title: Genomes of 'Candidatus Liberibacter solanacearum' Haplotype A from New Zealand and the United States Suggest Significant Genome Plasticity in the Species.
abstract: 'Candidatus Liberibacter solanacearum' contains two solanaceous crop-infecting haplotypes, A and B. Two haplotype A draft genomes were assembled and compared with ZC1 (haplotype B), revealing inversion and relocation genomic rearrangements, numerous single-nucleotide polymorphisms, and differences in phage-related regions. Differences in prophage location and sequence were seen both within and between haplotype comparisons. OrthoMCL and BLAST analyses identified 46 putative coding sequences present in haplotype A that were not present in haplotype B. Thirty-eight of these loci were not found in sequences from other Liberibacter spp. Quantitative polymerase chain reaction (qPCR) assays designed to amplify sequences from 15 of these loci were screened against a panel of 'Ca. L. solanacearum'-positive samples to investigate genetic diversity. Seven of the assays demonstrated within-haplotype diversity; five failed to amplify loci in at least one haplotype A sample while three assays produced amplicons from some haplotype B samples. Eight of the loci assays showed consistent A-B differentiation. Differences in genome arrangements, prophage, and qPCR results suggesting locus diversity within the haplotypes provide more evidence for genetic complexity in this emerging bacterial species.
authors.affiliation: First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand.
authors.forename: Sarah M
authors.initials: SM
authors.lastname: Thompson
authors.affiliation: First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand.
authors.forename: Chris P
authors.initials: CP
authors.lastname: Johnson
authors.affiliation: First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand.
authors.forename: Ashley Y
authors.initials: AY
authors.lastname: Lu
authors.affiliation: First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand.
authors.forename: Rebekah A
authors.initials: RA
authors.lastname: Frampton
authors.affiliation: First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand.
authors.forename: Kerry L
authors.initials: KL
authors.lastname: Sullivan
authors.affiliation: First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand.
authors.forename: Mark W E J
authors.initials: MW
authors.lastname: Fiers
authors.affiliation: First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand.
authors.forename: Ross N
authors.initials: RN
authors.lastname: Crowhurst
authors.affiliation: First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand.
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Pitman
authors.affiliation: First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand.
authors.forename: Ian A W
authors.initials: IA
authors.lastname: Scott
authors.affiliation: First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand.
authors.forename: Aimin
authors.initials: A
authors.lastname: Wen
authors.affiliation: First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand.
authors.forename: Neil C
authors.initials: NC
authors.lastname: Gudmestad
authors.affiliation: First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand.
authors.forename: Grant R
authors.initials: GR
authors.lastname: Smith
mesh_terms: D016680:Genome, Bacterial; D006239:Haplotypes; D008969:Molecular Sequence Data; D009520:New Zealand; D012230:Rhizobiaceae / Q000235:genetics*; D019657:Solanaceae / Q000382:microbiology*; D014481:United States