Cell Biology & Molecular Genetics

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    Re-annotation of the woodland strawberry (Fragaria vesca) genome
    (Springer Nature, 2015-01-27) Darwis, Omar; Shahan, Rachel; Liu, Zhongchi; Slovin, Janet P; Alkharouf, Nadim W
    Fragaria vesca is a low-growing, small-fruited diploid strawberry species commonly called woodland strawberry. It is native to temperate regions of Eurasia and North America and while it produces edible fruits, it is most highly useful as an experimental perennial plant system that can serve as a model for the agriculturally important Rosaceae family. A draft of the F. vesca genome sequence was published in 2011 [Nat Genet 43:223,2011]. The first generation annotation (version 1.1) were developed using GeneMark-ES+[Nuc Acids Res 33:6494,2005]which is a self-training gene prediction tool that relies primarily on the combination of ab initio predictions with mapping high confidence ESTs in addition to mapping gene deserts from transposable elements. Based on over 25 different tissue transcriptomes, we have revised the F. vesca genome annotation, thereby providing several improvements over version 1.1. The new annotation, which was achieved using Maker, describes many more predicted protein coding genes compared to the GeneMark generated annotation that is currently hosted at the Genome Database for Rosaceae (http://www.rosaceae.org/). Our new annotation also results in an increase in the overall total coding length, and the number of coding regions found. The total number of gene predictions that do not overlap with the previous annotations is 2286, most of which were found to be homologous to other plant genes. We have experimentally verified one of the new gene model predictions to validate our results. Using the RNA-Seq transcriptome sequences from 25 diverse tissue types, the re-annotation pipeline improved existing annotations by increasing the annotation accuracy based on extensive transcriptome data. It uncovered new genes, added exons to current genes, and extended or merged exons. This complete genome re-annotation will significantly benefit functional genomic studies of the strawberry and other members of the Rosaceae.
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    Simultaneous transcriptome profiling of Trypanosoma cruzi parasites and their human host cells.
    (2014) Li, Yuan; El-Sayed, Najib M; Cell Biology & Molecular Genetics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    The genome of the kinetoplastid parasite Trypanosoma cruzi, causative agent of Chagas disease, was published nine years ago, yet a systematic and comprehensive analysis of the transcriptomes of the parasite and the human host has not been conducted. The parasite responds rapidly to transmission between arthropod vectors and mammalian hosts by undergoing complex cellular differentiation processes that are not well understood. In this study, we generated the first transcriptome map for both T. cruzi and infected human host cells across the infection cycle including time points of 4, 6, 12, 24, 48 and 72 hours post invasion with the next generation RNA sequencing technology (RNA-Seq). We also captured the transcriptome of the parasite in its bloodstream form (trypomastigote) and its replicative form inside insect vector (epimastigote). We successfully mapped transcribed regions for the pathogen at single nucleotide resolution on a genomic scale and characterized the RNA processing (trans-splicing and polyadenylation) events across its various developmental stages. Here we report the prevalent heterogeneity of RNA processing sites across the genome. We also note the preference of different primary sites in various developmental stages presenting as a potential and interesting approach of posttranscriptional regulation, which may hypothetically contribute to the survival of the parasite across different environments. Our work has significantly enhanced the current genome annotation of T. cruzi. In addition, using the T. cruzi and human genome sequence as reference, we explored these data with informatics tools to identify genes with significant regulation and successfully profiled gene expressions from both species simultaneously. We examined the subsets of differentially expressed genes both in the parasite and the host cell over the course of the infection to understand the mechanisms of invasion and intracellular survival strategy as well as host-pathogen interactions. T. cruzi genes that were significantly regulated during the infection process might present as new targets for drug development, whereas human genes that were significantly regulated might signal the immunoinflammatory response triggered by the manipulation of the parasite. Furthermore, we investigated the gene expression patterns of T. cruzi across its different developmental stages, clustered gene with similar patterns, and identified possible sequence motifs in coexpressed gene clusters.