Rosselló-Mora R, Amann R. The species concept for prokaryotes. FEMS Microbiol Rev. 2001;25:39–67.
Article
PubMed
Google Scholar
Fraser C, Alm EJ, Polz MF, Spratt BG, Hanage WP. The bacterial species challenge: making sense of genetic and ecological diversity. Science. 2009;323:741–6.
Article
CAS
PubMed
Google Scholar
Bobay L-M, Ochman H. Biological species are universal across life’s domains. Genome Biol Evol. 2017;9:491–501.
Article
PubMed Central
Google Scholar
Konstantinidis K, Ramette A, Tiedje JM. The bacterial species definition in the genomic era. Philos Trans R Soc B Biol Sci. 2006;361:1929–40.
Article
Google Scholar
Popoff MY, Kersters K, Kiredjian M, Miras I, Coynault C. Position taxonomique de souches de Agrobacterium d’origine hospitalière. Ann Inst Pasteur Microbiol. 1984;135:427–42.
Article
Google Scholar
Costechareyre D, Bertolla F, Nesme X. Homologous recombination in Agrobacterium: potential implications for the genomic species concept in bacteria. Mol Biol Evol. 2009;26:167–76.
Article
CAS
PubMed
Google Scholar
Wu C-F, Santos MNM, Cho S-T, Chang H-H, Tsai Y-M, Smith DA, et al. Plant-pathogenic Agrobacterium tumefaciens strains have diverse type VI effector-immunity pairs and vary in in-planta competitiveness. Mol Plant Microbe Interact. 2019;32:961–71.
Article
CAS
PubMed
Google Scholar
Lassalle F, Planel R, Penel S, Chapulliot D, Barbe V, Dubost A, et al. Ancestral genome estimation reveals the history of ecological diversification in Agrobacterium. Genome Biol Evol. 2017;9:3413–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Weisberg AJ, Davis EW, Tabima J, Belcher MS, Miller M, Kuo C-H, et al. Unexpected conservation and global transmission of agrobacterial virulence plasmids. Science. 2020;368:eaba5256.
Article
CAS
PubMed
Google Scholar
Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90 K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9:5114.
Article
PubMed
PubMed Central
CAS
Google Scholar
Murray CS, Gao Y, Wu M. Re-evaluating the evidence for a universal genetic boundary among microbial species. Nat Commun. 2021;12:4059.
Article
CAS
PubMed
PubMed Central
Google Scholar
Young JM. Agrobacterium—taxonomy of plant-pathogenic Rhizobium species. In: Tzfira T, Citovsky V, editors. Agrobacterium Biol Biotechnol. New York: Springer; 2008. p. 183–220. Available from: http://link.springer.com/chapter/10.1007/978-0-387-72290-0_5.
Chapter
Google Scholar
Kado CI. Historical account on gaining insights on the mechanism of crown gall tumorigenesis induced by Agrobacterium tumefaciens. Front Microbiol. 2014;5:340.
Article
PubMed
PubMed Central
Google Scholar
Nester EW. Agrobacterium: nature’s genetic engineer. Front Plant Sci. 2015;5:730.
Article
PubMed
PubMed Central
Google Scholar
Hwang H-H, Yu M, Lai E-M. Agrobacterium-mediated plant transformation: biology and applications. Arab Book. 2017;15:e0186.
Article
Google Scholar
Mougel C, Thioulouse J, Perrière G, Nesme X. A mathematical method for determining genome divergence and species delineation using AFLP. Int J Syst Evol Microbiol. 2002;52:573–86.
Article
CAS
PubMed
Google Scholar
Portier P, Saux MF-L, Mougel C, Lerondelle C, Chapulliot D, Thioulouse J, et al. Identification of genomic species in Agrobacterium biovar 1 by AFLP genomic markers. Appl Environ Microbiol. 2006;72:7123–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Costechareyre D, Rhouma A, Lavire C, Portier P, Chapulliot D, Bertolla F, et al. Rapid and efficient identification of Agrobacterium species by recA allele analysis: Agrobacterium recA diversity. Microb Ecol. 2010;60:862–72.
Article
CAS
PubMed
Google Scholar
Hellens R, Mullineaux P, Klee H. A guide to Agrobacterium binary Ti vectors. Trends Plant Sci. 2000;5:446–51.
