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, 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 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. Conclusions The new camel genome assemblies were greatly improved in terms of contiguity and increased size with fewer scaffolds, which is of general value for the scientific community. This allowed us to perform in-depth studies on genetic diversity in immunity-related regions of the genome. Our results suggest that differences of diversity across classes of genes appear compatible with being caused by a combination of population history coupled with possible distinct exposures to pathogens and consequent different selective pressures.

The Genomic Organisation of the TRA/TRD Locus Validates the Peculiar Characteristics of Dromedary δ-Chain Expression

“…Indeed, large blocks of synteny are interrupted by shortest blocks, due to the presence of sequencing gaps (grey lines in Figure 5 ) or micro rearrangements (e.g., local inversion, blocks below the central line of each graphic in Figure 5 ) in some of the three genomic sequences. Taking into account that the present gaps are rightly estimated in size, the length of the entire TRA/TRD locus appears to be comparable in the recent draft of the genome sequences belonging to the three camel species [ 18 ]. Instead, sequence gap annotation is lacking in the assembly BCGSAC_Cfer_1.0 of the wild Bactrian camel [ 20 ].…”

“…In this work, the latest improved version of the genomic assembly [ 18 ] allowed us to fill the gap in our knowledge [ 5 ] regarding the genomic organisation of the dromedary TRA/TRD locus, which represents the most complex among the TR loci.…”

“…To determine the TRA/TRD locus location, the upgraded dromedary CamDro3 genome assembly [ 18 ] was searched using the BLAST algorithm. A sequence of 877,081 bp was retrieved directly from the reference sequence NC_044516.1 ( C. dromedarius chromosome 6 genomic sequence) available at NCBI from 31,696,654 to 32,573,734 positions.…”

“…The CamBac2 and CamFer2 genome assemblies, which are the improved versions of the two Old World camelid genome sequences, and BCGSAC_Cfer_1.0 [ 18 , 20 ] were screened for the presence of the TRA/TRD region. A sequence from TRAV1 to TRAC orthologous genes was retrieved from each assembly.…”

“…The latest release of a new high-quality version of dromedary reference genome assembly [ 18 ], which is chromosomally assigned and improved in terms of contiguity and increased size, prompted us to perform in-depth studies for understanding the genome architecture of the TRD locus that is critical for the discovery of the genetic basis of TR δ chain repertoire.…”