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Shi Y, Chen Z, Jiang J, Wu W, Yu W, Zhang S, Zeng W. The assembly and comparative analysis of the first complete mitogenome of Lindera aggregata. FRONTIERS IN PLANT SCIENCE 2024; 15:1439245. [PMID: 39290737 PMCID: PMC11405213 DOI: 10.3389/fpls.2024.1439245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 08/16/2024] [Indexed: 09/19/2024]
Abstract
Lindera aggregata, a member belongs to the genus Lindera of Lauraceae family. Its roots and leaves have been used as traditional Chinese medicine or functional food for thousands of years. However, its mitochondrial genome has not been explored. Our aim is to sequence and assemble the mitogenome of L. aggregata to elucidate the genetic mechanism and evolutionary pathway. The results had shown that the mitogenome was extremely complex and had a unique multi-branched conformation with total size of 912,473 bp. Comprehensive analysis of protein coding genes of 7 related species showed that there were 40 common genes in their mitogenome. Interestingly, positive selection had become an important factor in the evolution of ccmB, ccmFC, rps10, rps11 and rps7 genes. Furthermore, our data highlighted the repeated trend of homologous fragment migrations between chloroplast and mitochondrial organelles, and 38 homologous fragments were identified. Phylogenetic analysis identified a tree that was basically consistent with the phylogeny of Laurales species described in the APG IV system. To sum up, this study will be helpful to the study of population genetics and evolution of Lindera species.
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Affiliation(s)
- Yujie Shi
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, Taizhou, China
| | - Zhen Chen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, Taizhou, China
| | - Jingyong Jiang
- Institute of Horticulture, Taizhou Academy of Agricultural Sciences, Linhai, China
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang Agricultural and Forestry (A&F) University, Hangzhou, China
| | - Weifu Yu
- Zhejiang Hongshiliang Group Tiantai Mountain Wu-Yao Co., Ltd., RedRock Group, Taizhou, China
| | - Shumeng Zhang
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, Taizhou, China
| | - Wei Zeng
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, Taizhou, China
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Aktürk Dizman Y. Analysis of codon usage bias of exonuclease genes in invertebrate iridescent viruses. Virology 2024; 593:110030. [PMID: 38402641 DOI: 10.1016/j.virol.2024.110030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/04/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024]
Abstract
Invertebrate iridescent viruses (IIVs) are double-stranded DNA viruses that belong to the Iridoviridae family. IIVs result diseases that vary in severity from subclinical to lethal in invertebrate hosts. Codon usage bias (CUB) analysis is a versatile method for comprehending the genetic and evolutionary aspects of species. In this study, we analyzed the CUB in 10 invertebrate iridescent viruses exonuclease genes by calculating and comparing the nucleotide contents, effective number of codons (ENC), codon adaptation index (CAI), relative synonymous codon usage (RSCU), and others. The results revealed that IIVs exonuclease genes are rich in A/T. The ENC analysis displayed a low codon usage bias in IIVs exonuclease genes. ENC-plot, neutrality plot, and parity rule 2 plot demonstrated that besides mutational pressure, other factors like natural selection, dinucleotide content, and aromaticity also contributed to CUB. The findings could enhance our understanding of the evolution of IIVs exonuclease genes.
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Affiliation(s)
- Yeşim Aktürk Dizman
- Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdogan University, 53100, Rize, Türkiye.
