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Uddin A. Compositional Features and Codon Usage Pattern of Genes Associated with Parkinson's Disease. Mol Neurobiol 2024; 61:8279-8292. [PMID: 38488980 DOI: 10.1007/s12035-024-04091-x] [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: 11/04/2023] [Accepted: 02/29/2024] [Indexed: 03/17/2024]
Abstract
Codon usage bias (CUB) is the phenomenon of non-uniform usage of synonymous codons in which some codons are more used than others and it helps in understanding the molecular organization of genome. Bioinformatic approach was used to analyze the protein-coding sequences of genes associated with Parkinson's disease (PD) to explore compositional features and codon usage pattern as no details work was reported yet. The average improved effective number of codons (Nc) and Nc prime were 42.74 and 44.26 respectively, indicated that CUB was low in these genes. In most of the genes, the overall GC content was almost 50% and GC content at the 1st codon position was the highest while GC content at the 2nd codon position was lowest. Relative synonymous codon usage (RSCU) analysis elucidated over-represented (p > 1.6) and under-represented codons (p < 0.6). The GTG (Val) is the only codon over-represented in all genes. Over-represented codons except (GTG) were A or T ending while under-represented codons (except ACT) were G or C ending. The codons namely TTA (Leu), CTA (Leu), ATC (Ile), ATA (Ile), AGT (Ser), AAC (Asn), TGT (Cys), TGC (Cys), CGC (Arg), AGA (Arg), and AGG (Arg) were absent in SNCA1 to SNCA8 genes. The codon TCG (Ser) was absent in all genes except UCHL1 and PINK1. Correspondence analysis (COA) revealed that the pattern of codon usage differs among genes associated with PD. Neutrality plot analysis indicated some of the points are diagonal distribution suggested that mutation pressure influenced the CUB in genes associated with PD.
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Affiliation(s)
- Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi-788150, Assam, India.
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Shen Z, Liu Q, Hao J, Bi S, Fu Y, Zhang L. The Complete Chloroplast Genome Sequence of the Medicinal Moss Rhodobryum giganteum (Bryaceae, Bryophyta): Comparative Genomics and Phylogenetic Analyses. Genes (Basel) 2024; 15:900. [PMID: 39062679 PMCID: PMC11275618 DOI: 10.3390/genes15070900] [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: 06/13/2024] [Revised: 07/05/2024] [Accepted: 07/07/2024] [Indexed: 07/28/2024] Open
Abstract
Rhodobryum giganteum (Bryaceae, Bryophyta), a rare medicinal bryophyte, is valued for its cardiovascular therapeutic properties in traditional Chinese medicine. This study presents the first complete chloroplast genome sequence of R. giganteum, including its assembly and annotation. The circular chloroplast genome of R. giganteum is 124,315 bp in length, displaying a typical quadripartite structure with 128 genes: 83 protein-coding genes, 37 tRNAs, and 8 rRNAs. Analyses of codon usage bias, repetitive sequences, and simple sequence repeats (SSRs) revealed an A/U-ending codon preference, 96 repetitive sequences, and 385 SSRs in the R. giganteum chloroplast genome. Nucleotide diversity analysis identified 10 high mutational hotspots. Ka/Ks ratio analysis suggested potential positive selection in rpl20, rps18, petG, and psbM genes. Phylogenetic analysis of whole chloroplast genomes from 38 moss species positioned R. giganteum within Bryales, closely related to Rhodobryum laxelimbatum. This study augments the chloroplast genomic data for Bryales and provides a foundation for molecular marker development and genetic diversity analyses in medicinal bryophytes.
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Affiliation(s)
- Zhengyuan Shen
- Center for Eco-Environment Restoration Engineering of Hainan Province, School of Ecology, Hainan University, Haikou 570228, China; (Z.S.)
| | - Qin Liu
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Yulin Normal University, Yulin 537000, China
| | - Jiewei Hao
- Center for Eco-Environment Restoration Engineering of Hainan Province, School of Ecology, Hainan University, Haikou 570228, China; (Z.S.)
| | - Sheng Bi
- Center for Eco-Environment Restoration Engineering of Hainan Province, School of Ecology, Hainan University, Haikou 570228, China; (Z.S.)
| | - Yezhen Fu
- Bawangling Branch of Hainan Tropical Rainforest National Park Administration, Changjiang 572700, China
| | - Lina Zhang
- Center for Eco-Environment Restoration Engineering of Hainan Province, School of Ecology, Hainan University, Haikou 570228, China; (Z.S.)
- Ministry of Education Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Hainan University, Haikou 570228, China
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Ling L, Zhang S, Yang T. Analysis of Codon Usage Bias in Chloroplast Genomes of Dryas octopetala var. asiatica (Rosaceae). Genes (Basel) 2024; 15:899. [PMID: 39062678 PMCID: PMC11275609 DOI: 10.3390/genes15070899] [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: 06/22/2024] [Revised: 07/04/2024] [Accepted: 07/07/2024] [Indexed: 07/28/2024] Open
Abstract
Dryas octopetala var. asiatica, a dwarf shrub belonging to the Rosaceae family and native to Asia, exhibits notable plasticity in photosynthesis in response to temperature variations. However, the codon usage patterns and factors influencing them in the chloroplast genome of this species have not yet been documented. This study sequenced and assembled the complete genome of D. octopetala var. asiatica. The annotated genes in the chloroplast genome were analyzed for codon composition through multivariate statistical methods including a neutrality plot, a parity rule 2 (PR2) bias plot, and an effective number of codons (ENC) plot using CodonW 1.4.2 software. The results indicated that the mean GC content of 53 CDSs was 38.08%, with the average GC content at the third codon base position being 27.80%, suggesting a preference for A/U(T) at the third codon position in chloroplast genes. Additionally, the chloroplast genes exhibited a weak overall codon usage bias (CUB) based on ENC values and other indicators. Correlation analysis showed a significant negative correlation between ENC value and GC2, an extremely positive correlation with GC3, but no correlation with GC1 content. These findings highlight the importance of the codon composition at the third position in influencing codon usage bias. Furthermore, our analysis indicated that the CUB of the chloroplast genome of D. octopetala var. asiatica was primarily influenced by natural selection and other factors. Finally, this study identified UCA, CCU, GCU, AAU, GAU, and GGU as the optimal codons. These results offer a foundational understanding for genetic modification and evolutionary dynamics of the chloroplast genome of D. octopetala var. asiatica.
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Affiliation(s)
| | - Shudong Zhang
- Key Laboratory for Specialty Agricultural Germplasm Resources Development and Utilization of Guizhou Province, Liupanshui Normal University, Liupanshui 553004, China; (L.L.); (T.Y.)
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Liu D, Zhang Z, Hao Y, Li M, Yu H, Zhang X, Mi H, Cheng L, Zhao Y. Decoding the complete organelle genomic architecture of Stewartia gemmata: an early-diverging species in Theaceae. BMC Genomics 2024; 25:114. [PMID: 38273225 PMCID: PMC10811901 DOI: 10.1186/s12864-024-10016-8] [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: 09/02/2023] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Theaceae, comprising 300 + species, holds significance in biodiversity, economics, and culture, notably including the globally consumed tea plant. Stewartia gemmata, a species of the earliest diverging tribe Stewartieae, is critical to offer insights into Theaceae's origin and evolutionary history. RESULT We sequenced the complete organelle genomes of Stewartia gemmata using short/long reads sequencing technologies. The chloroplast genome (158,406 bp) exhibited a quadripartite structure including the large single-copy region (LSC), a small single-copy region (SSC), and a pair of inverted repeat regions (IRs); 114 genes encoded 80 proteins, 30 tRNAs, and four rRNAs. The mitochondrial genome (681,203 bp) exhibited alternative conformations alongside a monocyclic structure: 61 genes encoding 38 proteins, 20 tRNAs, three rRNAs, and RNA editing-impacting genes, including ATP6, RPL16, COX2, NAD4L, NAD5, NAD7, and RPS1. Comparative analyses revealed frequent recombination events and apparent rRNA gene gains and losses in the mitochondrial genome of Theaceae. In organelle genomes, the protein-coding genes exhibited a strong A/U bias at codon endings; ENC-GC3 analysis implies selection-driven codon bias. Transposable elements might facilitate interorganelle sequence transfer. Phylogenetic analysis confirmed Stewartieae's early divergence within Theaceae, shedding light on organelle genome characteristics and evolution in Theaceae. CONCLUSIONS We studied the detailed characterization of organelle genomes, including genome structure, composition, and repeated sequences, along with the identification of lateral gene transfer (LGT) events and complexities. The discovery of a large number of repetitive sequences and simple sequence repeats (SSRs) has led to new insights into molecular phylogenetic markers. Decoding the Stewartia gemmata organellar genome provides valuable genomic resources for further studies in tea plant phylogenomics and evolutionary biology.
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Affiliation(s)
- Daliang Liu
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High-Value Utilization, College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
- Key Laboratory of Functional Agriculture in Higher Education of Guizhou Province, College of Agriculture, Guizhou University, Guiyang, 550025, China
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang, 550025, China
| | - Zhihan Zhang
- Key Laboratory of Functional Agriculture in Higher Education of Guizhou Province, College of Agriculture, Guizhou University, Guiyang, 550025, China
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang, 550025, China
- College of Engineering and Technology, Northeast Forestry University, Harbin, 150040, China
| | - Yanlin Hao
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High-Value Utilization, College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Mengge Li
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High-Value Utilization, College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Houlin Yu
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA
- Present address: Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Xingruo Zhang
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Haoyang Mi
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Lin Cheng
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High-Value Utilization, College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China.
| | - Yiyong Zhao
- Key Laboratory of Functional Agriculture in Higher Education of Guizhou Province, College of Agriculture, Guizhou University, Guiyang, 550025, China.
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang, 550025, China.
