title: YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut.
abstract: The transcriptome provides a functional footprint of the genome by enumerating the molecular components of cells and tissues. The field of transcript discovery has been revolutionized through high-throughput mRNA sequencing (RNA-seq). Here, we present a methodology that replicates and improves existing methodologies, and implements a workflow for error estimation and correction followed by genome annotation and transcript abundance estimation for RNA-seq derived transcriptome sequences (YeATS - Yet Another Tool Suite for analyzing RNA-seq derived transcriptome). A unique feature of YeATS is the upfront determination of the errors in the sequencing or transcript assembly process by analyzing open reading frames of transcripts. YeATS identifies transcripts that have not been merged, result in broken open reading frames or contain long repeats as erroneous transcripts. We present the YeATS workflow using a representative sample of the transcriptome from the tissue at the heartwood/sapwood transition zone in black walnut. A novel feature of the transcriptome that emerged from our analysis was the identification of a highly abundant transcript that had no known homologous genes (GenBank accession: KT023102). The amino acid composition of the longest open reading frame of this gene classifies this as a putative extensin. Also, we corroborated the transcriptional abundance of proline-rich proteins, dehydrins, senescence-associated proteins, and the DNAJ family of chaperone proteins. Thus, YeATS presents a workflow for analyzing RNA-seq data with several innovative features that differentiate it from existing software.
authors.affiliation: Plant Sciences Department, University of California, Davis, CA, 95616, USA.
authors.forename: Sandeep
authors.initials: S
authors.lastname: Chakraborty
authors.affiliation: UC Davis Genome Center Bioinformatics Core Facility, University of California, Davis, CA, 95616, USA.
authors.forename: Monica
authors.initials: M
authors.lastname: Britton
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA.
authors.forename: Jill
authors.initials: J
authors.lastname: Wegrzyn
authors.affiliation: Plant Sciences Department, University of California, Davis, CA, 95616, USA.
authors.forename: Timothy
authors.initials: T
authors.lastname: Butterfield
authors.affiliation: Plant Sciences Department, University of California, Davis, CA, 95616, USA.
authors.forename: Pedro José
authors.initials: PJ
authors.lastname: Martínez-García
authors.affiliation: Plant Sciences Department, University of California, Davis, CA, 95616, USA.
authors.forename: Russell L
authors.initials: RL
authors.lastname: Reagan
authors.affiliation: Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhaba Road, Mumbai, 400, India.
authors.forename: Basuthkar J
authors.initials: BJ
authors.lastname: Rao
authors.affiliation: Plant Sciences Department, University of California, Davis, CA, 95616, USA.
authors.forename: Charles A
authors.initials: CA
authors.lastname: Leslie
authors.affiliation: Plant Sciences Department, University of California, Davis, CA, 95616, USA.
authors.forename: Mallikarjuna
authors.initials: M
authors.lastname: Aradhaya
authors.affiliation: Plant Sciences Department, University of California, Davis, CA, 95616, USA.
authors.forename: David
authors.initials: D
authors.lastname: Neale
authors.affiliation: USDA Forest Service Hardwood Tree Improvement and Regeneration Center, Purdue University, West Lafayette, IN, 47907, USA.
authors.forename: Keith
authors.initials: K
authors.lastname: Woeste
authors.affiliation: Plant Sciences Department, University of California, Davis, CA, 95616, USA.
authors.forename: Abhaya M
authors.initials: AM
authors.lastname: Dandekar
keywords: Computational genomics; Juglans nigra; RNA-seq; black walnut; dehydrins; extensin; heartwood/sapwood transition zone; open reading frame; proline-rich proteins; senescence-associated proteins; transcriptome