Gene models were predicted using ab initio and homology-based methods (FGENESH, GENEWISE, SNAP, PASA and Gnomon). pulex live for around 10-30 days, but can live up to 100 days in the absence of predation. We describe the draft genome of the microcrustacean Daphnia pulex , which is only 200 megabases and contains at least 30,907 genes. 2020 Apr 21;117(16):8948-8957. doi: 10.1073/pnas.1917303117. This genome sequence provides the toolkit.”Co-authors of the study include Pfrender, Jacqueline Lopez and Brent Harker of the Notre Dame Genomics and Bioinformatics Core Facility; Zhiqiang Ye, Ken Spitze, Xiaoqian Jiang, Matthew S. Ackerman and Michael Lynch at the Department of Biology at Indiana University; Sen Xu at the Department of Biology at Indiana University and the University of Texas at Arlington; Jana Asselman, Laboratory for Environmental Toxicology at Ghent University; R. Taylor Raborn at the Department of Biology and School of Informatics and Computing at Indiana University; and W. Kelley Thomas and Jordan Ramsdell at the Hubbard Center for Genome Studies at the University of New Hampshire.The study was funded through a grant from the National Institutes of Health to Michael Lynch at Indiana University, Bloomington and Notre Dame Research. Environ Commun. "We need this genomic infrastructure to add to the ecological context we already have to gain a better understanding of how Daphnia adapt.
2013;30(7):923–30.Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. But the tiny, transparent microcrustaceans have been studied intensively for more than 150 years, and new research published and featured on the cover of the journal G3 reveals scientists can now take a closer look at its genome.
The Daphnia Genomics Consortium and the JGI are coordinating a community-wide analysis of the data. However, from the clone-specific analyses, each independent clone has a higher number of unique DS genes than unique DE genes, with Clone D having the highest proportion of unique DS vs DE genes (82/6) followed by Clone S (56/9) and Clone K (39/16). The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. Genome Biol. Alternative splicing in plant stress response. Human Genomics. Functional diversification of duplicated genes, from 12 microarray experiments. A new reference genome assembly for the microcrustacean Gilbert D. Gene-omes built from mRNA-seq not genome DNA; 2013.Simon J-C, Pfrender ME, Tollrian R, Tagu D, Colbourne JK. You can also search for this author in Nat Genet.
Gene response profiles for Kim HJ, Koedrith P, Seo YR. Ecotoxicogenomic approaches for understanding molecular mechanisms of environmental chemical toxicity using aquatic invertebrate, Noguchi T, Inoue H, Tanaka T. The M1-and M2-type isozymes of rat pyruvate kinase are produced from the same gene by alternative RNA splicing. Environmental perturbations lead to extensive directional shifts in RNA processing. 2020 Jun 26;21(1):433. doi: 10.1186/s12864-020-06831-4.Proc Natl Acad Sci U S A. Daphnia pulex was the first crustacean to have its genome sequenced. pulex plays a vital role in Earth’s ecology. Bioinformatics. Trends Genet. Moreover, the D. pulex genome will prove a useful resource for characterising the D. magna genome, which is an ongoing sequencing project undertaken by the Daphnia Genomics Consortium. Intraspecific variation in the sensitivity of aquatic macrophytes to chemical contamination: the case of copper: Université Toulouse III Paul Sabatier (UT3 Paul Sabatier); 2018.Orsini L, Brown JB, Shams Solari O, Li D, He S, Podicheti R, et al. Evolutionary dynamics of gene and isoform regulation in mammalian tissues. They evolve quickly and are masters of responding to the conditions in their environment. Genome-wide analysis of alternative splicing in Gibilisco L, Zhou Q, Mahajan S, Bachtrog D. Alternative splicing within and between Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, et al.
The current study describes how scientists used the latest technology as part of a thorough and methodical process the result of which led to the identification of 18,440 genes.D.
1986;261(29):13807–12.Mullarky E, Cantley LC. Cross-kingdom patterns of alternative splicing and splice recognition. 2014;8(1):3.Florea L. Bioinformatics of alternative splicing and its regulation. More than a third of Daphnia's genes have no detectable h … J Hered. Alternative splicing in plants: directing traffic at the crossroads of adaptation and environmental stress. It represents the percentage of transcripts including a particular exon or splice site and is calculated from the read counts [Several studies have reported that alternative splicing plays an important role in abiotic stress tolerance in plants and mammals [In this study, we integrate an analysis of differential gene expression and differential splicing to identify the role of alternative splicing in mediating response to metal-induced acute stress in Across the three clonal lineages, a total of 6630 of the 17,761 expressed genes were identified to have alternative transcripts, accounting for ~ 37% of the Comparisons of the alternative splicing events between all 15 copper-exposed samples with all 6 control samples identified 16 significantly differentially spliced (DS) genes (FDR corrected To investigate the influence of genetic background on the molecular response to acute copper exposure, the gene expression and splicing patterns were compared between controls (Venn diagram showing the overlap of differentially expressed and differentially spliced genes.
2018;102(1):11–26.Hooper JE. These two species are quite similar with respect to effective population sizes and mutation rates, although some features of recombination appear to be … MC and TC designed the copper exposure experiment. Name must be less than 100 characters By using our site, you acknowledge that you have read and understand our
A3SS – alternate 3 prime splice site; A5SS – alternate 5 prime splice site; MXE – mutually exclusive exons; ES – exon skipping; IR – intron retentionDifferential splicing of gene14576 (pyruvate kinase-like isoform x). Most of the DS genes (13) were not found to be DE, suggesting unique transcriptional regulation in response to copper that went unnoticed with conventional DE analysis. eCollection 2020. Model of gene duplication under the preservation by entrainment (PBE) model. This Your feedback will go directly to Science X editors.Thank you for taking your time to send in your valued opinion to Science X editors. 2004;36(9):915–6.Kim E, Magen A, Ast G. Different levels of alternative splicing among eukaryotes.
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