Insect Innate Immunity Database (IIID): An Annotation Tool for Identifying Immune Genes in Insect Genomes

The innate immune system is an ancient component of host defense. Since innate immunity pathways are well conserved throughout many eukaryotes, immune genes in model animals can be used to putatively identify homologous genes in newly sequenced genomes of non-model organisms. With the initiation of...

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Main Authors:	Brucker, Robert M., Funkhouser, Lisa J., Setia, Shefali, Pauly, Rini, Bordenstein, Seth R.
Format:	Online
Language:	English
Published:	Public Library of Science 2012
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440344/

id	pubmed-3440344
recordtype	oai_dc
spelling	pubmed-34403442012-09-14 Insect Innate Immunity Database (IIID): An Annotation Tool for Identifying Immune Genes in Insect Genomes Brucker, Robert M. Funkhouser, Lisa J. Setia, Shefali Pauly, Rini Bordenstein, Seth R. Research Article The innate immune system is an ancient component of host defense. Since innate immunity pathways are well conserved throughout many eukaryotes, immune genes in model animals can be used to putatively identify homologous genes in newly sequenced genomes of non-model organisms. With the initiation of the “i5k” project, which aims to sequence 5,000 insect genomes by 2016, many novel insect genomes will soon become publicly available, yet few annotation resources are currently available for insects. Thus, we developed an online tool called the Insect Innate Immunity Database (IIID) to provide an open access resource for insect immunity and comparative biology research (http://www.vanderbilt.edu/IIID). The database provides users with simple exploratory tools to search the immune repertoires of five insect models (including Nasonia), spanning three orders, for specific immunity genes or genes within a particular immunity pathway. As a proof of principle, we used an initial database with only four insect models to annotate potential immune genes in the parasitoid wasp genus Nasonia. Results specify 306 putative immune genes in the genomes of N. vitripennis and its two sister species N. giraulti and N. longicornis. Of these genes, 146 were not found in previous annotations of Nasonia immunity genes. Combining these newly identified immune genes with those in previous annotations, Nasonia possess 489 putative immunity genes, the largest immune repertoire found in insects to date. While these computational predictions need to be complemented with functional studies, the IIID database can help initiate and augment annotations of the immune system in the plethora of insect genomes that will soon become available. Public Library of Science 2012-09-12 /pmc/articles/PMC3440344/ /pubmed/22984621 http://dx.doi.org/10.1371/journal.pone.0045125 Text en © 2012 Brucker et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Brucker, Robert M. Funkhouser, Lisa J. Setia, Shefali Pauly, Rini Bordenstein, Seth R.
spellingShingle	Brucker, Robert M. Funkhouser, Lisa J. Setia, Shefali Pauly, Rini Bordenstein, Seth R. Insect Innate Immunity Database (IIID): An Annotation Tool for Identifying Immune Genes in Insect Genomes
author_facet	Brucker, Robert M. Funkhouser, Lisa J. Setia, Shefali Pauly, Rini Bordenstein, Seth R.
author_sort	Brucker, Robert M.
title	Insect Innate Immunity Database (IIID): An Annotation Tool for Identifying Immune Genes in Insect Genomes
title_short	Insect Innate Immunity Database (IIID): An Annotation Tool for Identifying Immune Genes in Insect Genomes
title_full	Insect Innate Immunity Database (IIID): An Annotation Tool for Identifying Immune Genes in Insect Genomes
title_fullStr	Insect Innate Immunity Database (IIID): An Annotation Tool for Identifying Immune Genes in Insect Genomes
title_full_unstemmed	Insect Innate Immunity Database (IIID): An Annotation Tool for Identifying Immune Genes in Insect Genomes
title_sort	insect innate immunity database (iiid): an annotation tool for identifying immune genes in insect genomes
description	The innate immune system is an ancient component of host defense. Since innate immunity pathways are well conserved throughout many eukaryotes, immune genes in model animals can be used to putatively identify homologous genes in newly sequenced genomes of non-model organisms. With the initiation of the “i5k” project, which aims to sequence 5,000 insect genomes by 2016, many novel insect genomes will soon become publicly available, yet few annotation resources are currently available for insects. Thus, we developed an online tool called the Insect Innate Immunity Database (IIID) to provide an open access resource for insect immunity and comparative biology research (http://www.vanderbilt.edu/IIID). The database provides users with simple exploratory tools to search the immune repertoires of five insect models (including Nasonia), spanning three orders, for specific immunity genes or genes within a particular immunity pathway. As a proof of principle, we used an initial database with only four insect models to annotate potential immune genes in the parasitoid wasp genus Nasonia. Results specify 306 putative immune genes in the genomes of N. vitripennis and its two sister species N. giraulti and N. longicornis. Of these genes, 146 were not found in previous annotations of Nasonia immunity genes. Combining these newly identified immune genes with those in previous annotations, Nasonia possess 489 putative immunity genes, the largest immune repertoire found in insects to date. While these computational predictions need to be complemented with functional studies, the IIID database can help initiate and augment annotations of the immune system in the plethora of insect genomes that will soon become available.
publisher	Public Library of Science
publishDate	2012
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440344/
_version_	1611908092489891840

Insect Innate Immunity Database (IIID): An Annotation Tool for Identifying Immune Genes in Insect Genomes

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