Genome evolution of Buchnera aphidicola (Gammaproteobacteria): Insights into strand compositional asymmetry, codon usage bias, and phylogenetic implications.
暂无分享,去创建一个
X. Kan | Jianke Yang | Ran Yi | Hengwu Ding | Sijia Zhang | Shiyun Han | Jinming Gao | Y. Ye | Xianzhao Kan
[1] V. Barbe,et al. Co-obligate symbioses have repeatedly evolved across aphids, but partner identity and nutritional contributions vary across lineages , 2023, bioRxiv.
[2] X. Kan,et al. Mitogenomic Codon Usage Patterns of Superfamily Certhioidea (Aves, Passeriformes): Insights into Asymmetrical Bias and Phylogenetic Implications , 2022, Animals : an open access journal from MDPI.
[3] F. Gao,et al. DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes , 2022, Nucleic Acids Res..
[4] Li-li Jiang,et al. Deep decoding of codon usage strategies and host adaption preferences of soybean mosaic virus. , 2022, International journal of biological macromolecules.
[5] F. Gao,et al. Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins , 2022, bioRxiv.
[6] S. Shigenobu,et al. Complex host/symbiont integration of a multi-partner symbiotic system in the eusocial aphid Ceratovacuna japonica , 2022, bioRxiv.
[7] Longhua Wu,et al. Plastome evolution of Aeonium and Monanthes (Crassulaceae): insights into the variation of plastomic tRNAs, and the patterns of codon usage and aversion , 2022, Planta.
[8] Pei Xue,et al. Codon usage divergence of important functional genes in Mycobacterium tuberculosis. , 2022, International journal of biological macromolecules.
[9] Christopher L. Owen,et al. Phylogenomics of the Aphididae: Deep relationships between subfamilies clouded by gene tree discordance, introgression and the gene tree anomaly zone , 2022, Systematic Entomology.
[10] S. Chakraborty,et al. Influencing elements of codon usage bias in Birnaviridae and its evolutionary analysis. , 2022, Virus research.
[11] V. Bhadana,et al. Codon usage bias , 2021, Molecular Biology Reports.
[12] Donovan H. Parks,et al. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy , 2021, Nucleic Acids Res..
[13] H. Musto,et al. Codon Usage Bias: An Endless Tale , 2021, Journal of Molecular Evolution.
[14] X. Kan,et al. Codon usage patterns and evolution of HSP60 in birds. , 2021, International journal of biological macromolecules.
[15] Liyun Jiang,et al. Phylogeny of drepanosiphine aphids sensu lato (Hemiptera, Aphidoidea) inferred from molecular and morphological data , 2021, Current zoology.
[16] Quanming Xu,et al. Genome-wide analysis of the synonymous codon usage pattern of Streptococcus suis. , 2021, Microbial pathogenesis.
[17] Sisi Liu,et al. Analysis of synonymous codon usage of transcriptome database in Rheum palmatum , 2021, PeerJ.
[18] S. Chakraborty,et al. Composition, codon usage pattern, protein properties, and influencing factors in the genomes of members of the family Anelloviridae , 2021, Archives of virology.
[19] N. Lo,et al. Evolutionary Rates are Correlated Between Buchnera Endosymbionts and the Mitochondrial Genomes of Their Aphid Hosts , 2020, Journal of Molecular Evolution.
[20] Z. Ning,et al. Comprehensive analysis of synonymous codon usage patterns and influencing factors of porcine epidemic diarrhea virus , 2020, Archives of virology.
[21] Fan Song,et al. The complete mitochondrial genome of the mealy plum aphid, Hyalopterus pruni (Hemiptera: Aphididae) , 2020, Mitochondrial DNA. Part B, Resources.
[22] D. Gordenin,et al. Hypermutation in single-stranded DNA , 2020, DNA Repair.
[23] E. Kiers,et al. Parallel Evolution in the Integration of a Co-obligate Aphid Symbiosis , 2020, Current Biology.
[24] C. Pandey,et al. Application of Student's t-test, Analysis of Variance, and Covariance , 2019, Annals of cardiac anaesthesia.
[25] Lawrence S. Hon,et al. Description of soybean aphid (Aphis glycines Matsumura) mitochondrial genome and comparative mitogenomics of Aphididae (Hemiptera: Sternorrhyncha). , 2019, Insect biochemistry and molecular biology.
[26] Johannes L. Schönberger,et al. SciPy 1.0: fundamental algorithms for scientific computing in Python , 2019, Nature Methods.
[27] N. Moran,et al. Genome Evolution of the Obligate Endosymbiont Buchnera aphidicola. , 2019, Molecular biology and evolution.
[28] Alexey M. Kozlov,et al. ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models , 2019, bioRxiv.
[29] Jin Zhang,et al. PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies , 2018, bioRxiv.
[30] Alexey M. Kozlov,et al. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference , 2018, bioRxiv.
[31] Christa Boer,et al. Correlation Coefficients: Appropriate Use and Interpretation , 2018, Anesthesia and analgesia.
