The Koala Genome Consortium - the Utilization of de novo Genome and Transcriptome Sequencing for Applied Conservation Genomics of an Iconic Australian Marsupial

This presentation will report de novo koala transcriptome and genome sequencing, assembly, annotation and analysis and the unique molecular attributes we have discovered for this iconic, monotypic marsupial.  Two geographically separate koalas, have been RNA sequenced for 15 tissue types, to create the first comprehensive catalog of annotated transcripts for this species, which we estimate represents approximately 15,000 koala genes and also detected the presence of the Koala retrovirus (KoRV) in the transcriptome data from both animals.

Comparative analyses using other marsupial transcriptome data were used to investigate potential gene duplications and we report evidence for copy number expansion of the alpha amylase gene, and of an aldehyde reductase gene. Further, we will report how we are now using these data to develop a SNP chip to investigate koala population genomics, immune gene diversity, disease and retroviral status across the Australian east coast koala distribution as well as in captive animals.

In addition, these koala transcriptome data are being used to validate and annotate the full koala genome sequence assembly in preparation for koala genome release draft version 1 in 2015. Version 1 of the genome release will form the foundation of evolutionary genetic studies of marsupials in general, thorough analysis of koala immune genes and importantly the opportunity for genome level investigation of the koala retrovirus.

Keywords: Conservation genomics, population genetics, Transcriptome, Koala, Phascolarctos cinereus, Koala retrovirus, Alpha amylase, Aldehyde reductase, www.koalagenome.org