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Jacquat AG, Theumer MG, Dambolena JS. Selective and non-selective evolutionary signatures found in the simplest replicative biological entities. J Evol Biol 2024; 37:862-876. [PMID: 38822575 DOI: 10.1093/jeb/voae070] [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: 11/23/2023] [Accepted: 05/30/2024] [Indexed: 06/03/2024]
Abstract
Mitoviruses, which are considered evolutionary relics of extinct alpha-proteobacteria RNA phages, represent one of the simplest self-replicating biological systems. This study aims to quantitatively describe genomes and identify potential genomic signatures that support the protein phylogenetic-based classification criterion. Genomic variables, such as mononucleotide and dinucleotide composition, codon usage bias, and minimal free energy derived from optimized predicted RNA secondary structure, were analyzed. From the values obtained, the main evolutionary pressures were discussed, indicating that natural selection plays a significant role in shaping mitovirus genomes. However, neutral evolution also makes a significant contribution. This study reveals a significant discovery of structural divergence in Kvaramitovirus. The energy minimization approach employed to study 2D folding in this study reveals a distinct spatial organization of their genomes, providing evidence for the hypothesis of a single evolutionary event of circularization in the most recent common ancestor of the lineage. This hypothesis was discussed in light of recent discoveries by other researchers that partially support the existence of mitoviruses with circular genomes. Finally, this study represents a significant advancement in the understanding of mitoviruses, as it quantitatively describes the nucleotide sequence at the family and genus taxonomic levels. Additionally, we provide hypotheses that can be experimentally validated to inspire new research and address the gaps in knowledge of this fascinating, basally divergent RNA virus lineage.
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Affiliation(s)
- Andrés Gustavo Jacquat
- Facultad de Ciencias Exactas Físicas y Naturales (FCEFyN), Universidad Nacional de Córdoba (UNC), Córdoba, Argentina
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Martín Gustavo Theumer
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas (FCQ), Universidad Nacional de Córdoba (UNC), Córdoba, Argentina
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - José Sebastián Dambolena
- Facultad de Ciencias Exactas Físicas y Naturales (FCEFyN), Universidad Nacional de Córdoba (UNC), Córdoba, Argentina
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
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Song C, Zhu J, Li H. Complete chloroplast genomes of eight Delphinium taxa (Ranunculaceae) endemic to Xinjiang, China: insights into genome structure, comparative analysis, and phylogenetic relationships. BMC PLANT BIOLOGY 2024; 24:600. [PMID: 38926811 PMCID: PMC11201361 DOI: 10.1186/s12870-024-05279-y] [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: 07/26/2023] [Accepted: 06/10/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Delphinium L. represents a taxonomically intricate genus of significant phylogenetic and economic importance in Ranunculaceae. Despite the existence of few chloroplast genome datasets, a comprehensive understanding of genome structures and selective pressures within the genus remains unknown. Furthermore, several taxa in this genus are exclusively found in Xinjiang, China, a region renowned for its distribution and diversity of Chinese and Central Asian Delphinium species. Therefore, investigating the features of chloroplast genomes in this area will provide valuable insights into the evolutionary processes and phylogenetic relationships of the genus. RESULTS In this study, the eight newly completed chloroplast genomes are examined, ranging in length from 153,979 bp to 154,284 bp. Alongside these, analysing six previously reported taxa re-annotated in Delphinium, 111 unique genes are identified across all samples. Genome structure, distributions of simple sequence repeats and short dispersed repeats, as well as gene content are similar among these Delphinium taxa. Nine hypervariable intergenic spacers and protein coding regions, including ndhF-trnL(TAG), rpl16-intron, rpl33, rps15, rps18, trnK(TTT)-trnQ(TTG), trnP(TGG)-psaJ, trnT(GGT)-psbD and ycf1, are identified among 13 perennial Delphinium. Selective pressure and codon usage bias of all the plastid genes are performed within 14 Delphinium taxa. Phylogenetic analysis based on 14 Delphinium plastomes, alongside two Aconitum (Ranunculaceae) species serving as outgroup taxa, reveals the monophyletic nature of Delphinium. Our findings further discern Delphinium into two distinct clades: perennial species (clade I) and annual species (clade II). In addition, compared with the nrDNA ITS topology, cytological data and morphological characters, D. mollifolium and D. maackianum showed potential involvement in hybridization or polyploidization processes. Excluding these two species, the perennial Delphinium (clade I) exhibits a stronger consistency with the morphology-based system that utilized seed morphology. CONCLUSION This study represents the first comprehensive analysis of plastomic variations among Delphinium taxa, based on the examination of 14 complete plastomes. The chloroplast genome structure of Delphinium is similar to other angiosperms and possesses the typical quadripartite structure with the conserved genome arrangement and gene features. In addition, the variation of non-coding regions is larger than coding regions of the chloroplast genome. Through DNA sequence divergence across Delphinium plastomes and subsequent phylogenomic analyses ndhF-trnL(TAG) and ycf1 are identified as promising molecular markers. These highly variable loci held significant potential for future phylogenetic and phylogeographic studies on Delphinium. Our phylogenomic analyses based on the whole plastomes, concatenation of 132 unique intergenic spacer regions, concatenation of 77 unique protein-coding genes and nrDNA ITS, all support the monophyly of Delphinium and perennial taxa clusters together into one clade within this genus. These findings provide crucial data for systematic, phylogenomic and evolutionary research in the genus for future studies.
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Affiliation(s)
- Chunfeng Song
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat- Sen), Nanjing, 210014, Jiangsu, China
| | - Junwen Zhu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat- Sen), Nanjing, 210014, Jiangsu, China
| | - Huimin Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat- Sen), Nanjing, 210014, Jiangsu, China.
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Sun W, Wei Z, Gu Y, Wang T, Liu B, Yan Y. Chloroplast genome structure analysis of Equisetum unveils phylogenetic relationships to ferns and mutational hotspot region. FRONTIERS IN PLANT SCIENCE 2024; 15:1328080. [PMID: 38665369 PMCID: PMC11044155 DOI: 10.3389/fpls.2024.1328080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/02/2024] [Indexed: 04/28/2024]
Abstract
Equisetum is one of the oldest extant group vascular plants and is considered to be the key to understanding vascular plant evolution. Equisetum is distributed almost all over the world and has a high degree of adaptability to different environments. Despite the fossil record of horsetails (Equisetum, Equisetaceae) dating back to the Carboniferous, the phylogenetic relationship of this genus is not well, and the chloroplast evolution in Equisetum remains poorly understood. In order to fill this gap, we sequenced, assembled, and annotated the chloroplast genomes of 12 species of Equisetum, and compared them to 13 previously published vascular plants chloroplast genomes to deeply examine the plastome evolutionary dynamics of Equisetum. The chloroplast genomes have a highly conserved quadripartite structure across the genus, but these chloroplast genomes have a lower GC content than other ferns. The size of Equisetum plastomes ranges from 130,773 bp to 133,684 bp and they encode 130 genes. Contraction/expansion of IR regions and the number of simple sequences repeat regions underlie large genomic variations in size among them. Comparative analysis revealed we also identified 13 divergence hotspot regions. Additionally, the genes accD and ycf1 can be used as potential DNA barcodes for the identification and phylogeny of the genus Equisetum. Twelve photosynthesis-related genes were specifically selected in Equisetum. Comparative genomic analyses implied divergent evolutionary patterns between Equisetum and other ferns. Phylogenomic analyses and molecular dating revealed a relatively distant phylogenetic relationship between Equisetum and other ferns, supporting the division of pteridophyte into Lycophytes, Equisetaceae and ferns. The results show that the chloroplast genome can be used to solve phylogenetic problems within or between Equisetum species, and also provide genomic resources for the study of Equisetum systematics and evolution.
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Affiliation(s)
- Weiyue Sun
- Key Laboratory of Plant Biology, College of Heilongjiang Province, Harbin Normal University, Harbin, China
- Key Laboratory of National Forestry and Grassland Administration for Orehid Conservation and Utilization, the Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
| | - Zuoying Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Guangzhou, China
| | - Yuefeng Gu
- Key Laboratory of National Forestry and Grassland Administration for Orehid Conservation and Utilization, the Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
| | - Ting Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Guangzhou, China
| | - Baodong Liu
- Key Laboratory of Plant Biology, College of Heilongjiang Province, Harbin Normal University, Harbin, China
- Key Laboratory of National Forestry and Grassland Administration for Orehid Conservation and Utilization, the Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
| | - Yuehong Yan
- Key Laboratory of National Forestry and Grassland Administration for Orehid Conservation and Utilization, the Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
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Lao XL, Meng Y, Wu J, Wen J, Nie ZL. Plastid genomes provide insights into the phylogeny and chloroplast evolution of the paper daisy tribe Gnaphalieae (Asteraceae). Gene 2024; 901:148177. [PMID: 38242378 DOI: 10.1016/j.gene.2024.148177] [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: 01/03/2024] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
Chloroplast genomes, as an essential source of phylogenetic information, are increasingly utilized in the evolutionary study of angiosperms. Gnaphalieae is a medium-sized tribe of the sunflower family of Asteraceae, with about 2,100 species in 178 genera distributed in temperate habitats worldwide. There has been considerable progress in our understanding of their phylogenetic evolution using both nuclear and chloroplast sequences, but no focus on chloroplast genomic data. In this study, we performed sequencing, assembly, and annotation of 16 representative chloroplast genomes from all the major lineages of Gnaphalieae. Our results showed that the plastomes exhibited a typical circular tetrad structure with similar genomic structure gene content. But there were differences in genome size, SSRs, and codon usage within the tribe. Phylogenetic analysis revealed Relhania clade is the earliest diverged lineages with the Lasiopogon clade and the Gnaphalium s.s. clade diverged subsequently. The core group includes FLAG clade sister to the HAP and Australasian group. Compared with the outgroup species, chloroplast genome size of the FLAG clade is much reduced whereas those of Australasian, HAP, Gnaphalium s.s., Lasiopogon and Relhania clades are relatively expanded. Insertions and deletions in the intergenic regions associated with repetitive sequence variations are supposed to be the main factor leading to length variations in the chloroplast genomes of Gnaphalieae. The comparative analyses of chloroplast genomes would provide useful implications into understanding the taxonomic and evolutionary history of Gnaphalieae.
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Affiliation(s)
- Xiao-Lin Lao
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, China
| | - Ying Meng
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, China
| | - Jue Wu
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Ze-Long Nie
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, China.