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Mkala EM, Jost M, Dong X, Mwachala G, Musili PM, Wanke S, Hu GW, Wang QF. Phylogenetic and comparative analyses of Hydnora abyssinica plastomes provide evidence for hidden diversity within Hydnoraceae. BMC Ecol Evol 2023; 23:34. [PMID: 37464315 PMCID: PMC10353213 DOI: 10.1186/s12862-023-02142-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 07/06/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND To date, plastid genomes have been published for all but two holoparasitic angiosperm families. However, only a single or a few plastomes represent most of these families. Of the approximately 40 genera of holoparasitic angiosperms, a complete plastid genome sequence is available for only about half. In addition, less than 15 species are currently represented with more than one published plastid genome, most of which belong to the Orobanchaceae. Therefore, a significant portion of the holoparasitic plant plastome diversity remains unexplored. This limited information could hinder potential evolutionary pattern recognition as well as the exploration of inter- and intra-species plastid genome diversity in the most extreme holoparasitic angiosperms. RESULTS Here, we report the first plastomes of Kenyan Hydnora abyssinica accessions. The plastomes have a typical quadripartite structure and encode 24 unique genes. Phylogenetic tree reconstruction recovers the Kenyan accessions as monophyletic and together in a clade with the Namibian H. abyssinica accession and the recently published H. arabica from Oman. Hydnora abyssinica as a whole however is recovered as non-monophyletic, with H. arabica nested within. This result is supported by distinct structural plastome synapomorphies as well as pairwise distance estimates that reveal hidden diversity within the Hydnora species in Africa. CONCLUSION We propose to increase efforts to sample widespread holoparasitic species for their plastid genomes, as is the case with H. abyssinica, which is widely distributed in Africa. Morphological reinvestigation and further molecular data are needed to fully investigate the diversity of H. abyssinica along the entire range of distribution, as well as the diversity of currently synonymized taxa.
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Affiliation(s)
- Elijah Mbandi Mkala
- CAS Key Laboratory of Plant Germplasm and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, CN-430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, CN-430074, China
- University of Chinese Academy of Sciences, Beijing, CN-100049, China
| | - Matthias Jost
- Institut für Botanik, Technische Universität Dresden, 01062, Dresden, Germany
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, CN-430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, CN-430074, China
- University of Chinese Academy of Sciences, Beijing, CN-100049, China
| | - Geoffrey Mwachala
- East African Herbarium, National Museums of Kenya, P. O. Box 451660-0100, Nairobi, Kenya
| | - Paul Mutuku Musili
- East African Herbarium, National Museums of Kenya, P. O. Box 451660-0100, Nairobi, Kenya
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, 01062, Dresden, Germany
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, CN-430074, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, CN-430074, China.
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, CN-430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, CN-430074, China
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Tang C, Chen X, Deng Y, Geng L, Ma J, Wei X. Complete chloroplast genomes of Sorbus sensu stricto (Rosaceae): comparative analyses and phylogenetic relationships. BMC PLANT BIOLOGY 2022; 22:495. [PMID: 36273120 PMCID: PMC9587547 DOI: 10.1186/s12870-022-03858-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Sorbus sensu stricto (Sorbus s.s.) is a genus with important economical values because of its beautiful leaves, and flowers and especially the colorful fruits. It belongs to the tribe Maleae of the family Rosaceae, and comprises about 90 species mainly distributed in China. There is on-going dispute about its infrageneric classification and species delimitation as the species are morphologically similar. With the aim of shedding light on the circumscription of taxa within the genus, phylogenetic analyses were performed using 29 Sorbus s.s. chloroplast (cp) genomes (16 newly sequenced) representing two subgenera and eight sections. RESULTS The 16 cp genomes newly sequenced range between 159,646 bp and 160,178 bp in length. All the samples examined and 22 taxa re-annotated in Sorbus sensu lato (Sorbus s.l.) contain 113 unique genes with 19 of these duplicated in the inverted repeat (IR). Six hypervariable regions including trnR-atpA, petN-psbM, rpl32-trnL, trnH-psbA, trnT-trnL and ndhC-trnV were screened and 44-53 SSRs and 14-31 dispersed repeats were identified as potential molecular markers. Phylogenetic analyses under ML/BI indicated that Sorbus s.l. is polyphyletic, but Sorbus s.s. and the other five segregate genera, Aria, Chamaemespilus, Cormus, Micromeles and Torminalis are monophyletic. Two major clades and four sub-clades resolved with full-support within Sorbus s.s. are not consistent with the existing infrageneric classification. Two subgenera, subg. Sorbus and subg. Albocarmesinae are supported as monophyletic when S. tianschanica is transferred to subg. Albocarmesinae from subg. Sorbus and S. hupehensis var. paucijuga transferred to subg. Sorbus from subg. Albocarmesinae, respectively. The current classification at sectional level is not supported by analysis of cp genome phylogeny. CONCLUSION Phylogenomic analyses of the cp genomes are useful for inferring phylogenetic relationships in Sorbus s.s. Though genome structure is highly conserved in the genus, hypervariable regions and repeat sequences used are the most promising molecule makers for population genetics, species delimitation and phylogenetic studies.
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Affiliation(s)
- Chenqian Tang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Xin Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
| | - Yunfei Deng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Liyang Geng
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Jianhui Ma
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Xueyan Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
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Alqahtani T, Khandia R, Puranik N, Alqahtani AM, Chidambaram K, Kamal MA. Codon Usage is Influenced by Compositional Constraints in Genes Associated with Dementia. Front Genet 2022; 13:884348. [PMID: 36017501 PMCID: PMC9395603 DOI: 10.3389/fgene.2022.884348] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/18/2022] [Indexed: 11/28/2022] Open
Abstract
Dementia is a clinical syndrome characterized by progressive cognitive decline, and the symptoms could be gradual, persistent, and progressive. In the present study, we investigated 47 genes that have been linked to dementia. Compositional, selectional, and mutational forces were seen to be involved. Nucleotide components that influenced A- and GC-affected codon usages bias at all three codon positions. The influence of these two compositional constraints on codon usage bias (CUB) was positive for nucleotide A and negative for GC. Nucleotide A also experienced the highest mutational force, and GC-ending codons were preferred over AT-ending codons. A high bias toward GC-ending codons enhances the gene expression level, evidenced by the positive association between CAI- and GC-ending codons. Unusual behavior of the TTG codon showing an inverse relationship with the GC-ending codon and negative influence of gene expression, behavior contrary to all other GC-ending codons, shows an operative selectional force. Furthermore, parity analysis, higher translational selection value, preference of GC-ending codons over AT-ending codons, and association of gene length with gene expression refer to the dominant role of selection pressure with compositional constraint and mutational force-shaping codon usage.
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Affiliation(s)
- Taha Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Nidhi Puranik
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Ali M Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Kumarappan Chidambaram
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Amjad Kamal
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.,King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh.,Enzymoics, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
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Khandia R, Sharma A, Alqahtani T, Alqahtani AM, Asiri YI, Alqahtani S, Alharbi AM, Kamal MA. Strong Selectional Forces Fine-Tune CpG Content in Genes Involved in Neurological Disorders as Revealed by Codon Usage Patterns. Front Neurosci 2022; 16:887929. [PMID: 35757545 PMCID: PMC9226491 DOI: 10.3389/fnins.2022.887929] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/04/2022] [Indexed: 02/05/2023] Open
Abstract
Neurodegenerative disorders cause irreversible damage to the neurons and adversely affect the quality of life. Protein misfolding and their aggregation in specific parts of the brain, mitochondrial dysfunction, calcium load, proteolytic stress, and oxidative stress are among the causes of neurodegenerative disorders. In addition, altered metabolism has been associated with neurodegeneration as evidenced by reductions in glutamine and alanine in transient global amnesia patients, higher homocysteine-cysteine disulfide, and lower methionine decline in serum urea have been observed in Alzheimer's disease patients. Neurodegeneration thus appears to be a culmination of altered metabolism. The study's objective is to analyze various attributes like composition, physical properties of the protein, and factors like selectional and mutational forces, influencing codon usage preferences in a panel of genes involved directly or indirectly in metabolism and contributing to neurodegeneration. Various parameters, including gene composition, dinucleotide analysis, Relative synonymous codon usage (RSCU), Codon adaptation index (CAI), neutrality and parity plots, and different protein indices, were computed and analyzed to determine the codon usage pattern and factors affecting it. The correlation of intrinsic protein properties such as the grand average of hydropathicity index (GRAVY), isoelectric point, hydrophobicity, and acidic, basic, and neutral amino acid content has been found to influence codon usage. In genes up to 800 amino acids long, the GC3 content was highly variable, while GC12 content was relatively constant. An optimum CpG content is present in genes to maintain a high expression level as required for genes involved in metabolism. Also observed was a low codon usage bias with a higher protein expression level. Compositional parameters and nucleotides at the second position of codons played essential roles in explaining the extent of bias. Overall analysis indicated that the dominance of selection pressure and compositional constraints and mutational forces shape codon usage.
