Genome Sequencing: The Ripping Yarn of The Frozen Genome

AbstractThe completion of the genome sequence of the filamentous fungus Neurospora crassa reveals a gene number very much higher than those of yeasts. Of particular interest in this species are the effects of the repeat-induced point mutation (RIP) process, which appears to have prevented recent evolution through gene duplication in this lineage

Transposable element invasions

Transposable elements have an ongoing, largely parasitic interaction with their hosts. We are interested in the timescale of this interaction. In a recent publication, we have examined the sequence divergence between class II DNA transposons from mammalian genomes. We asked whether these sequences undergo a continuing process of turnover, keeping a family as an integrated whole, as members of the family are continually created and lost. Alternatively, we envisaged that elements might have been involved in a burst of amplification, soon after they first occupied a mammalian genome, and the shared ancestry of present-day elements harks back to this initial amplification, a process that we termed a “life cycle.” We resolved between these processes by estimating the time to common ancestry predicted from the genetic diversity of sequences found in a transposon family, and also estimating, from the mammalian orders that currently possess copies of the family, the time when the family first entered the mammalian genome. These times are approximately the same, supporting the “life cycle” model. This casts light on how far we can infer genetic changes in the past through the study of DNA sequences from the present

Alu elements in primates are preferentially lost from areas of high GC content

The currently-accepted dogma when analysing human Alu transposable elements is that ‘young’ Alu elements are found in low GC regions and ‘old’ Alus in high GC regions. The correlation between high GC regions and high gene frequency regions make this observation particularly difficult to explain. Although a number of studies have tackled the problem, no analysis has definitively explained the reason for this trend. These observations have been made by relying on the subfamily as a proxy for age of an element. In this study, we suggest that this is a misleading assumption and instead analyse the relationship between the taxonomic distribution of an individual element and its surrounding GC environment. An analysis of 103906 Alu elements across 6 human chromosomes was carried out, using the presence of orthologous Alu elements in other primate species as a proxy for age. We show that the previously-reported effect of GC content correlating with subfamily age is not reflected by the ages of the individual elements. Instead, elements are preferentially lost from areas of high GC content over time. The correlation between GC content and subfamily may be due to a change in insertion bias in the young subfamilies. The link between Alu subfamily age and GC region was made due to an over-simplification of the data and is incorrect. We suggest that use of subfamilies as a proxy for age is inappropriate and that the analysis of ortholog presence in other primate species provides a deeper insight into the data