Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Genome-scale methylome analysis of the desert locust, Schistocerca gregaria

ABSTRACT: DNA methylation is a widely conserved epigenetic modification that is established and maintained by the cooperative activity of DNA methyltransferases. While the complement of DNA methyltransferase genes can vary substantially between animal species, whole-genome methylation analyses have suggested that major features of animal methylomes are widely conserved. We have now used genome-scale bisulfite sequencing to analyze the methylome of the desert locust, Schistocerca gregaria, which represents an economically important pest with a high degree of phenotypic plasticity. Interestingly, in this system, DNA methylation appears to be both established and maintained by Dnmt1 methyltransferases, which distinguishes locusts from most other known organisms. Our results indicate that the S. gregaria methylome shares preferential methylation of CpG dinucleotides and exons with other animal methylomes. In contrast to other invertebrates, however, overall methylation levels were substantially higher and a significant fraction of transposons was methylated. Additionally, genes were densely methylated in a pronounced bimodal pattern, suggesting a role for DNA methylation in the regulation of locust gene expression. Altogether, our results uncover a unique pattern of genome methylation in locusts and also suggest that animal methylomes may be more diverse than previously thought. Whole exome methylation analysis of S. gregaria. Two samples were analyzed, one sample containing DNA from brain, one sample containing DNA from MTG. To date, there exists no sequenced genome of Schistocerca gregaria; thus, we could only map the data against an EST database (Locust2 EST project) representing the coding part of the genome.

ORGANISM(S): Schistocerca gregaria

SUBMITTER: Guenter Raddatz

PROVIDER: E-GEOD-41214 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Characterization of genome methylation patterns in the desert locust Schistocerca gregaria.

Falckenhayn Cassandra C Boerjan Bart B Raddatz Günter G Frohme Marcus M Schoofs Liliane L Lyko Frank F

The Journal of experimental biology 20121221 Pt 8

DNA methylation is a widely conserved epigenetic modification. The analysis of genome-scale DNA methylation patterns in various organisms suggests that major features of animal methylomes are widely conserved. However, based on the variation of DNA methyltransferase genes in invertebrates, it has also been proposed that DNA methylation could provide a molecular mechanism for ecological adaptation. We have now analyzed the methylome of the desert locust, Schistocerca gregaria, which represents an ...[more]

PMID: 23264491

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Project description:The migratory locust, Locusta migratoria, is a serious agricultural pest and important insect model to study insect digestion and feeding behavior. The gut is one of the primary interfaces between the insect and its environment. Nevertheless, knowledge on the gut transcriptome of L. migratoria is still very limited. With the development of two EST databases from L. migratoria (whole body and central nervous system (CNS)) and one EST database from Schistocerca gregaria (CNS), an abundance of transcript data was made available for locusts. In addition, the genome of Locusta was also recently published in an effort to create a better understanding of swarm formation and flight behavior (Wang et al., 2014). While the transcript composition of nervous tissue was relatively well studied after the development of the specific CNS-derived EST-databases from both L. migratoria and S. gregaria, little transcript profiling information is available for the digestive system at the moment. Locusts are, however, widely used as physiological model organisms regarding the regulation and control of feeding and digestion, and improved knowledge on the gut transcriptome could contribute significantly to a better understanding of their gut physiology. Therefore, we aimed to use the available sequence data to specifically identify gut-expressed transcripts in 5th larval locusts. By means of two independent self-self microarray hybridizations for two distinct tissues, the gut and the brain, a selection could be made of those ESTs that are present in the gut and/or the brain. Here, sequences that were found to be expressed in gut but not brain were further functionally annotated to shed new light on the complex physiology of the locust digestive system. Since the gut is the single most important organ in digestion, and both tissues are assumed to be involved in the regulation thereof, the resulting subset of sequences can also be valuable for further in-depth studies on the regulation of digestion. In addition, the method allowed us to rank the signal intensities, using them as a rough indicator to compare relative transcript abundance in the gut. Therefore, the data complement previously published transcript and genomic data, and provide a clear overview of the expressed portion of the genome in the gut. Taken together, the present data provide significant insight into locust larval gut physiology, and will be valuable for future studies on the insect gut. Self-self hybridisation of Cy5- and Cy3-labeled samples. One biological repeat per tissue type, i.e., brain and gut. Gut is a combination of foregut, midgut, gastric caeca and hindgut. Per tissue type, a pool was made from RNA from 3 pools of 5 locusts, and this for 3 different feeding conditions, resulting in samples derived from a total of 45 locust larvae. Feeding conditions were normally fed, fed with diet containing additional protease inhibitors (PIs), and starved locusts.

Dataset Information

Genome-scale methylome analysis of the desert locust, Schistocerca gregaria

Publications

Characterization of genome methylation patterns in the desert locust Schistocerca gregaria.

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