Improving the Alpaca Genome Sequence Assembly

The development of whole genome sequence maps is key for understanding the genome architecture of a species and is critical for the discovery of genetic blueprints of diseases, congenital disorders and traits of biological significance. Here we report our recent work improving the alpaca VicPac2.0 reference assembly by incorporating 100X Illumina HiSeq data from the same female individual. Annotation of the assembly was improved by mapping alpaca testis RNA-Seq reads to sequence scaffolds. This allowed discovery of missing exons, determining new splice sites and gene isoforms. RNA-Seq reads that did not map to the female alpaca genome sequence scaffolds were assembled de novo, resulting in 210,961 transcripts representing novel autosomal and X-linked genes, and the first 44 putative Y chromosome transcripts. The improved sequence scaffolds are currently anchored to alpaca chromosomes using the recently generated whole genome cytogenetic map and by additional FISH mapping of unassigned scaffolds. Our ultimate goal is to create a robust, annotated and chromosomally assigned sequence assembly for the alpaca genome.