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For: Robbertse B, Yoder RJ, Boyd A, Reeves J, Spatafora JW. Hal: an automated pipeline for phylogenetic analyses of genomic data. PLoS Curr 2011;3:RRN1213. [PMID: 21327165 PMCID: PMC3038436 DOI: 10.1371/currents.rrn1213] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 02/07/2011] [Indexed: 11/21/2022]
Number Cited by Other Article(s)
1
Vasan S, Srivastava D, Cahill D, Singh PP, Adholeya A. Important innate differences in determining symbiotic responsiveness in host and non-hosts of arbuscular mycorrhiza. Sci Rep 2021;11:14444. [PMID: 34262100 PMCID: PMC8280126 DOI: 10.1038/s41598-021-93626-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 06/29/2021] [Indexed: 11/09/2022]  Open
2
Fungi between extremotolerance and opportunistic pathogenicity on humans. FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0414-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
3
Shibl AA, Ngugi DK, Talarmin A, Thompson LR, Blom J, Stingl U. The genome of a novel isolate of Prochlorococcus from the Red Sea contains transcribed genes for compatible solute biosynthesis. FEMS Microbiol Ecol 2018;94:5090968. [PMID: 30188995 DOI: 10.1093/femsec/fiy182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/04/2018] [Indexed: 11/14/2022]  Open
4
Drori M, Rice A, Einhorn M, Chay O, Glick L, Mayrose I. OneTwoTree: An online tool for phylogeny reconstruction. Mol Ecol Resour 2018;18:1492-1499. [PMID: 30010236 DOI: 10.1111/1755-0998.12927] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/20/2018] [Accepted: 06/28/2018] [Indexed: 01/10/2023]
5
Landry ZC, Vergin K, Mannenbach C, Block S, Yang Q, Blainey P, Carlson C, Giovannoni S. Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface. Front Microbiol 2018;9:1152. [PMID: 29937754 PMCID: PMC6003095 DOI: 10.3389/fmicb.2018.01152] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 05/14/2018] [Indexed: 12/03/2022]  Open
6
Genome mining for peptidases in heat-tolerant and mesophilic fungi and putative adaptations for thermostability. BMC Genomics 2018;19:152. [PMID: 29463214 PMCID: PMC5819190 DOI: 10.1186/s12864-018-4549-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 02/13/2018] [Indexed: 12/17/2022]  Open
7
Landry Z, Swan BK, Herndl GJ, Stepanauskas R, Giovannoni SJ. SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter. mBio 2017;8:e00413-17. [PMID: 28420738 PMCID: PMC5395668 DOI: 10.1128/mbio.00413-17] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 03/20/2017] [Indexed: 01/09/2023]  Open
8
Mora-Ortiz M, Swain MT, Vickers MJ, Hegarty MJ, Kelly R, Smith LMJ, Skøt L. De-novo transcriptome assembly for gene identification, analysis, annotation, and molecular marker discovery in Onobrychis viciifolia. BMC Genomics 2016;17:756. [PMID: 27671367 PMCID: PMC5037894 DOI: 10.1186/s12864-016-3083-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 09/13/2016] [Indexed: 01/08/2023]  Open
9
Peter M, Kohler A, Ohm RA, Kuo A, Krützmann J, Morin E, Arend M, Barry KW, Binder M, Choi C, Clum A, Copeland A, Grisel N, Haridas S, Kipfer T, LaButti K, Lindquist E, Lipzen A, Maire R, Meier B, Mihaltcheva S, Molinier V, Murat C, Pöggeler S, Quandt CA, Sperisen C, Tritt A, Tisserant E, Crous PW, Henrissat B, Nehls U, Egli S, Spatafora JW, Grigoriev IV, Martin FM. Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum. Nat Commun 2016;7:12662. [PMID: 27601008 PMCID: PMC5023957 DOI: 10.1038/ncomms12662] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 07/21/2016] [Indexed: 12/13/2022]  Open
10
Brown NM, Mueller RS, Shepardson JW, Landry ZC, Morré JT, Maier CS, Hardy FJ, Dreher TW. Structural and functional analysis of the finished genome of the recently isolated toxic Anabaena sp. WA102. BMC Genomics 2016;17:457. [PMID: 27296936 PMCID: PMC4907049 DOI: 10.1186/s12864-016-2738-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 05/12/2016] [Indexed: 11/29/2022]  Open
