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Wang L, Zhao H, Wang Z, Ding S, Qin L, Jiang R, Deng X, He Z, Li L. An Evolutionary Perspective of Codon Usage Pattern, Dinucleotide Composition and Codon Pair Bias in Prunus Necrotic Ringspot Virus. Genes (Basel) 2023; 14:1712. [PMID: 37761852 PMCID: PMC10530913 DOI: 10.3390/genes14091712] [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: 07/31/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Prunus necrotic ringspot virus (PNRSV) is a significant virus of ornamental plants and fruit trees. It is essential to study this virus due to its impact on the horticultural industry. Several studies on PNRSV diversity and phytosanitary detection technology were reported, but the content on the codon usage bias (CUB), dinucleotide preference and codon pair bias (CPB) of PNRSV is still uncertain. We performed comprehensive analyses on a dataset consisting of 359 coat protein (CP) gene sequences in PNRSV to examine the characteristics of CUB, dinucleotide composition, and CPB. The CUB analysis of PNRSV CP sequences showed that it was not only affected by natural selection, but also affected by mutations, and natural selection played a more significant role compared to mutations as the driving force. The dinucleotide composition analysis showed an over-expression of the CpC/GpA dinucleotides and an under-expression of the UpA/GpC dinucleotides. The dinucleotide composition of the PNRSV CP gene showed a weak association with the viral lineages and hosts, but a strong association with viral codon positions. Furthermore, the CPB of PNRSV CP gene is low and is related to dinucleotide preference and codon usage patterns. This research provides reference for future research on PNRSV genetic diversity and gene evolution mechanism.
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Affiliation(s)
- Lingqi Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China;
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Haiting Zhao
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Zhilei Wang
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Shiwen Ding
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Lang Qin
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Runzhou Jiang
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Xiaolong Deng
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Zhen He
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Liangjun Li
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China;
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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Whittle CA, Kulkarni A, Chung N, Extavour CG. Adaptation of codon and amino acid use for translational functions in highly expressed cricket genes. BMC Genomics 2021; 22:234. [PMID: 33823803 PMCID: PMC8022432 DOI: 10.1186/s12864-021-07411-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/27/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND For multicellular organisms, much remains unknown about the dynamics of synonymous codon and amino acid use in highly expressed genes, including whether their use varies with expression in different tissue types and sexes. Moreover, specific codons and amino acids may have translational functions in highly transcribed genes, that largely depend on their relationships to tRNA gene copies in the genome. However, these relationships and putative functions are poorly understood, particularly in multicellular systems. RESULTS Here, we studied codon and amino acid use in highly expressed genes from reproductive and nervous system tissues (male and female gonad, somatic reproductive system, brain and ventral nerve cord, and male accessory glands) in the cricket Gryllus bimaculatus. We report an optimal codon, defined as the codon preferentially used in highly expressed genes, for each of the 18 amino acids with synonymous codons in this organism. The optimal codons were mostly shared among tissue types and both sexes. However, the frequency of optimal codons was highest in gonadal genes. Concordant with translational selection, a majority of the optimal codons had abundant matching tRNA gene copies in the genome, but sometimes obligately required wobble tRNAs. We suggest the latter may comprise a mechanism for slowing translation of abundant transcripts, particularly for cell-cycle genes. Non-optimal codons, defined as those least commonly used in highly transcribed genes, intriguingly often had abundant tRNAs, and had elevated use in a subset of genes with specialized functions (gametic and apoptosis genes), suggesting their use promotes the translational upregulation of particular mRNAs. In terms of amino acids, we found evidence suggesting that amino acid frequency, tRNA gene copy number, and amino acid biosynthetic costs (size/complexity) had all interdependently evolved in this insect model, potentially for translational optimization. CONCLUSIONS Collectively, the results suggest a model whereby codon use in highly expressed genes, including optimal, wobble, and non-optimal codons, and their tRNA abundances, as well as amino acid use, have been influenced by adaptation for various functional roles in translation within this cricket. The effects of expression in different tissue types and the two sexes are discussed.
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Affiliation(s)
- Carrie A Whittle
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Arpita Kulkarni
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Nina Chung
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA.
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, 02138, MA, USA.