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Jiao L, Jing Z, Zhang W, Su X, Yan H, Tian S. Codon Pattern and Context Analysis in Genes Triggering Alzheimer's Disease and Latent Tau Protein Aggregation Post-Anesthesia Exhibited Unique Molecular Patterns Associated with Functional Aspects. J Alzheimers Dis 2024; 97:1645-1660. [PMID: 38306048 DOI: 10.3233/jad-231142] [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] [Indexed: 02/03/2024]
Abstract
Background Previous reports have demonstrated post-operative dementia and Alzheimer's disease (AD), and increased amyloid-β levels and tau hyperphosphorylation have been observed in animal models post-anesthesia. Objective After surgical interventions, loss in memory has been observed that has been found linked with genes modulated after anesthesia. Present study aimed to study molecular pattern present in genes modulated post anesthesia and involved in characters progressing towards AD. Methods In the present study, 17 transcript variants belonging to eight genes, which have been found to modulate post-anesthesia and contribute to AD progression, were envisaged for their compositional features, molecular patterns, and codon and codon context-associated studies. Results The sequences' composition was G/C rich, influencing dinucleotide preference, codon preference, codon usage, and codon context. The G/C nucleotides being highly occurring nucleotides, CpGdinucleotides were also preferred; however, CpG was highly disfavored at p3-1 at the codon junction. The nucleotide composition of Cytosine exhibited a unique feature, and unlike other nucleotides, it did not correlate with codon bias. Contrarily, it correlated with the sequence lengths. The sequences were leucine-rich, and multiple leucine repeats were present, exhibiting the functional role of neuroprotection from neuroinflammation post-anesthesia. Conclusions The analysis pave the way to elucidate unique molecular patterns in genes modulated during anesthetic treatment and might help ameliorate the ill effects of anesthetics in the future.
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Affiliation(s)
- Liyuan Jiao
- Department of Anesthesiology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Ziye Jing
- Department of Anesthesiology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Wenjie Zhang
- Department of Anesthesiology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Xuesen Su
- Department of Anesthesiology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Hualei Yan
- Department of Anesthesiology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Shouyuan Tian
- Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Taiyuan, China
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Xiao F, Zhao Y, Wang X, Jian X. Full-length transcriptome characterization and comparative analysis of Gleditsia sinensis. BMC Genomics 2023; 24:757. [PMID: 38066414 PMCID: PMC10709882 DOI: 10.1186/s12864-023-09843-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 11/25/2023] [Indexed: 12/18/2023] Open
Abstract
As an economically important tree, Gleditsia sinensis Lam. is widely planted. A lack of background genetic information on G. sinensis hinders molecular breeding. Based on PacBio single-molecule real-time (SMRT) sequencing and analysis of G. sinensis, a total of 95,183 non-redundant transcript sequences were obtained, of which 93,668 contained complete open reading frames (ORFs), 2,858 were long non-coding RNAs (LncRNAs) and 18,855 alternative splicing (AS) events were identified. Genes orthologous to different Gleditsia species pairs were identified, stress-related genes had been positively selected during the evolution. AGA, AGG, and CCA were identified as the universal optimal codon in the genus of Gleditsia. EIF5A was selected as a suitable fluorescent quantitative reference gene. 315 Cytochrome P450 monooxygenases (CYP450s) and 147 uridine diphosphate (UDP)-glycosyltransferases (UGTs) were recognized through the PacBio SMRT transcriptome. Randomized selection of GsIAA14 for cloning verified the reliability of the PacBio SMRT transcriptome assembly sequence. In conclusion, the research data lay the foundation for further analysis of the evolutionary mechanism and molecular breeding of Gleditsia.
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Affiliation(s)
- Feng Xiao
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Yang Zhao
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China.
| | - Xiurong Wang
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Xueyan Jian
- School of Continuing Education, Yanbian University, Yanji, 133002, Jilin, China
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Zhou CY, Zeng MY, Gao X, Zhao Z, Li R, Wu Y, Liu ZJ, Zhang D, Li MH. Characteristics and Comparative Analysis of Seven Complete Plastomes of Trichoglottis s.l. (Aeridinae, Orchidaceae). Int J Mol Sci 2023; 24:14544. [PMID: 37833995 PMCID: PMC10572978 DOI: 10.3390/ijms241914544] [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: 08/17/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Trichoglottis exhibits a range of rich variations in colors and shapes of flower and is a valuable ornamental orchid genus. The genus Trichoglottis has been expanded by the inclusion of Staurochilus, but this Trichoglottis sensu lato (s.l.) was recovered as a non-monophyletic genus based on molecular sequences from one or a few DNA regions. Here, we present phylogenomic data sets, incorporating complete plastome sequences from seven species (including five species sequenced in this study) of Trichoglottis s.l. (including two species formerly treated as Staurochilus), to compare plastome structure and to reconstruct the phylogenetic relationships of this genus. The seven plastomes possessed the typical quadripartite structure of angiosperms and ranged from 149,402 bp to 149,841 bp with a GC content of 36.6-36.7%. These plastomes contain 120 genes, which comprise 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes, all ndh genes were pseudogenized or lost. A total of 98 (T. philippinensis) to 134 (T. ionosma) SSRs and 33 (T. subviolacea) to 46 (T. ionosma) long repeats were detected. The consistent and robust phylogenetic relationships of Trichoglottis were established using a total of 25 plastid genomes from the Aeridinae subtribe. The genus Trichoglottis s.l. was strongly supported as a monophyletic group, and two species formerly treated as Staurochilus were revealed as successively basal lineages. In addition, five mutational hotspots (trnNGUU-rpl32, trnLUAA, trnSGCU-trnGUCC, rbcL-accD, and trnTGGU-psbD) were identified based on the ranking of PI values. Our research indicates that plastome data is a valuable source for molecular identification and evolutionary studies of Trichoglottis and its related genera.
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Affiliation(s)
- Cheng-Yuan Zhou
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (M.-Y.Z.); (X.G.); (Z.Z.); (R.L.); (Y.W.); (Z.-J.L.)
| | - Meng-Yao Zeng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (M.-Y.Z.); (X.G.); (Z.Z.); (R.L.); (Y.W.); (Z.-J.L.)
| | - Xuyong Gao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (M.-Y.Z.); (X.G.); (Z.Z.); (R.L.); (Y.W.); (Z.-J.L.)
| | - Zhuang Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (M.-Y.Z.); (X.G.); (Z.Z.); (R.L.); (Y.W.); (Z.-J.L.)
| | - Ruyi Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (M.-Y.Z.); (X.G.); (Z.Z.); (R.L.); (Y.W.); (Z.-J.L.)
| | - Yuhan Wu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (M.-Y.Z.); (X.G.); (Z.Z.); (R.L.); (Y.W.); (Z.-J.L.)
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (M.-Y.Z.); (X.G.); (Z.Z.); (R.L.); (Y.W.); (Z.-J.L.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (M.-Y.Z.); (X.G.); (Z.Z.); (R.L.); (Y.W.); (Z.-J.L.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (M.-Y.Z.); (X.G.); (Z.Z.); (R.L.); (Y.W.); (Z.-J.L.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Zhao Z, Zeng MY, Wu YW, Li JW, Zhou Z, Liu ZJ, Li MH. Characterization and Comparative Analysis of the Complete Plastomes of Five Epidendrum (Epidendreae, Orchidaceae) Species. Int J Mol Sci 2023; 24:14437. [PMID: 37833887 PMCID: PMC10572996 DOI: 10.3390/ijms241914437] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/10/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023] Open
Abstract
Epidendrum, one of the three largest genera of Orchidaceae, exhibits significant horticultural and ornamental value and serves as an important research model in conservation, ecology, and evolutionary biology. Given the ambiguous identification of germplasm and complex evolutionary relationships within the genus, the complete plastome of this genus (including five species) were firstly sequenced and assembled to explore their characterizations. The plastomes exhibited a typical quadripartite structure. The lengths of the plastomes ranged from 147,902 bp to 150,986 bp, with a GC content of 37.16% to 37.33%. Gene annotation revealed the presence of 78-82 protein-coding genes, 38 tRNAs, and 8 rRNAs. A total of 25-38 long repeats and 130-149 SSRs were detected. Analysis of relative synonymous codon usage (RSCU) indicated that leucine (Leu) was the most and cysteine (Cys) was the least. The consistent and robust phylogenetic relationships of Epidendrum and its closely related taxa were established using a total of 43 plastid genomes from the tribe Epidendreae. The genus Epidendrum was supported as a monophyletic group and as a sister to Cattleya. Meanwhile, four mutational hotspots (trnCGCA-petN, trnDGUC-trnYGUA, trnSGCU-trnGUCC, and rpl32-trnLUAG) were identified for further phylogenetic studies. Our analysis demonstrates the promising utility of plastomes in inferring the phylogenetic relationships of Epidendrum.
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Affiliation(s)
- Zhuang Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
| | - Meng-Yao Zeng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
| | - Yu-Wei Wu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
| | - Jin-Wei Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
| | - Zhuang Zhou
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Yuan S, Nie C, Jia S, Liu T, Zhao J, Peng J, Kong W, Liu W, Gou W, Lei X, Xiong Y, Xiong Y, Yu Q, Ling Y, Ma X. Complete chloroplast genomes of three wild perennial Hordeum species from Central Asia: genome structure, mutation hotspot, phylogenetic relationships, and comparative analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1170004. [PMID: 37554563 PMCID: PMC10405828 DOI: 10.3389/fpls.2023.1170004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/05/2023] [Indexed: 08/10/2023]
Abstract
Hordeum L. is widely distributed in mountain or plateau of subtropical and warm temperate regions around the world. Three wild perennial Hordeum species, including H. bogdanii, H. brevisubulatum, and H. violaceum, have been used as forage and for grassland ecological restoration in high-altitude areas in recent years. To date, the degree of interspecies sequence variation in the three Hordeum species within existing gene pools is still not well-defined. Herein, we sequenced and assembled chloroplast (cp) genomes of the three species. The results revealed that the cp genome of H. bogdanii showed certain sequence variations compared with the cp genomes of the other two species (H. brevisubulatum and H. violaceum), and the latter two were characterized by a higher relative affinity. Parity rule 2 plot (PR2) analysis illuminated that most genes of all ten Hordeum species were concentrated in nucleotide T and G. Numerous single nucleotide polymorphism (SNP) and insertion/deletion (In/Del) events were detected in the three Hordeum species. A series of hotspots regions (tRNA-GGU ~ tRNA-GCA, tRNA-UGU ~ ndhJ, psbE ~ rps18, ndhF ~ tRNA-UAG, etc.) were identified by mVISTA procedures, and the five highly polymorphic genes (tRNA-UGC, tRNA-UAA, tRNA-UUU, tRNA-UAC, and ndhA) were proved by the nucleotide diversity (Pi). Although the distribution and existence of cp simple sequence repeats (cpSSRs) were predicted in the three Hordeum cp genomes, no rearrangement was found between them. A similar phenomenon has been found in the cp genome of the other seven Hordeum species, which has been published so far. In addition, evolutionary relationships were reappraised based on the currently reported cp genome of Hordeum L. This study offers a framework for gaining a better understanding of the evolutionary history of Hordeum species through the re-examination of their cp genomes, and by identifying highly polymorphic genes and hotspot regions that could provide important insights into the genetic diversity and differentiation of these species.
