Chromosomal rearrangements and karyotype evolution in carnivores revealed by chromosome painting

Abstract

Chromosomal evolution in carnivores has been revisited extensively using cross-species chromosome painting. Painting probes derived from flow-sorted chromosomes of the domestic dog, which has one of the most rearranged karyotypes in mammals and the highest dipoid number (2n=78) in carnivores, are a powerful tool in detecting both evolutionary intra- and inter-chromosomal rearrangements. However, only a few comparative maps have been established between dog and other non-Canidae species. Here, we extended cross-species painting with dog probes to seven more species representing six carnivore families: Eurasian lynx (Lynx lynx), the stone marten (Martes foina), the small Indian civet (Viverricula indica), the Asian palm civet (Paradoxurus hermaphrodites), Javan mongoose (Hepestes javanicas), the raccoon (Procyon lotor) and the giant panda (Ailuropoda melanoleuca). The numbers and positions of intra-chromosomal rearrangements were found to differ among these carnivore species. A comparative map between human and stone marten, and a map among the Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis), stone marten and human were also established to facilitate outgroup comparison and to integrate comparative maps between stone marten and other carnivores with such maps between human and other species. These comparative maps give further insight into genome evolution and karyotype phylogenetic relationships among carnivores, and will facilitate the transfer of gene mapping data from human, domestic dog and cat to other species.

The Juicebox Assembly Tools module facilitatesde novoassembly of mammalian genomes with chromosome-length scaffolds for under $1000

“…The analysis demonstrates a high degree of karyotype conservation between the raccoon and the cat, as well as a highly rearranged structure of the dog chromosomes. The results are in agreement with prior studies (Nie et al 2012). For this analysis, the cat (GCF_000181335.2), the dog (GCF_000002285.3) and the common raccoon (pl-1k) genome assemblies were aligned using the LastZ alignment algorithm (Robert S. Harris 2007) using "--notransition --step=20 -nogapped" command options; the cat and dog assemblies were used as targets.…”

“…Here, we show alignment blocks with scores larger than 50,000 (Robert S. Harris 2007), with direct synteny blocks colored red, and inverted blocks colored blue. Chromosome order and orientation of the common raccoon chromosomes has been modified in order to facilitate the comparison with (Nie et al 2012).…”

Comparative Chromosome Painting in Carnivora and Pholidota

“…Chromosome painting data for the Feliformia and Caniformia branches were recently reviewed [Nie et al, 2012]. A detailed tree depicting chromosomal evolution of both branches of Carnivora was presented in that study.…”

Summary of Laurasiatheria (Mammalia) Phylogeny

“…Early karyotype studies of Laurasiatheria have suggested there are significant differences in chromosome number, morphology and banding pattern among the six orders (Ao et al, 2007;Frönicke et al, 1997;Kulemzina et al, 2009;Nie et al, 2011;SoteroCaio et al, 2011;Trifonov et al, 2008;Yang & Graphodatsky, 2004;Yang et al, 2006;Ye et al, 2006). Kulemzina et al (2010) investigated the phylogenetic relationships among Laurasiatheria orders by comparing their karyotypes with human karyotype, and proposed the Laurasiatheria phylogeny as (Eulipotyphla, (Cetartiodactyla, ((Perissodactyla, Chiroptera), (Carnivora, Pholidota)))) ( Figure 1A, Table 1).…”