[32] M. Suchard,et al. Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 , 2018, Systematic biology.
[33] Dave Clarke,et al. Molecular phylogeny of Macrosiphini (Hemiptera: Aphididae): An evolutionary hypothesis for the Pterocomma-group habitat adaptation. , 2018, Molecular phylogenetics and evolution.
[34] Kazunori D. Yamada,et al. Parallelization of MAFFT for large-scale multiple sequence alignments , 2018, Bioinform..
[35] Yang Zhang,et al. Genetic Structure of the Bacterial Endosymbiont Buchnera aphidicola from Its Host Aphid Schlechtendalia chinensis and Evolutionary Implications , 2018, Current Microbiology.
[36] A. von Haeseler,et al. MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation , 2018, BMC Evolutionary Biology.
[37] N. Moran,et al. Evolutionary loss and replacement of Buchnera, the obligate endosymbiont of aphids , 2018, The ISME Journal.
[38] Yasukazu Nakamura,et al. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication , 2017, Bioinform..
[39] R. Asokan,et al. Reconstructing the macroevolutionary patterns of aphids (Hemiptera: Aphididae) using nuclear and mitochondrial DNA sequences , 2017 .
[40] Y. Wang,et al. Mitochondrial genome sequences effectively reveal deep branching events in aphids (Insecta: Hemiptera: Aphididae) , 2017 .
[41] X. Peng,et al. Analysis of transcriptome data reveals multifactor constraint on codon usage in Taenia multiceps , 2017, BMC Genomics.
[42] Peter D. Karp,et al. The EcoCyc database: reflecting new knowledge about Escherichia coli K-12 , 2016, Nucleic Acids Res..
[43] H. Zhang,et al. All 37 Mitochondrial Genes of Aphid Aphis craccivora Obtained from Transcriptome Sequencing: Implications for the Evolution of Aphids , 2016, PloS one.
[44] F. Guo,et al. Multiple Factors Drive Replicating Strand Composition Bias in Bacterial Genomes , 2015, International journal of molecular sciences.
[45] Zeyang Zhou,et al. Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes , 2015, PloS one.
[46] N. Moran,et al. The tiniest tiny genomes. , 2014, Annual review of microbiology.
[47] N. Moran,et al. Reconstructing the phylogeny of aphids (Hemiptera: Aphididae) using DNA of the obligate symbiont Buchnera aphidicola. , 2013, Molecular phylogenetics and evolution.
[48] R. Bambara,et al. Okazaki fragment metabolism. , 2013, Cold Spring Harbor perspectives in biology.
[49] C. Dutta,et al. Microbial Lifestyle and Genome Signatures , 2012, Current genomics.
[50] Maxim Teslenko,et al. MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space , 2012, Systematic biology.
[51] Y. Jang,et al. Macroevolutionary Patterns in the Aphidini Aphids (Hemiptera: Aphididae): Diversification, Host Association, and Biogeographic Origins , 2011, PloS one.
[52] A. Moya,et al. New Clues about the Evolutionary History of Metabolic Losses in Bacterial Endosymbionts, Provided by the Genome of Buchnera aphidicola from the Aphid Cinara tujafilina , 2011, Applied and Environmental Microbiology.
[53] F. Guo,et al. Strong Strand Composition Bias in the Genome of Ehrlichia canis Revealed by Multiple Methods , 2010, The open microbiology journal.
[54] S. K. Ray,et al. Strand‐specific mutational bias influences codon usage of weakly expressed genes in Escherichia coli , 2010, Genes to cells : devoted to molecular & cellular mechanisms.
[55] B. Ortiz-Rivas,et al. Combination of molecular data support the existence of three main lineages in the phylogeny of aphids (Hemiptera: Aphididae) and the basal position of the subfamily Lachninae. , 2010, Molecular phylogenetics and evolution.
[56] Igor Goryanin,et al. A fragile metabolic network adapted for cooperation in the symbiotic bacterium Buchnera aphidicola , 2009, BMC Systems Biology.
[57] F. Guo,et al. Codon Usages of Genes on Chromosome, and Surprisingly, Genes in Plasmid are Primarily Affected by Strand-specific Mutational Biases in Lawsonia intracellularis , 2009, DNA research : an international journal for rapid publication of reports on genes and genomes.
[58] E. Jousselin,et al. Fine-scale cospeciation between Brachycaudus and Buchnera aphidicola: bacterial genome helps define species and evolutionary relationships in aphids , 2009, Proceedings of the Royal Society B: Biological Sciences.
[59] N. Moran,et al. Genomics and evolution of heritable bacterial symbionts. , 2008, Annual review of genetics.
[60] Eduardo P C Rocha,et al. From GC skews to wavelets: a gentle guide to the analysis of compositional asymmetries in genomic data. , 2008, Biochimie.
[61] Gerard Talavera,et al. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. , 2007, Systematic biology.
[62] M. Cox. Regulation of Bacterial RecA Protein Function , 2007, Critical reviews in biochemistry and molecular biology.
