Patterns of microchromosome organization remain highly conserved throughout avian evolution

Abstract

The structure and organization of a species genome at a karyotypic level, and in interphase nuclei, have broad functional significance. Although regular sized chromosomes are studied extensively in this regard, microchromosomes, which are present in many terrestrial vertebrates, remain poorly explored. Birds have more cytologically indistinguishable microchromosomes (~ 30 pairs) than other vertebrates; however, the degree to which genome organization patterns at a karyotypic and interphase level differ between species is unknown. In species where microchromosomes have fused to other chromosomes, they retain genomic features such as gene density and GC content; however, the extent to which they retain a central nuclear position has not been investigated. In studying 22 avian species from 10 orders, we established that, other than in species where microchromosomal fusion is obvious ( Falconiformes and Psittaciformes ), there was no evidence of microchromosomal rearrangement, suggesting an evolutionarily stable avian genome (karyotypic) organization. Moreover, in species where microchromosomal fusion has occurred, they retain a central nuclear location, suggesting that the nuclear position of microchromosomes is a function of their genomic features rather than their physical size. Electronic supplementary material The online version of this article (10.1007/s00412-018-0685-6) contains supplementary material, which is available to authorized users.

Falcon genomics in the context of conservation, speciation, and human culture

“…As a general trend across diapsids (Lepidosaurs and Archosaurs), microchromosomes are concentrated closer to the center of the nucleus during interphase and are characterized by disproportionately high concentrations of genes, higher recombination rates, and a higher GC content accompanied by more CpG islands (Joseph, ). However, the extent to which these properties arise from physical aspects of microchromosomes themselves, or arise from aspects of the DNA sequences that occur on microchromosomes, remains unresolved (O'Connor et al, ). Lower chromosome counts in falcons are driven by fusions of microchromosomes into macrochromosomes; whereas most birds possess ~10 pairs of macrochromosomes and ~30 pairs of microchromosomes, falcons possess 7–11 pairs of macrochromosomes and 13–16 pairs of microchromosomes.…”

Automated nuclear cartography reveals conserved sperm chromosome territory localization across 2 million years of mouse evolution

“…To compare signal distributions between warped signals, we used an open source implementation of a multi-scale structural similarity index measure, MS-SSIM* [19,20], which quantifies visual similarity between images [21]. To further assess co-localization, we identified the chromosomal signals within the nuclei by thresholding [3], and measured the distances between the centres of mass of co-hybridised chromosomes. Statistical analyses were performed in R 3.5.1 [22], and charts were generated using the cividis colour palette [23].…”

“…If the nucleus is circular or elliptical, it is commonly divided into concentric shells of equal area and the proportion of signal in each shell is measured (e.g. [1–3]). This has been amenable to automation, allowing analysis of thousands of cells, which, with appropriate statistical treatment, can yield valuable data at a scale that is still beyond the scope of 3D imaging techniques in time and cost.…”

Chromosomal Evolution in the Phylogenetic Context: A Remarkable Karyotype Reorganization in Neotropical Parrot Myiopsitta monachus (Psittacidae)

“…For instance, it was possible to identify that their ancestral karyotype structure was kept stable over millions of years of evolution in many branches (Kretschmer et al, 2018a). This conservatism seems to count not only for macrochromosomes but also microchromosomes, as revealed by recent studies with chicken BACs from microchromosomes (O'Connor et al, 2018). Despite this, some avian groups such as Charadriiformes, Accipitriformes and Psittaciformes, exhibit highly reorganized karyotypes (de Oliveira et al, 2005(de Oliveira et al, , 2010Nie et al, 2009;Furo et al, 2015aFuro et al, , 2018.…”