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Gupta K, Dhawan R, Kajla M, Misra T, Kumar S, Gupta L. The evolutionary divergence of STAT transcription factor in different Anopheles species. Gene 2016; 596:89-97. [PMID: 27664587 DOI: 10.1016/j.gene.2016.09.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 08/28/2016] [Accepted: 09/14/2016] [Indexed: 12/27/2022]
Abstract
Anopheles mosquito transmits Plasmodium, the malaria causing parasite. Different species of Anopheles mosquito dominate in a particular geographical location and are capable of transmitting specific strains of Plasmodium. It is important to understand the biology of different anophelines to control the parasite transmission. STAT is an evolutionary conserved transcription factor that regulates the parasite development in African malaria vector Anopheles gambiae. Unlike Drosophila and Aedes aegypti, where a single STAT gene plays an important role in immunity, An. gambiae contains one evolutionary conserved STAT-A and another retro-duplicated, introns-less STAT-B gene. To find out whether other species of Anopheles also have two STATs, the available genomic data of different anophelines were used to annotate their STATs through in silico analyses. Our results revealed that Indian malaria vector An. stephensi genome contains two STATs, AsSTAT-A and AsSTAT-B genes. These genes were cloned and confirmed by sequencing. Both AsSTATs were found to be expressed in different development stages of mosquito. However, the relative mRNA levels of evolutionary conserved AsSTAT-A gene were always higher than the retroduplicated AsSTAT-B gene. STAT pathway was activated upon Plasmodium berghei infection, indicated its role in immunity. Furthermore, comparative in silico analysis of eighteen Anopheles species revealed that five species: An. sinensis, An. albimanus, An. darlingi, An. dirus andAn. farauti do not contain STAT-B gene in their genome. Interestingly, thirteen species of the subgenus Anopheles and Cellia that contain both STATs were also mutually diverged. This consequence leads to sequence variability in some significant protein motifs within the STAT-B genes. Phylogenetic analyses indicated that an independent, lineage-specific duplication occurred in the subgenus Cellia after the diversification of series Neomyzomyia from its last common ancestor. In An. atroparvus (subgenus Anopheles), STAT gene underwent recent lineage-specific duplication and give rise to a highly similar STAT-B gene. This suggested that the genetic divergence in various Anopheles species might appeared due to their adaptations to the altered environmental conditions or pathogen encounters.
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Affiliation(s)
- Kuldeep Gupta
- Molecular Parasitology and Vector Biology Laboratory, Department of Biological Sciences, Birla Institute of Technology & Sciences (BITS) - Pilani, Pilani 333031, Rajasthan, India
| | - Rini Dhawan
- Molecular Parasitology and Vector Biology Laboratory, Department of Biological Sciences, Birla Institute of Technology & Sciences (BITS) - Pilani, Pilani 333031, Rajasthan, India
| | - Mithilesh Kajla
- Molecular Parasitology and Vector Biology Laboratory, Department of Biological Sciences, Birla Institute of Technology & Sciences (BITS) - Pilani, Pilani 333031, Rajasthan, India
| | - Tripti Misra
- Molecular Parasitology and Vector Biology Laboratory, Department of Biological Sciences, Birla Institute of Technology & Sciences (BITS) - Pilani, Pilani 333031, Rajasthan, India
| | - Sanjeev Kumar
- Molecular Parasitology and Vector Biology Laboratory, Department of Biological Sciences, Birla Institute of Technology & Sciences (BITS) - Pilani, Pilani 333031, Rajasthan, India; Department of Biotechnology, Ch. Bansi Lal University, Bhiwani, Haryana, India
| | - Lalita Gupta
- Molecular Parasitology and Vector Biology Laboratory, Department of Biological Sciences, Birla Institute of Technology & Sciences (BITS) - Pilani, Pilani 333031, Rajasthan, India; Department of Zoology, Ch. Bansi Lal University, Bhiwani, Haryana, India.
