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

GigaScience
Marta FarréHarris A Lewin

Abstract

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. 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 hybridiza...Continue Reading

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Datasets Mentioned

BETA
OR1865
SRR7503155
RAWU00000000

Methods Mentioned

BETA
whole-genome shotgun sequencing
Illumina sequencing
PCR
Genome Sequencing

Key Resources (RRID) Mentioned

SCR_010752
SCR_010910
SCR_005476
SCR_015008
SCR_012954
SCR_002344
SCR_015054
SCR_008417
SCR_012902
SCR_007936

Software Mentioned

Chicago
BUSCO
lastZ
Bowtie2
SOAPdenovo
SA
Benchmarking Universal Single - Copy Orthologs ( BUSCO
UCSC Kent
UCSC Genome Browser LiftOver
PhyML

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