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Fu X, Xie DF, Zhou YY, Cheng RY, Zhang XY, Zhou SD, He XJ. Phylogeny and adaptive evolution of subgenus Rhizirideum (Amaryllidaceae, Allium) based on plastid genomes. BMC PLANT BIOLOGY 2023; 23:70. [PMID: 36726056 PMCID: PMC9890777 DOI: 10.1186/s12870-022-03993-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 12/09/2022] [Indexed: 06/01/2023]
Abstract
The subgenus Rhizirideum in the genus Allium consists of 38 species worldwide and forms five sections (A. sect. Rhizomatosa, A. sect. Tenuissima, A. sect. Rhizirideum, A. sect. Eduardia, and A. sect. Caespitosoprason), A. sect. Caespitosoprason being merged into A. sect. Rhizomatosa recently. Previous studies on this subgenus mainly focused on separate sections. To investigate the inter-section and inter-subgenera phylogenetic relationships and adaptive evolution of A. subg. Rhizirideum, we selected thirteen representative species, which cover five sections of this subgenus and can represent four typical phenotypes of it. We conducted the comparative plastome analysis with our thirteen plastomes. And phylogenetic inferences with CDSs and complete sequences of plastomes of our thirteen species and another fifty-four related species were also performed. As a result, the A. subg. Rhizirideum plastomes were relatively conservative in structure, IR/SC borders, codon usage, and repeat sequence. In phylogenetic results, the inter-subgenera relationships among A. subg. Rhizirideum and other genus Allium subgenera were generally similar to the previous reports. In contrast, the inter-section relationships within our subgenus A. subg. Rhizirideum were newly resolved in this study. A. sect. Rhizomatosa and A. sect. Tenuissima were sister branches, which were then clustered with A. sect. Rhizirideum and A. sect. Eduardia successively. However, Allium Polyrhizum Turcz. ex Regel, type species of A. sect. Caespitosoprason, was resolved as the basal taxon of A. subg. Rhizirideum. Allium siphonanthum J. M. Xu was also found in clade A. subg. Cyathophora instead of clade A. subg. Rhizirideum. The selective pressure analysis was also conducted, and most protein-coding genes were under purifying selection. At the same time, just one gene, ycf2, was found under positive selection, and another three genes (rbcL, ycf1a, ycf1b) presented relaxed selection, which were all involved in the photosynthesis. The low temperature, dry climate, and high altitude of the extreme habitats where A. subg. Rhizirideum species grow might impose intense natural selection forces on their plastome genes for photosynthesis. In summary, our research provides new insights into the phylogeny and adaptive evolution of A. subg. Rhizirideum. Moreover, we suggest that the positions of the A. subg. Rhizirideum species A. polyrhizum and A. siphonanthum should be reconsidered.
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Affiliation(s)
- Xiao Fu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, The People's Republic of China
| | - Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, The People's Republic of China
| | - Yu-Yang Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, The People's Republic of China
| | - Rui-Yu Cheng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, The People's Republic of China
| | - Xiang-Yi Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, The People's Republic of China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, The People's Republic of China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, The People's Republic of China.
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Wang CW, Chen YL, Mao SJT, Lin TC, Wu CW, Thongchan D, Wang CY, Wu HY. Pathogenicity of Avian Polyomaviruses and Prospect of Vaccine Development. Viruses 2022; 14:v14092079. [PMID: 36146885 PMCID: PMC9505546 DOI: 10.3390/v14092079] [Citation(s) in RCA: 2] [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: 06/27/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/23/2022] Open
Abstract
Polyomaviruses are nonenveloped icosahedral viruses with a double-stranded circular DNA containing approximately 5000 bp and 5–6 open reading frames. In contrast to mammalian polyomaviruses (MPVs), avian polyomaviruses (APVs) exhibit high lethality and multipathogenicity, causing severe infections in birds without oncogenicity. APVs are classified into 10 major species: Adélie penguin polyomavirus, budgerigar fledgling disease virus, butcherbird polyomavirus, canary polyomavirus, cormorant polyomavirus, crow polyomavirus, Erythrura gouldiae polyomavirus, finch polyomavirus, goose hemorrhagic polyomavirus, and Hungarian finch polyomavirus under the genus Gammapolyomavirus. This paper briefly reviews the genomic structure and pathogenicity of the 10 species of APV and some of their differences in terms of virulence from MPVs. Each gene’s genomic size, number of amino acid residues encoding each gene, and key biologic functions are discussed. The rationale for APV classification from the Polyomavirdae family and phylogenetic analyses among the 10 APVs are also discussed. The clinical symptoms in birds caused by APV infection are summarized. Finally, the strategies for developing an effective vaccine containing essential epitopes for preventing virus infection in birds are discussed. We hope that more effective and safe vaccines with diverse protection will be developed in the future to solve or alleviate the problems of viral infection.