11
Adelskov J, Patel BKC. A molecular phylogenetic framework for Bacillus subtilis using genome sequences and its application to Bacillus subtilis subspecies stecoris strain D7XPN1, an isolate from a commercial food-waste degrading bioreactor. 3 Biotech 2016;6:96. [PMID: 28330166 PMCID: PMC4809863 DOI: 10.1007/s13205-016-0408-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 02/28/2016] [Indexed: 11/25/2022]  Open
12
Araújo WL, Creason AL, Mano ET, Camargo-Neves AA, Minami SN, Chang JH, Loper JE. Genome Sequencing and Transposon Mutagenesis of Burkholderia seminalis TC3.4.2R3 Identify Genes Contributing to Suppression of Orchid Necrosis Caused by B. gladioli. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016;29:435-446. [PMID: 26959838 DOI: 10.1094/mpmi-02-16-0047-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
13
Ho WS, Yap KP, Yeo CC, Rajasekaram G, Thong KL. The Complete Sequence and Comparative Analysis of a Multidrug-Resistance and Virulence Multireplicon IncFII Plasmid pEC302/04 from an Extraintestinal Pathogenic Escherichia coli EC302/04 Indicate Extensive Diversity of IncFII Plasmids. Front Microbiol 2016;6:1547. [PMID: 26793180 PMCID: PMC4707298 DOI: 10.3389/fmicb.2015.01547] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 12/21/2015] [Indexed: 01/07/2023]  Open
14
Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs. Appl Environ Microbiol 2015;82:1215-1226. [PMID: 26655752 DOI: 10.1128/aem.02852-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/03/2015] [Indexed: 12/16/2022]  Open
15
Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement. Sci Rep 2015;5:17394. [PMID: 26617401 PMCID: PMC4663792 DOI: 10.1038/srep17394] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/29/2015] [Indexed: 01/19/2023]  Open
16
Prasad P, Varshney D, Adholeya A. Whole genome annotation and comparative genomic analyses of bio-control fungus Purpureocillium lilacinum. BMC Genomics 2015;16:1004. [PMID: 26607873 PMCID: PMC4658809 DOI: 10.1186/s12864-015-2229-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 11/18/2015] [Indexed: 01/11/2023]  Open
17
Duan J, Ladd T, Doucet D, Cusson M, vanFrankenhuyzen K, Mittapalli O, Krell PJ, Quan G. Transcriptome Analysis of the Emerald Ash Borer (EAB), Agrilus planipennis: De Novo Assembly, Functional Annotation and Comparative Analysis. PLoS One 2015;10:e0134824. [PMID: 26244979 PMCID: PMC4526369 DOI: 10.1371/journal.pone.0134824] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Accepted: 07/14/2015] [Indexed: 11/18/2022]  Open
18
Derks MFL, Smit S, Salis L, Schijlen E, Bossers A, Mateman C, Pijl AS, de Ridder D, Groenen MAM, Visser ME, Megens HJ. The Genome of Winter Moth (Operophtera brumata) Provides a Genomic Perspective on Sexual Dimorphism and Phenology. Genome Biol Evol 2015;7:2321-32. [PMID: 26227816 PMCID: PMC4558862 DOI: 10.1093/gbe/evv145] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]  Open
19
The genome of the truffle-parasite Tolypocladium ophioglossoides and the evolution of antifungal peptaibiotics. BMC Genomics 2015. [PMID: 26215153 PMCID: PMC4517408 DOI: 10.1186/s12864-015-1777-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
20
SAR11 lipid renovation in response to phosphate starvation. Proc Natl Acad Sci U S A 2015;112:7767-72. [PMID: 26056292 DOI: 10.1073/pnas.1505034112] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
21
Chang Y, Wang S, Sekimoto S, Aerts AL, Choi C, Clum A, LaButti KM, Lindquist EA, Yee Ngan C, Ohm RA, Salamov AA, Grigoriev IV, Spatafora JW, Berbee ML. Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants. Genome Biol Evol 2015;7:1590-601. [PMID: 25977457 PMCID: PMC4494064 DOI: 10.1093/gbe/evv090] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