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Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Anushri Sharma
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Taha Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Ali M Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Yahya I Asiri
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Saud Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Ahmed M Alharbi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Mohammad Amjad Kamal
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.,King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh.,Enzymoics, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
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9
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Cao Q, Gao Q, Ma X, Zhang F, Xing R, Chi X, Chen S. Plastome structure, phylogenomics and evolution of plastid genes in Swertia (Gentianaceae) in the Qing-Tibetan Plateau. BMC PLANT BIOLOGY 2022; 22:195. [PMID: 35413790 PMCID: PMC9004202 DOI: 10.1186/s12870-022-03577-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 03/28/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND The genus Swertia is of great medicinal importance and one of the most taxonomically challenging taxa within Gentianaceae, largely due to the morphological similarities of species within this genus and with its closely related genera. Previous molecular studies confirmed its polyphyly but suffered from low phylogenetic resolutions because only limited sequence loci were used. Thus, we conducted the structural, gene evolutionary, and phylogenetic analyses of 11 newly obtained plastomes of Swertia. Our result greatly improved the phylogenetic resolutions in Swertia, shed new light on the plastome evolution and phylogenetic relationships of this genus. RESULTS The 11 Swertia plastomes together with the published seven species proved highly similar in overall size, structure, gene order, and content, but revealed some structural variations caused by the expansion and contraction of the IRb region into the LSC region, due to the heterogeneous length of the ψycf1. The gene rps16 was found to be in a state flux with pseudogenes or completely lost. Similar situation was also documented in other genera of Gentianaceae. This might imply loss of the gene in the common ancestor of Gentianaceae. The distribution plot of ENC vs. GC3 showed all these plastomes arranging very close in the Wright line with an expected ENC value (49-52%), suggesting the codon usage of Swertia was mainly constrained by a GC mutation bias. Most of the genes remained under the purifying selection, however, the cemA was identified under positive selection, possibly reflecting an adaptive response to low CO2 atmospheric conditions during the Late Miocene. Our phylogenomic analyses, based on 74 protein-coding genes (CDS), supported the polyphyly of Swertia with its close allies in the subtribe Swertiinae, presumably due to recent rapid radiation. The topology inferred from our phylogenetic analyses partly supported the current taxonomic treatment. Finally, several highly variable loci were identified, which can be used in future phylogenetic studies and accurate identification of medicinal genuineness of Swertia. CONCLUSIONS Our study confirmed the polyphyly of Swertia and demonstrated the power of plastome phylogenomics in improvement of phylogenetic resolution, thus contributing to a better understanding of the evolutionary history of Swertia.
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Affiliation(s)
- Qian Cao
- Key Laboratory of Crop Molecular Breeding of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingbo Gao
- Key Laboratory of Crop Molecular Breeding of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Xiaolei Ma
- Key Laboratory of Crop Molecular Breeding of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Faqi Zhang
- Key Laboratory of Crop Molecular Breeding of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Rui Xing
- Key Laboratory of Crop Molecular Breeding of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Xiaofeng Chi
- Key Laboratory of Crop Molecular Breeding of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Shilong Chen
- Key Laboratory of Crop Molecular Breeding of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China.
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10
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Guo XX, Qu XJ, Zhang XJ, Fan SJ. Comparative and Phylogenetic Analysis of Complete Plastomes among Aristidoideae Species (Poaceae). BIOLOGY 2022; 11:biology11010063. [PMID: 35053061 PMCID: PMC8773369 DOI: 10.3390/biology11010063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/26/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022]
Abstract
Aristidoideae is a subfamily in the PACMAD clade of family Poaceae, including three genera, Aristida, Stipagrostis, and Sartidia. In this study, the plastomes of Aristida adscensionis and Stipagrostis pennata were newly sequenced, and a total of 16 Aristidoideae plastomes were compared. All plastomes were conservative in genome size, gene number, structure, and IR boundary. Repeat sequence analysis showed that forward and palindrome repeats were the most common repeat types. The number of SSRs ranged from 30 (Sartidia isaloensis) to 54 (Aristida purpurea). Codon usage analysis showed that plastome genes preferred to use codons ending with A/T. A total of 12 highly variable regions were screened, including four protein coding sequences (matK, ndhF, infA, and rpl32) and eight non-coding sequences (rpl16-1-rpl16-2, ccsA-ndhD, trnY-GUA-trnD-GUC, ndhF-rpl32, petN-trnC-GCA, trnT-GGU-trnE-UUC, trnG-GCC-trnfM-CAU, and rpl32-trnL-UAG). Furthermore, the phylogenetic position of this subfamily and their intergeneric relationships need to be illuminated. All Maximum Likelihood and Bayesian Inference trees strongly support the monophyly of Aristidoideae and each of three genera, and the clade of Aristidoideae and Panicoideae was a sister to other subfamilies in the PACMAD clade. Within Aristidoideae, Aristida is a sister to the clade composed of Stipagrostis and Sartidia. The divergence between C4 Stipagrostis and C3 Sartidia was estimated at 11.04 Ma, which may be associated with the drought event in the Miocene period. Finally, the differences in carbon fixation patterns, geographical distributions, and ploidy may be related to the difference of species numbers among these three genera. This study provides insights into the phylogeny and evolution of the subfamily Aristidoideae.
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Affiliation(s)
| | | | - Xue-Jie Zhang
- Correspondence: (X.-J.Z.); (S.-J.F.); Tel.: +86-531-86180718 (S.-J.F.)
| | - Shou-Jin Fan
- Correspondence: (X.-J.Z.); (S.-J.F.); Tel.: +86-531-86180718 (S.-J.F.)
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11
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Nair RR, Mohan M, Rudramurthy GR, Vivekanandam R, Satheshkumar PS. Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus. Pathogens 2021; 10:1649. [PMID: 34959603 PMCID: PMC8703355 DOI: 10.3390/pathogens10121649] [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: 11/24/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 11/22/2022] Open
Abstract
Trends associated with codon usage in molluscum contagiosum virus (MCV) and factors governing the evolution of codon usage have not been investigated so far. In this study, attempts were made to decipher the codon usage trends and discover the major evolutionary forces that influence the patterns of codon usage in MCV with special reference to sub-types 1 and 2, MCV-1 and MCV-2, respectively. Three hypotheses were tested: (1) codon usage patterns of MCV-1 and MCV-2 are identical; (2) SCUB (synonymous codon usage bias) patterns of MCV-1 and MCV-2 slightly deviate from that of human host to avoid affecting the fitness of host; and (3) translational selection predominantly shapes the SCUB of MCV-1 and MCV-2. Various codon usage indices viz. relative codon usage value, effective number of codons and codon adaptation index were calculated to infer the nature of codon usage. Correspondence analysis and correlation analysis were performed to assess the relative contribution of silent base contents and significance of codon usage indices in defining bias in codon usage. Among the tested hypotheses, only the second and third hypotheses were accepted.
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Affiliation(s)
- Rahul Raveendran Nair
- Centre for Evolutionary Ecology, Aushmath Biosciences, Vadavalli Post, Coimbatore 641041, India
| | - Manikandan Mohan
- College of Pharmacy, University of Georgia, Athens, GA 30605, USA;
| | | | - Reethu Vivekanandam
- Department of Biotechnology, Bharathiyar University, Coimbatore 641046, India;
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12
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Chakraborty S, Sophiarani Y, Uddin A. Free energy of mRNA positively correlates with GC content in chloroplast transcriptomes of edible legumes. Genomics 2021; 113:2826-2838. [PMID: 34147635 DOI: 10.1016/j.ygeno.2021.06.026] [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: 12/31/2018] [Revised: 01/01/2021] [Accepted: 06/16/2021] [Indexed: 11/20/2022]
Abstract
In the present study, the results of nucleotide composition analysis showed that the legume chloroplast (cp) transcriptomes were AT rich. From the neutrality plot, we observed that natural selection might have played a major role, while mutation pressure played a minor role in the CUB of cp transcriptomes. Highly significant (p < 0.05) negative correlation was found between mRNA free energy (mFE) and scaled chi-square for entire mRNA in Cicer arietinum and Lens culinaris suggesting that the release of higher energy by entire mRNA molecule might be associated with higher degree of codon usage bias in these two crop plants. Further, highly significant (p < 0.01, p < 0.05) positive correlation of mFE for entire mRNA was found with GC3 and that of mFE for 39 bases with GC, GC1, GC2 and GC3 contents among all the legumes. This indicated that higher GC content might induce the release of more free energy by cp transcriptomes.
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Affiliation(s)
- Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India.
| | | | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi 788150, India
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13
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Wu W, Li J, Liu Y, Jiang M, Lan M, Liu C. Peculiarities of the inverted repeats in the complete chloroplast genome of Strobilanthes bantonensis Lindau. Mitochondrial DNA B Resour 2021; 6:1440-1447. [PMID: 33969193 PMCID: PMC8079011 DOI: 10.1080/23802359.2021.1911699] [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] [Indexed: 11/24/2022] Open
Abstract
Strobilanthes bantonensis Lindau belongs to the family Acanthaceae. It is an antiviral herb that can be used to prevent Influenza virus infections in the border areas between China and Vietnam. Local people call it ‘Purple Ban-lan-gen’ because its root is very similar to that of Strobilanthes cusia (Nees) Kuntze, which is called ‘Southern Ban-lan-gen’ and is listed in Chinese Pharmacopeia. The two species have been used interchangeably locally. However, their pharmacological equivalence has caused concern for years. We have sequenced the chloroplast genome of S. cusia previously. In this study, we sequenced the complete chloroplast genome sequence of S. bantonensis to preform in-depth comparative genetic analysis of the two Strobilanthes species. The chloroplast genome of S. bantonensis is a circular DNA molecule with a total length of 144,591 bp and encodes 84 protein-coding, 8 ribosomes, and 37 transfer RNA genes. The chloroplast genome has a conservative quadripartite structure, including a large single-copy (LSC) region, a small single-copy (SSC) region, and a pair of inverted repeat (IR) regions, with lengths of 92,068 bp, 17,767 bp, and 17,378 bp, respectively. Phylogenetic analysis confirmed that S. bantonensis is closely related to the S. cusia. Compared with other species from Acanthaceae, S. bantonensis has a significantly shortened IR region, suggesting the occurrence of IR contraction events. This study will help future taxonomic, evolutionary, phylogenetic, and bioprospecting studies of the sizeable Strobilanthes genus, which contains over 400 species.
