Copy number polymorphism in the α-globin gene cluster of European rabbit (Oryctolagus cuniculus)

Abstract

Comparative genomic studies have revealed that mammals typically possess two or more tandemly duplicated copies of the a-globin (HBA) gene. The domestic rabbit represents an exception to this general rule, as this species was found to possess a single HBA gene. Previous electrophoretic surveys of HBA polymorphism in natural populations of the European rabbit (Oryctolagus cuniculus) revealed extensive geographic variation in the frequencies of three main electromorphs. The variation in frequency of two electromorphs is mainly partitioned between two distinct subspecies of European rabbit, and a third is restricted to the hybrid zone between the two rabbit subspecies in Iberia. Here we report the results of a survey of nucleotide polymorphism, which revealed HBA copy number polymorphism in Iberian populations of the European rabbit. By characterizing patterns of HBA polymorphism in populations from the native range of the European rabbit, we were able to identify the specific amino-acid substitutions that distinguish the previously characterized electromorphs. Within the hybrid zone, we observed the existence of a second HBA gene duplicate, named HBA2, that mostly represents a novel sequence haplotype, which occurs in higher frequency within the hybrid zone, and thus appears to have arisen in hybrids of the two distinct subspecies. Although this novel gene is also present in other wild Iberian populations, it is almost absent from French populations, which suggest a recent ancestry, associated with the establishment of the post-Pleistocene contact zone between the two European rabbit subspecies.

Status and origin of Egyptian local rabbits in comparison with Spanish common rabbits using mitochondrial DNA sequence analysis

“…Furthermore, the large population size increases the number of mutations (Bollback and Huelsenbeck, 2007;Peischl and Excoffier, 2015;Park et al,2019) which was also observed in EGS (117). We observed the highest levels of Sin EWR; the high value was consistent with Geraldes et al (2006) and Campos et al (2012). Tajima's D values were found to be significantly negative in EWR and EGS.…”

“…Meanwhile, we recorded 286 mutations (ETA) in EWR. This was because EWR samples were collected from the hybrid zone in Iberian Peninsula in which Albacete is located (Campos et al, 2012). Furthermore, the large population size increases the number of mutations (Bollback and Huelsenbeck, 2007;Peischl and Excoffier, 2015;Park et al,2019) which was also observed in EGS (117).…”

Exploring copy number variation in the rabbit (Oryctolagus cuniculus) genome by array comparative genome hybridization

“…Unfortunately this gene is not correctly assembled in the OryCun2.0 genome version and for this reason we could have missed it from our study even if it is still not clear if this variability is present only in wild rabbit populations or also in domesticated populations [42].…”

Relaxed functional constraints on triplicate α-globin gene in the bank vole suggest a different evolutionary history from other rodents

“…The high rate of gene duplication and loss in this family is likely mediated by unequal crossing-over and inactivation . Many of the gene duplicates within a species therefore have no 1:1 orthologues in other species (see, for example, Campos et al, 2012), and often have nearly identical sequence as the result of concerted evolution by means of interparalogue gene conversion . However, the a-globin genes of two rodents, the Norway rat (Rattus norvegicus) and the deer mouse (Peromyscus maniculatus), are a striking exception to this general pattern.…”