YeATS- a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut

Authors: CHAKRABORTY, SANDDEP - University Of California; BRITTON, MONICA - University Of California; WEGRZYN, JILL - University Of Connecticut; BUTTERFIELD, TIMOTHY - University Of California; MARTINEZ-GARCIA, PEDRO JOSE' - University Of California; REAGAN, RUSSELL - University Of California; RAO, BASUTHKAR - The Tata Institute Of Fundamental Research; LESLIE, CHUCK - University Of California; Aradhya, Mallikarjuna; NEALE, DAVID - University Of California; WOESTE, KEITH - Purdue University; DANDEKAR, ABHAYA - University Of California

Submitted to: F1000Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/30/2015
Publication Date: 11/6/2015
Publication URL: http://www.ars-grin.gov.dav
Citation: Chakraborty, S., Britton, M., Wegrzyn, J., Butterfield, T., Martinez-Garcia, P., Reagan, R.L., Rao, B.J., Leslie, C.A., Aradhya, M.K., Neale, D., Woeste, K., Dandekar, A.M. 2015. YeATS- a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut. F1000Research. 4:155. doi: 10.12688/f100research.6617.2.

Interpretive Summary: 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.

Technical 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.