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Affiliation(s)
- Wuwei Wu
- Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Yu Liu
- Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from the Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Mingsheng Lan
- Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from the Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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14
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Sawyer JK, Kabiri Z, Montague RA, Allen SR, Stewart R, Paramore SV, Cohen E, Zaribafzadeh H, Counter CM, Fox DT. Exploiting codon usage identifies intensity-specific modifiers of Ras/MAPK signaling in vivo. PLoS Genet 2020; 16:e1009228. [PMID: 33296356 PMCID: PMC7752094 DOI: 10.1371/journal.pgen.1009228] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/21/2020] [Accepted: 10/27/2020] [Indexed: 01/05/2023] Open
Abstract
Signal transduction pathways are intricately fine-tuned to accomplish diverse biological processes. An example is the conserved Ras/mitogen-activated-protein-kinase (MAPK) pathway, which exhibits context-dependent signaling output dynamics and regulation. Here, by altering codon usage as a novel platform to control signaling output, we screened the Drosophila genome for modifiers specific to either weak or strong Ras-driven eye phenotypes. Our screen enriched for regions of the genome not previously connected with Ras phenotypic modification. We mapped the underlying gene from one modifier to the ribosomal gene RpS21. In multiple contexts, we show that RpS21 preferentially influences weak Ras/MAPK signaling outputs. These data show that codon usage manipulation can identify new, output-specific signaling regulators, and identify RpS21 as an in vivo Ras/MAPK phenotypic regulator. Cellular communication is critical in controlling the growth of organs and must be carefully regulated to prevent disease. The Ras signaling pathway is frequently used for cellular communication of tissue growth regulation but can operate at different signaling strengths. Here, we used a novel strategy to identify genes that specifically tune weak or strong Ras signaling states. We find that the gene RpS21 preferentially tunes weak Ras signaling states.
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Affiliation(s)
- Jessica K. Sawyer
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Zahra Kabiri
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Ruth A. Montague
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Scott R. Allen
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Rebeccah Stewart
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Sarah V. Paramore
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Erez Cohen
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Hamed Zaribafzadeh
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Christopher M. Counter
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- * E-mail: (CMC); (DTF)
| | - Donald T. Fox
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- * E-mail: (CMC); (DTF)
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15
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Chakraborty S, Yengkhom S, Uddin A. Analysis of codon usage bias of chloroplast genes in Oryza species : Codon usage of chloroplast genes in Oryza species. PLANTA 2020; 252:67. [PMID: 32989601 DOI: 10.1007/s00425-020-03470-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 09/15/2020] [Indexed: 05/11/2023]
Abstract
The codon usage bias in chloroplast genes of Oryza species was low and AT rich. The pattern of codon usage was different among Oryza species and mainly influenced by mutation pressure and natural selection. Codon usage bias (CUB) is the unequal usage of synonymous codons in which some codons are more preferred to others in the coding sequences of genes. It shows a species-specific property. We studied the patterns of codon usage and the factors that influenced the CUB of protein-coding chloroplast (cp) genes in 18 Oryza species as no work was yet reported. The nucleotide composition analysis revealed that the overall GC content of cp genes in different species of Oryza was lower than 50%, i.e., Oryza cp genes were AT rich. Synonymous codon usage order (SCUO) suggested that CUB was weak in the cp genes of different Oryza species. A highly significant correlation was observed between overall nucleotides and its constituents at the third codon position suggesting that both, mutation pressure and natural selection, might influence the CUB. Correspondence analysis (COA) revealed that codon usage pattern differed across Oryza species. In the neutrality plot, a narrow range of GC3 distribution was recorded and some points were diagonally distributed in all the plots, suggesting that natural selection and mutation pressure might have influenced the CUB. The slope of the regression line was < 0.5, augmenting our inference that natural selection might have played a major role, while mutation pressure had a minor role in shaping the CUB of cp genes. The magnitudes of mutation pressure and natural selection on cp genes varied across Oryza species.
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Affiliation(s)
- Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar, 788011, Assam, India.
| | - Sophiarani Yengkhom
- 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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16
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Sarpan N, Taranenko E, Ooi SE, Low ETL, Espinoza A, Tatarinova TV, Ong-Abdullah M. DNA methylation changes in clonally propagated oil palm. PLANT CELL REPORTS 2020; 39:1219-1233. [PMID: 32591850 DOI: 10.1007/s00299-020-02561-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
Several hypomethylated sites within the Karma region of EgDEF1 and hotspot regions in chromosomes 1, 2, 3, and 5 may be associated with mantling. One of the main challenges faced by the oil palm industry is fruit abnormalities, such as the "mantled" phenotype that can lead to reduced yields. This clonal abnormality is an epigenetic phenomenon and has been linked to the hypomethylation of a transposable element within the EgDEF1 gene. To understand the epigenome changes in clones, methylomes of clonal oil palms were compared to methylomes of seedling-derived oil palms. Whole-genome bisulfite sequencing data from seedlings, normal, and mantled clones were analyzed to determine and compare the context-specific DNA methylomes. In seedlings, coding and regulatory regions are generally hypomethylated while introns and repeats are extensively methylated. Genes with a low number of guanines and cytosines in the third position of codons (GC3-poor genes) were increasingly methylated towards their 3' region, while GC3-rich genes remain demethylated, similar to patterns in other eukaryotic species. Predicted promoter regions were generally hypomethylated in seedlings. In clones, CG, CHG, and CHH methylation levels generally decreased in functionally important regions, such as promoters, 5' UTRs, and coding regions. Although random regions were found to be hypomethylated in clonal genomes, hypomethylation of certain hotspot regions may be associated with the clonal mantling phenotype. Our findings, therefore, suggest other hypomethylated CHG sites within the Karma of EgDEF1 and hypomethylated hotspot regions in chromosomes 1, 2, 3 and 5, are associated with mantling.
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Affiliation(s)
- Norashikin Sarpan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Elizaveta Taranenko
- Department of Biology, University of La Verne, La Verne, CA, USA
- Department of Fundamental Biology and Biotechnology, Siberian Federal University, 660074, Krasnoyarsk, Russia
| | - Siew-Eng Ooi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Eng-Ti Leslie Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | | | - Tatiana V Tatarinova
- Department of Biology, University of La Verne, La Verne, CA, USA.
- Department of Fundamental Biology and Biotechnology, Siberian Federal University, 660074, Krasnoyarsk, Russia.
- Vavilov Institute for General Genetics, Moscow, Russia.
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
| | - Meilina Ong-Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia.
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17
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Genetic evolution and codon usage analysis of NKX-2.5 gene governing heart development in some mammals. Genomics 2019; 112:1319-1329. [PMID: 31377427 DOI: 10.1016/j.ygeno.2019.07.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/26/2019] [Accepted: 07/31/2019] [Indexed: 11/21/2022]
Abstract
NKX-2.5 gene is responsible for cardiac development and its targeted disruption apprehends cardiac development at the linear heart tube stage. Bioinformatic analysis was employed to investigate the codon usage pattern and dN/dS of mammalian NKX-2.5 gene. The relative synonymous codon usage analysis revealed variation in codon usage and two synonymous codons namely ATA (Ile) and GTA (Val) were absent in NKX-2.5 gene across selected mammalian species suggesting that these two codons were possibly selected against during evolution. Parity rule 2 analysis of two and four fold amino acids showed CT bias whereas six-fold amino acids revealed GA bias. Neutrality analysis suggests that selection played a prominent role while mutation had a minor role. The dN/dS analysis suggests synonymous substitution played a significant role and it negatively correlated with p-distance of the gene. Purifying natural selection played a dominant role in the genetic evolution of NKX-2.5 gene in mammals.
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18
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Chiapella JO, Barfuss MHJ, Xue ZQ, Greimler J. The Plastid Genome of Deschampsia cespitosa (Poaceae). Molecules 2019; 24:E216. [PMID: 30634385 PMCID: PMC6359331 DOI: 10.3390/molecules24020216] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/28/2018] [Accepted: 01/04/2019] [Indexed: 01/03/2023] Open
Abstract
Plastid genome analysis of non-model organisms provides valuable information for basic research e.g., molecular evolutionary genomics, phylogeny and phylogeography. Deschampsia cespitosa is the most widespread species of the genus and it is a common grass that is found across Eurasia and North America. Scattered populations in regions of appropriate ecological conditions are also found in Australia, New Zealand and southern South America, where it is sympatric with D. antarctica. We analyzed the plastid genome of a sample of Deschampsia cespitosa of the Austrian Alps using high-throughput sequencing. The plastid (cp) genome shows the typical quadripartite structure with a length of 135,340 bp, comprising a large single-copy (LSC) region of 79,992 bp, a small single-copy (SSC) region of 12,572 bp and two inverted repeats (IR) regions of 21,388 bp each. It contains 115 genes, including 85 protein-coding genes, four ribosomal RNA genes and 30 transfer RNA genes. The GC content (%), number of repeats and microsatellites, RNA editing sites and codon usage were highly similar to those of D. antarctica. The results of this present study highlight the extremely conserved nature of the cp genome in this group, since the comparison involved individuals separated by about 13,000 km, from the Alps to Antarctica.
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Affiliation(s)
- Jorge O Chiapella
- Instituto Multidisciplinario de Biología Vegetal (IMBIV-CONICET), Universidad Nacional de Córdoba, POB 495, Córdoba 5000, Argentina.
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030 Vienna, Austria.
| | - Michael H J Barfuss
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030 Vienna, Austria.
| | - Zhi-Qing Xue
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030 Vienna, Austria.
| | - Josef Greimler
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030 Vienna, Austria.
