Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids

© 2012 Matyášek et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

Genome-wide repeat dynamics reflect phylogenetic distance in closely related allotetraploid Nicotiana (Solanaceae)

Nicotiana sect. Repandae is a group of four allotetraploid species originating from a single allopolyploidisation event approximately 5 million years ago. Previous phylogenetic analyses support the hypothesis of N. nudicaulis as sister to the other three species. This is concordant with changes in genome size, separating those with genome downsizing (N. nudicaulis) from those with genome upsizing (N. repanda, N. nesophila, N. stocktonii). However, a recent analysis reflecting genome dynamics of different transposable element families reconstructed greater similarity between N. nudicaulis and the Revillagigedo Island taxa (N. nesophila and N. stocktonii), thereby placing N. repanda as sister to the rest of the group. This could reflect a different phylogenetic hypothesis or the unique evolutionary history of these particular elements. Here we re-examine relationships in this group and investigate genome-wide patterns in repetitive DNA, utilising high-throughput sequencing and a genome skimming approach. Repetitive DNA clusters provide support for N. nudicaulis as sister to the rest of the section, with N. repanda sister to the two Revillagigedo Island species. Clade-specific patterns in the occurrence and abundance of particular repeats confirm the original (N. nudicaulis (N. repanda (N. nesophila ? N. stocktonii))) hypothesis. Furthermore, overall repeat dynamics in the island species N. nesophila and N. stocktonii confirm their similarity to N. repanda and the distinctive patterns between these three species and N. nudicaulis. Together these results suggest that broad-scale repeat dynamics do in fact reflect evolutionary history and could be predicted based on phylogenetic distance

Mass-loaded spherical accretion flows

We have calculated the evolution of spherical accretion flows undergoing mass-loading from embedded clouds through either conduction or hydrodynamical ablation. We have observed the effect of varying the ratios of the mass-loading timescale and the cooling timescale to the ballistic crossing timescale through the mass-loading region. We have also varied the ratio of the potential energy of a particle injected into the flow near the outer region of mass-loading to the temperature at which a minimum occurs in the cooling curve. The two types of mass-loading produce qualitatively different types of behaviour in the accretion flow, since mass-loading through conduction requires the ambient gas to be hot, whereas mass ablation from clumps occurs throughout the flow. Higher ratios of injected to accreted mass typically occur with hydrodynamical ablation, in agreement with previous work on wind-blown bubbles and supernova remnants. We find that mass-loading damps the radiative overstability of such flows, in agreement with our earlier work. If the mass-loading is high enough it can stabilize the accretion shock at a constant radius, yielding an almost isothermal subsonic post-shock flow. Such solutions may be relevant to cooling flows onto massive galaxies. Mass-loading can also lead to the formation of isolated shells of high temperature material, separated by gas at cooler temperatures

The role of the supervisor in pre-application doctoral communications : project brief

A briefing for doctoral supervisors based on the project 'Opening up the Black Box of Pre-Application Doctoral Communications', funded by the Research England Enhancing Research Culture Fund

The role of the institution in pre-application doctoral communications : project brief

A briefing for higher education institutions and academic departments based on the project 'Opening up the Black Box of Pre-Application Doctoral Communications', funded by the Research England Enhancing Research Culture Fund