Low Frequency of Microsatellites in the Avian Genome

Abstract

A better insight into the occurrence of microsatellites in a range of taxa may help to understand the evolution of simple repeats. Previous studies have found the relative abundance of several repeat motifs to differ among mammals, invertebrates, and plants. Absolute numbers of microsatellites also tend to correlate positively with genome size. We analyzed the occurrence, frequency, and distribution of microsatellites in birds, a taxon with one of the smallest known genome sizes among vertebrates. Dot-blot hybridization revealed that about half of 22 different di-, tri-, and tetranucleotide repeat motifs were clearly more common in human than in three species of birds: chicken, woodpecker, and swallow. For the remaining motifs no clear difference was found. From searching avian database sequences we estimated there to be 30,000-70,000 microsatellites longer than 20 bp in the avian genome. The number of (CA) ജ10 would be around 7000-9000 and the number of (CA) ജ14 about 3000. The calculated density of avian microsatellites (total, one every 20-39 kb; (CA) ജ10 , one every 136-150 kb) is much lower than that estimated for the human genome (one every 6 and 30 kb, respectively). This may be explained by the fact that the avian genome contains relatively less noncoding DNA than most mammals and that avian SINE/LINE elements do not terminate in poly(A) tails, which are known to provide a resource for the evolution of simple repeats in mammals. We found no association between microsatellites and SINEs in birds. Primed in situ labeling suggested fairly even distribution of (CA) n repeats over chicken macrochromosomes and intermediate chromosomes, whereas the microchromosomes, a large part of the Z and W chromosomes, and most telomeres and centromeres had very low concentrations of (CA) n microsatellites. The scarcity of microsatellites on the microchromosomes is compatible to these regions likely being unusually rich in coding sequences. The low microsatellite density in the genome in general and on the microchromosomes in particular imposes an obstacle for the development of marker-rich genetic maps of chicken and other birds, and for the localization of quantitative trait genes.Less than 10 years after their introduction, microsatellites have developed into the marker of choice in a number of genetic areas, including genome mapping and medical, evolutionary, and ecological genetics. Despite this widespread use, many questions still remain unresolved regarding the evolution of these simple, repeated sequences, not least the mutational processes involved (Amos et al. 1996;Primmer et al. 1996). Such understanding is important for the proper use of microsatellites in evolutionary contexts, for example, for phylogeny reconstruction (Jarne and Lagoda 1996) and also for addressing general questions relating to genome organization. Knowledge of the patterns of microsatellite evolution may also help to reveal whether these sequences are associated with a functional significance. One intriguing question in this respect is why ce...

A Bird's-Eye View of the C-Value Enigma: Genome Size, Cell Size, and Metabolic Rate in the Class Aves

“…Thus, genome size in bats is controlled by broad-based regulatory forces that maintain low copy numbers of repetitive DNA families (Van Den Bussche et al 1995). Microsatellites are even rarer in avian genomes (Primmer et al 1997), and repetitive DNA in general appears scarce in birds (Eden et al 1978;Epplen et al 1978;Wagenmann et al 1981;Venturini et al 1987;Bloom et al 1993). This general fact about bird genomes is even displayed in miniature within the major histocompatibility complex of chicken (Parham 1999).…”

Challenges and prospects of population genetic studies in terns (Charadriiformes, Aves)

“…Here, only the positive clones for the PCR screening were sequenced (16 for S. hirundinacea and 8 for R. niger) and none of them were found to be true microsatellite sequences. The percentage of positive clones using traditional methods of microsatellite isolation (non-enriched libraries) has been found to be lower in birds (0.46%), compared to other taxa, such as mammals (1.67%) and fish (3.1%; Primmer et al, 1997;Zane et al, 2002). Even considering that in our study a relatively low number of clones were screened (about 2000), our results suggested that the frequency of microsatellites in S. hirundinacea and R. niger may be than for other species of birds studied to date.…”

“…It is known that the abundance of microsatellites across the taxa varies by orders of magnitude (Nève and Meglécz, 2000), and in some groups, such as birds, their frequency is relatively low (Primmer et al, 1997;Neff and Gross, 2001). In addition, major difficulties in the isolation of these markers have been reported for groups such as leptidoptera (Saccheri and Bruford, 1993), birds (Beaumont and Bruford, 1999) and some plants (Squirrell et al, 2003).…”

AFLP linkage map of the Japanese quail Coturnix japonica

“…However, AFLP markers can be expected to provide a better coverage of microchromosomes than microsatellites. Indeed, as a result of the GC-rich and gene-dense nature of microchromosomes [22,38] together with the type of polymorphism revealed by each technique, microsatellites are underrepresented on these chromosomes [30], whereas the AFLP technique, using TaqI or other enzymes, such as MspI or HinP1I [17] with GC-rich recognition sites, could better target these zones.…”

“…[6,34]), and as a model for a variety of studies in embryonic development, genetics, In linkage studies, microsatellite markers are currently used because they are highly polymorphic and codominantly inherited. However, they occur at about a 5-7-fold lower frequency in avian genomes than in mammals [30] and are thought to be biased in their distribution [30,38]. In addition, cross-species microsatellite amplification in birds is successful only at a low rate.…”