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Gao X, Zhang X, Meng H, Li J, Zhang D, Liu C. Comparative chloroplast genomes of Paris Sect. Marmorata: insights into repeat regions and evolutionary implications. BMC Genomics 2018; 19:878. [PMID: 30598104 PMCID: PMC6311911 DOI: 10.1186/s12864-018-5281-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Species of Paris Sect. Marmorata are valuable medicinal plants to synthesize steroidal saponins with effective pharmacological therapy. However, the wild resources of the species are threatened by plundering exploitation before the molecular genetics studies uncover the genomes and evolutionary significance. Thus, the availability of complete chloroplast genome sequences of Sect. Marmorata is necessary and crucial to the understanding the plastome evolution of this section and facilitating future population genetics studies. Here, we determined chloroplast genomes of Sect. Marmorata, and conducted the whole chloroplast genome comparison. Results This study presented detailed sequences and structural variations of chloroplast genomes of Sect. Marmorata. Over 40 large repeats and approximately 130 simple sequence repeats as well as a group of genomic hotspots were detected. Inverted repeat contraction of this section was inferred via comparing the chloroplast genomes with the one of P. verticillata. Additionally, almost all the plastid protein coding genes were found to prefer ending with A/U. Mutation bias and selection pressure predominately shaped the codon bias of most genes. And most of the genes underwent purifying selection, whereas photosynthetic genes experienced a relatively relaxed purifying selection. Conclusions Repeat sequences and hotspot regions can be scanned to detect the intraspecific and interspecific variability, and selected to infer the phylogenetic relationships of Sect. Marmorata and other species in subgenus Daiswa. Mutation and natural selection were the main forces to drive the codon bias pattern of most plastid protein coding genes. Therefore, this study enhances the understanding about evolution of Sect. Marmorata from the chloroplast genome, and provide genomic insights into genetic analyses of Sect. Marmorata. Electronic supplementary material The online version of this article (10.1186/s12864-018-5281-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaoyang Gao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Science, Menglun, 666303, Yunnan, China
| | - Xuan Zhang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Science, Menglun, 666303, Yunnan, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Honghu Meng
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Jing Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Science, Menglun, 666303, Yunnan, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Di Zhang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Science, Menglun, 666303, Yunnan, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Science, Menglun, 666303, Yunnan, China.
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20
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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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21
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Karumathil S, Raveendran NT, Ganesh D, Kumar Ns S, Nair RR, Dirisala VR. Evolution of Synonymous Codon Usage Bias in West African and Central African Strains of Monkeypox Virus. Evol Bioinform Online 2018; 14:1176934318761368. [PMID: 29551886 PMCID: PMC5846927 DOI: 10.1177/1176934318761368] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 02/01/2018] [Indexed: 12/17/2022] Open
Abstract
The evolution of bias in synonymous codon usage in chosen monkeypox viral genomes and the factors influencing its diversification have not been reported so far. In this study, various trends associated with synonymous codon usage in chosen monkeypox viral genomes were investigated, and the results are reported. Identification of factors that influence codon usage in chosen monkeypox viral genomes was done using various codon usage indices, such as the relative synonymous codon usage, the effective number of codons, and the codon adaptation index. The Spearman rank correlation analysis and a correspondence analysis were used for correlating various factors with codon usage. The results revealed that mutational pressure due to compositional constraints, gene expression level, and selection at the codon level for utilization of putative optimal codons are major factors influencing synonymous codon usage bias in monkeypox viral genomes. A cluster analysis of relative synonymous codon usage values revealed a grouping of more virulent strains as one major cluster (Central African strains) and a grouping of less virulent strains (West African strains) as another major cluster, indicating a relationship between virulence and synonymous codon usage bias. This study concluded that a balance between the mutational pressure acting at the base composition level and the selection pressure acting at the amino acid level frames synonymous codon usage bias in the chosen monkeypox viruses. The natural selection from the host does not seem to have influenced the synonymous codon usage bias in the analyzed monkeypox viral genomes.
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Affiliation(s)
- Sudeesh Karumathil
- Centre for Evolutionary Ecology, Aushmath Biosciences, Coimbatore, India
| | - Nimal T Raveendran
- Amrita Centre for Nanosciences, Amrita Vishwa Vidyapeetham, Kochi, India
| | - Doss Ganesh
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | | | - Rahul R Nair
- Centre for Evolutionary Ecology, Aushmath Biosciences, Coimbatore, India
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Takaaki K, Tatsuo S. Analysis of factors affecting codon usage bias in human papillomavirus. ACTA ACUST UNITED AC 2018. [DOI: 10.5897/jbsa2017.0106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Mazumdar P, Binti Othman R, Mebus K, Ramakrishnan N, Ann Harikrishna J. Codon usage and codon pair patterns in non-grass monocot genomes. ANNALS OF BOTANY 2017; 120:893-909. [PMID: 29155926 PMCID: PMC5710610 DOI: 10.1093/aob/mcx112] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 09/19/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND AND AIMS Studies on codon usage in monocots have focused on grasses, and observed patterns of this taxon were generalized to all monocot species. Here, non-grass monocot species were analysed to investigate the differences between grass and non-grass monocots. METHODS First, studies of codon usage in monocots were reviewed. The current information was then extended regarding codon usage, as well as codon-pair context bias, using four completely sequenced non-grass monocot genomes (Musa acuminata, Musa balbisiana, Phoenix dactylifera and Spirodela polyrhiza) for which comparable transcriptome datasets are available. Measurements were taken regarding relative synonymous codon usage, effective number of codons, derived optimal codon and GC content and then the relationships investigated to infer the underlying evolutionary forces. KEY RESULTS The research identified optimal codons, rare codons and preferred codon-pair context in the non-grass monocot species studied. In contrast to the bimodal distribution of GC3 (GC content in third codon position) in grasses, non-grass monocots showed a unimodal distribution. Disproportionate use of G and C (and of A and T) in two- and four-codon amino acids detected in the analysis rules out the mutational bias hypothesis as an explanation of genomic variation in GC content. There was found to be a positive relationship between CAI (codon adaptation index; predicts the level of expression of a gene) and GC3. In addition, a strong correlation was observed between coding and genomic GC content and negative correlation of GC3 with gene length, indicating a strong impact of GC-biased gene conversion (gBGC) in shaping codon usage and nucleotide composition in non-grass monocots. CONCLUSION Optimal codons in these non-grass monocots show a preference for G/C in the third codon position. These results support the concept that codon usage and nucleotide composition in non-grass monocots are mainly driven by gBGC.
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Affiliation(s)
- Purabi Mazumdar
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, Malaysia
| | - RofinaYasmin Binti Othman
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, Malaysia
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Katharina Mebus
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, Malaysia
| | - N Ramakrishnan
- Electrical and Computer System Engineering, School of Engineering, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Jennifer Ann Harikrishna
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, Malaysia
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- For correspondence. E-mail:
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Bowman MJ, Pulman JA, Liu TL, Childs KL. A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa. BMC Bioinformatics 2017; 18:522. [PMID: 29178822 PMCID: PMC5702205 DOI: 10.1186/s12859-017-1942-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 11/15/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Accurate structural annotation depends on well-trained gene prediction programs. Training data for gene prediction programs are often chosen randomly from a subset of high-quality genes that ideally represent the variation found within a genome. One aspect of gene variation is GC content, which differs across species and is bimodal in grass genomes. When gene prediction programs are trained on a subset of grass genes with random GC content, they are effectively being trained on two classes of genes at once, and this can be expected to result in poor results when genes are predicted in new genome sequences. RESULTS We find that gene prediction programs trained on grass genes with random GC content do not completely predict all grass genes with extreme GC content. We show that gene prediction programs that are trained with grass genes with high or low GC content can make both better and unique gene predictions compared to gene prediction programs that are trained on genes with random GC content. By separately training gene prediction programs with genes from multiple GC ranges and using the programs within the MAKER genome annotation pipeline, we were able to improve the annotation of the Oryza sativa genome compared to using the standard MAKER annotation protocol. Gene structure was improved in over 13% of genes, and 651 novel genes were predicted by the GC-specific MAKER protocol. CONCLUSIONS We present a new GC-specific MAKER annotation protocol to predict new and improved gene models and assess the biological significance of this method in Oryza sativa. We expect that this protocol will also be beneficial for gene prediction in any organism with bimodal or other unusual gene GC content.
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Affiliation(s)
- Megan J Bowman
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, Room 166, East Lansing, MI, 48824, USA.,Van Andel Research Institute, Grand Rapids, MI, 49506, USA
| | - Jane A Pulman
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, Room 166, East Lansing, MI, 48824, USA.,Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, MI, 48824, USA.,Centre for Genomics Research, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Tiffany L Liu
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, Room 166, East Lansing, MI, 48824, USA
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, Room 166, East Lansing, MI, 48824, USA. .,Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, MI, 48824, USA.