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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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Behura SK, Sarro J, Li P, Mysore K, Severson DW, Emrich SJ, Duman-Scheel M. High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti. BMC Genomics 2016; 17:341. [PMID: 27161480 PMCID: PMC4862039 DOI: 10.1186/s12864-016-2468-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/12/2016] [Indexed: 12/15/2022] Open
Abstract
Background Despite substantial progress in mosquito genomic and genetic research, few cis-regulatory elements (CREs), DNA sequences that control gene expression, have been identified in mosquitoes or other non-model insects. Formaldehyde-assisted isolation of regulatory elements paired with DNA sequencing, FAIRE-seq, is emerging as a powerful new high-throughput tool for global CRE discovery. FAIRE results in the preferential recovery of open chromatin DNA fragments that are not bound by nucleosomes, an evolutionarily conserved indicator of regulatory activity, which are then sequenced. Despite the power of the approach, FAIRE-seq has not yet been applied to the study of non-model insects. In this investigation, we utilized FAIRE-seq to profile open chromatin and identify likely regulatory elements throughout the genome of the human disease vector mosquito Aedes aegypti. We then assessed genetic variation in the regulatory elements of dengue virus susceptible (Moyo-S) and refractory (Moyo-R) mosquito strains. Results Analysis of sequence data obtained through next generation sequencing of FAIRE DNA isolated from A. aegypti embryos revealed >121,000 FAIRE peaks (FPs), many of which clustered in the 1 kb 5’ upstream flanking regions of genes known to be expressed at this stage. As expected, known transcription factor consensus binding sites were enriched in the FPs, and of these FoxA1, Hunchback, Gfi, Klf4, MYB/ph3 and Sox9 are most predominant. All of the elements tested in vivo were confirmed to drive gene expression in transgenic Drosophila reporter assays. Of the >13,000 single nucleotide polymorphisms (SNPs) recently identified in dengue virus-susceptible and refractory mosquito strains, 3365 were found to map to FPs. Conclusion FAIRE-seq analysis of open chromatin in A. aegypti permitted genome-wide discovery of CREs. The results of this investigation indicate that FAIRE-seq is a powerful tool for identification of regulatory DNA in the genomes of non-model organisms, including human disease vector mosquitoes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2468-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Susanta K Behura
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Joseph Sarro
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, 1234 Notre Dame Ave., South Bend, IN, 46617, USA
| | - Ping Li
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, 1234 Notre Dame Ave., South Bend, IN, 46617, USA
| | - Keshava Mysore
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, 1234 Notre Dame Ave., South Bend, IN, 46617, USA
| | - David W Severson
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, 1234 Notre Dame Ave., South Bend, IN, 46617, USA
| | - Scott J Emrich
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA. .,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA. .,Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA.
| | - Molly Duman-Scheel
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA. .,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA. .,Department of Medical and Molecular Genetics, Indiana University School of Medicine, 1234 Notre Dame Ave., South Bend, IN, 46617, USA.
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Chakraborty P, Das S, Saha B, Sarkar P, Karmakar A, Saha A, Saha D, Saha A. Phylogeny and synonymous codon usage pattern of Papaya ringspot virus coat protein gene in the sub-Himalayan region of north-east India. Can J Microbiol 2015; 61:555-64. [DOI: 10.1139/cjm-2015-0172] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Sub-Himalayan West Bengal is favorable for the production of several fruits and vegetables. Papaya is one of the common plants cultivated in the area. Most of the papaya plants of the area are susceptible to Papaya ringspot virus (PRSV). Coat protein genes of 6 PRSV isolates of the area were sequenced following RT–PCR. Phylogenetic study of the PRSV isolates showed about 80%–90% similarity with Cuban isolates. The codon usage pattern of our isolates was also analyzed, along with several other isolates. PRSV isolates of our study showed a preference for 8 putative optimal codons. Correspondence analysis of the genes of different isolates along the first 2 major axes were done, as the first 2 axes contributed more in shaping codon usage pattern. In the phylogenetic tree constructed by the neighbour-joining method, our isolates clustered together with the east Indian, north Indian, and Bangladeshi isolates. The diversity and codon usage pattern of the PRSV isolates of different regions were studied, and it was observed that the codon usage pattern of PRSV isolates is probably influenced by translational selection along with mutational bias.
