Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies

Background

Immune-response (IR) genes have an important role in the defense against highly variable pathogens, and therefore, genetic diversity in these genomic regions is essential for species’ survival and adaptation. Although current genome assemblies from Old World camelids are very useful for investigating genome-wide diversity, demography and population structure, they have inconsistencies and gaps that limit analyses at local genomic scales. Improved and more accurate genome assemblies and annotations are needed to study complex genomic regions like adaptive and innate IR genes.

Results

In this work, we improved the genome assemblies in the three Old World camel species – domestic dromedary and Bactrian camel, and the two-humped wild camel – via different computational methods. The newly annotated dromedary genome assembly CamDro3 served as reference to scaffold the NCBI RefSeq genomes of domestic Bactrian and wild camels. These upgraded assemblies were then used to asse...