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Sablok G, Chen TW, Lee CC, Yang C, Gan RC, Wegrzyn JL, Porta NL, Nayak KC, Huang PJ, Varotto C, Tang P. ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications. DNA Res 2017; 24:327-332. [PMID: 28419256 PMCID: PMC5499650 DOI: 10.1093/dnares/dsw044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 09/14/2016] [Indexed: 01/01/2023] Open
Abstract
Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes for transgenic expression. From the overexpression point of view, it is critical to systematically analyze the codon usage patterns of the organelle genomes. In light of the importance of codon usage patterns in the development of hyper-expression organelle transgenics, we present ChloroMitoCU, the first-ever curated, web-based reference catalog of the codon usage patterns in organelle genomes. ChloroMitoCU contains the pre-compiled codon usage patterns of 328 chloroplast genomes (29,960 CDS) and 3,502 mitochondrial genomes (49,066 CDS), enabling genome-wide exploration and comparative analysis of codon usage patterns across species. ChloroMitoCU allows the phylogenetic comparison of codon usage patterns across organelle genomes, the prediction of codon usage patterns based on user-submitted transcripts or assembled organelle genes, and comparative analysis with the pre-compiled patterns across species of interest. ChloroMitoCU can increase our understanding of the biased patterns of codon usage in organelle genomes across multiple clades. ChloroMitoCU can be accessed at: http://chloromitocu.cgu.edu.tw/
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Affiliation(s)
- Gaurav Sablok
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige (TN), Italy
| | - Ting-Wen Chen
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Kweishan, Taoyuan 333, Taiwan
| | - Chi-Ching Lee
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Kweishan, Taoyuan 333, Taiwan
| | - Chi Yang
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Kweishan, Taoyuan 333, Taiwan
| | - Ruei-Chi Gan
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Kweishan, Taoyuan 333, Taiwan
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University 10 of Connecticut, 75 North Eagleville Road, Storrs, CT 06269-3043 USA
| | - Nicola L Porta
- Department of Sustainable Agrobiosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige (TN), Italy.,MOUNTFOR Project Centre, European Forest Institute, Via E. Mach 1, 38010 San Michele all'Adige, Trento, Italy
| | - Kinshuk C Nayak
- Bioinformatics Centre, Institute of Life Sciences, Department of Biotechnology, Govt. India, Nalco Square, Bhubaneswar - 751 023, India
| | - Po-Jung Huang
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Kweishan, Taoyuan 333, Taiwan
| | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige (TN), Italy
| | - Petrus Tang
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Kweishan, Taoyuan 333, Taiwan.,Molecular Infectious Diseases Research Center, Chang Gung Memorial Hospital, Kweishan, Taoyuan 333, Taiwan
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26
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Nath Choudhury M, Uddin A, Chakraborty S. Codon usage bias and its influencing factors for Y-linked genes in human. Comput Biol Chem 2017; 69:77-86. [DOI: 10.1016/j.compbiolchem.2017.05.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 05/04/2017] [Accepted: 05/20/2017] [Indexed: 11/30/2022]
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27
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Kong WQ, Yang JH. The complete chloroplast genome sequence of Morus cathayana and Morus multicaulis, and comparative analysis within genus Morus L. PeerJ 2017; 5:e3037. [PMID: 28286710 PMCID: PMC5345388 DOI: 10.7717/peerj.3037] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 01/27/2017] [Indexed: 11/20/2022] Open
Abstract
Trees in the Morus genera belong to the Moraceae family. To better understand the species status of genus Morus and to provide information for studies on evolutionary biology within the genus, the complete chloroplast (cp) genomes of M. cathayana and M. multicaulis were sequenced. The plastomes of the two species are 159,265 bp and 159,103 bp, respectively, with corresponding 83 and 82 simple sequence repeats (SSRs). Similar to the SSRs of M. mongolica and M. indica cp genomes, more than 70% are mononucleotides, ten are in coding regions, and one exhibits nucleotide content polymorphism. Results for codon usage and relative synonymous codon usage show a strong bias towards NNA and NNT codons in the two cp genomes. Analysis of a plot of the effective number of codons (ENc) for five Morus spp. cp genomes showed that most genes follow the standard curve, but several genes have ENc values below the expected curve. The results indicate that both natural selection and mutational bias have contributed to the codon bias. Ten highly variable regions were identified among the five Morus spp. cp genomes, and 154 single-nucleotide polymorphism mutation events were accurately located in the gene coding region.
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Affiliation(s)
- Wei Qing Kong
- Shaanxi Key Laboratory of Sericulture, Ankang University , Ankang , Shaanxi , China
| | - Jin Hong Yang
- Shaanxi Key Laboratory of Sericulture, Ankang University , Ankang , Shaanxi , China
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28
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Karumathil S, Dirisala VR, Srinadh U, Nikhil V, Kumar NSS, Nair RR. Evolution of Synonymous Codon Usage in the Mitogenomes of Certain Species of Bilaterian Lineage with Special Reference to Chaetognatha. Bioinform Biol Insights 2016; 10:167-84. [PMID: 27688709 PMCID: PMC5034883 DOI: 10.4137/bbi.s38192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/17/2016] [Accepted: 08/28/2016] [Indexed: 11/20/2022] Open
Abstract
Chaetognatha is a minor phylum, comprising transparent marine invertebrates varying in size from 0.5 to 12 cm. The exact phylogenetic position of Chaetognatha in Metazoa has not been deciphered as some embryological characteristics place chaetognaths among deuterostomes and some morphological characteristics place these among protostomes. In this study, the major factors that drive synonymous codon usage bias (SCUB) in the mitogenomes of representative species of Chaetognatha and chosen species of other closely related phyla were analyzed. Spearman’s rank correlation analyses of nucleotide contents suggested that mutational pressure and selection were acting in all examined mitogenomes but with varying intensities. The quantification of SCUB using effective number of codons vs. GC composition at the third codon position (GC3) plot suggested that mutational pressure due to GC compositional constraints might be one of the major influencing forces driving the SCUB in all chaetognaths except Sagitta enflata. However, neutrality plots revealed no significant correlation between GC3 and cumulative GC content at first and second codon positions (GC12) in all other species, except in Daphnia pulex. The parity rule 2 bias plot showed that significant compositional differences existed between C and G, as well as between A and T, contents in most of the protein-coding genes (PCGs) and, comparatively, A and T contents were used more proportionally than C and G contents in all chosen mitogenomes. Chi-square analysis revealed the presence of putative optimal codons in all species, except in S. enflata. The correspondence analysis identified that mutational pressure and selection act on the mitogenomes of the selected chaetognaths and other phyla with varying intensities. The cluster analysis based on relative synonymous codon usage (RSCU) values revealed that RSCU variations in the PCGs of mitogenomes of chaetognaths are more comparable with those of protostomes. Apart from mutational pressure and selection, certain unknown selective forces might be acting on the PCGs in the analyzed mitogenomes as the phenomenon of SCUB could not be explained by mutational pressure, by selection, or by both.
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Affiliation(s)
- Sudeesh Karumathil
- Aushmath Biosciences, Administrative office, Devaraj Corner, Vadavalli Post, Coimbatore, Tamil Nadu, India
| | - Vijaya R Dirisala
- Department of Biotechnology, Vignan's University (Vignan's Foundation for Science, Technology and Research University), Guntur, Andhra Pradesh, India
| | - Uthpala Srinadh
- Department of Biotechnology, Vignan's University (Vignan's Foundation for Science, Technology and Research University), Guntur, Andhra Pradesh, India
| | - Valaboju Nikhil
- Department of Biotechnology, Vignan's University (Vignan's Foundation for Science, Technology and Research University), Guntur, Andhra Pradesh, India
| | - N Satya Sampath Kumar
- Department of Biotechnology, Vignan's University (Vignan's Foundation for Science, Technology and Research University), Guntur, Andhra Pradesh, India
| | - Rahul R Nair
- Aushmath Biosciences, Administrative office, Devaraj Corner, Vadavalli Post, Coimbatore, Tamil Nadu, India
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29
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Malakar AK, Halder B, Paul P, Chakraborty S. Cytochrome P450 genes in coronary artery diseases: Codon usage analysis reveals genomic GC adaptation. Gene 2016; 590:35-43. [PMID: 27275533 DOI: 10.1016/j.gene.2016.06.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 04/12/2016] [Accepted: 06/03/2016] [Indexed: 10/21/2022]
Abstract
Establishing codon usage biases are imperative for understanding the etiology of coronary artery diseases (CAD) as well as the genetic factors associated with these diseases. The aim of this study was to evaluate the contribution of 18 responsible cytochrome P450 (CYP) genes for the risk of CAD. Effective number of codon (Nc) showed a negative correlation with both GC3 and synonymous codon usage order (SCUO) suggesting an antagonistic relationship between codon usage and Nc of genes. The dinucleotide analysis revealed that CG and TA dinucleotides have the lowest odds ratio in these genes. Principal component analysis showed that GC composition has a profound effect in separating the genes along the first major axis. Our findings revealed that mutational pressure and natural selection could possibly be the major factors responsible for codon bias in these genes. The study not only offers an insight into the mechanisms of genomic GC adaptation, but also illustrates the complexity of CYP genes in CAD.
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Affiliation(s)
- Arup Kumar Malakar
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Binata Halder
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Prosenjit Paul
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India.
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30
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Abstract
Codon adaptation is codon usage bias that results from selective pressure to increase the translation efficiency of a gene. Codon adaptation has been studied across a wide range of genomes and some early analyses of plastids have shown evidence for codon adaptation in a limited set of highly expressed plastid genes. Here we study codon usage bias across all fully sequenced plastid genomes which includes representatives of the Rhodophyta, Alveolata, Cryptophyta, Euglenozoa, Glaucocystophyceae, Rhizaria, Stramenopiles and numerous lineages within the Viridiplantae, including Chlorophyta and Embryophyta. We show evidence that codon adaptation occurs in all genomes except for two, Theileria parva and Heicosporidium sp., both of which have highly reduced gene contents and no photosynthesis genes. We also show evidence that selection for codon adaptation increases the representation of the same set of codons, which we refer to as the adaptive codons, across this wide range of taxa, which is probably due to common features descended from the initial endosymbiont. We use various measures to estimate the relative strength of selection in the different lineages and show that it appears to be fairly strong in certain Stramenopiles and Chlorophyta lineages but relatively weak in many members of the Rhodophyta, Euglenozoa and Embryophyta. Given these results we propose that codon adaptation in plastids is widespread and displays the same general features as adaptation in eubacterial genomes.
