Abstract Detail

Phylogenomics

Hartsock, Ryan H. [1], McKain, Michael [2], Wohl, Molly [1], Kellogg, Elizabeth [3].

Verdant: Automated Annotation, Alignment, and Phylogenetic Analysis for Whole Chloroplast Sequences.

Whole plastomes are a common byproduct of high-throughput sequencing projects and provide a reliable and readily obtainable locus for plant phylogenetics. Manipulation of large chloroplast genome datasets can be difficult and tedious, especially when annotation is necessary on hundreds of samples. Verdant is a database and workbench hosted in collaboration with iPlant that provides an easy-to-use environment for the manipulation and phylogenomic analysis of whole chloroplast genomes and their annotations. Verdant allows users to work in a secure environment, add other users to a collaborative project, and ultimately publish their plastomes to the database. Logins are secured and processed through the iPlant login system. Plastomes are available as downloadable files and viewable as fully annotated using JBrowse. Current features include a novel automated annotation program, annotation-based full plastome alignment using MAFFT, phylogeny estimation using RAxML, and publication-quality graphic representations of plastomes using Circos. Previously, these steps required considerable manual intervention and generally some computational ability. In contrast, Verdant is designed to be entirely automated with a focus on an intuitive graphical user experience. Full plastome alignment accommodates variation in plastome structure and arrangement through the individual alignment and ultimate concatenation of uniformly orientated, orthologous regions. This provides more accurate full plastome alignments than aligning full genomes as a whole. Future modules are in development for structural comparison of plastomes, analysis of evolutionary rates of protein coding genes, synonymous and nonsynonymous substitution rates of protein coding genes, and secondary structure analyses. We also expect user-derived modules to be integrated into Verdant as use increases. Verdant provides a reliable, fast, and easy-to-use method that will decrease the amount of user time needed to create whole plastome phylogenies and will be useful for both existing data and large sequencing projects. (Hartsock and McKain co-first authors)

Related Links:
Verdant

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

Keywords:
plastid genome
phylogenomics
annotation.

Presentation Type: Poster:Posters for Topics
Session: P
Location: Hall D/The Shaw Conference Centre
Date: Monday, July 27th, 2015
Time: 5:30 PM
Number: PPY004
Abstract ID:915
Candidate for Awards:None