Publications

  • Cheng, C-Y., Krishnakumar, V., Chan, A. P., Thibaud-Nissen, F., Schobel, S., Town, C. D. (2016). Araport11: a complete reannotation of the Arabidopsis thaliana reference genome. Plant J, Accepted Author Manuscript.

    Summary

    The flowering plant Arabidopsis thaliana is a dicot model organism for research in many aspects of plant biology. A comprehensive annotation of its genome paves the way for understanding the functions and activities of all types of transcripts, including mRNA, the various classes of non-coding RNA, and small RNA. The TAIR10 annotation update had a profound impact on Arabidopsis research but was released more than five years ago. Maintaining the accuracy of the annotation continues to be a prerequisite for future progress. Using an integrative annotation pipeline, we assembled tissue-specific RNA-Seq libraries from 113 datasets and constructed 48,359 transcript models of protein-coding genes in eleven tissues. In addition, we annotated various classes of non-coding RNA including microRNA, long intergenic RNA, small nucleolar RNA, natural antisense transcript, small nuclear RNA, and small RNA using published datasets and in-house analytic results. Altogether, we identified 635 novel protein-coding genes, 508 novel transcribed regions, 5,178 non-coding RNAs, and 35,846 small RNA loci that were formerly unannotated. Analysis of the splicing events and RNA-Seq based expression profiles revealed the landscapes of gene structures, untranslated regions, and splicing activities to be more intricate than previously appreciated. Furthermore, we present 692 uniformly expressed housekeeping genes, 43% of whose human orthologs are also housekeeping genes. This updated Arabidopsis genome annotation with a substantially increased resolution of gene models will not only further our understanding of the biological processes of this plant model but also of other species.

  • Krishnakumar, V., Hanlon, M. R., Contrino, S., Ferlanti, E. S., Karamycheva, S., Kim, M., Rosen, B. D., Cheng, C., Moreira, W., Mock, S. A., Stubbs, J., Sullivan, J. M., Krampis, K., Miller, J. R., Micklem, G., Vaughn, M. & Town, C. D. (2014). Araport: the Arabidopsis Information Portal. Nucl. Acids Res., 43(D1), D1003-D1009.

    Abstract

    The Arabidopsis Information Portal (https://www.araport.org) is a new online resource for plant biology research. It houses the Arabidopsis thaliana genome sequence and associated annotation. It was conceived as a framework that allows the research community to develop and release ‘modules’ that integrate, analyze and visualize Arabidopsis data that may reside at remote sites. The current implementation provides an indexed database of core genomic information. These data are made available through feature-rich web applications that provide search, data mining, and genome browser functionality, and also by bulk download and web services. Araport uses software from the InterMine and JBrowse projects to expose curated data from TAIR, GO, BAR, EBI, UniProt, PubMed and EPIC CoGe. The site also hosts ‘science apps,’ developed as prototypes for community modules that use dynamic web pages to present data obtained on-demand from third-party servers via RESTful web services. Designed for sustainability, the Arabidopsis Information Portal strategy exploits existing scientific computing infrastructure, adopts a practical mixture of data integration technologies and encourages collaborative enhancement of the resource by its user community.

  • Hanlon, M. R., Vaughn, M., Mock, S., Dooley, R., Moreira, W., Stubbs, J., Town, C., Miller, J., Krishnakumar, V., Ferlanti, E., and Pence, E. (2015). Araport: an application platform for data discovery. Concurrency Computat.: Pract. Exper., doi: 10.1002/cpe.3542.

    Abstract

    Araport is an open-source, online community resource for research on the Arabidopsis thaliana genome and related data. Araport is developed through a partnership between J. Craig Venter Institute, the Texas Advanced Computing Center at The University of Texas at Austin, and The University of Cambridge. Part of the open architecture of Araport is the Science Applications Workspace. Taking an ‘app store’ approach, users can choose applications developed both by the Araport team and community developers to create a customized environment for their work. Araport also provides tooling and support for developing applications for Araport, including an application generator, a rapid development and testing tool, and a straightforward deployment path for publishing applications into the Araport workspace.

  • International Arabidopsis Informatics Consortium. (2012). Taking the next step: building an Arabidopsis information portal. The Plant Cell, 24(6), 2248-2256.

    Abstract

    The Arabidopsis Information Portal (AIP), a resource expected to provide access to all community data and combine outputs into a single user-friendly interface, has emerged from community discussions over the last 23 months. These discussions began during two closely linked workshops in early 2010 that established the International Arabidopsis Informatics Consortium (IAIC). The design of the AIP will provide core functionality while remaining flexible to encourage multiple contributors and constant innovation. An IAIC-hosted Design Workshop in December 2011 proposed a structure for the AIP to provide a framework for the minimal components of a functional community portal while retaining flexibility to rapidly extend the resource to other species. We now invite broader participation in the AIP development process so that the resource can be implemented in a timely manner.

Contact Us

Have a question or comment? Send us a message at araport@jcvi.org or at our Contact Us page.

FAQ