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Affiliation(s)
- Haruo Suzuki
- Graduate School of Science and Engineering, Yamaguchi University, Yamaguchi, Japan
| | - Brian R. Morton
- Department of Biology, Barnard College, Columbia University, New York, New York, United States of America
- * E-mail:
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31
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Hu S, Sablok G, Wang B, Qu D, Barbaro E, Viola R, Li M, Varotto C. Plastome organization and evolution of chloroplast genes in Cardamine species adapted to contrasting habitats. BMC Genomics 2015; 16:306. [PMID: 25887666 PMCID: PMC4446112 DOI: 10.1186/s12864-015-1498-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 03/27/2015] [Indexed: 11/10/2022] Open
Abstract
Background Plastid genomes, also known as plastomes, are shaped by the selective forces acting on the fundamental cellular functions they code for and thus they are expected to preserve signatures of the adaptive path undertaken by different plant species during evolution. To identify molecular signatures of positive selection associated to adaptation to contrasting ecological niches, we sequenced with Solexa technology the plastomes of two congeneric Brassicaceae species with different habitat preference, Cardamine resedifolia and Cardamine impatiens. Results Following in-depth characterization of plastome organization, repeat patterns and gene space, the comparison of the newly sequenced plastomes between each other and with 15 fully sequenced Brassicaceae plastomes publically available in GenBank uncovered dynamic variation of the IR boundaries in the Cardamine lineage. We further detected signatures of positive selection in ten of the 75 protein-coding genes of the examined plastomes, identifying a range of chloroplast functions putatively involved in adaptive processes within the family. For instance, the three residues found to be under positive selection in RUBISCO could possibly be involved in the modulation of RUBISCO aggregation/activation and enzymatic specificty in Brassicaceae. In addition, our results points to differential evolutionary rates in Cardamine plastomes. Conclusions Overall our results support the existence of wider signatures of positive selection in the plastome of C. resedifolia, possibly as a consequence of adaptation to high altitude environments. We further provide a first characterization of the selective patterns shaping the Brassicaceae plastomes, which could help elucidate the driving forces underlying adaptation and evolution in this important plant family. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1498-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shiliang Hu
- Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy.
| | - Gaurav Sablok
- Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy.
| | - Bo Wang
- Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy.
| | - Dong Qu
- Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy. .,College of Horticulture, Northwest Agricultural and Forest University, 712100, Yangling, Shaanxi, PR China.
| | - Enrico Barbaro
- Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy.
| | - Roberto Viola
- Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy.
| | - Mingai Li
- Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy.
| | - Claudio Varotto
- Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy.
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Liu Q, Hu H, Wang H. Mutational bias is the driving force for shaping the synonymous codon usage pattern of alternatively spliced genes in rice (Oryza sativa L.). Mol Genet Genomics 2014; 290:649-60. [PMID: 25407289 DOI: 10.1007/s00438-014-0951-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 11/04/2014] [Indexed: 11/30/2022]
Abstract
Alternative splicing plays important roles in diverse aspects of plant development, metabolism, and stress responses. However, the regulatory mechanisms of alternative splicing of genes still remain incompletely elucidated, especially in plants. In this study, the synonymous codon usage pattern of alternatively spliced (AS) genes in rice was firstly explored using the combination of correspondence analysis (CA), internal CA, correlation and ANOVA analyses. The results show that alternatively and non-alternatively spliced (non-AS) genes have similar tendency for overall codon usage, but exhibit significant difference in 58 out of 64 codons. AS and non-AS genes are both under strong purifying selection, but the former ones have significant lower mutation rate and are prone to be enriched towards the chromosomal ends. In the group of AS genes, the variability in synonymous codon usage between genes is mainly due to the variations in GC content, CDS length, as well as gene functions. Mutational bias that accounts for 25.85 % of the total codon usage variability plays a major role in shaping the codon usage pattern of AS genes. In contrast, no obvious evidence is found for the contributions of translational selection, AS types, the conservation of AS events, and numbers of AS variants to the codon usage divergence between AS genes. These findings may be useful for further understanding the mechanisms of origination, differentiation and regulation of alternatively spliced genes in plants.
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Affiliation(s)
- Qingpo Liu
- Department of Agronomy, and the Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agriculture and Food Science, Zhejiang A & F University, Lin'an, 311300, Zhejiang, China,
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Kim HT, Chung MG, Kim KJ. Chloroplast genome evolution in early diverged leptosporangiate ferns. Mol Cells 2014; 37:372-82. [PMID: 24823358 PMCID: PMC4044308 DOI: 10.14348/molcells.2014.2296] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 04/11/2014] [Accepted: 04/14/2014] [Indexed: 12/02/2022] Open
Abstract
In this study, the chloroplast (cp) genome sequences from three early diverged leptosporangiate ferns were completed and analyzed in order to understand the evolution of the genome of the fern lineages. The complete cp genome sequence of Osmunda cinnamomea (Osmundales) was 142,812 base pairs (bp). The cp genome structure was similar to that of eusporangiate ferns. The gene/intron losses that frequently occurred in the cp genome of leptosporangiate ferns were not found in the cp genome of O. cinnamomea. In addition, putative RNA editing sites in the cp genome were rare in O. cinnamomea, even though the sites were frequently predicted to be present in leptosporangiate ferns. The complete cp genome sequence of Diplopterygium glaucum (Gleicheniales) was 151,007 bp and has a 9.7 kb inversion between the trnL-CAA and trnVGCA genes when compared to O. cinnamomea. Several repeated sequences were detected around the inversion break points. The complete cp genome sequence of Lygodium japonicum (Schizaeales) was 157,142 bp and a deletion of the rpoC1 intron was detected. This intron loss was shared by all of the studied species of the genus Lygodium. The GC contents and the effective numbers of codons (ENCs) in ferns varied significantly when compared to seed plants. The ENC values of the early diverged leptosporangiate ferns showed intermediate levels between eusporangiate and core leptosporangiate ferns. However, our phylogenetic tree based on all of the cp gene sequences clearly indicated that the cp genome similarity between O. cinnamomea (Osmundales) and eusporangiate ferns are symplesiomorphies, rather than synapomorphies. Therefore, our data is in agreement with the view that Osmundales is a distinct early diverged lineage in the leptosporangiate ferns.
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Affiliation(s)
- Hyoung Tae Kim
- Division of Life Sciences, School of Life Sciences, Korea University, Seoul 136-701,
Korea
| | | | - Ki-Joong Kim
- Division of Life Sciences, School of Life Sciences, Korea University, Seoul 136-701,
Korea
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Tatarinova T, Elhaik E, Pellegrini M. Cross-species analysis of genic GC3 content and DNA methylation patterns. Genome Biol Evol 2013; 5:1443-56. [PMID: 23833164 PMCID: PMC3762193 DOI: 10.1093/gbe/evt103] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The GC content in the third codon position (GC3) exhibits a unimodal distribution in many plant and animal genomes. Interestingly, grasses and homeotherm vertebrates exhibit a unique bimodal distribution. High GC3 was previously found to be associated with variable expression, higher frequency of upstream TATA boxes, and an increase of GC3 from 5′ to 3′. Moreover, GC3-rich genes are predominant in certain gene classes and are enriched in CpG dinucleotides that are potential targets for methylation. Based on the GC3 bimodal distribution we hypothesize that GC3 has a regulatory role involving methylation and gene expression. To test that hypothesis, we selected diverse taxa (rice, thale cress, bee, and human) that varied in the modality of their GC3 distribution and tested the association between GC3, DNA methylation, and gene expression. We examine the relationship between cytosine methylation levels and GC3, gene expression, genome signature, gene length, and other gene compositional features. We find a strong negative correlation (Pearson’s correlation coefficient r = −0.67, P value < 0.0001) between GC3 and genic CpG methylation. The comparison between 5′-3′ gradients of CG3-skew and genic methylation for the taxa in the study suggests interplay between gene-body methylation and transcription-coupled cytosine deamination effect. Compositional features are correlated with methylation levels of genes in rice, thale cress, human, bee, and fruit fly (which acts as an unmethylated control). These patterns allow us to generate evolutionary hypotheses about the relationships between GC3 and methylation and how these affect expression patterns. Specifically, we propose that the opposite effects of methylation and compositional gradients along coding regions of GC3-poor and GC3-rich genes are the products of several competing processes.
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Affiliation(s)
- Tatiana Tatarinova
- Laboratory of Applied Pharmacokinetics and Bioinformatics, University of Southern California.
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Nair RR, Nandhini MB, Sethuraman T, Doss G. Mutational pressure dictates synonymous codon usage in freshwater unicellular α - cyanobacterial descendant Paulinella chromatophora and β - cyanobacterium Synechococcus elongatus PCC6301. SPRINGERPLUS 2013; 2:492. [PMID: 24255825 PMCID: PMC3825069 DOI: 10.1186/2193-1801-2-492] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 09/27/2013] [Indexed: 11/10/2022]
Abstract
Background Comparative study of synonymous codon usage variations and factors influencing its diversification in α - cyanobacterial descendant Paulinella chromatophora and β - cyanobacterium Synechococcus elongatus PCC6301 has not been reported so far. In the present study, we investigated various factors associated with synonymous codon usage in the genomes of P. chromatophora and S. elongatus PCC6301 and findings were discussed. Results Mutational pressure was identified as the major force behind codon usage variation in both genomes. However, correspondence analysis revealed that intensity of mutational pressure was higher in S. elongatus than in P. chromatophora. Living habitats were also found to determine synonymous codon usage variations across the genomes of P. chromatophora and S. elongatus. Conclusions Whole genome sequencing of α-cyanobacteria in the cyanobium clade would certainly facilitate the understanding of synonymous codon usage patterns and factors contributing its diversification in presumed ancestors of photosynthetic endosymbionts of P. chromatophora.
