Novel tools for characterising inter and intra chromosomal rearrangements in avian microchromosomes

Abstract

Avian genome organisation is characterised, in part, by a set of microchromosomes that are unusually small in size and unusually large in number. Although containing about a quarter of the genome, they contain around half the genes and three quarters of the total chromosome number. Nonetheless, they continue to belie analysis by cytogenetic means. Chromosomal rearrangements play a key role in genome evolution, fertility and genetic disease and thus tools for analysis of the microchromosomes are essential to analyse such phenomena in birds. Here, we report the development of chicken microchromosomal paint pools, generation of pairs of specific microchromosome BAC clones in chicken, and computational tools for in silico comparison of the genomes of microchromosomes. We demonstrate the use of these molecular and computational tools across species, suggesting their use to generate a clear picture of microchromosomal rearrangements between avian species. With increasing numbers of avian genome sequences that are emerging, tools such as these will find great utility in assembling genomes de novo and for asking fundamental questions about genome evolution from a chromosomal perspective.

Chromosome mapping of the large elaenia (Elaenia spectabilis): evidence for a cytogenetic signature for passeriform birds?

“…Hence, the signals found on chromosome 3 in the genus Turdus probably indicate the same fusion found in ESP. Further studies using wcp corresponding to Gallus microchromosomes may clarify this point (Lithgow et al ., ).…”

Age-Related Variations in Intestinal Microflora of Free-Range and Caged Hens

“…Oakley et al (2014) reviewed to provide additional details regarding the taxonomic composition of microbial communities typically found in the different sections of the GI tract. Although the ceca is looked as organs that digesta resident for 12–20 h for longest time in the intestine and have fermentations contributing to intestinal health and nutrition, especially harbor the highest microbial cell densities in old studies (Lithgow et al, 2014; Sergeant et al, 2014), chickens can survive with experimentally removed ceca. In the present study, the microflora was found clearly separated in different intestinal sections of hens.…”

Molecular Cytogenetic Characterization of Multiple Intrachromosomal Rearrangements in Two Representatives of the Genus Turdus (Turdidae, Passeriformes)

“…Considering that chromosomal rearrangements play a key role in speciation and genome evolution, including also influence in social behavior in some species [11], [30], whole chromosome probes of species in which macrochromosomes are fissioned in multiple chromosome pairs provide an important tool for analysis of these phenoma in birds. For instance, our results illustrate well the advantage of using L. albicollis probes, considering that in this species, some chicken macrochromosomes are involved in several fission events, the most extreme example being GGA 1 chromosome, which is homologous to five distinct pairs of L. albicollis [10].…”

“…Indeed, the chromosome complement of Falconiformes species, which are characterized for presenting a few pairs of microchromosomes, at least 19 to 22 interchromosomal rearrangements have been already described in comparison to the putative ancestral avian karyotype (PAK) [2], [9], [10]. Furthermores, the use of the new developed GGA microchromosome specific probes might increase this average of chromosomal rearrangements, as most of the comparative chromosome painting analyses in birds have applied usually whole chromosome probes covering the macrochromosome GGA pairs 1 to 10 and Z chromosome [11].…”