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Affiliation(s)
- Chen-Wei Wang
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
- International Degree Program in Animal Vaccine Technology, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
| | - Yung-Liang Chen
- Department of Medical Laboratory Science and Biotechnology, Yuan Pei University of Medical Technology, Yuanpei Street, Hsinchu 300, Taiwan
| | - Simon J. T. Mao
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Tzu-Chieh Lin
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
- International Degree Program in Animal Vaccine Technology, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
| | - Ching-Wen Wu
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
- Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
| | - Duangsuda Thongchan
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
- Faculty of Agriculture and Technology, Rajamangala University of Technology Isan, Surin Campus, Nakhon Ratchasima 30000, Thailand
| | - Chi-Young Wang
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung 402, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
- Correspondence: (C.-Y.W.); (H.-Y.W.); Tel.: +886-4-22840369 (ext. 48) (C.-Y.W.); +886-8-7703202 (ext. 5072) (H.-Y.W.)
| | - Hung-Yi Wu
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
- Correspondence: (C.-Y.W.); (H.-Y.W.); Tel.: +886-4-22840369 (ext. 48) (C.-Y.W.); +886-8-7703202 (ext. 5072) (H.-Y.W.)
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Fan Y, Guo D, Zhao S, Wei Q, Li Y, Lin T. Human genes with relative synonymous codon usage analogous to that of polyomaviruses are involved in the mechanism of polyomavirus nephropathy. Front Cell Infect Microbiol 2022; 12:992201. [PMID: 36159639 PMCID: PMC9492876 DOI: 10.3389/fcimb.2022.992201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/12/2022] [Indexed: 11/28/2022] Open
Abstract
Human polyomaviruses (HPyVs) can cause serious and deleterious infections in human. Yet, the molecular mechanism underlying these infections, particularly in polyomavirus nephropathy (PVAN), is not well-defined. In the present study, we aimed to identify human genes with codon usage bias (CUB) similar to that of HPyV genes and explore their potential involvement in the pathogenesis of PVAN. The relative synonymous codon usage (RSCU) values of genes of HPyVs and those of human genes were computed and used for Pearson correlation analysis. The involvement of the identified correlation genes in PVAN was analyzed by validating their differential expression in publicly available transcriptomics data. Functional enrichment was performed to uncover the role of sets of genes. The RSCU analysis indicated that the A- and T-ending codons are preferentially used in HPyV genes. In total, 5400 human genes were correlated to the HPyV genes. The protein-protein interaction (PPI) network indicated strong interactions between these proteins. Gene expression analysis indicated that 229 of these genes were consistently and differentially expressed between normal kidney tissues and kidney tissues from PVAN patients. Functional enrichment analysis indicated that these genes were involved in biological processes related to transcription and in pathways related to protein ubiquitination pathway, apoptosis, cellular response to stress, inflammation and immune system. The identified genes may serve as diagnostic biomarkers and potential therapeutic targets for HPyV associated diseases, especially PVAN.
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Affiliation(s)
- Yu Fan
- Department of Urology, National Clinical Research Center for Geriatrics and Organ Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
| | - Duan Guo
- Department of Palliative Medicine, West China School of Public Health and West China fourth Hospital, Sichuan University, Chengdu, China
- Palliative Medicine Research Center, West China−Peking Union Medical College, Chen Zhiqian (PUMC C.C). Chen Institute of Health, Sichuan University, Chengdu, China
| | - Shangping Zhao
- Department of Urology, West China School of Nursing and Organ Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
| | - Qiang Wei
- Department of Urology, National Clinical Research Center for Geriatrics and Organ Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
| | - Yi Li
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Tao Lin, ; ; Yi Li,
| | - Tao Lin
- Department of Urology, National Clinical Research Center for Geriatrics and Organ Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
- *Correspondence: Tao Lin, ; ; Yi Li,
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Comparative Plastome Analysis of Three Amaryllidaceae Subfamilies: Insights into Variation of Genome Characteristics, Phylogeny, and Adaptive Evolution. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3909596. [PMID: 35372568 PMCID: PMC8970886 DOI: 10.1155/2022/3909596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/19/2022] [Accepted: 02/05/2022] [Indexed: 11/17/2022]
Abstract
In the latest APG IV classification system, Amaryllidaceae is placed under the order of Asparagus and includes three subfamilies: Agapanthoideae, Allioideae, and Amaryllidoideae, which include many economically important crops. With the development of molecular phylogeny, research on the phylogenetic relationship of Amaryllidaceae has become more convenient. However, the current comparative analysis of Amaryllidaceae at the whole chloroplast genome level is still lacking. In this study, we sequenced 18 Allioideae plastomes and combined them with publicly available data (a total of 41 plastomes), including 21 Allioideae species, 1 Agapanthoideae species, 14 Amaryllidoideae species, and 5 Asparagaceae species. Comparative analyses were performed including basic characteristics of genome structure, codon usage, repeat elements, IR boundary, and genome divergence. Phylogenetic relationships were detected using single-copy genes (SCGs) and ribosomal internal transcribed spacer sequences (ITS), and the branch-site model was also employed to conduct the positive selection analysis. The results indicated that all Amaryllidaceae species showed a highly conserved typical tetrad structure. The GC content and five codon usage indexes in Allioideae species were lower than those in the other two subfamilies. Comparison analysis of Bayesian and ML phylogeny based on SCGs strongly supports the monophyly of three subfamilies and the sisterhood among them. Besides, positively selected genes (PSGs) were detected in each of the three subfamilies. Almost all genes with significant posterior probabilities for codon sites were associated with self-replication and photosynthesis. Our study investigated the three subfamilies of Amaryllidaceae at the whole chloroplast genome level and suggested the key role of selective pressure in the adaptation and evolution of Amaryllidaceae.
