Abstract
BackgroundThe 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.FindingsUsing 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.ConclusionsWe 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.
Highlights
The Masai giraffe (Giraffa camelopardalis tippelskirchi) is the largest-bodied giraffe and the world’s tallest terrestrial animal
To evaluate the 146 scaffold joints introduced by Reference-Assisted Chromosome Assembly (RACA), a reliability score was further calculated considering 4 components: (i) the relative positions of the bacterial artificial chromosomes (BACs) in giraffe metaphase spreads compared to the predicted chromosome fragment (PCF) (Fig. 2), (ii) if the joint was supported by sequence reads from Chicago libraries, (iii) physical coverage of Illumina paired-end reads, and (iv) comparative syntenic information
These results show that the genome assemblies we generated are of high completeness and accuracy, as well as a significant improvement over the genome assembly currently available for Masai giraffe
Summary
Giraffes (Giraffa) are a genus of even-toed ungulate mammals comprising 4 species [1]. We report a chromosomescale assembly of a female Masai giraffe genome sequenced de novo This assembly will facilitate studies of ruminant genome evolution and will be a powerful resource for further elucidation of the genetic basis for the giraffe’s characteristic features. Having another Masai giraffe genome sequence will assist conservation efforts for this species, whose population has declined by more than 52% in recent decades [2, 10]. The cross-links were reversed and the DNA purified from chromatin These libraries were sequenced in 1 flow-cell lane using the Illumina HiSeq 4000 platform, resulting in the generation of ∼385 million read pairs or 114.60 Gbp of sequence data (Supplementary Table 1)
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