Patterns of cytosine methylation in the genome of Caenorhabditis elegans

Recent large-scale comparative analysis of cytosine DNA methylation across diverse eukaryotes suggest that early features of DNA methylation present in the last common ancestor of all eukaryotes some 1.6 to 1.8 billion years ago included the methylation of gene bodies and transposable elements (Zemach, McDaniel et al. 2010; Parfrey, Lahr et al. 2011). These potentially ancient patterns may reflect a primitive role of methylation in transcriptional fidelity and as a mechanism to protect the germ line from transposon, or repeat, mediated mutation. Because spurious transcription and mutation are hypothesized to be among the critical limiting factors to genome size, an ancient role for methylation in support of fidelity of transcription and genome stability suggests a possible link with the origin of eukaryotes. As a consequence, understanding the roles of methylation across diverse eukaryotes will be critical to understanding the evolution of methylation and its role in the evolution of genome complexity. In light of these observations it is perplexing that one of our key model eukaryotes, the nematode (Caenorhabditis elegans) is assumed to lack active DNA methylation. In fact, C. elegans is often invoked to suggest the dispensability of methylation in multicellular animals (Feng, Cokus et al. 2010; Zemach, McDaniel et al. 2010). Historically, this view has been based on crude assays using methylation sensitive restriction enzymes (Simpson, Johnson et al. 1986) that lack the sensitivity to identify low levels of methylation. While it is clear that the genome of C. elegans is not highly methylated, in this thesis we used comparative genomics and genome wide bisulfite sequencing to show that: 1) The genome of C. elegans appears to encode at least three DNA methyltrasferases and a DNA methyltransferase associated protein; 2) the genome of C. elegans is methylated in a pattern consistent with the proposed basal eukaryotic pattern and 3) that that cytosine methylation is not a major contributor to the basal rate and pattern of mutation in the genome of C. elegans. Based on these observations we contend that C. elegans represents an ideal model for the study of the basal roles of DNA methylation shared by all eukaryotes

Shifting patterns of natural variation in the nuclear genome of caenorhabditis elegans

<p>Abstract</p> <p>Background</p> <p>Genome wide analysis of variation within a species can reveal the evolution of fundamental biological processes such as mutation, recombination, and natural selection. We compare genome wide sequence differences between two independent isolates of the nematode <it>Caenorhabditis elegans </it>(CB4856 and CB4858) and the reference genome (N2).</p> <p>Results</p> <p>The base substitution pattern when comparing N2 against CB4858 reveals a transition over transversion bias (1.32:1) that is not present in CB4856. In CB4856, there is a significant bias in the direction of base substitution. The frequency of A or T bases in N2 that are G or C bases in CB4856 outnumber the opposite frequencies for transitions as well as transversions. These differences were not observed in the N2/CB4858 comparison. Similarly, we observed a strong bias for deletions over insertions in CB4856 (1.44: 1) that is not present in CB4858. In both CB4856 and CB4858, there is a significant correlation between SNP rate and recombination rate on the autosomes but not on the X chromosome. Furthermore, we identified numerous significant hotspots of variation in the CB4856-N2 comparison.</p> <p>In both CB4856 and CB4858, based on a measure of the strength of selection (k_a/k_s), all the chromosomes are under negative selection and in CB4856, there is no difference in the strength of natural selection in either the autosomes versus X or between any of the chromosomes. By contrast, in CB4858, k_a/k_svalues are smaller in the autosomes than in the X chromosome. In addition, in CB4858, k_a/k_svalues differ between chromosomes.</p> <p>Conclusions</p> <p>The clear bias of deletions over insertions in CB4856 suggests that either the CB4856 genome is becoming smaller or the N2 genome is getting larger. We hypothesize the hotspots found represent alleles that are shared between CB4856 and CB4858 but not N2. Because the k_a/k_sratio in the X chromosome is higher than the autosomes on average in CB4858, purifying selection is reduced on the X chromosome.</p

Review and future prospects for DNA barcoding methods in forensic palynology

© 2015 Elsevier Ireland Ltd. All rights reserved. Pollen can be a critical forensic marker in cases where determining geographic origin is important, including investigative leads, missing persons cases, and intelligence applications. However, its use has previously been limited by the need for a high level of specialization by expert palynologists, slow speeds of identification, and relatively poor taxonomic resolution (typically to the plant family or genus level). By contrast, identification of pollen through DNA barcoding has the potential to overcome all three of these limitations, and it may seem surprising that the method has not been widely implemented. Despite what might seem a straightforward application of DNA barcoding to pollen, there are technical issues that have delayed progress. However, recent developments of standard methods for DNA barcoding of pollen, along with improvements in high-throughput sequencing technology, have overcome most of these technical issues. Based on these recent methodological developments in pollen DNA barcoding, we believe that now is the time to start applying these techniques in forensic palynology. In this article, we discuss the potential for these methods, and outline directions for future research to further improve on the technology and increase its applicability to a broader range of situations

