An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi)

Abstract

Background: 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 suboptimal for genome analysis. Herein we report an improved giraffe genome assembly to facilitate evolutionary analysis of the giraffe and other ruminant genomes.

Findings: Using SOAPdenovo2 and 170 Gbp of Illumina paired-end and mate-pair reads, we generated a 2.6-Gbp male 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 placed 153 cattle bacterial artificial chromosomes onto giraffe metaphase spreads to assess and assign the PCFs on 14 giraffe autosomes and the X chromosome resulting in the final assembly with an N50 of 177.94 Mbp. In this assembly, 21,621 protein-coding genes were identified using both de novo and homology-based predictions.

Conclusions: We have produced the first chromosome-scale genome assembly for a Giraffidae species. This assembly provides a valuable resource for the study of artiodactyl evolution and for understanding the molecular basis of the unique adaptive traits of giraffes. In addition, the assembly will provide a powerful resource to assist conservation efforts of Masai giraffe, whose population size has declined by 52% in recent years.

Keywords: Giraffa camelopardalis tippelskirchi; annotation; assembly; giraffe; ruminant.

Figure 1:

A representative adult female Masai giraffe (Giraffa camelopardalis tippelskirchi) in the Masai Mara national park, Kenya. Picture taken by Bjørn Christian Tørrissen, licence CC BY-SA 3.0.

Figure 2:

Syntenic relationships between giraffe and cattle genomes. (A) Circos plot showing syntenic relationships between cattle autosomes (labeled as BTA) and giraffe chromosomes. Chromosomes are colored based on cattle homologies. Ribbons inside the plot show syntenic relationships, while lines inside each ribbon indicate inversions. (B) Placement of cattle BACs onto the giraffe karyotype. The first column of numbers on the right of each pair of giraffe chromosomes corresponds to cattle (BTA) chromosomes, while the second column locates the cattle BAC IDs hybridized to giraffe chromosomes. (C) Giraffe chromosome 14 from the final assembly (Table1) showing homologous synteny blocks (HSBs) between giraffe and cattle. SOAPdenovo and SOAPdenovo + Chicago scaffolds are also displayed. Blue blocks indicate positive (+) orientation of tracks compared with the giraffe chromosome, while red blocks indicate negative (−) orientation. Numbers inside each block represent cattle chromosomes or giraffe scaffold IDs. BTA: Bos taurus, cattle. Images of all giraffe chromosomes can be found in Supplementary Fig. 1.

Figure 3:

Benchmarking of genome completeness for the 4 giraffe assemblies using BUSCO. The BUSCO data set of the mammalia_odb9 including 4,104 genes was used to assess the completeness of the 4 giraffe genome assemblies, as well as the previously published giraffe genome (ASM165123v1 [9]). The newly released cattle (ARS−UCD1.2, GCA_0 022 63795.2) and goat (ARS1, GCA_0 017 04415.1) assemblies are included for comparison.

Figure 4:

Phylogenetic relationships of the giraffe. Phylogenetic tree constructed with orthologous genes. Divergence times were extracted from the TimeTree database for calibration. Blue bars indicate the estimated divergence times in millions of years, and red circle indicates the calibration time.