Poplar: a phylogenomics pipeline

Abstract

Motivation: Generating phylogenomic trees from the genomic data is essential in understanding biological systems. Each step of this complex process has received extensive attention and has been significantly streamlined over the years. Given the public availability of data, obtaining genomes for a wide selection of species is straightforward. However, analyzing that data to generate a phylogenomic tree is a multistep process with legitimate scientific and technical challenges, often requiring a significant input from a domain-area scientist.

Results: We present Poplar, a new, streamlined computational pipeline, to address the computational logistical issues that arise when constructing the phylogenomic trees. It provides a framework that runs state-of-the-art software for essential steps in the phylogenomic pipeline, beginning from a genome with or without an annotation, and resulting in a species tree. Running Poplar requires no external databases. In the execution, it enables parallelism for execution for clusters and cloud computing. The trees generated by Poplar match closely with state-of-the-art published trees. The usage and performance of Poplar is far simpler and quicker than manually running a phylogenomic pipeline.

Availability and implementation: Freely available on GitHub at https://github.com/sandialabs/poplar. Implemented using Python and supported on Linux.

Figure 1.

Illustration of the Poplar pipeline from input sequence to species tree.

Figure 2.

Reference tree of Kickxellomycotina genomes, according to JGI’s MycoCosm.

Figure 3.

Poplar generated tree of Kickxellomycotina genomes with triplet error rate of 0.594, according to one run of Poplar with 50 gene trees given the coding sequences.

Figure 4.

Reference Rhodophyta tree from JGI’s MycoCosm.

Figure 5.

Rhodophyta tree generated by Poplar with 200 gene trees given coding sequences as input.

Figure 6.

Reference tree for NCBI commonly studied organisms, from NCBI.

Figure 7.

Tree generated by Poplar from the NCBI genomes given 200 gene trees and coding sequence input.

Figure 8.

Puccinia graminis reference tree from MycoCosm (top) and Poplar with 100 or 500 gene trees (bottom).

Figure 9.

Graph of CPU usage during execution of Poplar on 14 Kickxellomycotina genomes using 500 gene trees.