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Pouresmaeil M, Azizi-Dargahlou S. Investigation of CaMV-host co-evolution through synonymous codon pattern. J Basic Microbiol 2024; 64:e2300664. [PMID: 38436477 DOI: 10.1002/jobm.202300664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/20/2024] [Accepted: 02/10/2024] [Indexed: 03/05/2024]
Abstract
Cauliflower mosaic virus (CaMV) has a double-stranded DNA genome and is globally distributed. The phylogeny tree of 121 CaMV isolates was categorized into two primary groups, with Iranian isolates showing the greatest genetic variations. Nucleotide A demonstrated the highest percentage (36.95%) in the CaMV genome and the dinucleotide odds ratio analysis revealed that TC dinucleotide (1.34 ≥ 1.23) and CG dinucleotide (0.63 ≤ 0.78) are overrepresented and underrepresented, respectively. Relative synonymous codon usage (RSCU) analysis confirmed codon usage bias in CaMV and its hosts. Brassica oleracea and Brassica rapa, among the susceptible hosts of CaMV, showed a codon adaptation index (CAI) value above 0.8. Additionally, relative codon deoptimization index (RCDI) results exhibited the highest degree of deoptimization in Raphanus sativus. These findings suggest that the genes of CaMV underwent codon adaptation with its hosts. Among the CaMV open reading frames (ORFs), genes that produce reverse transcriptase and virus coat proteins showed the highest CAI value of 0.83. These genes are crucial for the creation of new virion particles. The results confirm that CaMV co-evolved with its host to ensure the optimal expression of its genes in the hosts, allowing for easy infection and effective spread. To detect the force behind codon usage bias, an effective number of codons (ENC)-plot and neutrality plot were conducted. The results indicated that natural selection is the primary factor influencing CaMV codon usage bias.
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Affiliation(s)
- Mahin Pouresmaeil
- Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Shahnam Azizi-Dargahlou
- Agricultural Biotechnology, Seed and Plant Certification and Registration Institute, Ardabil Agricultural and Natural Resources Research Center, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
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Li T, Ma Z, Ding T, Yang Y, Wang F, Wan X, Liang F, Chen X, Yao H. Codon usage bias and phylogenetic analysis of chloroplast genome in 36 gracilariaceae species. Funct Integr Genomics 2024; 24:45. [PMID: 38429550 DOI: 10.1007/s10142-024-01316-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 03/03/2024]
Abstract
Gracilariaceae is a group of marine large red algae and main source of agar with important economic and ecological value. The codon usage patterns of chloroplast genomes in 36 species from Graciliaceae show that GC range from 0.284 to 0.335, the average GC3 range from 0.135 to 0.243 and the value of ENC range from 35.098 to 42.327, which indicates these genomes are rich in AT and prefer to use codons ending with AT in these species. Nc plot, PR2 plot, neutrality plot analyses and correlation analysis indicate that these biases may be caused by multiple factors, such as natural selection and mutation pressure, but prolonged natural selection is the main driving force influencing codon usage preference. The cluster analysis and phylogenetic analysis show that the differentiation relationship of them is different and indicate that codons with weak or unbiased preferences may also play an irreplaceable role in these species' evolution. In addition, we identified 26 common high-frequency codons and 8-18 optimal codons all ending in A/U in these 36 species. Our results will not only contribute to carrying out transgenic work in Gracilariaceae species to maximize the protein yield in the future, but also lay a theoretical foundation for further exploring systematic classification of them.
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Affiliation(s)
- 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
| | - Tiemei Ding
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Yanxin Yang
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Fei Wang
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Xinjing Wan
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Fangyun Liang
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Xi Chen
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Huipeng Yao
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China.