Article
CAS
PubMed
Google Scholar
Lee L-Y, Gelvin SB. T-DNA binary vectors and systems. Plant Physiol. 2008;146:325–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lassalle F, Campillo T, Vial L, Baude J, Costechareyre D, Chapulliot D, et al. Genomic species are ecological species as revealed by comparative genomics in Agrobacterium tumefaciens. Genome Biol Evol. 2011;3:762–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Young JM, Pennycook SR, Watson DRW. Proposal that Agrobacterium radiobacter has priority over Agrobacterium tumefaciens. Request for an Opinion. Int J Syst Evol Microbiol. 2006;56:491–3.
Article
CAS
PubMed
Google Scholar
Slater SC, Goldman BS, Goodner B, Setubal JC, Farrand SK, Nester EW, et al. Genome sequences of three Agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria. J Bacteriol. 2009;191:2501–11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Goodner B, Hinkle G, Gattung S, Miller N, Blanchard M, Qurollo B, et al. Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science. 2001;294:2323–8.
Article
CAS
PubMed
Google Scholar
Wood DW, Setubal JC, Kaul R, Monks DE, Kitajima JP, Okura VK, et al. The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science. 2001;294:2317–23.
Article
CAS
PubMed
Google Scholar
Haryono M, Cho S-T, Fang M-J, Chen A-P, Chou S-J, Lai E-M, et al. Differentiations in gene content and expression response to virulence induction between two Agrobacterium strains. Front Microbiol. 2019;10:1554.
Article
PubMed
PubMed Central
Google Scholar
Ma L-S, Hachani A, Lin J-S, Filloux A, Lai E-M. Agrobacterium tumefaciens deploys a superfamily of type VI secretion DNase effectors as weapons for interbacterial competition in planta. Cell Host Microbe. 2014;16:94–104.
Article
CAS
PubMed
PubMed Central
Google Scholar
Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Ostell J, Pruitt KD, et al. GenBank. Nucleic Acids Res. 2018;46:D41–7.
Article
CAS
PubMed
Google Scholar
Ormeño-Orrillo E, Servín-Garcidueñas LE, Rogel MA, González V, Peralta H, Mora J, et al. Taxonomy of rhizobia and agrobacteria from the Rhizobiaceae family in light of genomics. Syst Appl Microbiol. 2015;38:287–91.
Article
PubMed
Google Scholar
Hernandez RE, Gallegos-Monterrosa R, Coulthurst SJ. Type VI secretion system effector proteins: effective weapons for bacterial competitiveness. Cell Microbiol. 2020;22:e13241.
Article
CAS
PubMed
Google Scholar
Jurėnas D, Journet L. Activity, delivery, and diversity of type VI secretion effectors. Mol Microbiol. 2021;115:383–94.
Article
PubMed
CAS
Google Scholar
Smith WPJ, Vettiger A, Winter J, Ryser T, Comstock LE, Basler M, et al. The evolution of the type VI secretion system as a disintegration weapon. PLoS Biol. 2020;18:e3000720.
Article
CAS
PubMed
PubMed Central
Google Scholar
Santos MNM, Cho S-T, Wu C-F, Chang C-J, Kuo C-H, Lai E-M. Redundancy and specificity of type VI secretion vgrG loci in antibacterial activity of Agrobacterium tumefaciens 1D1609 strain. Front Microbiol. 2020;10:3004.
Article
PubMed
PubMed Central
Google Scholar
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wu H-Y, Chung P-C, Shih H-W, Wen S-R, Lai E-M. Secretome analysis uncovers an Hcp-family protein secreted via a type VI secretion system in Agrobacterium tumefaciens. J Bacteriol. 2008;190:2841–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bondage DD, Lin J-S, Ma L-S, Kuo C-H, Lai E-M. VgrG C terminus confers the type VI effector transport specificity and is required for binding with PAAR and adaptor–effector complex. Proc Natl Acad Sci. 2016;113:E3931–40.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lin J-S, Ma L-S, Lai E-M. Systematic dissection of the Agrobacterium type VI secretion system reveals machinery and secreted components for subcomplex formation. PLoS One. 2013;8:e67647.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pukatzki S, Ma AT, Revel AT, Sturtevant D, Mekalanos JJ. Type VI secretion system translocates a phage tail spike-like protein into target cells where it cross-links actin. Proc Natl Acad Sci. 2007;104:15508–13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Leiman PG, Basler M, Ramagopal UA, Bonanno JB, Sauder JM, Pukatzki S, et al. Type VI secretion apparatus and phage tail-associated protein complexes share a common evolutionary origin. Proc Natl Acad Sci. 2009;106:4154–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wu C-F, Weisberg AJ, Davis EW, Chou L, Khan S, Lai E-M, et al. Diversification of the type VI secretion system in agrobacteria. mBio. 2021;12:e01927-21.
