Karyotype Differentiation between Two Stickleback Species (Gasterosteidae)

Abstract

The stickleback family (Gasterosteidae) of fish is less than 40 million years old, yet stickleback species have diverged in both diploid chromosome number (2n) and morphology. We used comparative fluorescence in situ hybridization (FISH) on 2 stickleback species, Gasterosteus aculeatus (2n = 42) and Apeltes quadracus (2n = 46), to ascertain the types of chromosome rearrangements that differentiate these species. The A. quadracus karyotype contains more acrocentric and telocentric chromosomes than the G. aculeatus karyotype. By using bacterial artificial chromosome probes from G. aculeatus in our FISH screen, we found that 6 pericentric inversions and 2 chromosome fusions/fissions are responsible for the greater number of acrocentric and telocentric chromosomes in A. quadracus. While most populations of G. aculeatus have an XX/XY sex chromosome system, A. quadracus has a ZZ/ZW sex chromosome system, as previously reported. However, we discovered that a population of A. quadracus from Connecticut lacks heteromorphic sex chromosomes, providing evidence for unexpected sex chromosome diversity in this species.

A RAD-Tag Genetic Map for the Platyfish (Xiphophorus maculatus) Reveals Mechanisms of Karyotype Evolution Among Teleost Fish

“…Platyfish has 24 chromosome pairs, as do about one-quarter of all teleosts, but fourspine stickleback (Apeltes quadracus) has 23 pairs (Figure 1), while ninespine stickleback (Pungitius pungitius) and threespine stickleback both have just 21 pairs (Ross et al 2009). Because ninespine stickleback (21 pairs) and fourspine stickleback (23 pairs) are more closely related to each other than either is to threespine stickleback (21 pairs) (Urton et al 2011), it is not clear whether the ancestral condition in stickleback was 21 or 23 chromosome pairs.…”

“…Two additional stickleback chromosomes show a similar pattern: GacVII, which harbors a major quantitative trait locus for pelvic spine (Shapiro et al 2004), is a fusion of Xma11 and Xma14, and GacI is a fusion of chromosomes with orthologs on Xma18 and Xma24 (Figure S6). The threespine stickleback sex chromosome GacXIX Urton et al 2011) was not involved in these fusions and its genetic content lies almost completely on Xma15 (the platyfish sex chromosome is Xma21) ( Figure S7). Thus, the reduced stickleback karyotype evolved from the fusion of three pairs of chromosomes present in the last common ancestor of platyfish and stickleback (GacIV = Xma23 + Xma17; GacVII = Xma11 + Xma14; and GacI = Xma18 + Xma24).…”

“…We conclude that three simple pairwise fusions of six ancestral chromosomes produced the threespine stickleback karyotype. Two of these, GacIV and GacVII, have been shown to be involved in what had been called chromosome fusion/fission events comparing threespine (n = 21) to fourspine stickleback (n = 23) (Urton et al 2011). Platyfish comparative data can distinguish between fission and fusion events because they define the condition at the root of the tree.…”

Identification of the centromeric repeat in the threespine stickleback fish (Gasterosteus aculeatus)

“…Only reads with a score >30 were counted where the score is dependent on the following: To find assembled scaffolds that contain sequence homologous to the centromeric repeat sequence, we conducted a BLAST search for the CEN sequence in the threespine stickleback genome assembly (Ensembl BROAD S1; Feb 2006). We identified sequences with homology to the CEN sequence in scaffolds from regions of the genome that were not assigned to chromosome assemblies and in scaffolds at the edges of gaps in chromosome assemblies that correspond to the putative position of centromeres as determined using the p/q chromosome arm length ratios (Urton et al 2011). Up to 5 kb of sequence data from each region was extracted, and the consensus centromeric repeat was aligned to these sequences in Geneious (Biomatters, New Zealand) to identify tandem repeats and to determine percent identity between the consensus centromere repeat and the repeats present in the genome assembly.…”

“…The threespine stickleback has an assembled genome (Jones et al 2012), yet the centromere sequence is still unknown. Gaps in the genome assembly correspond with the cytological constriction on most chromosomes (Urton et al 2011), suggesting that the stickleback centromere is comprised of repetitive sequences (Henikoff 2002;Rudd and Willard 2004). To identify the threespine stickleback centromere sequence, we first identified the complete threespine stickleback CENP-A coding sequence and then performed ChIP-seq using a threespine stickleback specific CENP-A antibody.…”