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Tikhomirova TS, Matyunin MA, Lobanov MY, Galzitskaya OV. In-depth analysis of amino acid and nucleotide sequences of Hsp60: how conserved is this protein? Proteins 2021; 90:1119-1141. [PMID: 34964171 DOI: 10.1002/prot.26294] [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: 09/10/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 11/07/2022]
Abstract
Chaperonin Hsp60, as a protein found in all organisms, is of great interest in medicine, since it is present in many tissues and can be used both as a drug and as an object of targeted therapy. Hence, Hsp60 deserves a fundamental comparative analysis to assess its evolutionary characteristics. It was found that the percent identity of Hsp60 amino acid sequences both within and between phyla was not high enough to identify Hsp60s as highly conserved proteins. However, their ATP binding sites are largely conserved. The amino acid composition of Hsp60s remained relatively constant. At the same time, the analysis of the nucleotide sequences showed that GC content in the Hsp60 genes was comparable to or greater than the genomic values, which may indicate a high resistance to mutations due to tight control of the nucleotide composition by DNA repair systems. Natural selection plays a dominant role in the evolution of Hsp60 genes. The degree of mutational pressure affecting the Hsp60 genes is quite low, and its direction does not depend on taxonomy. Interestingly, for the Hsp60 genes from Chordata, Arthropoda, and Proteobacteria the exact direction of mutational pressure could not be determined. However, upon further division into classes, it was found that the direction of the mutational pressure for Hsp60 genes from Fish differs from that for other chordates. The direction of the mutational pressure affects the synonymous codon usage bias. The number of high and low represented codons increases with increasing GC content, which can improve codon usage. Special server has been created for bioinformatics analysis of Hsp60: http://oka.protres.ru:4202/.
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Affiliation(s)
- Tatyana S Tikhomirova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, Russia
| | - Maxim A Matyunin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Michail Yu Lobanov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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Cho M, Kim H, Son HS. Analysis of protein determinants of host-specific infection properties of polyomaviruses using machine learning. Genes Genomics 2021; 43:407-420. [PMID: 33646531 DOI: 10.1007/s13258-021-01059-2] [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: 09/11/2020] [Accepted: 01/27/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND The large tumor antigen (LT-Ag) and major capsid protein VP1 are known to play important roles in determining the host-specific infection properties of polyomaviruses (PyVs). OBJECTIVE The objective of this study was to investigate the physicochemical properties of amino acids of LT-Ag and VP1 that have important effects on host specificity, as well as classification techniques used to predict PyV hosts. METHODS We collected and used reference sequences of 86 viral species for analysis. Based on the clustering pattern of the reconstructed phylogenetic tree, the dataset was divided into three groups: mammalian, avian, and fish. We then used random forest (RF), naïve Bayes (NB), and k-nearest neighbors (kNN) algorithms for host classification. RESULTS Among the three algorithms, classification accuracy using kNN was highest in both LT-Ag (ACC = 98.83) and VP1 (ACC = 96.51). The amino acid physicochemical property most strongly correlated with host classification was charge, followed by solvent accessibility, polarity, and hydrophobicity in LT-Ag. However, in VP1, amino acid composition showed the highest correlation with host classification, followed by charge, normalized van der Waals volume, and solvent accessibility. CONCLUSIONS The results of the present study suggest the possibility of determining or predicting the host range and infection properties of PyVs at the molecular level by identifying the host species of active and emerging PyVs that exhibit different infection properties among diverse host species. Structural and biochemical differences of LT-Ag and VP1 proteins in host species that reflect these amino acid properties can be considered primary factors that determine the host specificity of PyV.
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Affiliation(s)
- Myeongji Cho
- Laboratory of Computational Virology & Viroinformatics, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
- Institute of Health and Environment, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
| | - Hayeon Kim
- Department of Biomedical Laboratory Science, Kyungdong University, 815 Gyeonhwon-ro, Munmak, Wonju, Gangwondo, 24695, Korea
| | - Hyeon S Son
- Laboratory of Computational Virology & Viroinformatics, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.
- Institute of Health and Environment, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.
- Interdisciplinary Graduate Program in Bioinformatics, College of National Science, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.
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