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Affiliation(s)
- Shuai Yuan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Cong Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Tianqi Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Junming Zhao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jinghan Peng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Weixia Kong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wei Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wenlong Gou
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Xiong Lei
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qingqing Yu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yao Ling
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
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10
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Khandia R, Pandey MK, Rzhepakovsky IV, Khan AA, Alexiou A. Synonymous Codon Variant Analysis for Autophagic Genes Dysregulated in Neurodegeneration. Mol Neurobiol 2023; 60:2252-2267. [PMID: 36637744 DOI: 10.1007/s12035-022-03081-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 09/27/2022] [Indexed: 01/14/2023]
Abstract
Neurodegenerative disorders are often a culmination of the accumulation of abnormally folded proteins and defective organelles. Autophagy is a process of removing these defective proteins, organelles, and harmful substances from the body, and it works to maintain homeostasis. If autophagic removal of defective proteins has interfered, it affects neuronal health. Some of the autophagic genes are specifically found to be associated with neurodegenerative phenotypes. Non-functional, mutated, or gene copies having silent mutations, often termed synonymous variants, might explain this. However, these synonymous variant which codes for exactly similar proteins have different translation rates, stability, and gene expression profiling. Hence, it would be interesting to study the pattern of synonymous variant usage. In the study, synonymous variant usage in various transcripts of autophagic genes ATG5, ATG7, ATG8A, ATG16, and ATG17/FIP200 reported to cause neurodegeneration (if dysregulated) is studied. These genes were analyzed for their synonymous variant usage; nucleotide composition; any possible nucleotide skew in a gene; physical properties of autophagic protein including GRAVY and AROMA; hydropathicity; instability index; and frequency of acidic, basic, neutral amino acids; and gene expression level. The study will help understand various evolutionary forces acting on these genes and the possible augmentation of a gene if showing unusual behavior.
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Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, 462026, India.
| | - Megha Katare Pandey
- Department of Translational Medicine, All India Institute of Medical Sciences, Bhopal, 462020, India
| | | | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia.
| | - Athanasios Alexiou
- Novel Global Community Educational Foundation, Hebersham, Australia
- AFNP Med, Wien, Austria
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11
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AbdAlla HAM, Wanga VO, Mkala EM, Amenu SG, Amar MH, Chen L, Wang QF. Comparative genomics analysis of endangered wild Egyptian Moringa peregrina (Forssk.) Fiori plastome, with implications for the evolution of Brassicales order. Front Genet 2023; 14:1131644. [PMID: 36992699 PMCID: PMC10040795 DOI: 10.3389/fgene.2023.1131644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 02/27/2023] [Indexed: 03/14/2023] Open
Abstract
Moringa is a mono-genus belonging to the Moringaceae family, which includes 13 species. Among them, Moringa peregrina is plant species native to the Arabian Peninsula, Southern Sinai in Egypt, and the Horn of Africa, and comprehensive studies on its nutritional, industrial, and medicinal values have been performed. Herein, we sequenced and analyzed the initial complete chloroplast genome of Moringa peregrina. Concurrently, we analyzed the new chloroplast genome along with 25 chloroplast genomes related to species representing eight families in the Brassicales order. The results indicate that the plastome sequence of M. peregrina consists of 131 genes, with an average GC content of 39.23%. There is a disparity in the IR regions of the 26 species ranging from 25,804 to 31,477 bp. Plastome structural variations generated 20 hotspot regions that could be considered prospective DNA barcode locations in the Brassicales order. Tandem repeats and SSR structures are reported as significant evidence of structural variations among the 26 tested specimens. Furthermore, selective pressure analysis was performed to estimate the substitution rate within the Moringaceae family, which revealing that the ndhA and accD genes are under positive selective pressure. The phylogenetic analysis of the Brassicales order produced an accurate monophyletic annotation cluster of the Moringaceae and Capparaceae species, offering unambiguous identification without overlapping groups between M. oleifera and M. peregrina, which are genetically strongly associated. Divergence time estimation suggests that the two Moringa species recently diversified, 0.467 Ma. Our findings highlight the first complete plastome of the Egyptian wild-type of M. peregrina, which can be used for determining plastome phylogenetic relationships and systematic evolution history within studies on the Moringaceae family.
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Affiliation(s)
- Heba A. M. AbdAlla
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Plant Biodiversity and Evolution Research Group, University of Chinese Academy of Sciences, Beijing, China
- Botany Department, Agriculture and Biological Institute, National Research Centre, Giza, Egypt
| | - Vincent Okelo Wanga
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Plant Biodiversity and Evolution Research Group, University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Elijah Mbandi Mkala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Plant Biodiversity and Evolution Research Group, University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Sara Getachew Amenu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Plant Biodiversity and Evolution Research Group, University of Chinese Academy of Sciences, Beijing, China
| | - Mohamed Hamdy Amar
- Egyptian Deserts Gene Bank, Desert Research Center, Cairo, Egypt
- *Correspondence: Qing-Feng Wang, ; Lingyun Chen, ; Mohamed Hamdy Amar,
| | - Lingyun Chen
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
- *Correspondence: Qing-Feng Wang, ; Lingyun Chen, ; Mohamed Hamdy Amar,
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Plant Biodiversity and Evolution Research Group, University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- *Correspondence: Qing-Feng Wang, ; Lingyun Chen, ; Mohamed Hamdy Amar,
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12
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Ramadan AM, Mohammed T, Al-Ghamdi KM, Alghamdi AJ, Atef A. The first report describes features of the chloroplast genome of Withania frutescens. Saudi J Biol Sci 2023; 30:103600. [PMID: 36874202 PMCID: PMC9975694 DOI: 10.1016/j.sjbs.2023.103600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/29/2023] [Accepted: 02/08/2023] [Indexed: 02/17/2023] Open
Abstract
Genomic studies not only help researcher not only to identify genomic features in organisms, but also facilitate understanding of evolutionary relationships. Species in the Withania genus have medicinal benefits, and one of them is Withania frutescens, which is used to treat various diseases. This report investigates the nucleotides and genic features of chloroplast genome of Withania frutescens and trying to clarify the evolutionary relationship with Withania sp and family Solanaceae. We found that the total size of Withania frutescens chloroplast genome was 153.771 kb (the smallest chloroplast genome in genus Withania). A large single-copy region (91.285 kb), a small single-copy region (18.373 kb) form the genomic region, and are distinct from each other by a large inverted repeat (22.056 kb). 137 chloroplast genes are found including 4 rRNAs, 38 tRNAs and 83 protein-coding genes. The Withania frutescens chloroplast genome as well as four closest relatives was compared for features such as structure, nucleotide composition, simple sequence repeats (SSRs) and codon bias. Compared to other Withania species, Withania frutescens has unique characteristics. It has the smallest chloroplast genome of any Withania species, isoleucine is the major amino acid, and tryptophan is the minor, In addition, there are no ycf3 and ycf4 genes, fourth, there are only fifteen replicative genes, while in most other species there are more. Using fast minimum evolution and neighbor joining, we have reconstructed the trees to confirm the relationship with other Solanacaea species. The Withania frutescens chloroplast genome is submitted under accession no. ON153173.
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Affiliation(s)
- Ahmed M Ramadan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Najla bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
- Plant Molecular Biology Department, Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt
- Corresponding author at: Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia.
| | - Taimyiah Mohammed
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khalid M Al-Ghamdi
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdullah J Alghamdi
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Atef
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Najla bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
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13
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Rahman SU, Rehman HU, Rahman IU, Khan MA, Rahim F, Ali H, Chen D, Ma W. Evolution of codon usage in Taenia saginata genomes and its impact on the host. Front Vet Sci 2023; 9:1021440. [PMID: 36713873 PMCID: PMC9875090 DOI: 10.3389/fvets.2022.1021440] [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: 08/17/2022] [Accepted: 10/03/2022] [Indexed: 01/13/2023] Open
Abstract
The beef tapeworm, also known as Taenia saginata, is a zoonotic tapeworm from the genus Taenia in the order Cyclophyllidea. Taenia saginata is a food-borne zoonotic parasite with a worldwide distribution. It poses serious health risks to the host and has a considerable negative socioeconomic impact. Previous studies have explained the population structure of T. saginata within the evolutionary time scale and adaptive evolution. However, it is still unknown how synonymous codons are used by T. saginata. In this study, we used 90 T. saginata strains, applying the codon usage bias (CUB). Both base content and relative synonymous codon usage (RSCU) analysis revealed that AT-ended codons were more frequently used in the genome of T. saginata. Further low CUB was observed from the effective number of codons (ENC) value. The neutrality plot analysis suggested that the dominant factor of natural selection was involved in the structuring of CUB in T. saginata. Further analysis showed that T. saginata has adapted host-specific codon usage patterns to sustain successful replication and transmission chains within hosts (Bos taurus and Homo sapiens). Generally, both natural selection and mutational pressure have an impact on the codon usage patterns of the protein-coding genes in T. saginata. This study is important because it characterized the codon usage pattern in the T. saginata genomes and provided the necessary data for a basic evolutionary study on them.
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Affiliation(s)
- Siddiq Ur Rahman
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Pakistan
| | - Hassan Ur Rehman
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Pakistan
| | - Inayat Ur Rahman
- Department of Botany, Khushal Khan Khattak University, Karak, Pakistan
| | - Muazzam Ali Khan
- Department of Botany, Bacha Khan University, Charsadda, KP, Pakistan
| | - Fazli Rahim
- Department of Botany, Bacha Khan University, Charsadda, KP, Pakistan
| | - Hamid Ali
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
| | - Dekun Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Wentao Ma
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China,*Correspondence: Wentao Ma ✉
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14
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Rahman SU, Rehman HU, Rahman IU, Rauf A, Alshammari A, Alharbi M, Haq NU, Suleria HAR, Raza SHA. Analysis of codon usage bias of lumpy skin disease virus causing livestock infection. Front Vet Sci 2022; 9:1071097. [PMID: 36544551 PMCID: PMC9762553 DOI: 10.3389/fvets.2022.1071097] [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: 10/15/2022] [Accepted: 11/10/2022] [Indexed: 12/07/2022] Open
Abstract
Lumpy skin disease virus (LSDV) causes lumpy skin disease (LSD) in livestock, which is a double-stranded DNA virus that belongs to the genus Capripoxvirus of the family Poxviridae. LSDV is an important poxvirus that has spread out far and wide to become distributed worldwide. It poses serious health risks to the host and causes considerable negative socioeconomic impact on farmers financially and on cattle by causing ruminant-related diseases. Previous studies explained the population structure of the LSDV within the evolutionary time scale and adaptive evolution. However, it is still unknown and remains enigmatic as to how synonymous codons are used by the LSDV. Here, we used 53 LSDV strains and applied the codon usage bias (CUB) analysis to them. Both the base content and the relative synonymous codon usage (RSCU) analysis revealed that the AT-ended codons were more frequently used in the genome of LSDV. Further low codon usage bias was calculated from the effective number of codons (ENC) value. The neutrality plot analysis suggested that the dominant factor of natural selection played a role in the structuring of CUB in LSDV. Additionally, the results from a comparative analysis suggested that the LSDV has adapted host-specific codon usage patterns to sustain successful replication and transmission chains within hosts (Bos taurus and Homo sapiens). Both natural selection and mutational pressure have an impact on the codon usage patterns of the protein-coding genes in LSDV. This study is important because it has characterized the codon usage pattern in the LSDV genomes and has provided the necessary data for a basic evolutionary study on them.
