Abstract Detail

Genomics / Proteomics

Blischak, Paul [1], Wenzel, Aaron [2], Stevens, Mikel [3], Wolfe, Andrea [4].

How low can you go? Gene predictions and putative annotations in four species of Penstemon (Plantaginaceae) from ultra low coverage 454 sequencing.

Genomic reduction in combination with next-generation sequencing (NGS) is allowing for many labs to begin developing marker systems that are specific to their organisms of interest. However, the amount of sequence data generated from NGS platforms can be daunting, and the question of what to do with the thousands of resulting sequences still remains a challenge. Here we utilize several software packages (MAKER2, MUMmer, BLAST+, Blast2GO) in an attempt to analyze whole genome shotgun sequences (WGS) for four species of Penstemon (P. fruticosus, P. davidsonii, P. dissectus, P. cyananthus) to develop nuclear and chloroplast markers. Using the MAKER2 annotation pipeline and publicly available data from closely related species, we show that even with extremely low coverage of the genome (~0.005x) and no prior genomic information, it is possible to predict and annotate genes for use in designing primers and sequence capture probes. Downstream analyses included functional annotation of predicted and annotated gene sequences using BLASTX, with GO terms added using Blast2GO and additional characterization of chloroplast sequences using the MUMmer suite of alignment tools. This analytical pipeline, therefore, offers a solution for analyzing thousands of sequences from organisms with no additional genomic resources, and will hopefully demonstrate to other researchers interested in marker development how to conduct similar analyses on their own datasets.

Broader Impacts:

Related Links:
Tutorial for MAKER annotation pipeline

1 - Ohio State University, Evolution, Ecology & Organismal Biology, 318 W. 12th Avenue, Columbus, OH, 43210, USA
2 - Ohio State University, Department of EEOB, 1242 Neil Ave, Apt. G, Columbus, OH, 43201, USA
3 - Brigham Yound University, Plant and Wildlife Sciences, Provo, UT, 84602
4 - Ohio State University, Department of Ecology, Evolution, And Organismal Biology, 318 W. 12th Avenue, COLUMBUS, OH, 43210-1293, USA

Keywords:
sequence annotation
marker development
Plantaginaceae
Penstemon
nuclear markers
pentatricopeptide repeats
MAKER annotation pipeline.

Presentation Type: Oral Paper:Papers for Topics
Session: 24
Location: Newberry/Riverside Hilton
Date: Tuesday, July 30th, 2013
Time: 10:45 AM
Number: 24004
Abstract ID:369
Candidate for Awards:Margaret Menzel Award