Supporting data for "An integrated chromosome-scale genome assembly of the Masai Giraffe (Giraffa camelopardalis tippelskirchi)"

The Masai giraffe (Giraffa camelopardalis tippelskirchi) is the largest-bodied giraffe and the world’s tallest terrestrial animal. With its extreme size and height, the giraffe’s unique anatomical and physiological adaptations have long been of interest to diverse research fields. Giraffes are also critical to ecosystems of sub-Saharan Africa, with their long neck serving as a conduit to food sources not shared by other herbivores. Although the genome of a Masai giraffe has been sequenced, the assembly was highly fragmented and unsuitable for the analysis of chromosome evolution. Herein we report an improved giraffe genome assembly to facilitate evolutionary analysis of the giraffe and other ruminant genomes.
Using SOAPdenovo2 and 170 Gbp of Illumina paired-end and mate-pair reads we generated a 2.6 Gbp female Masai giraffe genome assembly, with a scaffold N50 of 3 Mbp. The incorporation of 114.6 Gbp of Chicago library sequencing data resulted in a HiRise SOAPdenovo + Chicago assembly with an N50 of 48 Mbp and containing 95% of expected genes according to BUSCO analysis. Using the Reference-Assisted Chromosome Assembly tool, we were able to order and orient scaffolds into 42 predicted chromosome fragments (PCFs). Using fluorescence in situ hybridization we hybridized 153 cattle BACs onto giraffe metaphase spreads to assess and place the PCFs on 14 giraffe autosome and 10 sex chromosome fragments. In this assembly, 21,621 protein-coding genes were identified and 1 Gbp of repetitive sequences annotated using both de novo and homology-based predictions.
Our results provide the first chromosome-scale genome assembly for the Masai giraffe. This assembly will be a valuable tool to elucidate the evolution and molecular basis of adaptive traits of the Giraffidae, and will provide a new genomic resource to assist conservation efforts.