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Affiliation(s)
- Siddiq Ur Rahman
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Pakistan,*Correspondence: Siddiq Ur Rahman
| | - Hassan Ur Rehman
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Pakistan
| | - Inayat Ur Rahman
- Department of Botany, Khushal Khan Khattak University, Karak, Pakistan
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Swabi, Pakistan
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Noor ul Haq
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Pakistan
| | - Hafiz Ansar Rasul Suleria
- Faculty of Veterinary and Agricultural Sciences, School of Agriculture and Food, The University of Melbourne, Melbourne, VIC, Australia
| | - Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China,Safety of Livestock and Poultry Products, College of Food Science, South China Agricultural University, Guangzhou, China
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15
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Xie DF, Xie C, Ren T, Song BN, Zhou SD, He XJ. Plastid phylogenomic insights into relationships, divergence, and evolution of Apiales. PLANTA 2022; 256:117. [PMID: 36376499 DOI: 10.1007/s00425-022-04031-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 11/06/2022] [Indexed: 06/16/2023]
Abstract
Members of Apiales are monophyletic and radiated in the Late Cretaceous. Fruit morphologies are critical for Apiales evolution and negative selection and mutation pressure play important roles in environmental adaptation. Apiales include many foods, spices, medicinal, and ornamental plants, but the phylogenetic relationships, origin and divergence, and adaptive evolution remain poorly understood. Here, we reconstructed Apiales phylogeny based on 72 plastid genes from 280 species plastid genomes representing six of seven families of this order. Highly supported phylogenetic relationships were detected, which revealed that each family of Apiales is monophyletic and confirmed that Pennanticeae is a member of Apiales. Genera Centella and Dickinsia are members of Apiaceae, and the genus Hydrocotyle previously classified into Apiaceae is confirmed to belong to Araliaceae. Besides, coalescent phylogenetic analysis and gene trees cluster revealed ten genes that can be used for distinguishing species among families of Apiales. Molecular dating suggested that the Apiales originated during the mid-Cretaceous (109.51 Ma), with the families' radiation occurring in the Late Cretaceous. Apiaceae species exhibit higher differentiation compared to other families. Ancestral trait reconstruction suggested that fruit morphological evolution may be related to shifts in plant types (herbaceous or woody), which in turn is related to the distribution areas and species numbers. Codon bias and positive selection analyses suggest that negative selection and mutation pressure may play important roles in environmental adaptation of Apiales members. Our results improve the phylogenetic framework of Apiales and provide insights into the origin, divergence, and adaptive evolution of this order and its members.
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Affiliation(s)
- Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Chuan Xie
- Sichuan Academy of Forestry, Chengdu, 610081, Sichuan, People's Republic of China
| | - Ting Ren
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Bo-Ni Song
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, 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, Chengdu, 610065, Sichuan, 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, Chengdu, 610065, Sichuan, People's Republic of China.
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16
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Khandia R, Pandey MK, Khan AA, Rzhepakovsky IV, Gurjar P, Karobari MI. Codon Usage and Context Analysis of Genes Modulated during SARS-CoV-2 Infection and Dental Inflammation. Vaccines (Basel) 2022; 10:1874. [PMID: 36366382 PMCID: PMC9695912 DOI: 10.3390/vaccines10111874] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/30/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2024] Open
Abstract
The overexpression of SARS-CoV-2 primary receptors and co-receptors (ACE2, TMPRSS2, FURIN, and CD147) enhance the likeliness of SARS-CoV-2 infection. The genes for same receptors are overexpressed in the periodontal tissues of periodontitis patients. On the other hand, BMAL1 is recognized to play a crucial role in regulating pulmonary inflammation and enhancing susceptibility to viral infection. Silenced BMAL1 disrupts circadian transcriptional regulations, enhances vulnerability to SARS-CoV-2 infections, and may trigger the further production of TNF-α and other pro-inflammatory cytokines that propagate the cytokine storm and exacerbate periodontal inflammation. Therefore ACE2, TMPRSS2, FURIN, CD147, and BMAL1 are the crossroads between SARS-CoV-2 and Periodontitis genes. The enhanced expression of ACE2, TMPRSS2, FURIN, and CD147 and the diminished expression of BMAL1 may be a strategy to check both ailments simultaneously. In gene manipulation techniques, oligos are introduced, which contain all the necessary information to manipulate gene expression. The data are derived from the studies on genes' molecular patterns, including nucleotide composition, dinucleotide patterns, relative synonymous codon usage, codon usage bias, codon context, and rare and abundant codons. Such information may be used to manipulate the overexpression and underexpression of the genes at the time of SARS-CoV-2 infection and periodontitis to mitigate both ailments simultaneously; it can be explored to uncover possible future treatments.
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Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal 462026, India
| | - Megha Katare Pandey
- Department of Translational Medicine, All India Institute of Medical Sciences, Bhopal 462020, India
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | | | - Pankaj Gurjar
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW 2770, Australia
| | - Mohmed Isaqali Karobari
- Conservative Dentistry Unit, School of Dental Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
- Department of Conservative Dentistry & Endodontics, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences University, Chennai 600077, India
- Department of Restorative Dentistry & Endodontics, University of Puthisastra, Phnom Penh 12211, Cambodia
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17
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Bansal S, Mallikarjuna MG, Balamurugan A, Nayaka SC, Prakash G. Composition and Codon Usage Pattern Results in Divergence of the Zinc Binuclear Cluster ( Zn(II)2Cys6) Sequences among Ascomycetes Plant Pathogenic Fungi. J Fungi (Basel) 2022; 8:1134. [PMID: 36354901 PMCID: PMC9694491 DOI: 10.3390/jof8111134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/22/2022] [Accepted: 10/23/2022] [Indexed: 07/29/2023] Open
Abstract
Zinc binuclear cluster proteins (ZBC; Zn(II)2Cys6) are unique to the fungi kingdom and associated with a series of functions, viz., the utilization of macromolecules, stress tolerance, and most importantly, host-pathogen interactions by imparting virulence to the pathogen. Codon usage bias (CUB) is the phenomenon of using synonymous codons in a non-uniform fashion during the translation event, which has arisen because of interactions among evolutionary forces. The Zn(II)2Cys6 coding sequences from nine Ascomycetes plant pathogenic species and model system yeast were analysed for compositional and codon usage bias patterns. The clustering analysis diverged the Ascomycetes fungi into two clusters. The nucleotide compositional and relative synonymous codon usage (RSCU) analysis indicated GC biasness toward Ascomycetes fungi compared with the model system S. cerevisiae, which tends to be AT-rich. Further, plant pathogenic Ascomycetes fungi belonging to cluster-2 showed a higher number of GC-rich high-frequency codons than cluster-1 and was exclusively AT-rich in S. cerevisiae. The current investigation also showed the mutual effect of the two evolutionary forces, viz. natural selection and compositional constraints, on the CUB of Zn(II)2Cys6 genes. The perseverance of GC-rich codons of Zn(II)2Cys6 in Ascomycetes could facilitate the invasion process. The findings of the current investigation show the role of CUB and nucleotide composition in the evolutionary divergence of Ascomycetes plant pathogens and paves the way to target specific codons and sequences to modulate host-pathogen interactions through genome editing and functional genomics tools.
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Affiliation(s)
- Shilpi Bansal
- Division of Plant Pathology, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India
| | | | - Alexander Balamurugan
- Division of Plant Pathology, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India
| | - S. Chandra Nayaka
- Department of Studies in Applied Botany and Biotechnology, University of Mysore, Mysore 570005, India
| | - Ganesan Prakash
- Division of Plant Pathology, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India
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18
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Analysis of the Compositional Features and Codon Usage Pattern of Genes Involved in Human Autophagy. Cells 2022; 11:cells11203203. [PMID: 36291071 PMCID: PMC9601114 DOI: 10.3390/cells11203203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
Autophagy plays an intricate role in paradigmatic human pathologies such as cancer, and neurodegenerative, cardiovascular, and autoimmune disorders. Autophagy regulation is performed by a set of autophagy-related (ATG) genes, first recognized in yeast genome and subsequently identified in other species, including humans. Several other genes have been identified to be involved in the process of autophagy either directly or indirectly. Studying the codon usage bias (CUB) of genes is crucial for understanding their genome biology and molecular evolution. Here, we examined the usage pattern of nucleotide and synonymous codons and the influence of evolutionary forces in genes involved in human autophagy. The coding sequences (CDS) of the protein coding human autophagy genes were retrieved from the NCBI nucleotide database and analyzed using various web tools and software to understand their nucleotide composition and codon usage pattern. The effective number of codons (ENC) in all genes involved in human autophagy ranges between 33.26 and 54.6 with a mean value of 45.05, indicating an overall low CUB. The nucleotide composition analysis of the autophagy genes revealed that the genes were marginally rich in GC content that significantly influenced the codon usage pattern. The relative synonymous codon usage (RSCU) revealed 3 over-represented and 10 under-represented codons. Both natural selection and mutational pressure were the key forces influencing the codon usage pattern of the genes involved in human autophagy.
