DNA methylation, a common modification of genomic DNA, is known to influence the expression of transposable elements as well as some genes. Although commonly viewed as an epigenetic mark, evidence has shown that underlying genetic variation, such as transposable element polymorphisms, often associate with differential DNA methylation states. To investigate the role of DNA methylation variation, transposable element polymorphism, and genomic diversity, whole genome bisulfite sequencing was performed on genetically diverse lines of the model cereal Brachypodium distachyon. Although DNA methylation profiles are broadly similar, thousands of differentially methylated regions are observed between lines. An analysis of novel transposable element indel variation highlighted hundreds of new polymorphisms not seen in the reference sequence. DNA methylation and transposable element variation is correlated with the genome-wide amount of genetic variation present between samples. However, there was minimal evidence that novel transposon insertion or deletions are associated with nearby differential methylation. This study highlights the importance of genetic variation when assessing DNA methylation variation between samples and provides a valuable map of DNA methylation across diverse re-sequenced accessions of this model cereal species.
A simple, general result for the variance of substitution number in molecular evolution
Bahram Houchmandzadeh, Marcel Vallade
(Submitted on 16 Feb 2016)
The number of substitutions (of nucleotides, amino acids, …) that take place during the evolution of a sequence is a stochastic variable of fundamental importance in the field of molecular evolution. Although the mean number of substitutions during molecular evolution of a sequence can be estimated for a given substitution model, no simple solution exists for the variance of this random variable. We show in this article that the computation of the variance is as simple as that of the mean number of substitutions for both short and long times. Apart from its fundamental importance, this result can be used to investigate the dispersion index R , i.e. the ratio of the variance to the mean substitution number, which is of prime importance in the neutral theory of molecular evolution. By investigating large classes of substitution models, we demonstrate that although R\ge1 , to obtain R significantly larger than unity necessitates in general additional hypotheses on the structure of the substitution model.
Maximum likelihood estimates of pairwise rearrangement distances
Stuart Serdoz, Attila Egri-Nagy, Jeremy Sumner, Barbara R. Holland, Peter Jarvis, Mark M. Tanaka, Andrew R. Francis
Accurate estimation of evolutionary distances between taxa is important for many phylogenetic reconstruction methods. Specifically, in the case of bacteria, distances can be estimated using a range of different evolutionary models, from single nucleotide polymorphisms to large-scale genome rearrangements. Most such methods use the minimal distance as a proxy for true distance, and only occasionally are improvements such as a Jukes-Cantor correction (for SNP models) available to improve this underestimate. In particular, for genome rearrangement models such as inversion, there is currently no way to correct for such underestimates. Here we introduce a maximum likelihood estimator for the inversion distance between a pair of genomes, using the group-theoretic approach to modelling inversions introduced recently. This MLE functions as a corrected distance in its ability to correct for multiple changes. In particular, we show that because of the way sequences of inversions interact with each other, it is quite possible for minimal distance and MLE distance to differently order the distances of two genomes from a third. This has an obvious implication for the use of minimal distance in phylogeny reconstruction.