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Affiliation(s)
| | - Shibu Das
- Department of Botany, University of North Bengal, Siliguri 734013, India
| | - Bikram Saha
- Department of Botany, University of North Bengal, Siliguri 734013, India
| | - Piyali Sarkar
- Department of Botany, University of North Bengal, Siliguri 734013, India
| | - Arup Karmakar
- Department of Botany, University of North Bengal, Siliguri 734013, India
| | - Arnab Saha
- Department of Botany, University of North Bengal, Siliguri 734013, India
| | - Dipanwita Saha
- Department of Biotechnology, University of North Bengal, Siliguri 734013, India
| | - Aniruddha Saha
- Department of Botany, University of North Bengal, Siliguri 734013, India
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Kessler MD, Dean MD. Effective population size does not predict codon usage bias in mammals. Ecol Evol 2014; 4:3887-900. [PMID: 25505518 PMCID: PMC4242573 DOI: 10.1002/ece3.1249] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/04/2014] [Accepted: 08/07/2014] [Indexed: 12/20/2022] Open
Abstract
Synonymous codons are not used at equal frequency throughout the genome, a phenomenon termed codon usage bias (CUB). It is often assumed that interspecific variation in the intensity of CUB is related to species differences in effective population sizes (Ne), with selection on CUB operating less efficiently in species with small Ne. Here, we specifically ask whether variation in Ne predicts differences in CUB in mammals and report two main findings. First, across 41 mammalian genomes, CUB was not correlated with two indirect proxies of Ne (body mass and generation time), even though there was statistically significant evidence of selection shaping CUB across all species. Interestingly, autosomal genes showed higher codon usage bias compared to X-linked genes, and high-recombination genes showed higher codon usage bias compared to low recombination genes, suggesting intraspecific variation in Ne predicts variation in CUB. Second, across six mammalian species with genetic estimates of Ne (human, chimpanzee, rabbit, and three mouse species: Mus musculus, M. domesticus, and M. castaneus), Ne and CUB were weakly and inconsistently correlated. At least in mammals, interspecific divergence in Ne does not strongly predict variation in CUB. One hypothesis is that each species responds to a unique distribution of selection coefficients, confounding any straightforward link between Ne and CUB.
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Affiliation(s)
- Michael D Kessler
- Molecular and Computational Biology, University of Southern California 1050 Childs Way, Los Angeles, California, 90089
| | - Matthew D Dean
- Molecular and Computational Biology, University of Southern California 1050 Childs Way, Los Angeles, California, 90089
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Large-scale genomic analysis of codon usage in dengue virus and evaluation of its phylogenetic dependence. BIOMED RESEARCH INTERNATIONAL 2014; 2014:851425. [PMID: 25136631 PMCID: PMC4124757 DOI: 10.1155/2014/851425] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 06/05/2014] [Accepted: 06/11/2014] [Indexed: 12/04/2022]
Abstract
The increasing number of dengue virus (DENV) genome sequences available allows identifying the contributing factors to DENV evolution. In the present study, the codon usage in serotypes 1–4 (DENV1–4) has been explored for 3047 sequenced genomes using different statistics methods. The correlation analysis of total GC content (GC) with GC content at the three nucleotide positions of codons (GC1, GC2, and GC3) as well as the effective number of codons (ENC, ENCp) versus GC3 plots revealed mutational bias and purifying selection pressures as the major forces influencing the codon usage, but with distinct pressure on specific nucleotide position in the codon. The correspondence analysis (CA) and clustering analysis on relative synonymous codon usage (RSCU) within each serotype showed similar clustering patterns to the phylogenetic analysis of nucleotide sequences for DENV1–4. These clustering patterns are strongly related to the virus geographic origin. The phylogenetic dependence analysis also suggests that stabilizing selection acts on the codon usage bias. Our analysis of a large scale reveals new feature on DENV genomic evolution.
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Zhou D, Zhang D, Ding G, Shi L, Hou Q, Ye Y, Xu Y, Zhou H, Xiong C, Li S, Yu J, Hong S, Yu X, Zou P, Chen C, Chang X, Wang W, Lv Y, Sun Y, Ma L, Shen B, Zhu C. Genome sequence of Anopheles sinensis provides insight into genetics basis of mosquito competence for malaria parasites. BMC Genomics 2014; 15:42. [PMID: 24438588 PMCID: PMC3901762 DOI: 10.1186/1471-2164-15-42] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 01/16/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Anopheles sinensis is an important mosquito vector of Plasmodium vivax, which is the most frequent and widely distributed cause of recurring malaria throughout Asia, and particularly in China, Korea, and Japan. RESULTS We performed 454 next-generation sequencing and obtained a draft sequence of A. sinensis assembled into scaffolds spanning 220.8 million base pairs. Analysis of this genome sequence, we observed expansion and contraction of several immune-related gene families in anopheline relative to culicine mosquito species. These differences suggest that species-specific immune responses to Plasmodium invasion underpin the biological differences in susceptibility to Plasmodium infection that characterize these two mosquito subfamilies. CONCLUSIONS The A. sinensis genome produced in this study, provides an important resource for analyzing the genetic basis of susceptibility and resistance of mosquitoes to Plasmodium parasites research which will ultimately facilitate the design of urgently needed interventions against this debilitating mosquito-borne disease.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Bo Shen
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu 210029, P,R, China.
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