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Huang X, Coulibaly D, Tan W, Ni Z, Shi T, Li H, Hayat F, Gao Z. The analysis of genetic structure and characteristics of the chloroplast genome in different Japanese apricot germplasm populations. BMC PLANT BIOLOGY 2022; 22:354. [PMID: 35864441 PMCID: PMC9306182 DOI: 10.1186/s12870-022-03731-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/04/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Chloroplast (cp) genomes are generally considered to be conservative and play an important role in population diversity analysis in plants, but the characteristics and diversity of the different germplasm populations in Japanese apricot are still not clear. RESULTS A total of 146 cp genomes from three groups of wild, domesticated, and bred accessions of Japanese apricot were sequenced in this study. The comparative genome analysis revealed that the 146 cp genomes were divided into 41 types, and ranged in size from 157,886 to 158,167 bp with a similar structure and composition to those of the genus Prunus. However, there were still minor differences in the cp genome that were mainly caused by the contraction and expansion of the IR region, and six types of SSR in which mono-nucleotide repeats were the most dominant type of repeats in the cp genome. The genes rpl33 and psbI, and intergenic regions of start-psbA, rps3-rpl22, and ccsA-ndhD, showed the highest nucleotide polymorphism in the whole cp genome. A total of 325 SNPs were detected in the 146 cp genomes, and more than 70% of the SNPs were in region of large single-copy (LSC). The SNPs and haplotypes in the cp genome indicated that the wild group had higher genetic diversity than the domesticated and bred groups. In addition, among wild populations, Southwest China, including Yunnan, Tibet, and Bijie of Guizhou, had the highest genetic diversity. The genetic relationship of Japanese apricot germplasm resources in different regions showed a degree of correlation with their geographical distribution. CONCLUSION Comparative analysis of chloroplast genomes of 146 Japanese apricot resources was performed to analyze the used to explore the genetic relationship and genetic diversity among Japanese apricot resources with different geographical distributions, providing some reference for the origin and evolution of Japanese apricot.
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Affiliation(s)
- Xiao Huang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Daouda Coulibaly
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Wei Tan
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Zhaojun Ni
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Hantao Li
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Faisal Hayat
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
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He X, Dong S, Gao C, Wang Q, Zhou M, Cheng R. The complete chloroplast genome of Carpesium abrotanoides L. (Asteraceae): structural organization, comparative analysis, mutational hotspots and phylogenetic implications within the tribe Inuleae. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01038-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Comparative Chloroplast Genome Analysis of Wax Gourd (Benincasa hispida) with Three Benincaseae Species, Revealing Evolutionary Dynamic Patterns and Phylogenetic Implications. Genes (Basel) 2022; 13:genes13030461. [PMID: 35328015 PMCID: PMC8954987 DOI: 10.3390/genes13030461] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/01/2022] [Indexed: 12/13/2022] Open
Abstract
Benincasa hispida (wax gourd) is an important Cucurbitaceae crop, with enormous economic and medicinal importance. Here, we report the de novo assembly and annotation of the complete chloroplast genome of wax gourd with 156,758 bp in total. The quadripartite structure of the chloroplast genome comprises a large single-copy (LSC) region with 86,538 bp and a small single-copy (SSC) region with 18,060 bp, separated by a pair of inverted repeats (IRa and IRb) with 26,080 bp each. Comparison analyses among B. hispida and three other species from Benincaseae presented a significant conversion regarding nucleotide content, genome structure, codon usage, synonymous and non-synonymous substitutions, putative RNA editing sites, microsatellites, and oligonucleotide repeats. The LSC and SSC regions were found to be much more varied than the IR regions through a divergent analysis of the species within Benincaseae. Notable IR contractions and expansions were observed, suggesting a difference in genome size, gene duplication and deletion, and the presence of pseudogenes. Intronic gene sequences, such as trnR-UCU–atpA and atpH–atpI, were observed as highly divergent regions. Two types of phylogenetic analysis based on the complete cp genome and 72 genes suggested sister relationships between B. hispida with the Citrullus, Lagenaria, and Cucumis. Variations and consistency with previous studies regarding phylogenetic relationships are discussed. The cp genome of B. hispida provides valuable genetic information for the detection of molecular markers, research on taxonomic discrepancies, and the inference of the phylogenetic relationships of Cucurbitaceae.
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Morton BR. Context-Dependent Mutation Dynamics, Not Selection, Explains the Codon Usage Bias of Most Angiosperm Chloroplast Genes. J Mol Evol 2022; 90:17-29. [PMID: 34932159 PMCID: PMC8821512 DOI: 10.1007/s00239-021-10038-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 11/17/2021] [Indexed: 01/12/2023]
Abstract
Two competing proposals about the degree to which selection affects codon usage of angiosperm chloroplast genes are examined. The first, based on observations that codon usage does not match expectations under the naïve assumption that base composition will be identical at all neutral sites, is that selection plays a significant role. The second is that codon usage is determined almost solely by mutation bias and drift, with selection influencing only one or two highly expressed genes, in particular psbA. First it is shown that, as a result of an influence of neighboring base composition on mutation dynamics, compositional biases are expected to be widely divergent at different sites in the absence of selection. The observed mutation properties are then used to predict expected neutral codon usage biases and to show that observed deviations from the naïve expectations are in fact expected given the context-dependent mutational dynamics. It is also shown that there is a match between the observed and expected codon usage when context effects are taken into consideration, with psbA being a notable exception. Overall, the data support the model that selection is not a widespread factor affecting the codon usage of angiosperm chloroplast genes and highlight the need to have an accurate model of mutational dynamics.
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Affiliation(s)
- Brian R Morton
- Department of Biology, Barnard College, Columbia University, 3009 Broadway, New York, NY, 10027, USA.
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Gu L, Hou Y, Wang G, Liu Q, Ding W, Weng Q. Characterization of the chloroplast genome of Lonicera ruprechtiana Regel and comparison with other selected species of Caprifoliaceae. PLoS One 2022; 17:e0262813. [PMID: 35077482 PMCID: PMC8789150 DOI: 10.1371/journal.pone.0262813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 01/05/2022] [Indexed: 11/19/2022] Open
Abstract
Lonicera ruprechtiana Regel is widely used as a greening tree in China and also displays excellent pharmacological activities. The phylogenetic relationship between L. ruprechtiana and other members of Caprifoliaceae remains unclear. In this study, the complete cp genome of L. ruprechtiana was identified using high-throughput Illumina pair-end sequencing data. The circular cp genome was 154,611 bp long and has a large single-copy region of 88,182 bp and a small single-copy region of 18,713 bp, with the two parts separated by two inverted repeat (IR) regions (23,858 bp each). A total of 131 genes were annotated, including 8 ribosomal RNAs, 39 transfer RNAs, and 84 protein-coding genes (PCGs). In addition, 49 repeat sequences and 55 simple sequence repeat loci of 18 types were also detected. Codon usage analysis demonstrated that the Leu codon is preferential for the A/U ending. Maximum-likelihood phylogenetic analysis using 22 Caprifoliaceae species revealed that L. ruprechtiana was closely related to Lonicera insularis. Comparison of IR regions revealed that the cp genome of L. ruprechtiana was largely conserved with that of congeneric species. Moreover, synonymous (Ks) and non-synonymous (Ka) substitution rate analysis showed that most genes were under purifying selection pressure; ycf3, and some genes associated with subunits of NADH dehydrogenase, subunits of the cytochrome b/f complex, and subunits of the photosystem had been subjected to strong purifying selection pressure (Ka/Ks < 0.1). This study provides useful genetic information for future study of L. ruprechtiana evolution.
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Affiliation(s)
- Lei Gu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yunyan Hou
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Guangyi Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Qiuping Liu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Wei Ding
- Colleage of plant protection, Southwest University, Chongqing, China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, China
- Qiannan Normal University for Nationalities, Duyun, China
- * E-mail:
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Luo Y, He J, Lyu R, Xiao J, Li W, Yao M, Pei L, Cheng J, Li J, Xie L. Comparative Analysis of Complete Chloroplast Genomes of 13 Species in Epilobium, Circaea, and Chamaenerion and Insights Into Phylogenetic Relationships of Onagraceae. Front Genet 2021; 12:730495. [PMID: 34804117 PMCID: PMC8600051 DOI: 10.3389/fgene.2021.730495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/20/2021] [Indexed: 02/01/2023] Open
Abstract
The evening primrose family, Onagraceae, is a well defined family of the order Myrtales, comprising 22 genera widely distributed from boreal to tropical areas. In this study, we report and characterize the complete chloroplast genome sequences of 13 species in Circaea, Chamaenerion, and Epilobium using a next-generation sequencing method. We also retrieved chloroplast sequences from two other Onagraceae genera to characterize the chloroplast genome of the family. The complete chloroplast genomes of Onagraceae encoded an identical set of 112 genes (with exclusion of duplication), including 78 protein-coding genes, 30 transfer RNAs, and four ribosomal RNAs. The chloroplast genomes are basically conserved in gene arrangement across the family. However, a large segment of inversion was detected in the large single copy region of all the samples of Oenothera subsect. Oenothera. Two kinds of inverted repeat (IR) region expansion were found in Oenothera, Chamaenerion, and Epilobium samples. We also compared chloroplast genomes across the Onagraceae samples in some features, including nucleotide content, codon usage, RNA editing sites, and simple sequence repeats (SSRs). Phylogeny was inferred by the chloroplast genome data using maximum-likelihood (ML) and Bayesian inference methods. The generic relationship of Onagraceae was well resolved by the complete chloroplast genome sequences, showing potential value in inferring phylogeny within the family. Phylogenetic relationship in Oenothera was better resolved than other densely sampled genera, such as Circaea and Epilobium. Chloroplast genomes of Oenothera subsect. Oenothera, which are biparental inheritated, share a syndrome of characteristics that deviate from primitive pattern of the family, including slightly expanded inverted repeat region, intron loss in clpP, and presence of the inversion.
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Affiliation(s)
- Yike Luo
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jian He
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Rudan Lyu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jiamin Xiao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Wenhe Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Min Yao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Linying Pei
- Beijing Engineering Research Center for Landscape Plant, Beijing Forestry University Forest Science Co. Ltd., Beijing, China
| | - Jin Cheng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jinyu Li
- Beijing Institute of Landscape Architecture, Beijing, China
| | - Lei Xie
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
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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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Mazumder GA, Uddin A, Chakraborty S. Analysis of codon usage bias in mitochondrial CO gene among platyhelminthes. Mol Biochem Parasitol 2021; 245:111410. [PMID: 34487743 DOI: 10.1016/j.molbiopara.2021.111410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/19/2021] [Accepted: 08/27/2021] [Indexed: 11/17/2022]
Abstract
The phenomenon of non-uniform usage of the synonymous codons, where some codons are given more preference to others, is known as codon usage bias (CUB). CUB is known to be determined by two major evolutionary forces i.e. mutation pressure and selection. We used various approaches to understand the codon usage pattern in mitochondrial CO (MT-CO) genes involved in complex IV of the respiratory chain (RC) as no work was reported yet. Our present study revealed that CUB was relatively high and the coding sequences were rich in A and T. Correspondence analysis further indicated that A/T compositional properties under mutational pressure might be affecting the codon usage pattern and was different in different classes for MT-CO gene. A highly significant correlation between A% and A3%, T% and T3%, G% and G3%, C% and C3%, GC% and GC3% in all the classes indicated that compositional constraints under mutational pressure and natural selection might affect the CUB. Neutrality plot indicated that both natural selection and mutational bias affected the CUB, where, natural selection played the major role as compared to mutational pressure.