22
Kumar S, Krabberød AK, Neumann RS, Michalickova K, Zhao S, Zhang X, Shalchian-Tabrizi K. BIR Pipeline for Preparation of Phylogenomic Data. Evol Bioinform Online 2015;11:79-83. [PMID: 25987827 PMCID: PMC4412416 DOI: 10.4137/ebo.s10189] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 12/03/2014] [Accepted: 12/08/2014] [Indexed: 11/05/2022]  Open
23
Quandt CA, Kohler A, Hesse CN, Sharpton TJ, Martin F, Spatafora JW. Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria-rich microbiome. Environ Microbiol 2015;17:2952-68. [PMID: 25753751 DOI: 10.1111/1462-2920.12840] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/13/2015] [Accepted: 02/28/2015] [Indexed: 01/06/2023]
24
Dvořák P, Casamatta DA, Poulíčková A, Hašler P, Ondřej V, Sanges R. Synechococcus: 3 billion years of global dominance. Mol Ecol 2014;23:5538-51. [PMID: 25283338 DOI: 10.1111/mec.12948] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/23/2014] [Accepted: 09/26/2014] [Indexed: 01/08/2023]
25
Creason AL, Davis EW, Putnam ML, Vandeputte OM, Chang JH. Use of whole genome sequences to develop a molecular phylogenetic framework for Rhodococcus fascians and the Rhodococcus genus. FRONTIERS IN PLANT SCIENCE 2014;5:406. [PMID: 25237311 PMCID: PMC4154481 DOI: 10.3389/fpls.2014.00406] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 07/30/2014] [Indexed: 06/03/2023]
26
Gostinčar C, Ohm RA, Kogej T, Sonjak S, Turk M, Zajc J, Zalar P, Grube M, Sun H, Han J, Sharma A, Chiniquy J, Ngan CY, Lipzen A, Barry K, Grigoriev IV, Gunde-Cimerman N. Genome sequencing of four Aureobasidium pullulans varieties: biotechnological potential, stress tolerance, and description of new species. BMC Genomics 2014;15:549. [PMID: 24984952 PMCID: PMC4227064 DOI: 10.1186/1471-2164-15-549] [Citation(s) in RCA: 205] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 06/20/2014] [Indexed: 11/29/2022]  Open
27
The genome of Eucalyptus grandis. Nature 2014;510:356-62. [DOI: 10.1038/nature13308] [Citation(s) in RCA: 553] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Accepted: 04/02/2014] [Indexed: 12/20/2022]
28
Jimenez-Infante F, Ngugi DK, Alam I, Rashid M, Baalawi W, Kamau AA, Bajic VB, Stingl U. Genomic differentiation among two strains of the PS1 clade isolated from geographically separated marine habitats. FEMS Microbiol Ecol 2014;89:181-97. [PMID: 24785133 DOI: 10.1111/1574-6941.12348] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 03/20/2014] [Accepted: 04/12/2014] [Indexed: 12/18/2022]  Open
29
Salavirta H, Oksanen I, Kuuskeri J, Mäkelä M, Laine P, Paulin L, Lundell T. Mitochondrial genome of Phlebia radiata is the second largest (156 kbp) among fungi and features signs of genome flexibility and recent recombination events. PLoS One 2014;9:e97141. [PMID: 24824642 PMCID: PMC4019555 DOI: 10.1371/journal.pone.0097141] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 04/15/2014] [Indexed: 01/28/2023]  Open
30
Discovery of a SAR11 growth requirement for thiamin's pyrimidine precursor and its distribution in the Sargasso Sea. ISME JOURNAL 2014;8:1727-38. [PMID: 24781899 DOI: 10.1038/ismej.2014.61] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 03/11/2014] [Accepted: 03/12/2014] [Indexed: 12/11/2022]
31
Grant JR, Katz LA. Building a phylogenomic pipeline for the eukaryotic tree of life - addressing deep phylogenies with genome-scale data. PLOS CURRENTS 2014;6. [PMID: 24707447 PMCID: PMC3973741 DOI: 10.1371/currents.tol.c24b6054aebf3602748ac042ccc8f2e9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
32