Article
PubMed Central
Google Scholar
Liang X, Moore R, Wilton M, Wong MJQ, Lam L, Dong TG. Identification of divergent type VI secretion effectors using a conserved chaperone domain. Proc Natl Acad Sci. 2015;112:9106–11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Unterweger D, Kostiuk B, Ötjengerdes R, Wilton A, Diaz-Satizabal L, Pukatzki S. Chimeric adaptor proteins translocate diverse type VI secretion system effectors in Vibrio cholerae. EMBO J. 2015;34:2198–210.
Article
CAS
PubMed
PubMed Central
Google Scholar
Weisberg AJ, Miller M, Ream W, Grünwald NJ, Chang JH. Diversification of plasmids in a genus of pathogenic and nitrogen-fixing bacteria. Philos Trans R Soc B Biol Sci. 2022;377:20200466.
Article
CAS
Google Scholar
Li X, Tu H, Pan SQ. Agrobacterium delivers anchorage protein VirE3 for companion VirE2 to aggregate at host entry sites for T-DNA protection. Cell Rep. 2018;25:302–11.e6.
Article
CAS
PubMed
Google Scholar
Jarchow E, Grimsley NH, Hohn B. virF, the host-range-determining virulence gene of Agrobacterium tumefaciens, affects T-DNA transfer to Zea mays. Proc Natl Acad Sci. 1991;88:10426–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vogel AM, Das A. The Agrobacterium tumefaciens virD3 gene is not essential for tumorigenicity on plants. J Bacteriol. 1992;174:5161–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lin T-S, Kado CI. The virD4 gene is required for virulence while virD3 and orf5 are not required for virulence of Agrobacterium tumefaciens. Mol Microbiol. 1993;9:803–12.
Article
CAS
PubMed
Google Scholar
Pan SQ, Jin S, Boulton MI, Hawes M, Gordon MP, Nester EW. An Agrobacterium virulence factor encoded by a Ti plasmid gene or a chromosomal gene is required for T-DNA transfer into plants. Mol Microbiol. 1995;17:259–69.
Article
CAS
PubMed
Google Scholar
Hwang H-H, Wu ET, Liu S-Y, Chang S-C, Tzeng K-C, Kado CI. Characterization and host range of five tumorigenic Agrobacterium tumefaciens strains and possible application in plant transient transformation assays. Plant Pathol. 2013;62:1384–97.
Article
CAS
Google Scholar
de Lajudie PM, Andrews M, Ardley J, Eardly B, Jumas-Bilak E, Kuzmanović N, et al. Minimal standards for the description of new genera and species of rhizobia and agrobacteria. Int J Syst Evol Microbiol. 2019;69:1852–63.
Article
PubMed
CAS
Google Scholar
Kuzmanović N, Puławska J, Prokić A, Ivanović M, Zlatković N, Jones JB, et al. Agrobacterium arsenijevicii sp. nov., isolated from crown gall tumors on raspberry and cherry plum. Syst Appl Microbiol. 2015;38:373–8.
Article
PubMed
CAS
Google Scholar
Mousavi SA, Willems A, Nesme X, de Lajudie P, Lindström K. Revised phylogeny of Rhizobiaceae: proposal of the delineation of Pararhizobium gen. nov., and 13 new species combinations. Syst Appl Microbiol. 2015;38:84–90.
Article
PubMed
Google Scholar
Mafakheri H, Taghavi SM, Puławska J, de Lajudie P, Lassalle F, Osdaghi E. Two novel genomospecies in the Agrobacterium tumefaciens species complex associated with rose crown gall. Phytopathology. 2019;109:1859–68.
Article
CAS
PubMed
Google Scholar
Valdes Franco JA, Collier R, Wang Y, Huo N, Gu Y, Thilmony R, et al. Draft genome sequence of Agrobacterium rhizogenes strain NCPPB2659. Genome Announc. 2016;4:e00746-16.
Article
PubMed
PubMed Central
Google Scholar
Singh NK, Lavire C, Nesme J, Vial L, Nesme X, Mason CE, et al. Comparative genomics of novel Agrobacterium G3 strains isolated from the International Space Station and description of Agrobacterium tomkonis sp. nov. Front Microbiol. 2021;12:3369.