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Affiliation(s)
- Gulshana A Mazumder
- Department of Biotechnology, Assam University, Silchar, 788011, Assam, India
| | - Arif Uddin
- Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, 788150, Assam, India
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar, 788011, Assam, India.
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Paudel YP, Hu Z, Khatiwada JR, Fan L, Pradhan S, Liu B, Qin W. Chloroplast genome analysis of Chrysotila dentata. Gene 2021; 804:145871. [PMID: 34363887 DOI: 10.1016/j.gene.2021.145871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/20/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022]
Abstract
Chrysotila dentata is an ecologically important marine alga contributing to the coccolith formation. In this study, a complete chloroplast (cp DNA) genome of Chrysotila dentata was sequenced by using Illumina Hiseq and was analyzed with the help of a bioinformatics tool CPGAVAS2. The circular chloroplast genome of Chrysotila dentata has a size of 109,017 bp with two inverted repeats (IRs) regions (4513 bp each) which is a common feature in most land plants and algal species. The Chrysotila dentata cp genome consists of 61 identified protein-coding genes, 30 tRNA genes and 6 rRNAs with 21 microsatellites. The phylogenetic relationship with other select algal species revealed a close phylogeny of Chrysotila dentata with Phaeocystis antarctica. This is the first report of the cp genome analysis of genus Chrysotila and the results from this study will be helpful for understanding the genetic structure and function of chloroplast in other species of Chrysotila.
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Affiliation(s)
- Yagya Prasad Paudel
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, ON P7B 5E1, Canada
| | - Zixuan Hu
- Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, ON P7B 5E1, Canada
| | - Janak Raj Khatiwada
- Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, ON P7B 5E1, Canada
| | - Lu Fan
- School of Civil Engineering, Architecture and Environment, Hubei University of Technology, Wuhan 430068, China
| | - Shreeti Pradhan
- Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, ON P7B 5E1, Canada
| | - Benwen Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| | - Wensheng Qin
- Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, ON P7B 5E1, Canada.
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Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB. Genes (Basel) 2021; 12:genes12081169. [PMID: 34440343 PMCID: PMC8393687 DOI: 10.3390/genes12081169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 12/03/2022] Open
Abstract
Giardia duodenalis, a flagellated parasitic protozoan, the most common cause of parasite-induced diarrheal diseases worldwide. Codon usage bias (CUB) is an important evolutionary character in most species. However, G. duodenalis CUB remains unclear. Thus, this study analyzes codon usage patterns to assess the restriction factors and obtain useful information in shaping G. duodenalis CUB. The neutrality analysis result indicates that G. duodenalis has a wide GC3 distribution, which significantly correlates with GC12. ENC-plot result—suggesting that most genes were close to the expected curve with only a few strayed away points. This indicates that mutational pressure and natural selection played an important role in the development of CUB. The Parity Rule 2 plot (PR2) result demonstrates that the usage of GC and AT was out of proportion. Interestingly, we identified 26 optimal codons in the G. duodenalis genome, ending with G or C. In addition, GC content, gene expression, and protein size also influence G. duodenalis CUB formation. This study systematically analyzes G. duodenalis codon usage pattern and clarifies the mechanisms of G. duodenalis CUB. These results will be very useful to identify new genes, molecular genetic manipulation, and study of G. duodenalis evolution.
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Uddin A, Chakraborty S. Analysis of mitochondrial protein-coding genes of Antheraea assamensis: Muga silkworm of Assam. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2021; 106:e21750. [PMID: 33075174 DOI: 10.1002/arch.21750] [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: 07/23/2020] [Revised: 09/18/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
To understand the synonymous codon usage pattern in mitochondrial genome of Antheraea assamensis, we analyzed the 13 mitochondrial protein-coding genes of this species using a bioinformatic approach as no work was reported yet. The nucleotide composition analysis suggested that the percentages of A, T, G,and C were 33.73, 46.39, 9.7 and 10.17, respectively and the overall GC content was 19.86, that is, lower than 50% and the genes were AT rich. The mean effective number of codons of mitochondrial protein-coding genes was 36.30 and it indicated low codon usage bias (CUB). Relative synonymous codon usage analysis suggested overrepresented and underrepresented codons in each gene and the pattern of codon usage was different among genes. Neutrality plot analysis revealed a narrow range of distribution for GC content at the third codon position and some points were diagonally distributed, suggesting both mutation pressure and natural selection influenced the CUB.
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Affiliation(s)
- Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Assam, India
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Barbhuiya PA, Uddin A, Chakraborty S. Codon usage pattern and evolutionary forces of mitochondrial ND genes among orders of class Amphibia. J Cell Physiol 2020; 236:2850-2868. [PMID: 32960450 DOI: 10.1002/jcp.30050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 08/07/2020] [Accepted: 08/31/2020] [Indexed: 12/18/2022]
Abstract
In this study, we used a bioinformatics approach to analyze the nucleotide composition and pattern of synonymous codon usage in mitochondrial ND genes in three amphibian groups, that is, orders Anura, Caudata, and Gymnophiona to identify the commonality and the differences of codon usage as no research work was reported yet. The high value of the effective number of codons revealed that the codon usage bias (CUB) was low in mitochondrial ND genes among the orders. Nucleotide composition analysis suggested that for each gene, the compositional features differed among Anura, Caudata, and Gymnophiona and the GC content was lower than AT content. Furthermore, a highly significant difference (p < .05) for GC content was found in each gene among the orders. The heat map showed contrasting patterns of codon usage among different ND genes. The regression of GC12 on GC3 suggested a narrow range of GC3 distribution and some points were located in the diagonal, indicating both mutation pressure and natural selection might influence the CUB. Moreover, the slope of the regression line was less than 0.5 in all ND genes among orders, indicating natural selection might have played the dominant role whereas mutation pressure had played a minor role in shaping CUB of ND genes across orders.
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Affiliation(s)
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Hailakandi, Assam, India
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Mazumder GA, Uddin A, Chakraborty S. Analysis of codon usage pattern of mitochondrial ND genes in Platyhelminthes. Mol Biochem Parasitol 2020; 238:111294. [PMID: 32592756 DOI: 10.1016/j.molbiopara.2020.111294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/18/2020] [Accepted: 06/20/2020] [Indexed: 01/24/2023]
Abstract
Codon usage bias (CUB) is the nonrandom usage of synonymous codons in which some codons are more preferred to others.CUB can be determined by mutation pressure and selection. Various approaches have been used to understand the pattern of CUB in the mitochondrial ND (MT-ND or ND) genes involved in complex I of respiratory chain in five different classes of Platyhelminthes as no work was reported yet. The present study revealed that the CUB varies across MT-ND genes and the coding sequences showed the richness of A and T. Correspondence analysis implied the effect of mutational pressure and also the pattern of codon usage was different in different classes of platyhelminthes for MT-ND genes. Highly significant correlation was observed between overall nucleotide composition and its 3rd codon position in most of the homogeneous nucleotides such as A% and A3%, T% and T3%, G% and G3%, C% and C3%, GC% and GC3% and also some significant correlations observed among heterogeneous nucleotides in all the five classes for MT-ND genes suggested the role of mutational pressure as well as natural selection in affecting the CUB. Neutrality plot suggested that the contributions of natural selection and mutational pressure varied across different classes of platyhelminthes and also differed in different MT-ND genes.
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Affiliation(s)
| | - Arif Uddin
- Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, 788150 Assam, India
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar, 788011 Assam, India.
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Barbhuiya PA, Uddin A, Chakraborty S. Analysis of compositional properties and codon usage bias of mitochondrial CYB gene in anura, urodela and gymnophiona. Gene 2020; 751:144762. [PMID: 32407767 DOI: 10.1016/j.gene.2020.144762] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/24/2020] [Accepted: 05/08/2020] [Indexed: 01/17/2023]
Abstract
We delineated the pattern of synonymous codon usage bias (CUB) and its determinants in mitochondrial CYB gene of respiratory chain across different amphibian groups namely orders anura, urodela and gymnophiona. We observed that CUB was low in CYB gene of amphibia. The gymnophionans had comparatively high bias followed by urodeles and anurans. The codons namely TCA, CCA, CAA, CGA, TGA, AAA and ACA were over-represented in all three orders. The codons such as GCC and TCC were over-represented in anura whereas in urodela, the over-represented codons were TTA, CTA, ATA, GTA, GAA, GGA and GCA. In gymnophiona, GCC, TTA, CTA, ATA, GTA, GAA and GGA codons were over-represented. The regression analysis between effective number of codons (ENC) and nucleobase at the 3rd position revealed that nucleobase A and C influenced CUB positively in order anura, while in urodela and gymnophiona, nucleobase A and T influenced the CUB positively. Mutation pressure and natural selection mutually illustrate the CUB of CYB gene (complex III gene) of amphibia as elucidated by correlation analysis between 3rd nucleotide in a codon and overall nucleotide content of the gene. However, neutrality plot showed that natural selection was the dominant evolutionary factor of CUB.
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Affiliation(s)
- Parvin A Barbhuiya
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakand 788150, Assam, India
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India.
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Uddin A, Mazumder TH, Barbhuiya PA, Chakraborty S. Similarities and dissimilarities of codon usage in mitochondrial ATP genes among fishes, aves, and mammals. IUBMB Life 2020; 72:899-914. [DOI: 10.1002/iub.2231] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/05/2020] [Indexed: 11/06/2022]
Affiliation(s)
- Arif Uddin
- Department of ZoologyMoinul Hoque Choudhury Memorial Science College Hailakandi Assam India
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Chakraborty S, Paul S, Nath D, Choudhury Y, Ahn Y, Cho YS, Uddin A. Synonymous codon usage and context analysis of genes associated with pancreatic cancer. Mutat Res 2020; 821:111719. [PMID: 32919141 DOI: 10.1016/j.mrfmmm.2020.111719] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/24/2020] [Accepted: 08/04/2020] [Indexed: 01/22/2023]
Abstract
Pancreatic cancer is a fatal disorder which originates in pancreas. Its mortality rate is increasing with time. Some studies also reported that pancreatic cancer would be ranked 2nd by the year 2030. Codon usage bias (CUB) arises when synonymous codons for each amino acid are not used randomly in the coding sequences of genes. We used bioinformatic methods to analyze the compositional properties, codon context and codon usage trend of the genes associated with pancreatic cancer as no work was reported yet. From the base composition analysis, the pancreatic cancer genes were found to be GC-rich and at the 3rd codon position the G/C ending codons were more preferred to A/T ending ones. The CUB was low in genes associated with pancreatic cancer. Correspondence analysis proposed that other than base constraints, CUB might also be affected by some other factors such as natural selection. Moreover, results of correlation analysis indicated that CUB and various GC contents i.e. GC, GC1, GC2, GC3 played important role in the release of free energy by transcripts of the genes associated with pancreatic cancer. The low compAI values of coding sequences suggested a low translation rate of the genes.
