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For: Chen WH, Lu G, Bork P, Hu S, Lercher MJ. Energy efficiency trade-offs drive nucleotide usage in transcribed regions. Nat Commun 2016;7:11334. [PMID: 27098217 PMCID: PMC4844684 DOI: 10.1038/ncomms11334] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 03/16/2016] [Indexed: 01/29/2023]  Open
Number Cited by Other Article(s)
1
Jeena NS, Rahuman S, Sebastian W, Kumar R, Sajeela KA, Kizhakudan JK, Menon KK, Roul SK, Gopalakrishnan A, Radhakrishnan EV. Mitogenomic recognition of incognito lineages in the mud spiny lobster Panulirus polyphagus (Herbst, 1793): A tale of unique genetic structuring and diversification. Int J Biol Macromol 2024;277:134327. [PMID: 39098694 DOI: 10.1016/j.ijbiomac.2024.134327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024]
2
Wang Z, Zhang S, Geng Z, Li C, Sun L, Zhang L, Cao Z. Soil bacterial community diversity and life strategy during slope restoration on an uninhabited island: changes under the aggregate spray-seeding technique. J Appl Microbiol 2024;135:lxae132. [PMID: 38830801 DOI: 10.1093/jambio/lxae132] [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: 02/07/2024] [Revised: 05/29/2024] [Accepted: 05/31/2024] [Indexed: 06/05/2024]
3
Kapoor S, Yang YT, Hall RN, Gasser RB, Bowles VM, Perry T, Anstead CA. Complete Mitochondrial Genome for Lucilia cuprina dorsalis (Diptera: Calliphoridae) from the Northern Territory, Australia. Genes (Basel) 2024;15:506. [PMID: 38674440 PMCID: PMC11050061 DOI: 10.3390/genes15040506] [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: 03/20/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]  Open
4
Wu Y, Gao N, Sun C, Feng T, Liu Q, Chen WH. A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments. MICROBIOME 2024;12:69. [PMID: 38576042 PMCID: PMC10993611 DOI: 10.1186/s40168-024-01784-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
5
Kaplan NA, Islam KN, Kanis FC, Verderber JR, Wang X, Jones JA, Koffas MAG. Simultaneous glucose and xylose utilization by an Escherichia coli catabolite repression mutant. Appl Environ Microbiol 2024;90:e0216923. [PMID: 38289128 PMCID: PMC10880614 DOI: 10.1128/aem.02169-23] [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: 12/01/2023] [Accepted: 12/11/2023] [Indexed: 02/22/2024]  Open
6
Aliperti L, Aptekmann AA, Farfañuk G, Couso LL, Soler-Bistué A, Sánchez IE. r/K selection of GC content in prokaryotes. Environ Microbiol 2023;25:3255-3268. [PMID: 37813828 DOI: 10.1111/1462-2920.16511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/16/2023] [Indexed: 10/11/2023]
7
Madrid I, Zheng Z, Gerbelot C, Fujiwara A, Li S, Grall S, Nishiguchi K, Kim SH, Chovin A, Demaille C, Clement N. Ballistic Brownian Motion of Nanoconfined DNA. ACS NANO 2023;17:17031-17040. [PMID: 37700490 DOI: 10.1021/acsnano.3c04349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
8
Li J, Li N, Roellig DM, Zhao W, Guo Y, Feng Y, Xiao L. High subtelomeric GC content in the genome of a zoonotic Cryptosporidium species. Microb Genom 2023;9:mgen001052. [PMID: 37399068 PMCID: PMC10438818 DOI: 10.1099/mgen.0.001052] [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: 01/06/2023] [Accepted: 05/24/2023] [Indexed: 07/04/2023]  Open
9
Moeckel C, Zaravinos A, Georgakopoulos-Soares I. Strand Asymmetries Across Genomic Processes. Comput Struct Biotechnol J 2023;21:2036-2047. [PMID: 36968020 PMCID: PMC10030826 DOI: 10.1016/j.csbj.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023]  Open
10
Pu F, Wang R, Yang X, Hu X, Wang J, Zhang L, Zhao Y, Zhang D, Liu Z, Liu J. Nucleotide and codon usage biases involved in the evolution of African swine fever virus: A comparative genomics analysis. J Basic Microbiol 2023;63:499-518. [PMID: 36782108 DOI: 10.1002/jobm.202200624] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/05/2023] [Accepted: 01/21/2023] [Indexed: 02/15/2023]
11
Shi F, Yu T, Xu Y, Zhang S, Niu Y, Ge S, Tao J, Zong S. Comparative mitochondrial genomic analysis provides new insights into the evolution of the subfamily Lamiinae (Coleoptera: Cerambycidae). Int J Biol Macromol 2023;225:634-647. [PMID: 36403761 DOI: 10.1016/j.ijbiomac.2022.11.125] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/23/2022] [Accepted: 11/12/2022] [Indexed: 11/18/2022]
