Abstract Detail

Phylogenomics

McKain, Michael [1], Wilson, Mark [2], Kellogg, Elizabeth Anne [1].

Fast-Plast: Rapid de novo assembly and finishing for whole chloroplast genomes.

Chloroplast genome sequences are often seen as a by-product of many sequencing projects. Whole genome shotgun, genome survey, and target enrichment sequencing in angiosperms all have a relatively high percentage of chloroplast genome sequence present for most species. Besides being a by-product, chloroplast genome datasets are often generated for phylogenetic studies as they represent a locus that has a simple orthology, often uni-parental history, and almost ubiquitous presence across angiosperms. Many chloroplast genome phylogenies use only protein-coding genes as they are relatively easy to assemble and provide a large proportion of the total chloroplast genome sequence. Protein-coding genes are limiting when dealing with closely related species or population-level chloroplast sequences due to the relatively low mutation rate of most chloroplast genomes. Assembling whole chloroplast genomes can be a challenge due to variability of coverage across the genome caused by AT-rich regions, low sequence complexity, and higher indel variation in intergenic regions of the plastome. Here, we present Fast-Plast, a software package that leverages existing and novel programs to quickly assemble, orient, and verify whole chloroplast genomes. With input of sufficient amounts of raw sequencing reads, Fast-Plast will assemble complete chloroplast genomes using a de novo assembly method and output a chloroplast genome oriented in the large single copy—inverted repeat—small single copy—inverted repeated format, assuming the sequenced species exhibits the typical chloroplast genome structure. Final genome sequences are verified using a coverage analysis of the raw reads against the proposed chloroplast genome sequence. We explore the limits of Fast-Plast using datasets from previous studies and simulations. We also demonstrate the breadth of Fast-Plast’s capabilities by assembling plastomes with non-traditional architectures. For most datasets, Fast-Plast is able to produce a full-length chloroplast genome assembly in approximately 30 minutes with no user mediation. This software provides a much needed de novo, high-throughput assembly for whole chloroplast genomes allowing for further utilization of existing data.

1 - Donald Danforth Plant Science Center, Department Of Biology, 975 North Warson Road, St. Louis, MO, 63132, USA
2 - Donald Danforth Plant Science Center, Department of Biology, 975 N Warson, St Louis, Missouri, 63132, United States

Keywords:
Chloroplast Genome
de novo assembly
automated.

Presentation Type: Poster
Session: P, Phylogenomics Posters
Location: Exhibit Hall/Savannah International Trade and Convention Center
Date: Monday, August 1st, 2016
Time: 5:30 PM This poster will be presented at 5:30 pm. The Poster Session runs from 5:30 pm to 7:00 pm. Posters with odd poster numbers are presented at 5:30 pm, and posters with even poster numbers are presented at 6:15 pm.
Number: PPY009
Abstract ID:708
Candidate for Awards:None