Avian comparative genomics: reciprocal chromosome painting between domestic chicken (Gallus gallus) and the stone curlew (Burhinus oedicnemus, Charadriiformes)--an atypical species with low diploid number

Abstract

The chicken is the most extensively studied species in birds and thus constitutes an ideal reference for comparative genomics in birds. Comparative cytogenetic studies indicate that the chicken has retained many chromosome characters of the ancestral avian karyotype. The homology between chicken macrochromosomes (1-9 and Z) and their counterparts in more than 40 avian species of 10 different orders has been established by chromosome painting. However, the avian homologues of chicken microchromosomes remain to be defined. Moreover, no reciprocal chromosome painting in birds has been performed due to the lack of chromosome-specific probes from other avian species. Here we have generated a set of chromosome-specific paints using flow cytometry that cover the whole genome of the stone curlew (Burhinus oedicnemus, Charadriiformes), a species with one of the lowest diploid number so far reported in birds, as well as paints from more microchromosomes of the chicken. A genome-wide comparative map between the chicken and the stone curlew has been constructed for the first time based on reciprocal chromosome painting. The results indicate that extensive chromosome fusions underlie the sharp decrease in the diploid number in the stone curlew. To a lesser extent, chromosome fissions and inversions occurred also during the evolution of the stone curlew. It is anticipated that this complete set of chromosome painting probes from the first Neoaves species will become an invaluable tool for avian comparative cytogenetics.

Fig. 1

(a) The DAPI-banded karyotype of the stone curlew (Burhinus oedicnemus, BOE, 2n=42). (b) The BOE metaphase stained with PI (propidium iodide). (c) The same metaphase as (b) stained with DAPI; arrows point to the dot-like microchromosomes. (d) The probe from BOE 17+18+19+20 hybridized to BOE 17, 18, 19 and 20; note the cross-hybridization signals on BOE 13 and W chromosomes. (e) The same metaphase as (d) stained with DAPI; arrows indicates the dot-like microchromosomes. Scale bar represents 10 μm

Fig. 2

(a) The G-banded karyotype of BOE with hybridization patterns of the chicken (Gallus gallus, GGA, 2n=78) painting probes to the right of each BOE chromosome. Chromosome numbers of BOE are indicated below the chromosomes. (b) Comparison of homologous G-banded macrochromosomes between GGA and BOE. GGA macrochromosomes (1–9, Z and W chromosomes) are on the right, and their chromosome numbers are given below. The homologous BOE chromosomes are on the left, and their chromosomal numbers are given to the left

Fig. 3

C-banding, Ag-NOR staining, and FISH examples. (a) C-banded BOE metaphase (the arrow shows the W chromosome). (b) Ag-NOR staining of BOE chromosomes (the arrow indicates the association of the two chromosomes with NORs). (c) The probe from a Chinese pangolin (Manis pentadactyla) BAC clone containing ribosomal DNA hybridized to BOE chromosome 13. (d) BOE 15+16 (red) and 17+18+19+20 (green) probes hybridized to BOE metaphase; note that the latter also gave cross-hybridization signals to BOE 13p proximal and W (see Fig. 1d and e for details); arrows show BOE 17–20. (e) BOE 7 (red) probe hybridized to BOE metaphase. (f) GGA probes R7 (green) and R9 (red) hybridized to GGA metaphase. (g) GGA 9 (green), R3 (red) and R6 (pink) probes hybridized to BOE chromosomes 7, 13q and 16q. (h) GGA probes R7 (green) and R9 (red) hybridized to BOE chromosomes 11, 13, 15, 17–20; (i) GGA probes 4 (green) and 9 (red) hybridized to BOE chromosomes 4, 7 and 8. (j) BOE probes 6 (green) and 10 (red) hybridized to GGA chromosomes 5 and two pairs of microchromosomes. (k) BOE probe 7 hybridized to GGA chromosomes 9 and two pairs of microchromosomes. (l) BOE probes 15+16 (green) and 17+18+19+20 (red) hybridized to 4 pairs of GGA microchromosomes. Scale bar represents 10 μm

Fig. 4

(a) Bivariate flow karyotype of the stone curlew (B. oedicnemus) with chromosome assignments. (b) Seven-color chromosome painting of the stone curlew metaphase. (c) The same metaphase with DAPI counterstain. Scale bar represents 10 μm

Fig. 5

Bivariate flow karyotypes of the chicken (G. gallus) with chromosome assignments: (a) macrochromosomes; (b) microchromosomes

Fig. 6

(a) The Z probe of GGA painted the Z and W chromosomes of BOE. (b) The W probe of GGA gave signals on the W chromosome of BOE; note the cross-hybridization signals on some microchromosomes of BOE. (c) The Z probe of BOE painted onto the Z chromosomes of GGA. (d) The W probe of GGA gave signals on the W chromosome; note the cross-hybridization signals on Zqter and some microchromosomes of GGA. Scale bar represents 10 μm