12
The Mitochondrial Genome of the Globally Invasive Barnacle Megabalanus coccopoma Darwin 1854 (Crustacea: Balanomorpha): Rearrangement and Phylogenetic Consideration within Balanomorpha. DIVERSITY 2023. [DOI: 10.3390/d15010117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
13
Dong MJ, Luo H, Gao F. DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes. Nucleic Acids Res 2022;51:D117-D120. [PMID: 36305822 PMCID: PMC9825612 DOI: 10.1093/nar/gkac964] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/08/2022] [Accepted: 10/13/2022] [Indexed: 01/29/2023]  Open
14
Dong MJ, Luo H, Gao F. Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022;20:1207-1213. [PMID: 36257484 DOI: 10.1016/j.gpb.2022.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 09/21/2022] [Accepted: 10/11/2022] [Indexed: 12/26/2022]
15
Yang Y, Kang Y, Tong J, Ge X, Yang X, Liu H. Mitochondrial gene rearrangements suggest a new genus in the subfamily Cantharinae (Coleoptera). ZOOL SCR 2022. [DOI: 10.1111/zsc.12572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
16
Complete Mitogenomes of Polypedates Tree Frogs Unveil Gene Rearrangement and Concerted Evolution within Rhacophoridae. Animals (Basel) 2022;12:ani12182449. [PMID: 36139309 PMCID: PMC9494961 DOI: 10.3390/ani12182449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/10/2022] [Accepted: 09/13/2022] [Indexed: 11/28/2022]  Open
17
Bharti R, Siebert D, Blombach B, Grimm DG. Systematic analysis of the underlying genomic architecture for transcriptional-translational coupling in prokaryotes. NAR Genom Bioinform 2022;4:lqac074. [PMID: 36186922 PMCID: PMC9514032 DOI: 10.1093/nargab/lqac074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 09/05/2022] [Accepted: 09/15/2022] [Indexed: 11/12/2022]  Open
18
Mitochondrial Genomes Provide New Phylogenetic and Evolutionary Insights into Psilidae (Diptera: Brachycera). INSECTS 2022;13:insects13060518. [PMID: 35735855 PMCID: PMC9224655 DOI: 10.3390/insects13060518] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/29/2022] [Accepted: 05/30/2022] [Indexed: 02/05/2023]
19
Consistent Clustering Pattern of Prokaryotic Genes Based on Base Frequency at the Second Codon Position and its Association with Functional Category Preference. Interdiscip Sci 2022;14:349-357. [PMID: 34817803 PMCID: PMC9124167 DOI: 10.1007/s12539-021-00493-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 11/02/2021] [Accepted: 11/07/2021] [Indexed: 10/26/2022]
20
Jin YT, Pu DK, Guo HX, Deng Z, Chen LL, Guo FB. T-G-A Deficiency Pattern in Protein-Coding Genes and Its Potential Reason. Front Microbiol 2022;13:847325. [PMID: 35602045 PMCID: PMC9116502 DOI: 10.3389/fmicb.2022.847325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 03/30/2022] [Indexed: 11/20/2022]  Open
21
Merrikh H, Merrikh C. Reply to: Testing the adaptive hypothesis of lagging-strand encoding in bacterial genomes. Nat Commun 2022;13:2627. [PMID: 35551437 PMCID: PMC9098457 DOI: 10.1038/s41467-022-30014-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 03/08/2022] [Indexed: 11/09/2022]  Open
22
Liu H, Zhang J. Testing the adaptive hypothesis of lagging-strand encoding in bacterial genomes. Nat Commun 2022;13:2628. [PMID: 35552380 PMCID: PMC9098844 DOI: 10.1038/s41467-022-30000-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 04/12/2021] [Indexed: 11/24/2022]  Open
23
Markosian C, Staquicini DI, Dogra P, Dodero-Rojas E, Lubin JH, Tang FH, Smith TL, Contessoto VG, Libutti SK, Wang Z, Cristini V, Khare SD, Whitford PC, Burley SK, Onuchic JN, Pasqualini R, Arap W. Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection. Mol Biol Evol 2022;39:msac091. [PMID: 35511693 PMCID: PMC9129195 DOI: 10.1093/molbev/msac091] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
24
Yuan L, Liu H, Ge X, Yang G, Xie G, Yang Y. A Mitochondrial Genome Phylogeny of Cleridae (Coleoptera, Cleroidea). INSECTS 2022;13:insects13020118. [PMID: 35206692 PMCID: PMC8878092 DOI: 10.3390/insects13020118] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/16/2022] [Accepted: 01/19/2022] [Indexed: 01/22/2023]
25
Cost-Efficiency Optimization Serves as a Conserved Mechanism that Promotes Osteosarcoma in Mammals. J Mol Evol 2022;90:139-148. [DOI: 10.1007/s00239-022-10047-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 01/06/2022] [Indexed: 10/19/2022]