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Benson CW, Sheltra MR, Huff DR. The genome of Salmacisia buchloëana, the parasitic puppet master pulling strings of sexual phenotypic monstrosities in buffalograss. G3 (BETHESDA, MD.) 2024; 14:jkad238. [PMID: 37847611 PMCID: PMC10849329 DOI: 10.1093/g3journal/jkad238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/19/2023]
Abstract
To complete its parasitic lifecycle, Salmacisia buchloëana, a biotrophic fungus, manipulates reproductive organ development, meristem determinacy, and resource allocation in its dioecious plant host, buffalograss (Bouteloua dactyloides; Poaceae). To gain insight into S. buchloëana's ability to manipulate its host, we sequenced and assembled the 20.1 Mb genome of S. buchloëana into 22 chromosome-level pseudomolecules. Phylogenetic analysis suggests that S. buchloëana is nested within the genus Tilletia and diverged from Tilletia caries and Tilletia walkeri ∼40 MYA. We find that S. buchloëana contains a novel chromosome arm with no syntenic relationship to other publicly available Tilletia genomes, and that genes on the novel arm are upregulated upon infection, suggesting that this unique chromosomal segment may have played a critical role in S. buchloëana's evolution and host specificity. Salmacisia buchloëana has one of the largest fractions of serine peptidases (1.53% of the proteome) and one of the highest GC contents (62.3%) in all classified fungi. Analysis of codon base composition indicated that GC content is controlled more by selective constraints than directional mutation, and that S. buchloëana has a unique bias for the serine codon UCG. Finally, we identify 3 inteins within the S. buchloëana genome, 2 of which are located in a gene often used in fungal taxonomy. The genomic and transcriptomic resources generated here will aid plant pathologists and breeders by providing insight into the extracellular components contributing to sex determination in dioecious grasses.
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Affiliation(s)
- Christopher W Benson
- Department of Plant Science, Pennsylvania State University, University Park, PA 16801, USA
- Intercollegiate Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA 16801, USA
| | - Matthew R Sheltra
- Department of Plant Science, Pennsylvania State University, University Park, PA 16801, USA
- Intercollegiate Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA 16801, USA
| | - David R Huff
- Department of Plant Science, Pennsylvania State University, University Park, PA 16801, USA
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Li M, Liu T, Cao R, Cao Q, Tong W, Song W. Evolution and Expression of the Expansin Genes in Emmer Wheat. Int J Mol Sci 2023; 24:14120. [PMID: 37762423 PMCID: PMC10531347 DOI: 10.3390/ijms241814120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Expansin proteins, a crucial class of intracellular proteins, are known to play a vital role in facilitating processes like cell wall relaxation and cell growth. Recent discoveries have revealed that expansin proteins also have significant functions in plant growth, development, and response to resistance. However, the expansin gene family, particularly in emmer wheat, has not been thoroughly studied, particularly in terms of evolution. In this study, we identified 63 TdEXPs and 49 TtEXPs from the latest genome versions of wild emmer wheat (WEW) and durum wheat (DW), respectively. The physicochemical properties of the encoded expansin proteins exhibited minimal differences, and the gene structures remained relatively conserved. Phylogenetic analysis categorized the proteins into three subfamilies, namely EXPA, EXPB, and EXLA, in addition to the EXLB subfamily. Furthermore, codon preference analysis revealed an increased usage frequency of the nucleotide "T" in expansin proteins throughout the evolution of WEW and DW. Collinearity analysis demonstrated higher orthology between the expansin proteins of WEW and DW, with a Ka/Ks ratio ranging from 0.4173 to 0.9494, indicating purifying selection during the evolution from WEW to DW. Haplotype analysis of the expansin gene family identified five genes in which certain haplotypes gradually became dominant over the course of evolution, enabling adaptation for survival and improvement. Expression pattern analysis indicated tissue-specific expression of expansin genes in emmer wheat, and some of these genes were quantified through qRT-PCR to assess their response to salt stress. These comprehensive findings present the first systematic analysis of the expansin protein gene family during the evolution from WEW to DW, providing a foundation for further understanding the functions and biological roles of expansin protein genes in emmer wheat.
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Affiliation(s)
| | | | | | | | - Wei Tong
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China; (M.L.); (T.L.); (R.C.); (Q.C.)
| | - Weining Song
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China; (M.L.); (T.L.); (R.C.); (Q.C.)
