Faculty of Veterinary Sciences, University of Sydney, NSW, Australia.
BMC Immunol. 2011 Aug 19;12:48. doi: 10.1186/1471-2172-12-48.
To understand the evolutionary origins of our own immune system, we need to characterise the immune system of our distant relatives, the marsupials and monotremes. The recent sequencing of the genomes of two marsupials (opossum and tammar wallaby) and a monotreme (platypus) provides an opportunity to characterise the immune gene repertoires of these model organisms. This was required as many genes involved in immunity evolve rapidly and fail to be detected by automated gene annotation pipelines.
We have developed a database of immune genes from the tammar wallaby, red-necked wallaby, northern brown bandicoot, brush-tail possum, opossum, echidna and platypus. The resource contains 2,235 newly identified sequences and 3,197 sequences which had been described previously. This comprehensive dataset was built from a variety of sources, including EST projects and expert-curated gene predictions generated through a variety of methods including chained-BLAST and sensitive HMMER searches. To facilitate systems-based research we have grouped sequences based on broad Gene Ontology categories as well as by specific functional immune groups. Sequences can be extracted by keyword, gene name, protein domain and organism name. Users can also search the database using BLAST.
The Immunome Database for Marsupials and Monotremes (IDMM) is a comprehensive database of all known marsupial and monotreme immune genes. It provides a single point of reference for genomic and transcriptomic datasets. Data from other marsupial and monotreme species will be added to the database as it become available. This resource will be utilized by marsupial and monotreme immunologists as well as researchers interested in the evolution of mammalian immunity.
为了了解我们自身免疫系统的进化起源，我们需要对远亲有袋类动物和单孔类动物的免疫系统进行特征描述。最近对两种有袋动物（负鼠和塔马尔袋鼠）和一种单孔类动物（鸭嘴兽）的基因组进行了测序，这为我们提供了一个机会来描述这些模式生物的免疫基因库。这是因为许多参与免疫的基因进化迅速，无法通过自动基因注释管道检测到。
我们从塔马尔袋鼠、红颈袋鼠、北部棕色袋狸、帚尾袋貂、负鼠、针鼹和鸭嘴兽中开发了一个免疫基因数据库。该资源包含 2235 个新鉴定的序列和 3197 个以前描述过的序列。这个全面的数据集是通过各种来源构建的，包括 EST 项目和通过各种方法（包括连锁 BLAST 和敏感 HMMER 搜索）生成的专家 curated 基因预测。为了便于基于系统的研究，我们根据广泛的基因本体类别以及特定的功能免疫组对序列进行了分组。序列可以通过关键字、基因名称、蛋白质结构域和生物体名称进行提取。用户还可以使用 BLAST 在数据库中进行搜索。
有袋动物和单孔类动物免疫数据库（IDMM）是所有已知有袋动物和单孔类动物免疫基因的综合数据库。它为基因组和转录组数据集提供了一个单一的参考点。随着其他有袋动物和单孔类动物物种的数据可用，将把这些数据添加到数据库中。这个资源将被有袋动物和单孔类动物免疫学家以及对哺乳动物免疫进化感兴趣的研究人员利用。