Hooykaas PJJ, Klapwijk PM, Nuti MP, Schilperoort RA, Rörsch A. Transfer of the Agrobacterium tumefaciens Ti plasmid to avirulent agrobacteria and to Rhizobium ex planta. J Gen Microbiol. 1977;98:477–84.
Article
Google Scholar
Haryono M, Tsai Y-M, Lin C-T, Huang F-C, Ye Y-C, Deng W-L, et al. Presence of an Agrobacterium-type tumor-inducing plasmid in Neorhizobium sp. NCHU2750 and the link to phytopathogenicity. Genome Biol Evol. 2018;10:3188–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rathore DS, Mullins E. Alternative non-Agrobacterium based methods for plant transformation. In: Roberts JA, editor. Annu Plant Rev Online. Hoboken, New Jersey: John Wiley & Sons, Ltd.; 2018. p. 891–908. Available from: https://onlinelibrary.wiley.com/doi/abs/10.1002/9781119312994.apr0659.
Chapter
Google Scholar
Barco RA, Garrity GM, Scott JJ, Amend JP, Nealson KH, Emerson D. A genus definition for Bacteria and Archaea based on a standard genome relatedness index. mBio. 2020;11:e02475-19.
Article
PubMed
PubMed Central
Google Scholar
Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil P-A, et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol. 2018;36:996–1004.
Article
CAS
PubMed
Google Scholar
Parks DH, Chuvochina M, Chaumeil P-A, Rinke C, Mussig AJ, Hugenholtz P. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat Biotechnol. 2020;38:1079–86.
Article
CAS
PubMed
Google Scholar
Kuo C-H, Ochman H. Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria. Biol Direct. 2009;4:35.
Article
PubMed
PubMed Central
CAS
Google Scholar
Okasha S. Evolution and the Levels of Selection. Oxford: Oxford University Press; 2006. Available from: https://oxford.universitypressscholarship.com/view/10.1093/acprof:oso/9780199267972.001.0001/acprof-9780199267972
Daubin V, Moran NA, Ochman H. Phylogenetics and the cohesion of bacterial genomes. Science. 2003;301:829–32.
Article
CAS
PubMed
Google Scholar
Choi I-G, Kim S-H. Global extent of horizontal gene transfer. Proc Natl Acad Sci. 2007;104:4489–94.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial innovation. Nature. 2000;405:299–304.
Article
CAS
PubMed
Google Scholar
Dagan T, Artzy-Randrup Y, Martin W. Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc Natl Acad Sci. 2008;105:10039–44.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chan CX, Beiko RG, Darling AE, Ragan MA. Lateral transfer of genes and gene fragments in prokaryotes. Genome Biol Evol. 2009;1:429–38.
Article
PubMed
PubMed Central
CAS
Google Scholar
Pál C, Papp B, Lercher MJ. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet. 2005;37:1372–5.
Article
PubMed
CAS
Google Scholar
Kuo C-H, Ochman H. The fate of new bacterial genes. FEMS Microbiol Rev. 2009;33:38–43.
Article
CAS
PubMed
Google Scholar
Wiedenbeck J, Cohan FM. Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiol Rev. 2011;35:957–76.
Article
CAS
PubMed
Google Scholar
Mira A, Ochman H, Moran NA. Deletional bias and the evolution of bacterial genomes. Trends Genet. 2001;17:589–96.
Article
CAS
PubMed
Google Scholar
Kuo C-H, Ochman H. Deletional bias across the three domains of life. Genome Biol Evol. 2009;1:145–52.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sundin GW. Genomic insights into the contribution of phytopathogenic bacterial plasmids to the evolutionary history of their hosts. Annu Rev Phytopathol. 2007;45:129–51.
Article
CAS
PubMed
Google Scholar
Bennett PM. Plasmid encoded antibiotic resistance: acquisition and transfer of antibiotic resistance genes in bacteria. Br J Pharmacol. 2009;153:S347–57.
Article
CAS
Google Scholar
Smillie C, Garcillán-Barcia MP, Francia MV, Rocha EPC, de la Cruz F. Mobility of plasmids. Microbiol Mol Biol Rev. 2010;74:434–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Redondo-Salvo S, Fernández-López R, Ruiz R, Vielva L, de Toro M, Rocha EPC, et al. Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids. Nat Commun. 2020;11:3602.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ramírez-Bahena MH, Vial L, Lassalle F, Diel B, Chapulliot D, Daubin V, et al. Single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the Agrobacterium/Rhizobium supercluster characterized by the presence of a linear chromid. Mol Phylogenet Evol. 2014;73:202–7.