[63] Andrés Moya,et al. A Small Microbial Genome: The End of a Long Symbiotic Relationship? , 2006, Science.
[64] Qingpo Liu. Analysis of codon usage pattern in the radioresistant bacterium Deinococcus radiodurans. , 2006, Bio Systems.
[65] S. Andersson,et al. Strong asymmetric mutation bias in endosymbiont genomes coincide with loss of genes for replication restart pathways. , 2006, Molecular biology and evolution.
[66] C. Dutta,et al. Evolutionary Constraints on Codon and Amino Acid Usage in Two Strains of Human Pathogenic Actinobacteria Tropheryma whipplei , 2006, Journal of Molecular Evolution.
[67] A. Douglas. Phloem-sap feeding by animals: problems and solutions. , 2006, Journal of experimental botany.
[68] T. Ghosh,et al. Evolutionary Forces in Shaping the Codon and Amino Acid Usages in Blochmannia floridanus , 2004, Journal of Biomolecular Structure and Dynamics.
[69] Eduardo P C Rocha,et al. The replication-related organization of bacterial genomes. , 2004, Microbiology.
[70] T. Fukatsu,et al. Changing partners in an obligate symbiosis: a facultative endosymbiont can compensate for loss of the essential endosymbiont Buchnera in an aphid , 2003, Proceedings of the Royal Society of London. Series B: Biological Sciences.
[71] A. Moya,et al. Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids. , 2003, Genome research.
[72] N. Sueoka,et al. Asymmetric directional mutation pressures in bacteria , 2002, Genome Biology.
[73] Andrés Moya,et al. Extreme genome reduction in Buchnera spp.: Toward the minimal genome needed for symbiotic life , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[74] A. Moya,et al. Molecular systematics of aphids and their primary endosymbionts. , 2001, Molecular phylogenetics and evolution.
[75] H. Ochman,et al. Deamination as the basis of strand-asymmetric evolution in transcribed Escherichia coli sequences. , 2001, Molecular biology and evolution.
[76] N. Moran,et al. Molecular data support a rapid radiation of aphids in the Cretaceous and multiple origins of host alternation , 2000 .
[77] H. Romero,et al. Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces. , 2000, Nucleic acids research.
[78] J. Lobry,et al. Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. , 1999, Gene.
[79] N. Sueoka. Two Aspects of DNA Base Composition: G+C Content and Translation-Coupled Deviation from Intra-Strand Rule of A=T and G=C , 1999, Journal of Molecular Evolution.
[80] P. Sharp,et al. Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases. , 1999, Nucleic acids research.
[81] N. Moran,et al. How nutritionally imbalanced is phloem sap for aphids? , 1999 .
[82] J O McInerney,et al. Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[83] A. Moya,et al. Putative evolutionary origin of plasmids carrying the genes involved in leucine biosynthesis in Buchnera aphidicola (endosymbiont of aphids) , 1997, Journal of bacteriology.
[84] H. Ochman,et al. Strand asymmetries in DNA evolution. , 1997, Trends in genetics : TIG.
[85] T. Fukatsu,et al. Phylogenetic position of yeast-like symbiont of Hamiltonaphis styraci (Homoptera, Aphididae) based on 18S rDNA sequence. , 1996, Insect biochemistry and molecular biology.
[86] N. Moran,et al. A molecular clock in endosymbiotic bacteria is calibrated using the insect hosts , 1993, Proceedings of the Royal Society of London. Series B: Biological Sciences.
[87] F. Wright. The 'effective number of codons' used in a gene. , 1990, Gene.
[88] N. Sueoka. Directional mutation pressure and neutral molecular evolution. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[89] T. Okazaki,et al. Mechanism of DNA chain growth. I. Possible discontinuity and unusual secondary structure of newly synthesized chains. , 1968, Proceedings of the National Academy of Sciences of the United States of America.
[90] G. Qiao,et al. Is the subfamily Eriosomatinae (Hemiptera: Aphididae) monophyletic? , 2014 .
[91] A. Alzohairy. BioEdit: An important software for molecular biology , 2011 .
[92] C. Dutta,et al. Codon and amino acid usage in two major human pathogens of genus Bartonella--optimization between replicational-transcriptional selection, translational control and cost minimization. , 2005, DNA research : an international journal for rapid publication of reports on genes and genomes.
[93] A. Moya,et al. Molecular systematics of aphids (Homoptera: Aphididae): new insights from the long-wavelength opsin gene. , 2004, Molecular phylogenetics and evolution.
[94] Pierre Legendre,et al. Statistical comparison of univariate tests of homogeneity of variances , 2001 .
[95] A. Douglas,et al. Nutritional interactions in insect-microbial symbioses: aphids and their symbiotic bacteria Buchnera. , 1998, Annual review of entomology.
[96] N. Moran,et al. Genetics, physiology, and evolutionary relationships of the genus Buchnera: intracellular symbionts of aphids. , 1995, Annual review of microbiology.
[97] A. K. Minks,et al. Paleontology and phylogeny , 1987 .