Towards the delineation of the ancestral eutherian genome organization: comparative genome maps of human and the African elephant (Loxodonta africana) generated by chromosome painting

Abstract

This study presents a whole-genome comparison of human and a representative of the Afrotherian clade, the African elephant, generated by reciprocal Zoo-FISH. An analysis of Afrotheria genomes is of special interest, because recent DNA sequence comparisons identify them as the oldest placental mammalian clade. Complete sets of whole-chromosome specific painting probes for the African elephant and human were constructed by degenerate oligonucleotide-primed PCR amplification of flow-sorted chromosomes. Comparative genome maps are presented based on their hybridization patterns. These maps show that the elephant has a moderately rearranged chromosome complement when compared to humans. The human paint probes identified 53 evolutionary conserved segments on the 27 autosomal elephant chromosomes and the X chromosome. Reciprocal experiments with elephant probes delineated 68 conserved segments in the human genome. The comparison with a recent aardvark and elephant Zoo-FISH study delineates new chromosomal traits which link the two Afrotherian species phylogenetically. In the absence of any morphological evidence the chromosome painting data offer the first non-DNA sequence support for an Afrotherian clade. The comparative human and elephant genome maps provide new insights into the karyotype organization of the proto-afrotherian, the ancestor of extant placental mammals, which most probably consisted of 2n = 46 chromosomes.

Cross-species chromosome painting in the golden mole and elephant-shrew: support for the mammalian clades Afrotheria and Afroinsectiphillia but not Afroinsectivora

“…In addition, the recent human : xenarthran data from Richard et al (2003b) allow us to further clarify the presumed synapomorphies uniting the Afrotheria. However, confirmation that these cytogenetic characters constitute Afrotherian synapomorphies as opposed to ancestral placental states would be strengthened by outgroup comparison to a marsupial representative which is lacking (Frönicke et al 2003;Yang et al 2003). Frönicke et al (2003) identified HSA 5/21 in the elephant, suggesting that this composite, together with HSA 1/19p, may be a synapomorphy that unites Afrotheria.…”

Origins of primate chromosomes – as delineated by Zoo-FISH and alignments of human and mouse draft genome sequences

“…some species in several recent publications (Korstanje et al, 1999;Froenicke et al, 2003;Yang et al, 2003) indicates the presence of rearrangement hotspots at the junction of HSA4 and 8 orthologous segments. The reciprocal Zoo-FISH data identify this association as a combination of HSA4 with the p-arm of HSA8 (Fig.…”

Molecular cytogenetic and genomic insights into chromosomal evolution

“…The differences in interpretation are primarily related to the recognition of a single large chromosome (corresponding to HSA 1) in the placental ancestor (Murphy et al, 2003), the detection of the 10q/12p/22q conserved syntenic segmental association , and fusion of HSA1/19p (Yang et al, 2003, n¼22) based on its presence in Afrotheria (aardvark, elephant, golden mole and elephant shrew), at the time regarded as the most basal split in the eutherian tree (Murphy et al, 2001a, b). The more recent studies appear, however, to have converged on n¼23 for Placentalia (that is, the eutherian ancestral karyotypes of Froenicke et al, 2003;Wienberg, 2004;Ferguson-Smith and Trifonov, 2007), and an identical n¼23 in the boreoeutherian ancestral karyotype (BAK; Froenicke, 2005;Froenicke et al, 2006;Robinson et al, 2006).…”