IDMM Immunome Database for Marsupials and Monotremes

Full description

IMDD is a database of marsupial and monotreme immune gene sequences. The main goal of IMDD is to fill gaps in our curation of immune genes by providing immune gene sequence annotations for published genome-wide expression studies and sequence information for divergent immune genes that are not hosted on any other public database.

Content

A total of 2,935 genes, 602 expressed (538 tammar wallaby, 24 opossum, 16 platypus, 11 echidna, 6 red-necked wallaby, 4 brushtail possum and 3 bandicoot) and 2,333 predicted (1,639 opossum, 694 platypus), are currently stored in the database. This includes protein and DNA sequences. DNA sequences are coding sequences to the best of our knowledge.

The database includes 1,985 published sequences. We have integrated data from various published resources, which include expressed and predicted genes from opossum (1,663), tammar (37), brushtail possum (4) echidna (11), bandicoot (3), red-necked wallaby (6) and platypus (261).

Manually annotated gene families include: major histocompatibility complex (MHC), leucocyte receptor complex (LRC), cytokine, defensin, cathelicidin, natural killer complex (NKC) and Fc receptor genes.

For predicted genes, candidate gene regions were first identified using either BLAST or HMMER hidden Markov model searches. Following this, best hits were either concatenated into genes or used to predict a full gene model using a gene prediction program.

516 wallaby genes were annotated based on opossum genes identified in Wong et al. 2006 [1] and Belov et al. 2007 [2]. Of these, at least 217 were not annotated by Ensembl. Wallaby reads were derived from the pyrosequencing of wallaby thymus transcriptomes and annotated using the wallaby (v1.0) genome assembly (1,786 wallaby reads in total).

449 platypus gene sequences were obtained by concatenation of the highest-scoring IRIS [3] BLAST hits against the platypus genome assembly (v5.0) (Unpublished). Of these, 366 genes were not annotated by Ensembl (version 58).

The human immune gene set comprises of 1,528 genes [3]. If we expect a similar number of genes in marsupials, the percentages of immune-related genes annotated are: >90% in opossum, ~46% in platypus and ~38% in the tammar wallaby.