26
Kelly S. The economics of organellar gene loss and endosymbiotic gene transfer. Genome Biol 2021;22:345. [PMID: 34930424 PMCID: PMC8686548 DOI: 10.1186/s13059-021-02567-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/06/2021] [Indexed: 01/09/2023]  Open
27
A novel statistical method predicts mutability of the genomic segments of the SARS-CoV-2 virus. QRB DISCOVERY 2021;3:e1. [PMID: 35106478 PMCID: PMC8795775 DOI: 10.1017/qrd.2021.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 05/28/2021] [Accepted: 11/26/2021] [Indexed: 11/06/2022]  Open
28
High-Fructose Diet Alters Intestinal Microbial Profile and Correlates with Early Tumorigenesis in a Mouse Model of Barrett’s Esophagus. Microorganisms 2021;9:microorganisms9122432. [PMID: 34946037 PMCID: PMC8708753 DOI: 10.3390/microorganisms9122432] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/12/2022]  Open
29
Comparative Analysis of Eight Mitogenomes of Bark Beetles and Their Phylogenetic Implications. INSECTS 2021;12:insects12100949. [PMID: 34680718 PMCID: PMC8538572 DOI: 10.3390/insects12100949] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 11/23/2022]
30
Markosian C, Staquicini DI, Dogra P, Dodero-rojas E, Tang FHF, Smith TL, Contessoto VG, Libutti SK, Wang Z, Cristini V, Whitford PC, Burley SK, Onuchic JN, Pasqualini R, Arap W. Apropos of Universal Epitope Discovery for COVID-19 Vaccines: A Framework for Targeted Phage Display-Based Delivery and Integration of New Evaluation Tools.. [PMID: 34676381 PMCID: PMC8529634 DOI: 10.1101/2021.08.30.458222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
31
Yu Y, Li Y, Dong Y, Wang X, Li C, Jiang W. Natural selection on synonymous mutations in SARS-CoV-2 and the impact on estimating divergence time. Future Virol 2021. [PMCID: PMC8132620 DOI: 10.2217/fvl-2021-0078] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
32
Ge X, Yuan L, Kang Y, Liu T, Liu H, Yang Y. Characterization of the First Complete Mitochondrial Genome of Cyphonocerinae (Coleoptera: Lampyridae) with Implications for Phylogeny and Evolution of Fireflies. INSECTS 2021;12:570. [PMID: 34206376 PMCID: PMC8307346 DOI: 10.3390/insects12070570] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/11/2021] [Accepted: 06/19/2021] [Indexed: 11/16/2022]
33
Veldsman WP, Ma KY, Hui JHL, Chan TF, Baeza JA, Qin J, Chu KH. Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation. BMC Genomics 2021;22:313. [PMID: 33931033 PMCID: PMC8086120 DOI: 10.1186/s12864-021-07636-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 04/21/2021] [Indexed: 11/17/2022]  Open
34
Gao NL, He Z, Zhu Q, Jiang P, Hu S, Chen WH. Selection for Cheaper Amino Acids Drives Nucleotide Usage at the Start of Translation in Eukaryotic Genes. GENOMICS PROTEOMICS & BIOINFORMATICS 2021;19:949-957. [PMID: 33741525 PMCID: PMC9403032 DOI: 10.1016/j.gpb.2021.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 05/30/2019] [Accepted: 08/18/2019] [Indexed: 12/04/2022]
35
Majda S, Beisser D, Boenigk J. Nutrient-driven genome evolution revealed by comparative genomics of chrysomonad flagellates. Commun Biol 2021;4:328. [PMID: 33712682 PMCID: PMC7954800 DOI: 10.1038/s42003-021-01781-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 01/28/2021] [Indexed: 01/31/2023]  Open
36
Ge Z, Li X, Cao X, Wang R, Hu W, Gen L, Han S, Shang Y, Liu Y, Zhou JH. Viral adaption of staphylococcal phage: A genome-based analysis of the selective preference based on codon usage Bias. Genomics 2020;112:4657-4665. [PMID: 32818632 DOI: 10.1016/j.ygeno.2020.08.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/19/2020] [Accepted: 08/11/2020] [Indexed: 12/09/2022]
37
Interplay between Position-Dependent Codon Usage Bias and Hydrogen Bonding at the 5' End of ORFeomes. mSystems 2020;5:5/4/e00613-20. [PMID: 32788408 PMCID: PMC7426154 DOI: 10.1128/msystems.00613-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
38
Selection for Reducing Energy Cost of Protein Production Drives the GC Content and Amino Acid Composition Bias in Gene Transfer Agents. mBio 2020;11:mBio.01206-20. [PMID: 32665274 PMCID: PMC7360931 DOI: 10.1128/mbio.01206-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]  Open
39