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Khandia R, Pandey MK, Zaki MEA, Al-Hussain SA, Baklanov I, Gurjar P. Application of codon usage and context analysis in genes up- or down-regulated in neurodegeneration and cancer to combat comorbidities. Front Mol Neurosci 2023; 16:1200523. [PMID: 37383425 PMCID: PMC10293642 DOI: 10.3389/fnmol.2023.1200523] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/23/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction Neurodegeneration and cancer present in comorbidities with inverse effects due to the expression of genes and pathways acting in opposition. Identifying and studying the genes simultaneously up or downregulated during morbidities helps curb both ailments together. Methods This study examines four genes. Three of these (Amyloid Beta Precursor Protein (APP), Cyclin D1 (CCND1), and Cyclin E2 (CCNE2) are upregulated, and one protein phosphatase 2 phosphatase activator (PTPA) is simultaneously downregulated in both disorders. We investigated molecular patterns, codon usage, codon usage bias, nucleotide bias in the third codon position, preferred codons, preferred codon pairs, rare codons, and codon context. Results Parity analysis revealed that T is preferred over A, and G is preferred over C in the third codon position, suggesting composition plays no role in nucleotide bias in both the upregulated and downregulated gene sets and that mutational forces are stronger in upregulated gene sets than in downregulated ones. Transcript length influenced the overall %A composition and codon bias, and the codon AGG exerted the strongest influence on codon usage in both the upregulated and downregulated gene sets. Codons ending in G/C were preferred for 16 amino acids, and glutamic acid-, aspartic acid-, leucine-, valine-, and phenylalanine-initiated codon pairs were preferred in all genes. Codons CTA (Leu), GTA (Val), CAA (Gln), and CGT (Arg) were underrepresented in all examined genes. Discussion Using advanced gene editing tools such as CRISPR/Cas or any other gene augmentation technique, these recoded genes may be introduced into the human body to optimize gene expression levels to augment neurodegeneration and cancer therapeutic regimens simultaneously.
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Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, Madhya Pradesh, India
| | - Megha Katare Pandey
- Translational Medicine Center, All India Institute of Medical Sciences, Bhopal, India
| | - Magdi E. A. Zaki
- Department of Chemistry, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Sami A. Al-Hussain
- Department of Chemistry, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Igor Baklanov
- Department of Philosophy, North Caucasus Federal University, Stavropol, Russia
| | - Pankaj Gurjar
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
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Wang ZK, Liu Y, Zheng HY, Tang MQ, Xie SQ. Comparative Analysis of Codon Usage Patterns in Nuclear and Chloroplast Genome of Dalbergia (Fabaceae). Genes (Basel) 2023; 14:genes14051110. [PMID: 37239470 DOI: 10.3390/genes14051110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/04/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
The Dalbergia plants are widely distributed across more than 130 tropical and subtropical countries and have significant economic and medicinal value. Codon usage bias (CUB) is a critical feature for studying gene function and evolution, which can provide a better understanding of biological gene regulation. In this study, we comprehensively analyzed the CUB patterns of the nuclear genome, chloroplast genome, and gene expression, as well as systematic evolution of Dalbergia species. Our results showed that the synonymous and optimal codons in the coding regions of both nuclear and chloroplast genome of Dalbergia preferred ending with A/U at the third codon base. Natural selection was the primary factor affecting the CUB features. Furthermore, in highly expressed genes of Dalbergia odorifera, we found that genes with stronger CUB exhibited higher expression levels, and these highly expressed genes tended to favor the use of G/C-ending codons. In addition, the branching patterns of the protein-coding sequences and the chloroplast genome sequences were very similar in the systematic tree, and different with the cluster from the CUB of the chloroplast genome. This study highlights the CUB patterns and features of Dalbergia species in different genomes, explores the correlation between CUB preferences and gene expression, and further investigates the systematic evolution of Dalbergia, providing new insights into codon biology and the evolution of Dalbergia plants.
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Affiliation(s)
- Zu-Kai Wang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, School of Forestry, Hainan University, Haikou 570228, China
| | - Yi Liu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, School of Forestry, Hainan University, Haikou 570228, China
| | - Hao-Yue Zheng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, School of Forestry, Hainan University, Haikou 570228, China
| | - Min-Qiang Tang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, School of Forestry, Hainan University, Haikou 570228, China
| | - Shang-Qian Xie
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, School of Forestry, Hainan University, Haikou 570228, China
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