Article
PubMed
CAS
Google Scholar
Treangen TJ, Rocha EPC. Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet. 2011;7:e1001284.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huang Y-Y, Cho S-T, Lo W-S, Wang Y-C, Lai E-M, Kuo C-H. Complete genome sequence of Agrobacterium tumefaciens Ach5. Genome Announc. 2015;3:e00570-15.
Article
PubMed
PubMed Central
Google Scholar
Cho S-T, Haryono M, Chang H-H, Santos MNM, Lai E-M, Kuo C-H. Complete genome sequence of Agrobacterium tumefaciens 1D1609. Genome Announc. 2018;6:e00253-18.
Article
PubMed
Google Scholar
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Darling ACE, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004;14:1394–403.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016;44:6614–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lo W-S, Chen L-L, Chung W-C, Gasparich GE, Kuo C-H. Comparative genome analysis of Spiroplasma melliferum IPMB4A, a honeybee-associated bacterium. BMC Genomics. 2013;14:22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lo W-S, Gasparich GE, Kuo C-H. Convergent evolution among ruminant-pathogenic Mycoplasma involved extensive gene content changes. Genome Biol Evol. 2018;10:2130–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cho S-T, Kung H-J, Huang W, Hogenhout SA, Kuo C-H. Species boundaries and molecular markers for the classification of 16SrI phytoplasmas inferred by genome analysis. Front Microbiol. 2020;11:1531.
Article
PubMed
PubMed Central
Google Scholar
Guy L, Roat Kultima J, Andersson SGE. genoPlotR: comparative gene and genome visualization in R. Bioinformatics. 2010;26:2334–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003;13:2178–89.
Article
CAS
PubMed
PubMed Central
Google Scholar
Popescu A-A, Huber KT, Paradis E. ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R. Bioinformatics. 2012;28:1536–7.
Article
CAS
PubMed
Google Scholar
Wickham H. ggplot2: Elegant Graphics for Data Analysis. New York, NY: Springer-Verlag New York; 2016. Available from: https://ggplot2.tidyverse.org.
Book
Google Scholar
Suzuki R, Shimodaira H. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics. 2006;22:1540–2.
Article
CAS
PubMed
Google Scholar
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003;52:696–704.
Article
PubMed
Google Scholar
Marchler-Bauer A, Zheng C, Chitsaz F, Derbyshire MK, Geer LY, Geer RC, et al. CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res. 2013;41:D348–52.
Article
CAS
PubMed
Google Scholar
Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJE. The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc. 2015;10:845–58.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, et al. MEME Suite: tools for motif discovery and searching. Nucleic Acids Res. 2009;37:W202–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ. Jalview version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009;25:1189–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Crooks GE, Hon G, Chandonia J-M, Brenner SE. WebLogo: a sequence logo generator. Genome Res. 2004;14:1188–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Conner AJ, Barrell PJ, Baldwin SJ, Lokerse AS, Cooper PA, Erasmuson AK, et al. Intragenic vectors for gene transfer without foreign DNA. Euphytica. 2007;154:341–53.
Article
CAS
Google Scholar
Vladimirov IA, Matveeva TV, Lutova LA. Opine biosynthesis and catabolism genes of Agrobacterium tumefaciens and Agrobacterium rhizogenes. Russ J Genet. 2015;51:121–9.
Article
CAS
Google Scholar
Bhatty M, Laverde Gomez JA, Christie PJ. The expanding bacterial type IV secretion lexicon. Res Microbiol. 2013;164:620–39.
Article
CAS
PubMed
Google Scholar
Wang Y, Wei X, Bao H, Liu S-L. Prediction of bacterial type IV secreted effectors by C-terminal features. BMC Genomics. 2014;15:50.
Article
PubMed
PubMed Central
Google Scholar
Eichinger V, Nussbaumer T, Platzer A, Jehl M-A, Arnold R, Rattei T. EffectiveDB—updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems. Nucleic Acids Res. 2016;44:D669–74.
Article
CAS
PubMed
Google Scholar
Wu H-Y, Chen C-Y, Lai E-M. Expression and functional characterization of the Agrobacterium VirB2 amino acid substitution variants in T-pilus biogenesis, virulence, and transient transformation efficiency. PLoS One. 2014;9:e101142.
Article
PubMed
PubMed Central
CAS
Google Scholar