The Mitochondrial Genomes of the Nudibranch Mollusks, Melibe leonina and Tritonia diomedea, and Their Impact on Gastropod Phylogeny.

The phylogenetic relationships among certain groups of gastropods have remained unresolved in recent studies, especially in the diverse subclass Opisthobranchia, where nudibranchs have been poorly represented. Here we present the complete mitochondrial genomes of Melibe leonina and Tritonia diomedea (more recently named T. tetraquetra), two nudibranchs from the unrepresented Cladobranchia group, and report on the resulting phylogenetic analyses. Both genomes coded for the typical thirteen protein-coding genes, twenty-two transfer RNAs, and two ribosomal RNAs seen in other species. The twelve-nucleotide deletion previously reported for the cytochrome oxidase 1 gene in several other Melibe species was further clarified as three separate deletion events. These deletions were not present in any opisthobranchs examined in our study, including the newly sequenced M. leonina or T. diomedea, suggesting that these previously reported deletions may represent more recently divergent taxa. Analysis of the secondary structures for all twenty-two tRNAs of both M. leonina and T. diomedea indicated truncated d arms for the two serine tRNAs, as seen in some other heterobranchs. In addition, the serine 1 tRNA in T. diomedea contained an anticodon not yet reported in any other gastropod. For phylogenetic analysis, we used the thirteen protein-coding genes from the mitochondrial genomes of M. leonina, T. diomedea, and seventy-one other gastropods. Phylogenetic analyses were performed for both the class Gastropoda and the subclass Opisthobranchia. Both Bayesian and maximum likelihood analyses resulted in similar tree topologies. In the Opisthobranchia, the five orders represented in our study were monophyletic (Anaspidea, Cephalaspidea, Notaspidea, Nudibranchia, Sacoglossa). In Gastropoda, two of the three traditional subclasses, Opisthobranchia and Pulmonata, were not monophyletic. In contrast, four of the more recently named gastropod clades (Vetigastropoda, Neritimorpha, Caenogastropoda, and Heterobranchia) were all monophyletic, and thus appear to be better classifications for this diverse group

Gastropod mitochondrial genomes used in this study.

<p>(*) indicates a classification that was not supported by this study.</p><p>Gastropod mitochondrial genomes used in this study.</p

Cytochrome oxidase 1 sequence differences in <i>Melibe</i> genus.

<p>Nucleotide (A) and amino acid (B) alignments of a portion of the cytochrome oxidase 1 gene for <i>M</i>. <i>leonina</i> and other members of the <i>Melibe</i> genus indicate that <i>M</i>. <i>leonina</i> lacks the twelve nucleotide deletion present in other species.</p

Bayesian and maximum likelihood consensus tree for gastropod phylogeny.

<p>All deep nodes for Bayesian and maximum likelihood analyses were identical, and are illustrated here as a consensus tree showing the relationship among the major gastropod groups. The more recently distinguished gastropod groups are all monophyletic and are highly supported. Posterior probability and bootstrap values are located at the nodes.</p

Bayesian analysis of gastropod phylogeny, based on amino acid alignment of 72 gastropods.

<p>Posterior probability values indicate the confidence of each node. The bivalve, <i>Venustaconcha ellipsiformis</i>, was used an outgroup. The traditional subclasses are highlighted (pulmonates in red, opisthobranchs in green, and prosobranchs in blue). Two of the three traditional subclasses (pulmonates and opisthobranchs) were not monophyletic. In contrast, the four more recently distinguished gastropod groups (Heterobranchia, Caenogastropoda, Vetigastropoda, and Neritimorpha) were all monophyletic.</p

The complete mitochondrial genomes of <i>Melibe leonina</i> (A) and <i>Tritonia diomedea</i> (B).

<p>Both mitochondrial genomes were found to code for the expected 22 transfer RNA, 13 protein-coding genes, and a short and large ribosomal subunit. The 13 protein-coding gene order was found to be identical to all other opisthobranchs.</p