Toome M, Ohm RA, Riley RW, James TY, Lazarus KL, Henrissat B, Albu S, Boyd A, Chow J, Clum A, Heller G, Lipzen A, Nolan M, Sandor L, Zvenigorodsky N, Grigoriev IV, Spatafora JW, Aime MC. Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogen Mixia osmundae. THE NEW PHYTOLOGIST 2014;202:554-564. [PMID: 24372469 DOI: 10.1111/nph.12653] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 11/19/2013] [Indexed: 05/06/2023]
33
Rusin LY, Lyubetskaya EV, Gorbunov KY, Lyubetsky VA. Reconciliation of gene and species trees. BIOMED RESEARCH INTERNATIONAL 2014;2014:642089. [PMID: 24800245 PMCID: PMC3985182 DOI: 10.1155/2014/642089] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Accepted: 11/27/2013] [Indexed: 11/18/2022]
34
Thrash JC, Temperton B, Swan BK, Landry ZC, Woyke T, DeLong EF, Stepanauskas R, Giovannoni SJ. Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype. ISME JOURNAL 2014;8:1440-51. [PMID: 24451205 DOI: 10.1038/ismej.2013.243] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 11/07/2013] [Accepted: 12/10/2013] [Indexed: 11/09/2022]
35
Rochette NC, Brochier-Armanet C, Gouy M. Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes. Mol Biol Evol 2014;31:832-45. [PMID: 24398320 PMCID: PMC3969559 DOI: 10.1093/molbev/mst272] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
36
Proteomic and transcriptomic analyses of "Candidatus Pelagibacter ubique" describe the first PII-independent response to nitrogen limitation in a free-living Alphaproteobacterium. mBio 2013;4:e00133-12. [PMID: 24281717 PMCID: PMC3870248 DOI: 10.1128/mbio.00133-12] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
37
Comparative and phylogenomic evidence that the alphaproteobacterium HIMB59 is not a member of the oceanic SAR11 clade. PLoS One 2013;8:e78858. [PMID: 24223857 PMCID: PMC3815206 DOI: 10.1371/journal.pone.0078858] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 09/05/2013] [Indexed: 11/19/2022]  Open
38
Kolton M, Sela N, Elad Y, Cytryn E. Comparative genomic analysis indicates that niche adaptation of terrestrial Flavobacteria is strongly linked to plant glycan metabolism. PLoS One 2013;8:e76704. [PMID: 24086761 PMCID: PMC3784431 DOI: 10.1371/journal.pone.0076704] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 08/26/2013] [Indexed: 11/17/2022]  Open
39
Genome and transcriptome sequencing of the halophilic fungus Wallemia ichthyophaga: haloadaptations present and absent. BMC Genomics 2013;14:617. [PMID: 24034603 PMCID: PMC3849046 DOI: 10.1186/1471-2164-14-617] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 09/04/2013] [Indexed: 01/03/2023]  Open
40
Sharma A, Rai A, Lal SB. Workflow management systems for gene sequence analysis and evolutionary studies - A Review. Bioinformation 2013;9:663-72. [PMID: 23930017 PMCID: PMC3732438 DOI: 10.6026/97320630009663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 02/23/2013] [Indexed: 11/23/2022]  Open
41
Gan HM, Hudson AO, Rahman AYA, Chan KG, Savka MA. Comparative genomic analysis of six bacteria belonging to the genus Novosphingobium: insights into marine adaptation, cell-cell signaling and bioremediation. BMC Genomics 2013;14:431. [PMID: 23809012 PMCID: PMC3704786 DOI: 10.1186/1471-2164-14-431] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 06/17/2013] [Indexed: 12/03/2022]  Open
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Bushley KE, Raja R, Jaiswal P, Cumbie JS, Nonogaki M, Boyd AE, Owensby CA, Knaus BJ, Elser J, Miller D, Di Y, McPhail KL, Spatafora JW. The genome of tolypocladium inflatum: evolution, organization, and expression of the cyclosporin biosynthetic gene cluster. PLoS Genet 2013;9:e1003496. [PMID: 23818858 PMCID: PMC3688495 DOI: 10.1371/journal.pgen.1003496] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 03/20/2013] [Indexed: 01/07/2023]  Open
