Citrus Greening-HLB Genome Resources
Genome sequence data and analyses for registered users
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March, 2010: Please note that all data on this page is presentlyaccessible via the GBrowse genome viewer and Additional Genome Resources links. Users will be notified when unpublished sequence data is added to this page. |
Reference #: |
2 | |
Date generated: |
09-07-21 | Documentation |
Source sequence and documentation: |
CP001677 (Las Psy62 complete genome) |
Complete Genome Sequence of Citrus Huanglongbing Bacterium, ‘Candidatus Liberibacter asiaticus’ Obtained Through Metagenomics. Duan, et al. MPMI 22:1011-1020 (abstract) |
Source annotation file: |
included in sequence record | same |
Output annotation/feature file(s): |
CP001677-pseudogenes.txt |
Feature file listing open reading frame and functional predictions for previously unannotated pseudogenes identified in the Las Psy62 sequence (CP001677) To view, open the CP001677-pseudogenes.txt feature file and save to your hard drive. Follow instructions at launching the Artemis Genome viewer to open source sequence CP001677 and load the saved feature file. |
Summary data: |
CP001677-pseudogene_summary (09-10-13) |
Pseudogenes in the Las Psy62 sequence (CP001677) were identified by BLAST analysis against Genbank nr of unannotated gaps deposited sequence. |
Summary data: |
CP001677-KEGG_summary
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CP001677 sequence was analyzed using the RAST server pipeline (09-09-21). Predicted functional roles were mapped on the KEGG metabolic maps and numbers of gene products in each metabolic category determined for HLB Psy62. Numbers of gene products in each metabolic category are also shown for selected fastidious plant pathogens, insect endosymbionts, and representative Rhizobiaceae for purposes of comparison. |
Reference #: |
1 ---------- replaced by Reference #2 ----------- | ||
Date generated: |
08-11-13 | Documentation |
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Source sequence and documentation: |
ABQW00000000 (Las Psy62 draft genome) |
Sequence deposited in GenBank by Duan,Y.P., Zhou,L.J., Hall,D., Li,W.B. Liu,L. and Gottwald,T.R., on 08-10-31 |
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Source annotation file: |
none | The 34 contigs that compose the ABQW00000000 deposition are numbered and annotated independently, preventing easy transfer of the annotations to the pseudomolecule generated from the sequence contigs | |
Output sequence: |
las0001-pseudomol.txt (sequence only) |
The 34 contigs in the source sequence were concatenated in order from largest to smallest to create a single pseudomolecule for the purpose of annotation and genome viewing. | |
Output annotation/feature file(s): |
las001-RAST-annotation.txt
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Open reading frame and functional predictions generated with the MG-RAST server pipeline (08-12-16) from the las0001-pseudomol.txt pseudomolecule. tRNA and rRNA predictions included.
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| las0001-ORFs.txt (features only in gff format) |
Open reading frame predictions generated with GLIMMER v3 for the las0001-pseudomol.txt pseudomolecule.tRNA and rRNA predictions not included.
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| las0001-delims.txt (features only in tab format) |
locations of the NNNNNTTAATTAATTAANNNNN sequences inserted as delimiters between concatenated contigs and indicating contig boundaries for the las0001-pseudomol.txt pseudomolecule | ||
| las0001-bacteria_nr.txt (features only in tab format) |
output of BLASTN analysis of the las0001-pseudomol.txt pseudomolecule against all non-redundant bacterial sequences in RefSeq (08-11-13 download) with a cutoff of e-20. This file is particularly useful for viewing the range of BLAST hits independent of ORF predictions | ||
Summary data: |
las0001-KEGG_summary
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Mapping of functional roles predicted by the MG-RAST server pipeline (08-12-16) to KEGG metabolic maps was performed and absolute counts generated by the MG-RAST KEGG utility. Assignments made to different KEGG maps are provided for HLB and selected fastidious plant pathogens and insect endosymbionts for the purpose of comparison. | |
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