Nuclear ribosomal DNA diversity of a cotton pest (Rotylenchulus reniformis) in the United States

The reniform nematode (Rotylenchulus reniformis) has emerged as a major cotton pest in the United States. A recent analysis of over 20 amphimictic populations of this pest from the US and three othercountries has shown no sequence variation at the nuclear ribosomal internal transcribed spacer (ITS) despite the region’s usual variability. We investigated this unexpected outcome by amplifying, cloningand sequencing two regions of the nuclear ribosomal DNA (18S, ITS1) to ascertain whether any variation occurred within and among populations of reniform nematodes in Alabama, US. Both thenrITS1 and the relatively conserved 18S region showed a fairly substantial amount of variation among populations. The identity among ITS sequences ranged from 1.00 to 0.86, while sequence identity at the18S ranged from 1.00 to 0.948. We conclude that variation does exist in these sequences in reniform nematodes, and the earlier report showing no ribosomal ITS variation in this pest might have beencaused by preferential amplification of a conserved ITS paralog. Current and future application towards resistance in cotton varieties to this pest requires reliable information on the molecular variability of thenematode in cotton-growing areas

Conserved and variable correlated mutations in the plant MADS protein network

<p>Abstract</p> <p>Background</p> <p>Plant MADS domain proteins are involved in a variety of developmental processes for which their ability to form various interactions is a key requisite. However, not much is known about the structure of these proteins or their complexes, whereas such knowledge would be valuable for a better understanding of their function. Here, we analyze those proteins and the complexes they form using a correlated mutation approach in combination with available structural, bioinformatics and experimental data.</p> <p>Results</p> <p>Correlated mutations are affected by several types of noise, which is difficult to disentangle from the real signal. In our analysis of the MADS domain proteins, we apply for the first time a correlated mutation analysis to a family of interacting proteins. This provides a unique way to investigate the amount of signal that is present in correlated mutations because it allows direct comparison of mutations in various family members and assessing their conservation. We show that correlated mutations in general are conserved within the various family members, and if not, the variability at the respective positions is less in the proteins in which the correlated mutation does not occur. Also, intermolecular correlated mutation signals for interacting pairs of proteins display clear overlap with other bioinformatics data, which is not the case for non-interacting protein pairs, an observation which validates the intermolecular correlated mutations. Having validated the correlated mutation results, we apply them to infer the structural organization of the MADS domain proteins.</p> <p>Conclusion</p> <p>Our analysis enables understanding of the structural organization of the MADS domain proteins, including support for predicted helices based on correlated mutation patterns, and evidence for a specific interaction site in those proteins.</p