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This Week in Genome Biology: Apr 17, 2019

Researchers from the University of Cologne, Baylor College of Medicine, and elsewhere report findings from a genomic analysis of the Hemiptera insect order, advanced by sequencing the genome for the milkweed bug, Oncopeltus fasciatus. The team assembled a 926 megabase genome for Oncopeltus containing more than 19,600 predicted protein-coding genes—sequences complemented by transcriptome sequences from across the bug's life cycle as well as milkweed bug RNA interference results. The sequences offered a look at lineage-specific expansions and other features in the Hemiptera tree, the authors say, while providing a resource for exploring interactions between feeding strategies in hemipteran insects and their genome features. "Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes," they say.

A University of Edinburgh team presents a single-cell methylome analysis tool called "Methylation Inference for Single cell Analysis," or Melissa. The Bayesian hierarchical approach is designed to computationally cluster cells based on single-cell whole-genome bisulfite sequencing or single-cell reduced-representation bisulfite sequencing data to get a look at the cytosine methylation variability from one cell to the next, the researchers say. They demonstrate the veracity of the approach by applying it to simulated and real sequence data for individual mouse embryonic cells and single cells from human cell lines profiled for ENCODE. "We show both on simulated and real data sets that Melissa provides accurate and biologically meaningful clusterings and state-of-the-art imputation performance," the authors report. 

Finally, researchers at the Wellcome Sanger Institute, BGI-Shenzhen, and elsewhere present a benchmark comparison between single-cell RNA sequencing on the BGI SEQ-500 platform and scRNA-seq on an Illumina HiSeq instrument. Using SMARTer and Smart-seq2 library preparation protocols, the researchers prepared single cell libraries for hundreds of individual mouse embryonic stem cells, along with matched complementary DNA samples, sequencing the libraries with single- and paired-end approaches on both the BGI SEQ-500 and Illumina platforms. From their results, the authors say the platforms "have comparable sensitivity and accuracy in terms of quantification of gene expression, and low technical variability."