Journal Club 20 Sept 2016: Novel Insights into Chromosome Evolution in Birds, Archosaurs, and Reptiles
It is known from work on mammals that genome structure and chromosome breakpoints are enriched for distinct DNA features, contributing to distinct phenotypes. This has been less studied in birds, but a new study by Farre et al. (2016) make an important contribution. They compared whole-genome sequences of 21 birds and 5 outgroup species. They found that genes involved in the regulation of gene expression and biosynthetic processes were more often located conserved genomic regions, than outside such regions. Concerning breakpoints, they suggest that lineage-specific changes have rearranged genes related to some distinct phenotypes (e.g. forebrain development in parrots).
Figure 1 from Farre et al. (2016): multispecies alignment of chicken chromosome 5 in 21 birds and 5 outgroups showing conserved genome structures and breakpoints.
Delmore et al. (2016) use NGS to find migration genes in light-logger-equipped Swainson’s thrushes. As amazingly as it may sound, they do find a migration-associated candidate region on chromosome 4. This would thus mean that this region of the genome may hold genes that trigger individuals to go either west or east of the Rocky mountains during their migration to Central America. They have worked in an area where hybrids and backcrosses occur which may have been key to find such a genotype-phenotype association in otherwise genetically well-differentiated subspecies.
Figure 2A from Delmore et al. (2016) showing the association between SNPs at chromosome 4 and the phenotype of interest - migratory direction in Swainson’s thrushes.
A study by Wang et al. (2013) tells that two chromosome variants in fire ants, called the social B and social b (SB and Sb), are characterized by a large region of approximately 13 megabases in which recombination is completely suppressed between SB and Sb. Recombination occurs normally between SB:s but not between Sb:s because Sb/Sb individuals are non-viable. Genomic comparisons revealed limited differentiation between SB and Sb, and the majority of 616 genes identified in the non-recombining region are present in the both variants. The lack of recombination over more than half of the two heteromorphic social chromosomes can be explained by at least one large inversion of around 9 megabases. So again inversions seem to play a large role in causing recombination suppression and the Sb chromosome shows similarities with sex chromosomes in other systems (X and Y, Z and W) and in particular with U and V of algea and bryophytes.
Figure 2 in Wang et al. showing the fire ant's 16 chromosomes with the social chromosome S and its non recombining part.
Journal Club 6 Sept 2016: Specific alleles at immune genes, rather than genome-wide heterozygosity, are related to immunity and survival in the critically endangered Attwater’s prairie-chicken
A recent paper in Molecular Ecology (Bateson et al. 2016) evaluates the association between genome-wide heterozygosity (GWH; i.e. inbreeding), immune gene variation and survival in prairie-chicken. They found no association between GWH and any survival related trait, but in contrast some immune gene alleles associate to survival. The question is whether this means that we should use e.g. immune genes as markers in conservation biological decisions? I do not agree with this conclusion, because it would mean avoiding some individuals, the ones not carrying these alleles, in breeding programs, rather than trying to keep a large and genome-wide pool of variation into the future generation. By the way, one may ask why GWH did not correlate with survivial - could it be that the double digest RAD approach created unreliable genotypes, or could it be that the individuals were similarly inbred?