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Affiliation(s)
- Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India.
| | - Sunanda Paul
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Durbba Nath
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Yashmin Choudhury
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Yeongseon Ahn
- Department of Biomedical Science, Hallym University, Hallymdachak-gil, Chuncheon, Gangwon-do 24252, South Korea
| | - Yoon Shin Cho
- Department of Biomedical Science, Hallym University, Hallymdachak-gil, Chuncheon, Gangwon-do 24252, South Korea
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi 788150, Assam, India
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Mehmood F, Abdullah, Shahzadi I, Ahmed I, Waheed MT, Mirza B. Characterization of Withania somnifera chloroplast genome and its comparison with other selected species of Solanaceae. Genomics 2020; 112:1522-1530. [DOI: 10.1016/j.ygeno.2019.08.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/19/2019] [Accepted: 08/26/2019] [Indexed: 01/04/2023]
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Majeed A, Kaur H, Bhardwaj P. Selection constraints determine preference for A/U-ending codons in Taxus contorta. Genome 2020; 63:215-224. [PMID: 31986060 DOI: 10.1139/gen-2019-0165] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Unequal utilization of synonymous codons is a well-known phenomenon among living organisms. This phenomenon plays a major role in the enhancement of the accuracy and efficiency of translation. Gymnosperms are rarely paid attention in this aspect. Understanding the degree of and determining the forces influencing codon usage bias (CUB) in Taxus contorta, an endangered Himalayan gymnosperm, will prove useful in interpreting the evolutionary characteristics of this species. Using RNAseq data, 93 790 assembled transcripts were clustered into 32 701 unigenes. Around 13 061 full-length sequences were utilized for the analysis of CUB. Compositional properties showed that GC-content ranged from 28.76% to 65.22%, with an average value of 44.28%, suggesting an AT-rich genome. The mean effective number of codons (ENC) value revealed that CUB is not strong in T. contorta. The preferred codons tended to be A/U ending, whereas the avoided codons tended to be G/C ending. A P2 index of 0.54 and a Mutation Responsive Index (MRI) value of -0.02 in addition to the results revealed by the neutrality, ENC, and parity plots showed that natural selection is a predominating factor governing CUB. Mutational pressure, gene length, hydropathiciy, aromaticity, and nucleotide composition influence CUB weakly.
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Affiliation(s)
- Aasim Majeed
- Molecular Genetics Laboratory, Department of Botany, Central University of Punjab, City Campus, Mansa Road, Bathinda-151001, India.,Molecular Genetics Laboratory, Department of Botany, Central University of Punjab, City Campus, Mansa Road, Bathinda-151001, India
| | - Harpreet Kaur
- Molecular Genetics Laboratory, Department of Botany, Central University of Punjab, City Campus, Mansa Road, Bathinda-151001, India.,Molecular Genetics Laboratory, Department of Botany, Central University of Punjab, City Campus, Mansa Road, Bathinda-151001, India
| | - Pankaj Bhardwaj
- Molecular Genetics Laboratory, Department of Botany, Central University of Punjab, City Campus, Mansa Road, Bathinda-151001, India.,Molecular Genetics Laboratory, Department of Botany, Central University of Punjab, City Campus, Mansa Road, Bathinda-151001, India
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Chloroplast genome of Hibiscus rosa-sinensis (Malvaceae): Comparative analyses and identification of mutational hotspots. Genomics 2020; 112:581-591. [DOI: 10.1016/j.ygeno.2019.04.010] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 04/09/2019] [Accepted: 04/13/2019] [Indexed: 12/21/2022]
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38
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Comparative analyses of chloroplast genomes of Theobroma cacao and Theobroma grandiflorum. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00388-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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39
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Mazumder TH, Uddin A, Chakraborty S. Insights into the nucleotide composition and codon usage pattern of human tumor suppressor genes. Mol Carcinog 2019; 59:15-23. [PMID: 31583785 DOI: 10.1002/mc.23124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 09/05/2019] [Accepted: 09/21/2019] [Indexed: 01/21/2023]
Abstract
Tumor suppressor genes encode different proteins that inhibit the uncontrolled proliferation of cell growth and tumor development. To acquire clues for predicting gene expression level, it is essential to understand the codon usage bias (CUB) of genes to characterize genome which possesses its own compositional characteristics and unique coding sequences. We used bioinformatic tools to analyze the codon usage patterns of 637 human tumor suppressor genes as no work was reported earlier. The mean effective number of codons of these genes was 48, indicating low CUB. Our results exhibited a significant positive correlation among different nucleotide compositions and the codons ending with C base was most frequently used along with the most over-represented codon CTG and GTG codifying leucine and valine amino acid, respectively, in human tumor suppressor genes. The neutrality plot showed a significant positive correlation (Pearson, r = 0. 646; P < .01) suggesting that mutation on GC bias might affect the CUB. However, the linear regression coefficient of GC12 on GC3 in human tumor suppressor genes suggested that natural selection played a major role while mutation pressure played a minor role in the codon usage patterns of tumor suppressor genes in human. Our study would throw light into the factors that affect CUB and the codon usage patterns in the human tumor suppressor genes.
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Affiliation(s)
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Hailakandi, Assam, India
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40
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Lamolle G, Fontenla S, Rijo G, Tort JF, Smircich P. Compositional Analysis of Flatworm Genomes Shows Strong Codon Usage Biases Across All Classes. Front Genet 2019; 10:771. [PMID: 31543897 PMCID: PMC6739440 DOI: 10.3389/fgene.2019.00771] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/22/2019] [Indexed: 11/13/2022] Open
Abstract
In the present work, we performed a comparative genome-wide analysis of 22 species representative of the main clades and lifestyles of the phylum Platyhelminthes. We selected a set of 700 orthologous genes conserved in all species, measuring changes in GC content, codon, and amino acid usage in orthologous positions. Values of 3rd codon position GC spanned over a wide range, allowing to discriminate two distinctive clusters within freshwater turbellarians, Cestodes and Trematodes respectively. Furthermore, a hierarchical clustering of codon usage data differs remarkably from the phylogenetic tree. Additionally, we detected a synonymous codon usage bias that was more dramatic in extreme GC-poor or GC-rich genomes, i.e., GC-poor Schistosomes preferred to use AT-rich terminated synonymous codons, while GC-rich M. lignano showed the opposite behavior. Interestingly, these biases impacted the amino acidic usage, with preferred amino acids encoded by codons following the GC content trend. These are associated with non-synonymous substitutions at orthologous positions. The detailed analysis of the synonymous and non-synonymous changes provides evidence for a two-hit mechanism where both mutation and selection forces drive the diverse coding strategies of flatworms.
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Affiliation(s)
- Guillermo Lamolle
- Departamento de Genética, Facultad de Medicina, Universidad de la Republica, UDELAR, Montevideo, Uruguay
| | - Santiago Fontenla
- Departamento de Genética, Facultad de Medicina, Universidad de la Republica, UDELAR, Montevideo, Uruguay
| | - Gastón Rijo
- Departamento de Genética, Facultad de Medicina, Universidad de la Republica, UDELAR, Montevideo, Uruguay
| | - Jose F Tort
- Departamento de Genética, Facultad de Medicina, Universidad de la Republica, UDELAR, Montevideo, Uruguay
| | - Pablo Smircich
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, IIBCE, MEC, Montevideo, Uruguay.,Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la Republica, UDELAR, Montevideo, Uruguay
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Shahzadi I, Abdullah, Mehmood F, Ali Z, Ahmed I, Mirza B. Chloroplast genome sequences of Artemisia maritima and Artemisia absinthium: Comparative analyses, mutational hotspots in genus Artemisia and phylogeny in family Asteraceae. Genomics 2019; 112:1454-1463. [PMID: 31450007 DOI: 10.1016/j.ygeno.2019.08.016] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/16/2019] [Accepted: 08/21/2019] [Indexed: 12/14/2022]
Abstract
Artemisia L. is a complex genus of medicinal importance. Publicly available chloroplast genomes of few Artemisia species are insufficient to resolve taxonomic discrepancies at species level. We report chloroplast genome sequences of two further Artemisia species: A. maritima (151,061 bp) and A. absinthium (151,193 bp). Both genomes possess typical quadripartite structure comprising of a large single copy, a small single copy and a pair of long inverted repeats. The two genomes exhibited high similarities in genome sizes, gene synteny, GC content, synonymous and non-synonymous substitutions, codon usage, amino acids frequencies, RNA editing sites, microsatellites, and oligonucleotide repeats. Transition to transversion ratio was <1. Maximum likelihood tree showed Artemisia a monophyletic genus, sister to genus Chrysanthemum. We also identified 20 highly polymorphic regions including rpoC2-rps2, trnR-UCU-trnG-UCC, rps18-rpl20, and trnL-UAG-rpl32 that could be used to develop authentic and cost-effective markers to resolve taxonomic discrepancies and infer phylogenetic relationships among Artemisia species.
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Affiliation(s)
- Iram Shahzadi
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Abdullah
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Furrukh Mehmood
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Zain Ali
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, Pakistan
| | - Bushra Mirza
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan.
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Barbhuiya RI, Uddin A, Chakraborty S. Compositional properties and codon usage pattern of mitochondrial ATP gene in different classes of Arthropoda. Genetica 2019; 147:231-248. [PMID: 31152294 DOI: 10.1007/s10709-019-00067-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 05/22/2019] [Indexed: 12/17/2022]
Abstract
Codon usage bias (CUB) is defined as the usage of synonymous codons unequally for an amino acid in a gene transcript. It is influenced by both mutation pressure and natural selection and is a species-specific property. In our current study, we used bioinformatic methods to investigate the coding sequences of mitochondrial adenosine triphosphate gene (MT-ATP) in different classes of arthropoda to know the codon usage pattern of the gene as no work was described earlier. The analysis of compositional properties suggested that the gene is AT rich. The effective number of codons revealed the CUB of both ATP6 and ATP8 gene was moderate. Heat map showed that the codons ending with AT were negatively associated with GC3 while the codons ending with GC were positively associated with GC3 in all the classes of arthropoda. Correspondence study revealed that the pattern of codon usage of ATP6 and ATP8 genes differed across classes. Neutrality plot suggested the codon usage bias of these two genes in phylum arthropoda was influenced by both mutation pressure and natural selection.
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Affiliation(s)
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Science College, Algapur, Hailakandi, Assam, 788150, India
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar, Assam, 788011, India.
