Computational protocol: Annotation of the Asian Citrus Psyllid Genome Reveals a Reduced Innate Immune System

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Protocol publication

[…] The comprehensive list of D. citri genes related to immune defenses was curated by screening for immune genes within the D. citri draft genome version 1.1 previously annotated by the NCBI automated refseq eukaryote genome annotation pipeline (Hunter et al., ). Also included were published sequences produced by recent deep sequencing surveys of D. citri (Hunter et al., ; Vyas et al., ). Immune related genes of interest were selected based on previous surveys of arthropod immune pathways and immunological defenses (Gerardo et al., ; González-Santoyo and Córdoba-Aguilar, ; Buchon et al., ; Smith and Pal, ). In addition to screening published sequences, a manual search for D. citri immune related genes was performed to search for genes not identified in previous annotations and to check the validity of the automated pipeline annotations. The manual search was implemented by first locally blasting D. citri predicted transcripts against a locally curated list of immune related genes from Drosophila melanogaster (flybase.org), A. pisum, Apis mellifera, Aedes aegypti (vectorbase.org), Bombyx mori, and Nilaparvata lugens with the tblastx search algorithm. Geneious software (http://www.geneious.com, version 7.1.5) was used to conduct BLAST searches (Kearse et al., ) with results limited to hits with e-values of <1e−5. The identities of predicted transcripts with positive matches in the initial tblastx search were validated performing a BLAST search of all insect protein sequences in the NCBI nr database using blastp. Immune genes identified with the manual search were submitted to NCBI and sequences mislabeled by the automated annotation pipeline were updated. […]

Pipeline specifications

Software tools TBLASTX, Geneious, BLASTP
Databases FlyBase VectorBase
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Diaphorina citri, Candidatus Liberibacter asiaticus, Pediculus humanus
Diseases Infection
Chemicals Nitric Oxide