Origin and ascendancy of a chimeric fusion gene: the beta/delta-globin gene of paenungulate mammals

Abstract

The delta-globin gene (HBD) of eutherian mammals exhibits a propensity for recombinational exchange with the closely linked beta-globin gene (HBB) and has been independently converted by the HBB gene in multiple lineages. Here we report the presence of a chimeric beta/delta fusion gene in the African elephant (Loxodonta africana) that was created by unequal crossing-over between misaligned HBD and HBB paralogs. The recombinant chromosome that harbors the beta/delta fusion gene in elephants is structurally similar to the "anti-Lepore" duplication mutant of humans (the reciprocal exchange product of the hemoglobin Lepore deletion mutant). However, the situation in the African elephant is unique in that the chimeric beta/delta fusion gene supplanted the parental HBB gene and is therefore solely responsible for synthesizing the beta-chain subunits of adult hemoglobin. A phylogenetic survey of beta-like globin genes in afrotherian and xenarthran mammals revealed that the origin of the chimeric beta/delta fusion gene and the concomitant inactivation of the HBB gene predated the radiation of "Paenungulata," a clade of afrotherian mammals that includes three orders: Proboscidea (elephants), Sirenia (dugongs and manatees), and Hyracoidea (hyraxes). The reduced fitness of the human Hb Lepore deletion mutant helps to explain why independently derived beta/delta fusion genes (which occur on an anti-Lepore chromosome) have been fixed in a number of mammalian lineages, whereas the reciprocal delta/beta fusion gene (which occurs on a Lepore chromosome) has yet to be documented in any nonhuman mammal. This illustrates how the evolutionary fates of chimeric fusion genes can be strongly influenced by their recombinational mode of origin.

FIG. 1.—

Genomic structure of the β-globin gene cluster in afrotherians (African elephant and lesser hedgehog tenrec), xenarthrans (nine-banded armadillo and two-toed sloth), two representative boreoeutherian species (human and European rabbit), and two marsupial outgroups (gray short-tailed opossum and North American opossum).

FIG. 2.—

Dot plot of pairwise sequence similarity between the 3′ ends of the β-globin gene clusters of African elephant, Loxodonta africana, and human.

FIG. 3.—

Diagram showing the inferred unequal crossing-over event that produced the 5′-HBD, HBB/D, HBBps-3′ anti-Lepore chromosome in the evolutionary ancestry of elephants.

FIG. 4.—

An alignment of β-chain amino acid sequences from human, rabbit, and African elephant. The crossover breakpoint that produced the chimeric HBB/D gene of the African elephant is located within the shaded interval. The boxes with dotted lines denote the breakpoint intervals associated with three different Hb Lepore deletion mutants in humans.

FIG. 5.—

Maximum likelihood phylograms depicting relationships among adult β-like globin genes based on 0.8 kb of 5′ flanking sequence, 5,028 bp of intron 2, and 1 kb of 3′ flanking sequence. The analysis included data from two afrotherians (African elephant, Loxodonta africana, and the lesser hedgehog tenrec, Echinops telfairi), two xenarthrans (nine-banded armadillo, Dasypus novemcinctus, and Hoffmann's two-toed sloth, Choloepus didactylus), two representative boreoeutherian species (human, Homo sapiens, and European rabbit, Oryctalagus cuniculus), and two marsupial species (the gray short-tailed opossum, Monodelphis domestica, and the North American opossum, Didelphis virginiana). All HBB and HBD sequences were retrieved from full genomic contigs (see text for details). The 5′ flanking sequence of the elephant HBBps pseudogene was not included in the analysis due to missing data (i.e., the upstream region, together with exon 1, intron 1, and part of exon 2 was deleted in the Loxodonta genome; see fig. 3). Because the β-like globin genes of mammals have undergone multiple rounds of duplication that have resulted in tandemly repeated sets of paralogous gene copies, we index each paralog with the symbol—T followed by a number that corresponds to the linkage order in the 5′ to 3′ orientation (Aguileta et al. 2006).

FIG. 6.—

Maximum likelihood phylogram depicting relationships among adult β-like globin genes based on 5,510 bp of intron 2 sequence. The analysis included sequence data from 15 atlantogenatan species in addition to two boreoeutherian outgroups (Oryctolagus and Homo) and two marsupial outgroups (Monodelphis and Didelphis).

FIG. 7.—

Dot plots of sequence similarity between the chimeric HBB/D (β/δ) fusion genes of paenungulate mammals and the HBD and HBB genes of human. Top row: Asian elephant β/δ fusion gene versus human HBD and HBB; Middle row: Dugong β/δ fusion gene versus human HBD and HBB; Bottom row: Rock hyrax β/δ fusion gene versus human HBD and HBB.