Ohbayashi R, Hirooka S, Onuma R, Kanesaki Y, Hirose Y, Kobayashi Y, Fujiwara T, Furusawa C, Miyagishima SY. Evolutionary Changes in DnaA-Dependent Chromosomal Replication in Cyanobacteria. Front Microbiol 2020;11:786. [PMID: 32411117 PMCID: PMC7198777 DOI: 10.3389/fmicb.2020.00786] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/02/2020] [Indexed: 12/02/2022]  Open
40
Syeda AH, Dimude JU, Skovgaard O, Rudolph CJ. Too Much of a Good Thing: How Ectopic DNA Replication Affects Bacterial Replication Dynamics. Front Microbiol 2020;11:534. [PMID: 32351461 PMCID: PMC7174701 DOI: 10.3389/fmicb.2020.00534] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 03/12/2020] [Indexed: 12/15/2022]  Open
41
Zu H, Zhang H, Yao M, Zhang J, Di H, Zhang L, Dong L, Wang Z, Zhou Y. Molecular characteristics of segment 5, a unique fragment encoding two partially overlapping ORFs in the genome of rice black-streaked dwarf virus. PLoS One 2019;14:e0224569. [PMID: 31697693 PMCID: PMC6837423 DOI: 10.1371/journal.pone.0224569] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 10/16/2019] [Indexed: 02/04/2023]  Open
42
Gao NL, Chen J, Wang T, Lercher MJ, Chen WH. Prokaryotic Genome Expansion Is Facilitated by Phages and Plasmids but Impaired by CRISPR. Front Microbiol 2019;10:2254. [PMID: 31681190 PMCID: PMC6805729 DOI: 10.3389/fmicb.2019.02254] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 09/17/2019] [Indexed: 12/02/2022]  Open
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Yanai I, Lercher M. Night science. Genome Biol 2019;20:179. [PMID: 31462323 PMCID: PMC6712672 DOI: 10.1186/s13059-019-1800-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 08/23/2019] [Indexed: 12/14/2022]  Open
44
Mordret E, Dahan O, Asraf O, Rak R, Yehonadav A, Barnabas GD, Cox J, Geiger T, Lindner AB, Pilpel Y. Systematic Detection of Amino Acid Substitutions in Proteomes Reveals Mechanistic Basis of Ribosome Errors and Selection for Translation Fidelity. Mol Cell 2019;75:427-441.e5. [DOI: 10.1016/j.molcel.2019.06.041] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 03/05/2019] [Accepted: 06/26/2019] [Indexed: 11/26/2022]
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Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the pmoCAB Operon of Type Ia Methanotrophs. mSystems 2019;4:4/4/e00342-19. [PMID: 31337658 PMCID: PMC6650546 DOI: 10.1128/msystems.00342-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]  Open
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Wang J, Li X, Do Kim K, Scanlon MJ, Jackson SA, Springer NM, Yu J. Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean. Genome Biol 2019;20:74. [PMID: 31018867 PMCID: PMC6482504 DOI: 10.1186/s13059-019-1683-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/28/2019] [Indexed: 01/21/2023]  Open
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Bohlin J, Pettersson JHO. Evolution of Genomic Base Composition: From Single Cell Microbes to Multicellular Animals. Comput Struct Biotechnol J 2019;17:362-370. [PMID: 30949307 PMCID: PMC6429543 DOI: 10.1016/j.csbj.2019.03.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 01/07/2023]  Open
48
Su HJ, Barkman TJ, Hao W, Jones SS, Naumann J, Skippington E, Wafula EK, Hu JM, Palmer JD, dePamphilis CW. Novel genetic code and record-setting AT-richness in the highly reduced plastid genome of the holoparasitic plant Balanophora. Proc Natl Acad Sci U S A 2019;116:934-943. [PMID: 30598433 PMCID: PMC6338844 DOI: 10.1073/pnas.1816822116] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
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Synonymous Codon Usages as an Evolutionary Dynamic for Chlamydiaceae. Int J Mol Sci 2018;19:ijms19124010. [PMID: 30545112 PMCID: PMC6321445 DOI: 10.3390/ijms19124010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/06/2018] [Accepted: 12/10/2018] [Indexed: 01/08/2023]  Open
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Du MZ, Zhang C, Wang H, Liu S, Wei W, Guo FB. The GC Content as a Main Factor Shaping the Amino Acid Usage During Bacterial Evolution Process. Front Microbiol 2018;9:2948. [PMID: 30581420 PMCID: PMC6292993 DOI: 10.3389/fmicb.2018.02948] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/16/2018] [Indexed: 11/13/2022]  Open
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