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Affiliation(s)
- Rahul Raveendran Nair
- Department of Biotechnology, Vignan University, Vadlamudi, 522 213 Guntur, Andhra Pradesh India
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Wang X, Wu L, Zhou P, Zhu S, An W, Chen Y, Zhao L. Analysis of synonymous codon usage patterns in the genus Rhizobium. World J Microbiol Biotechnol 2013; 29:2015-24. [PMID: 23653263 DOI: 10.1007/s11274-013-1364-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 04/25/2013] [Indexed: 10/26/2022]
Abstract
The codon usage patterns of rhizobia have received increasing attention. However, little information is available regarding the conserved features of the codon usage patterns in a typical rhizobial genus. The codon usage patterns of six completely sequenced strains belonging to the genus Rhizobium were analysed as model rhizobia in the present study. The relative neutrality plot showed that selection pressure played a role in codon usage in the genus Rhizobium. Spearman's rank correlation analysis combined with correspondence analysis (COA) showed that the codon adaptation index and the effective number of codons (ENC) had strong correlation with the first axis of the COA, which indicated the important role of gene expression level and the ENC in the codon usage patterns in this genus. The relative synonymous codon usage of Cys codons had the strongest correlation with the second axis of the COA. Accordingly, the usage of Cys codons was another important factor that shaped the codon usage patterns in Rhizobium genomes and was a conserved feature of the genus. Moreover, the comparison of codon usage between highly and lowly expressed genes showed that 20 unique preferred codons were shared among Rhizobium genomes, revealing another conserved feature of the genus. This is the first report of the codon usage patterns in the genus Rhizobium.
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Affiliation(s)
- Xinxin Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, People's Republic of China,
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Ahmad T, Sablok G, Tatarinova TV, Xu Q, Deng XX, Guo WW. Evaluation of codon biology in citrus and Poncirus trifoliata based on genomic features and frame corrected expressed sequence tags. DNA Res 2013; 20:135-50. [PMID: 23315666 PMCID: PMC3628444 DOI: 10.1093/dnares/dss039] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Citrus, as one of the globally important fruit trees, has been an object of interest for understanding genetics and evolutionary process in fruit crops. Meta-analyses of 19 Citrus species, including 4 globally and economically important Citrus sinensis, Citrus clementina, Citrus reticulata, and 1 Citrus relative Poncirus trifoliata, were performed. We observed that codons ending with A- or T- at the wobble position were preferred in contrast to C- or G- ending codons, indicating a close association with AT richness of Citrus species and P. trifoliata. The present study postulates a large repertoire of a set of optimal codons for the Citrus genus and P. trifoliata and demonstrates that GCT and GGT are evolutionary conserved optimal codons. Our observation suggested that mutational bias is the dominating force in shaping the codon usage bias (CUB) in Citrus and P. trifoliata. Correspondence analysis (COA) revealed that the principal axis [axis 1; COA/relative synonymous codon usage (RSCU)] contributes only a minor portion (∼10.96%) of the recorded variance. In all analysed species, except P. trifoliata, Gravy and aromaticity played minor roles in resolving CUB. Compositional constraints were found to be strongly associated with the amino acid signatures in Citrus species and P. trifoliata. Our present analysis postulates compositional constraints in Citrus species and P. trifoliata and plausible role of the stress with GC3 and coevolution pattern of amino acid.
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Affiliation(s)
- Touqeer Ahmad
- Key Laboratory of Horticultural Plant Biology MOE, Huazhong Agricultural University, Wuhan 430070, China
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Nair RR, Nandhini MB, Monalisha E, Murugan K, Sethuraman T, Nagarajan S, Rao NSP, Ganesh D. Synonymous codon usage in chloroplast genome of Coffea arabica. Bioinformation 2012; 8:1096-104. [PMID: 23251044 PMCID: PMC3523224 DOI: 10.6026/97320630081096] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 10/26/2012] [Indexed: 01/27/2023] Open
Abstract
Synonymous codon usage of 53 protein coding genes in chloroplast genome of Coffea arabica was analyzed for the first time to find out the possible factors contributing codon bias. All preferred synonymous codons were found to use A/T ending codons as chloroplast genomes are rich in AT. No difference in preference for preferred codons was observed in any of the two strands, viz., leading and lagging strands. Complex correlations between total base compositions (A, T, G, C, GC) and silent base contents (A(3), T(3), G(3), C(3), GC(3)) revealed that compositional constraints played crucial role in shaping the codon usage pattern of C. arabica chloroplast genome. ENC Vs GC(3) plot grouped majority of the analyzed genes on or just below the left side of the expected GC(3) curve indicating the influence of base compositional constraints in regulating codon usage. But some of the genes lie distantly below the continuous curve confirmed the influence of some other factors on the codon usage across those genes. Influence of compositional constraints was further confirmed by correspondence analysis as axis 1 and 3 had significant correlations with silent base contents. Correlation of ENC with axis 1, 4 and CAI with 1, 2 prognosticated the minor influence of selection in nature but exact separation of highly and lowly expressed genes could not be seen. From the present study, we concluded that mutational pressure combined with weak selection influenced the pattern of synonymous codon usage across the genes in the chloroplast genomes of C. arabica.
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Affiliation(s)
- Rahul R Nair
- Plant Genetic Improvement Laboratory, Department of Biotechnology, SPK Centre for Environmental
Sciences, Manonmaniam Sundaranar University, Alwarkurichi 627 412, Tirunelveli District, Tamil Nadu. India
| | - Manivasagam B Nandhini
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Palkalai Nagar 625 021, Madurai, Tamil Nadu, India
| | - Elango Monalisha
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Palkalai Nagar 625 021, Madurai, Tamil Nadu, India
| | - Kavitha Murugan
- Plant Genetic Improvement Laboratory, Department of Biotechnology, SPK Centre for Environmental
Sciences, Manonmaniam Sundaranar University, Alwarkurichi 627 412, Tirunelveli District, Tamil Nadu. India
| | - Thilaga Sethuraman
- Plant Genetic Improvement Laboratory, Department of Biotechnology, SPK Centre for Environmental
Sciences, Manonmaniam Sundaranar University, Alwarkurichi 627 412, Tirunelveli District, Tamil Nadu. India
| | - Sangeetha Nagarajan
- Plant Genetic Improvement Laboratory, Department of Biotechnology, SPK Centre for Environmental
Sciences, Manonmaniam Sundaranar University, Alwarkurichi 627 412, Tirunelveli District, Tamil Nadu. India
| | - Nayani Surya Prakash Rao
- Division of Plant Breeding, Central Coffee Research Institute, Coffee Research Station Post 577 117, Chikmagalur District, Karnataka, India
| | - Doss Ganesh
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Palkalai Nagar 625 021, Madurai, Tamil Nadu, India
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Abstract
Human metapneumovirus (HMPV) is an important agent of acute respiratory tract infection in children, while its pathogenicity and molecular evolution are lacking. Herein, we firstly report the synonymous codon usage patterns of HMPV genome. The relative synonymous codon usage (RSCU) values, effective number of codon (ENC) values, nucleotide contents, and correlation analysis were performed among 17 available whole genome of HMPV, including different genotypes. All preferred codons in HMPV are ended with A/U nucleotide and exhibited a great association with its high proportion of these two nucleotides in their genomes. Mutation pressure rather than natural selection is the main influence factor that determines the bias of synonymous codon usage in HMPV. The complementary pattern of codon usage bias between HMPV and human cell was observed, and this phenomenon suggests that host cells might be also act as an important factor to affect the codon usage bias. Moreover, the codon usage biases in each HMPV genotypes are separated into different clades, which suggest that phylogenetic distance might involve in codon usage bias formation as well. These analyses of synonymous codon usage bias in HMPV provide more information for better understanding its evolution and pathogenicity.
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Selva Kumar C, Nair RR, Sivaramakrishnan KG, Ganesh D, Janarthanan S, Arunachalam M, Sivaruban T. Influence of certain forces on evolution of synonymous codon usage bias in certain species of three basal orders of aquatic insects. ACTA ACUST UNITED AC 2012; 23:447-60. [PMID: 22943112 DOI: 10.3109/19401736.2012.710203] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Forces that influence the evolution of synonymous codon usage bias are analyzed in six species of three basal orders of aquatic insects. The rationale behind choosing six species of aquatic insects (three from Ephemeroptera, one from Plecoptera, and two from Odonata) for the present analysis is based on phylogenetic position at the basal clades of the Order Insecta facilitating the understanding of the evolution of codon bias and of factors shaping codon usage patterns in primitive clades of insect lineages and their subtle differences in some of their ecological and environmental requirements in terms of habitat-microhabitat requirements, altitudinal preferences, temperature tolerance ranges, and consequent responses to climate change impacts. The present analysis focuses on open reading frames of the 13 protein-coding genes in the mitochondrial genome of six carefully chosen insect species to get a comprehensive picture of the evolutionary intricacies of codon bias. In all the six species, A and T contents are observed to be significantly higher than G and C, and are used roughly equally. Since transcription hypothesis on codon usage demands A richness and T poorness, it is quite likely that mutation pressure may be the key factor associated with synonymous codon usage (SCU) variations in these species because the mutation hypothesis predicts AT richness and GC poorness in the mitochondrial DNA. Thus, AT-biased mutation pressure seems to be an important factor in framing the SCU variation in all the selected species of aquatic insects, which in turn explains the predominance of A and T ending codons in these species. This study does not find any association between microhabitats and codon usage variations in the mitochondria of selected aquatic insects. However, this study has identified major forces, such as compositional constraints and mutation pressure, which shape patterns of codon usage in mitochondrial genes in the primitive clades of insect lineages.
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Affiliation(s)
- C Selva Kumar
- Department of Zoology, University of Madras, Chennai 600 025, Tamil Nadu, India
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Genome dynamics in three different geographical isolates of white spot syndrome virus (WSSV). Arch Virol 2012; 157:2357-62. [PMID: 22836599 DOI: 10.1007/s00705-012-1395-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 05/21/2012] [Indexed: 10/28/2022]
Abstract
White spot syndrome virus (WSSV), the sole member of the monotypic family Nimaviridae, is considered an extremely lethal shrimp pathogen. Despite its impact, some essential biological characteristics related to WSSV genome dynamics, such as the synonymous codon usage pattern and selection pressure in genes, remain to be elucidated. The results show that compositional limitations and mutational pressure determine the codon usage bias and base composition in WSSV. Furthermore, different forces of selective pressure are acting across various regions of the WSSV genome. Finally, this study points out the possible occurrence of two major recombination events.
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