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Kimbrel JA, Thomas WJ, Jiang Y, Creason AL, Thireault CA, Sachs JL, Chang JH. Mutualistic co-evolution of type III effector genes in Sinorhizobium fredii and Bradyrhizobium japonicum. PLoS Pathog 2013;9:e1003204. [PMID: 23468637 PMCID: PMC3585131 DOI: 10.1371/journal.ppat.1003204] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/08/2013] [Indexed: 12/16/2022]  Open
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Thakur K, Chawla V, Bhatti S, Swarnkar MK, Kaur J, Shankar R, Jha G. De novo transcriptome sequencing and analysis for Venturia inaequalis, the devastating apple scab pathogen. PLoS One 2013;8:e53937. [PMID: 23349770 PMCID: PMC3547962 DOI: 10.1371/journal.pone.0053937] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 12/04/2012] [Indexed: 11/28/2022]  Open
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Manning VA, Pandelova I, Dhillon B, Wilhelm LJ, Goodwin SB, Berlin AM, Figueroa M, Freitag M, Hane JK, Henrissat B, Holman WH, Kodira CD, Martin J, Oliver RP, Robbertse B, Schackwitz W, Schwartz DC, Spatafora JW, Turgeon BG, Yandava C, Young S, Zhou S, Zeng Q, Grigoriev IV, Ma LJ, Ciuffetti LM. Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence. G3 (BETHESDA, MD.) 2013;3:41-63. [PMID: 23316438 PMCID: PMC3538342 DOI: 10.1534/g3.112.004044] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 11/02/2012] [Indexed: 12/31/2022]
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Streamlining and core genome conservation among highly divergent members of the SAR11 clade. mBio 2012;3:mBio.00252-12. [PMID: 22991429 PMCID: PMC3448164 DOI: 10.1128/mbio.00252-12] [Citation(s) in RCA: 191] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
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Loper JE, Hassan KA, Mavrodi DV, Davis EW, Lim CK, Shaffer BT, Elbourne LDH, Stockwell VO, Hartney SL, Breakwell K, Henkels MD, Tetu SG, Rangel LI, Kidarsa TA, Wilson NL, van de Mortel JE, Song C, Blumhagen R, Radune D, Hostetler JB, Brinkac LM, Durkin AS, Kluepfel DA, Wechter WP, Anderson AJ, Kim YC, Pierson LS, Pierson EA, Lindow SE, Kobayashi DY, Raaijmakers JM, Weller DM, Thomashow LS, Allen AE, Paulsen IT. Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions. PLoS Genet 2012;8:e1002784. [PMID: 22792073 PMCID: PMC3390384 DOI: 10.1371/journal.pgen.1002784] [Citation(s) in RCA: 398] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 05/10/2012] [Indexed: 12/11/2022]  Open
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Padamsee M, Kumar TKA, Riley R, Binder M, Boyd A, Calvo AM, Furukawa K, Hesse C, Hohmann S, James TY, LaButti K, Lapidus A, Lindquist E, Lucas S, Miller K, Shantappa S, Grigoriev IV, Hibbett DS, McLaughlin DJ, Spatafora JW, Aime MC. The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction. Fungal Genet Biol 2012;49:217-26. [PMID: 22326418 DOI: 10.1016/j.fgb.2012.01.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2011] [Revised: 01/19/2012] [Accepted: 01/26/2012] [Indexed: 12/27/2022]
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Trautwein MD, Wiegmann BM, Beutel R, Kjer KM, Yeates DK. Advances in insect phylogeny at the dawn of the postgenomic era. ANNUAL REVIEW OF ENTOMOLOGY 2012;57:449-468. [PMID: 22149269 DOI: 10.1146/annurev-ento-120710-100538] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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Sun J, Steindler L, Thrash JC, Halsey KH, Smith DP, Carter AE, Landry ZC, Giovannoni SJ. One carbon metabolism in SAR11 pelagic marine bacteria. PLoS One 2011;6:e23973. [PMID: 21886845 PMCID: PMC3160333 DOI: 10.1371/journal.pone.0023973] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 07/28/2011] [Indexed: 12/13/2022]  Open
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