Transcriptome data obtained from developing chia seeds were assembled into contigs. Sequence contigs containing an open reading frame (ORF) that showed amino acid identities with a viral RNA-dependent RNA polymerase (RdRp) were identified and analyzed. RESULTS A genomic sequence of a novel plant RNA virus named Salvia hispanica RNA virus 1 (ShRV1) was identified in a chia seed transcriptome dataset. The ShRV1 genome sequence has two ORFs that showed high sequence identities with ORFs of known members of the genus Amalgavirus in the family Amalgaviridae. Amalgaviridae is a family of positive-sense double-stranded non-segmented RNA viruses that infect plants, fungi, and animals. The ShRV1 genome encodes two proteins: a putative replication factory matrix-like protein from ORF1 and an RdRp from the fused ORF of ORF1 and ORF2 by a + 1 programmed ribosomal frameshifting (PRF) mechanism. A conserved + 1 PRF motif sequence UUU_CGU was found at the ORF1/ORF2 boundary. A comparison of 31 amalgavirus ORF1 + 2 fusion proteins revealed that only three positions were repeatedly used as a + 1 PRF site during amalgavirus evolution. CONCLUSION ShRV1 is a novel virus found to be associated with chia and may be useful for studying the molecular features of amalgaviruses.
Collapse
Affiliation(s)
- Ji Seok Lee
- Department of Life Science, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, South Korea
| | - Chul Jun Goh
- Department of Life Science, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, South Korea
| | - Dongbin Park
- Department of Life Science, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, South Korea
| | - Yoonsoo Hahn
- Department of Life Science, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, South Korea.
| |
Collapse
|
11
|
Song H, Gao H, Liu J, Tian P, Nan Z. Comprehensive analysis of correlations among codon usage bias, gene expression, and substitution rate in Arachis duranensis and Arachis ipaënsis orthologs. Sci Rep 2017; 7:14853. [PMID: 29093502 PMCID: PMC5665869 DOI: 10.1038/s41598-017-13981-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 10/04/2017] [Indexed: 11/22/2022] Open
Abstract
The relationship between evolutionary rates and gene expression in model plant orthologs is well documented. However, little is known about the relationships between gene expression and evolutionary trends in Arachis orthologs. We identified 7,435 one-to-one orthologs, including 925 single-copy and 6,510 multiple-copy sequences in Arachis duranensis and Arachis ipaënsis. Codon usage was stronger for shorter polypeptides, which were encoded by codons with higher GC contents. Highly expressed coding sequences had higher codon usage bias, GC content, and expression breadth. Additionally, expression breadth was positively correlated with polypeptide length, but there was no correlation between gene expression and polypeptide length. Inferred selective pressure was also negatively correlated with both gene expression and expression breadth in all one-to-one orthologs, while positively but non-significantly correlated with gene expression in sequences with signatures of positive selection. Gene expression levels and expression breadth were significantly higher for single-copy genes than for multiple-copy genes. Similarly, the gene expression and expression breadth in sequences with signatures of purifying selection were higher than those of sequences with positive selective signatures. These results indicated that gene expression differed between single-copy and multiple-copy genes as well as sequences with signatures of positive and purifying selection.
Collapse
Affiliation(s)
- Hui Song
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China.
| | - Hongjuan Gao
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China
| | - Jing Liu
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China
| | - Pei Tian
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China
| | - Zhibiao Nan
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China.
| |
Collapse
|