Data from: Horizontal gene acquisitions, mobile element proliferation, and genome decay in the host - restricted plant pathogen Erwinia tracheiphila

Shapiro LR, Scully ED, Straub TJ, Park J, Stephenson AG, Beattie GA, Gleason ML, Kolter R, Coelho MC, De Moraes CM, Mescher MC, Zhaxybayeva O

Date Published: March 25, 2016

DOI: http://dx.doi.org/10.5061/dryad.v7h28

 

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Title HopV1-trim
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Description Aligned and trimmed alignment of putative T3SS effector HopVI found in the E. tracheiphila genome
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Title BHKY-assembly
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Description E. tracheiphila strain BHKY hybrid mapping + deNovo assembly fasta file
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Title MISpSq-assembly
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Description E. tracheiphila strain MISpSq hybrid assembly from mapping + deNovo assembly of Illumina short reads
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Title NYZuch1-assembly
Downloaded 1 time
Description Hybrid mapping and deNovo assembly file for E. tracheiphila strain NYZuch1
Download NYZuch1-assembly.fasta (5.251 Mb)
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Title ppHow2-assembly
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Description E. tracheiphila genome assembly for strain ppHow2, from a hybrid mapping + deNovo assembly
Download ppHow2-assembly.fasta (5.200 Mb)
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Title GZ4-assembly
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Description E. tracheiphila strain GZ4 assembly file in fasta format, generated by a hybrid mapping + deNovo strategy
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Title core_Enterobactericeae_alignment
Downloaded 3 times
Description Core Enterobacteriaceae alignment used to create figure 2. Relevant methods are in the 'Methods' section of the publication
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Title core_Erwinia_Pantoea_Alignments
Description Core genome alignment of the Erwinia/Pantoea clade used to create figure 4. Relevant methods are in the 'methods' section of the publication
Download core_Erwinia_Pantoea_Alignments.fasta (3.173 Mb)
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Title Supplemental_File_1
Downloaded 4 times
Description File describing the exact parameters for the hybrid mapping + deNovo assembly using Mira 4.1, as described in the 'Methods' section of the accompanying publication
Download Supplemental_File_1.txt (2.819 Kb)
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Title Et.Etrach_0.final
Downloaded 2 times
Description Manual annotation of Contig 0, E. tracheiphila reference strain BuffGH
Download Et.Etrach_0.final.embl (581.5 Kb)
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Title Et.Etrach_1.final
Downloaded 1 time
Description Manually corrected annotation of Contig 1, reference strain BuffGH
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Title Et.Etrach_2.final
Downloaded 1 time
Description Manually corrected annotation of E. tracheiphila BuffGH contig 2
Download Et.Etrach_2.final.embl (8.355 Mb)
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Title Et.Etrach_3.final
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Description Manual corrections of annotations for E. tracheiphila BuffGH reference strain, contig 3
Download Et.Etrach_3.final.embl (158.3 Kb)
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Title Et.Etrach_4.final
Downloaded 1 time
Description Manually corrected annotation file for contig 4 of E. tracheiphila reference genome BuffGH
Download Et.Etrach_4.final.embl (642.0 Kb)
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Title Et.Etrach_5.final
Downloaded 2 times
Description E. tracheiphila manual annotations of reference strain BuffGH, contig 5
Download Et.Etrach_5.final.embl (57.51 Kb)
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Title Et.Etrach_6.final
Downloaded 2 times
Description Manual annotations of E. tracheiphila reference genome BuffGH, contig 6
Download Et.Etrach_6.final.embl (96.92 Kb)
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Title Etracheiphila_BuffGH
Downloaded 1 time
Description Erwinia tracheiphila embl file with four merged chromosomal contigs for viewing and editing as a single file in Artemis software from Sanger Institute.
Download Etracheiphila_BuffGH.embl (9.655 Mb)
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When using this data, please cite the original publication:

Shapiro LR, Scully ED, Straub TJ, Park J, Stephenson AG, Beattie GA, Gleason ML, Kolter R, Coelho MC, De Moraes CM, Mescher MC, Zhaxybayeva O (2016) Horizontal gene acquisitions, mobile element proliferation, and genome decay in the host - restricted plant pathogen Erwinia tracheiphila. Genome Biology and Evolution 8(3): 649-664. http://dx.doi.org/10.1093/gbe/evw016

Additionally, please cite the Dryad data package:

Shapiro LR, Scully ED, Straub TJ, Park J, Stephenson AG, Beattie GA, Gleason ML, Kolter R, Coelho MC, De Moraes CM, Mescher MC, Zhaxybayeva O (2016) Data from: Horizontal gene acquisitions, mobile element proliferation, and genome decay in the host - restricted plant pathogen Erwinia tracheiphila. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.v7h28
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