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Tao J, Yao H. Comprehensive analysis of the codon usage patterns of polyprotein of Zika virus. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 150:43-49. [PMID: 31054849 DOI: 10.1016/j.pbiomolbio.2019.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 02/25/2019] [Accepted: 05/01/2019] [Indexed: 01/05/2023]
Abstract
Zika virus (ZIKV) is a mosquito-borne virus in the family Flaviviridae, and the massive outbreak of ZIKV has endangered public health. Codon usage patterns of viruses reflect a series of evolutionary changes that enable viruses to shape their survival rates and fitness toward the external environment and, most importantly, their hosts. In this study, 90 ZIKV isolates were used for a comprehensive analysis on the codon usage patterns. The overall codon usage among ZIKV strains is similar and slightly biased. The value of effective number of codons (ENC) showed that the overall extent of codon usage bias in ZIKV is relatively low. Nucleotide analysis showed that the overall codon usage is biased toward A- and G-ending codons. The phylogenetic analysis indicated that their independent evolutionary origins from a common ancestor. The RSCU analysis showed that the codon usage pattern of ZIKV is more similar to that of Homo sapiens. Correlation analysis, Correspondence analysis, ENC-GC3S plot, and PR2 plot indicated that the codon usage patterns of the viruses are not only influenced by mutational pressure but also by natural selection, but neutrality plot analysis showed that the latter plays a major role. These results built the base for further research on the molecular evolution of ZIKV.
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Affiliation(s)
- Jun Tao
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, PR China
| | - Huipeng Yao
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, PR China.
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44
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Barbhuiya PA, Uddin A, Chakraborty S. Genome‐wide comparison of codon usage dynamics in mitochondrial genes across different species of amphibian genus
Bombina. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2019; 332:99-112. [DOI: 10.1002/jez.b.22852] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 03/10/2019] [Accepted: 03/20/2019] [Indexed: 01/16/2023]
Affiliation(s)
| | - Arif Uddin
- Department of ZoologyMoinul Hoque Choudhury Memorial Science CollegeHailakandi Assam India
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Uddin A, Paul N, Chakraborty S. The codon usage pattern of genes involved in ovarian cancer. Ann N Y Acad Sci 2019; 1440:67-78. [PMID: 30843242 DOI: 10.1111/nyas.14019] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 01/04/2019] [Accepted: 01/14/2019] [Indexed: 12/20/2022]
Abstract
In this study, we analyzed the compositional dynamics and codon usage pattern of genes involved in ovarian cancer (OC) using a computational method. Mutations in specific genes are associated with OC, and some genes are risk factors for progression of OC, but no work has been reported yet on the codon usage pattern of genes involved in OC. Nucleotide composition analysis of OC-related genes suggested that the overall GC content was higher than AT content; that is, the genes were GC rich. The improved effective number of codons indicated that the overall extent of codon usage bias of genes involved in OC was low. The codons AGC, CTG, ATC, ACC, GTG, and GCC were overrepresented, while the codons TCG, TTA, CTA, CCG, CAA, CGT, ATA, ACG, GTA, GTT, GCG, and GGT were underrepresented in the genes. Correspondence analysis suggested that the codon usage pattern was different in different genes. A highly significant correlation was observed between GC12 and GC3 (r = 0.587, P < 0.01) of genes, suggesting that directional mutation affected the three codon positions. Our report on the codon usage pattern of genes involved in OC includes a new perspective for elucidating the mechanisms of biased usage of synonymous codons, as well as providing useful clues for molecular genetic engineering.
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Affiliation(s)
- Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Assam, India
| | - Nirmal Paul
- Department of Biotechnology, Assam University, Assam, India
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Khan MS, Guan DL, Ma LB, Xie JY, Xu SQ. Analysis of synonymous codon usage pattern of genes in unique non-blood-sucking leech Whitmania pigra. J Cell Biochem 2019; 120:9850-9858. [PMID: 30681200 DOI: 10.1002/jcb.28267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 11/19/2018] [Indexed: 12/17/2022]
Abstract
Whitmania pigra is a unique, fluid-sucking ectoparasite and an anticoagulant medical leech. The codon usage bias (CUB) is the nonuniform usage of synonymous codons in which some codons are more preferred than others. Here, we performed a comprehensive analysis of CUB of genes in W. pigra, analyzing 140 780 transcripts, 59 553 unigenes, and 20 304 qualified coding sequences (CDSs) from the transcriptomic data of W. pigra. The effective number of codons values suggested that the CUB was low in these genes. We recognized profoundly favored codons in W. pigra that have a G/C-ending. Parity rule two-bias plots suggested that both mutation pressure and natural selection might have influenced the CUB. However, neutrality plots revealed that natural selection might have played a major role while mutation pressure might have played a minor role in shaping the CUB. We applied principal component analysis to relative synonymous codon usage values for divided CDSs based on GC content and codon-ending bases. Codon usage in W. pigra had a general inclination toward C-ending codons and natural selection rather than mutation pressure is the dominant force in the genetic evolution of W. pigra. To our knowledge, this is the first study to describe a complete codon usage analysis of W. pigra; this will increase the understanding of CUB and evolution in W. pigra. The analysis of codon usage patterns in W. pigra aids in understanding its evolution and genetic architecture.
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Affiliation(s)
- Muhammad Salabat Khan
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, People's Republic of China
| | - De-Long Guan
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, People's Republic of China
| | - Li-Bin Ma
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, People's Republic of China
| | - Juan-Ying Xie
- School of Computer Science, Shaanxi Normal University, Xi'an, Shaanxi, People's Republic of China
| | - Sheng-Quan Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, People's Republic of China
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Chakraborty S, Deb B, Barbhuiya PA, Uddin A. Analysis of codon usage patterns and influencing factors in Nipah virus. Virus Res 2019; 263:129-138. [PMID: 30664908 PMCID: PMC7114725 DOI: 10.1016/j.virusres.2019.01.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/18/2019] [Accepted: 01/18/2019] [Indexed: 11/28/2022]
Abstract
Nipah virus (NiV) genes are AT-rich. Codon usage bias of NiV genes is low. Patterns of codon usage bias differ across the genomes of NiV. Both mutation pressure and natural selection influenced codon usage bias of NiV genes.
Codon usage bias (CUB) is the unequal usage of synonymous codons of an amino acid in which some codons are used more often than others and is widely used in understanding molecular biology, genetics, and functional regulation of gene expression. Nipah virus (NiV) is an emerging zoonotic paramyxovirus that causes fatal disease in both humans and animals. NiV was first identified during an outbreak of a disease in Malaysia in 1998 and then occurred periodically since 2001 in India, Bangladesh, and the Philippines. We used bioinformatics tools to analyze the codon usage patterns in a genome-wide manner among 11 genomes of NiV as no work was reported yet. The compositional properties revealed that the overall GC and AT contents were 41.96 and 58.04%, respectively i.e. Nipah virus genes were AT-rich. Correlation analysis between overall nucleotide composition and its 3rd codon position suggested that both mutation pressure and natural selection might influence the CUB across Nipah genomes. Neutrality plot revealed natural selection might have played a major role while mutation pressure had a minor role in shaping the codon usage bias in NiV genomes.
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Affiliation(s)
- Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India.
| | - Bornali Deb
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Parvin A Barbhuiya
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi 788150, Assam, India
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Uddin A, Mazumder TH, Chakraborty S. Understanding molecular biology of codon usage in mitochondrial complex IV genes of electron transport system: Relevance to mitochondrial diseases. J Cell Physiol 2018; 234:6397-6413. [DOI: 10.1002/jcp.27375] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/17/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Arif Uddin
- Department of Zoology Moinul Hoque Choudhury Memorial Science College Hailakandi Assam India
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Deka H, Nath D, Uddin A, Chakraborty S. DNA compositional dynamics and codon usage patterns of M1 and M2 matrix protein genes in influenza A virus. INFECTION GENETICS AND EVOLUTION 2018; 67:7-16. [PMID: 30367980 DOI: 10.1016/j.meegid.2018.10.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/11/2018] [Accepted: 10/23/2018] [Indexed: 11/30/2022]
Abstract
Influenza A virus subtype H3N2 has been a serious health issue across the globe with approximately 36 thousand annual casualties in the United States of America only. Co-circulation in avian, swine and human hosts has led to frequent mutations in the virus genome, due to which development of successful antivirals against the virus has become a formidable challenge. Recently, focussed research is being carried out targeting the matrix proteins of this strain as vaccine candidates. This study is carried out to unravel the key features of the genes encoding the matrix proteins that manoeuvre the codon usage profile in the H3N2 strains. The findings reveal differential codon choice for both matrix protein 1 and matrix protein 2. The overall codon usage bias is less pronounced in both the datasets which is evident from higher value of effective number of codons (>55). Comparison of the codon usage for both the genes under study with that of humans revealed that the viral codon usage is not fully optimized for the human host conditions. Both the genes enrolled in the study showed variation which was reflected in almost all the indices used for codon usage studies. Neutrality analysis revealed a weak role of mutation pressure while selection was the major contributor towards codon usage.
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Affiliation(s)
- Himangshu Deka
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Durbba Nath
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Hailakandi 788150, Assam, India.
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India.
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Barbhuiya PA, Uddin A, Chakraborty S. Compositional properties and codon usage of TP73 gene family. Gene 2018; 683:159-168. [PMID: 30316927 DOI: 10.1016/j.gene.2018.10.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 10/03/2018] [Accepted: 10/11/2018] [Indexed: 12/19/2022]
Abstract
The TP73 gene is considered as one of the members of TP53 gene family and shows much homology to p53 gene. TP73 gene plays a pivotal role in cancer studies in addition to other biological functions. Codon usage bias (CUB) is the phenomenon of unequal usage of synonymous codons for an amino acid wherein some codons are more frequently used than others and it reveals the evolutionary relationship of a gene. Here, we report the pattern of codon usage in TP73 gene using various bioinformatic tools as no work was reported yet. Nucleotide composition analysis suggested that the mean nucleobase C was the highest, followed by G and the gene was GC rich. Correlation analysis between codon usage and GC3 suggested that most of the GC-ending codons showed positive correlation while most of the AT-ending codons showed negative correlation with GC3 in the coding sequences of TP73 gene variants in human. The CUB is moderate in human TP73 gene as evident from intrinsic codon deviation index (ICDI) analysis. Nature selected against two codons namely ATA (isoleucine) and AGA (arginine) in the coding sequences of TP73 gene during the course of evolution. A significant correlation (p < 0.05) was found between overall nucleotide composition and its composition at the 3rd codon position, indicating that both mutation pressure and natural selection might influence the CUB. The correlation analysis between ICDI and biochemical properties of protein suggested that variation of CUB was associated with degree of hydrophobicity and length of protein.
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Affiliation(s)
- Parvin A Barbhuiya
- Departments of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi 788150, Assam, India
| | - Supriyo Chakraborty
- Departments of Biotechnology, Assam University, Silchar 788011, Assam, India.
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