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

Abstract

Background: Immune-response (IR) genes have an important role in the defense against highly variable pathogens, and therefore, 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 of the three Old World camel speciesdomestic dromedary and Bactrian camel, and the two-humped wild camelvia 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 assess nucleotide diversity of IR genes within and between species, and to compare the diversity found in immune genes and the rest of the genes in the genome. We detected differences in the nucleotide diversity among the three Old World camelid species and between IR gene groups, i.e., innate versus adaptive. Among the three species, domestic Bactrian camels showed the highest mean nucleotide diversity. Among the functionally different IR gene groups, the highest mean nucleotide diversity was observed in the major histocompatibility complex.

A Deadly Cargo: Gene Repertoire of Cytotoxic Effector Proteins in the Camelidae

“…At this stage, our data provide more information about the immunogenome in camels, representing in many regards a special immunological model [ 43 ]. The data on genetic polymorphisms may contribute to a better understanding of an apparently unusually low diversity of camelid genomes with a special focus on the position of immunity genes [ 44 ]. SNP loci and haplotypes identified in the genes analyzed may also serve as helpful markers in various types of association studies.…”

Recent Advances in Camel Immunology

“…Recently, high quality genome assemblies have been developed for domestic and wild camel species ( 6 , 29 ). Computational methods were employed for the improvement of genome assemblies of the three Old World camel species ( 6 ). The authors used the upgraded genome assemblies to investigate nucleotide diversity of immune response genes in the three species.…”

“…The highest mean nucleotide diversity was identified in the domestic Bactrian camel. The comparison between several innate and adaptive immune response gene groups revealed the highest mean nucleotide diversity in the major histocompatibility complex ( 6 ).…”

“…The Old World camelids include two domesticated species: the dromedary or one humped camel ( Camelus dromedarius ) and the two humped camel or Bactrian camel ( Camelus bactrianus ) ( 4 , 5 ). The wild camel ( Camelus ferus ) is a third species of Old World camelids, which is a double-humped camel living in central Asia and closely related to the Bactrian camel ( 6 ). The New World camelids, which live in the high altitudes of South America, comprise four main species including two wild species (guanaco and vicuña) and two domesticated species (llama and alpaca) ( 7 ).…”

The impact of COVID-19 on Old World Camelids and their potential role to combat a human pandemic

“…As the consumption of camel milk and meat is on the rise and camel products gain access to wider markets, the impact of camel-associated zoonotic diseases on public health and economy will also grow with increasing urbanization. Recent releases of whole-camel genomes include detailed information on immune response regions ( Lado et al, 2020 , Fitak et al 2020 , Ming et al 2020 ), while ongoing studies aim to understand patterns of immunogenetic diversity in dromedaries in response to MERS-CoV infection (Burger, unpublished data). The knowledge gained with all these studies during and after the SARS and MERS outbreaks has been essential for fighting COVID-19 as the scientific community has been better prepared to deal with the new pandemic.…”