A composite genome approach to identify phylogenetically informative data from next-generation sequencing

Abstract

BackgroundImprovements in sequencing technology now allow easy acquisition of large datasets; however, analyzing these data for phylogenetics can be challenging. We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps of de novo whole genome assembly, multiple genome alignment, and annotation.ResultsFor simulations SISRS is able to identify large numbers of loci containing variable sites with phylogenetic signal. For genomic data from apes, SISRS identified thousands of variable sites, from which we produced an accurate phylogeny. Finally, we used SISRS to identify phylogenetic markers that we used to estimate the phylogeny of placental mammals. We recovered eight phylogenies that resolved the basal relationships among mammals using datasets with different levels of missing data. The three alternate resolutions of the basal relationships are consistent with the major hypotheses for the relationships among mammals, all of which have been supported previously by different molecular datasets.ConclusionsSISRS has the potential to transform phylogenetic research. This method eliminates the need for expensive marker development in many studies by using whole genome shotgun sequence data directly. SISRS is open source and freely available at https://github.com/rachelss/SISRS/releases.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0632-y) contains supplementary material, which is available to authorized users.

Genome-scale profiling reveals higher proportions of phylogenetic signal in non-coding data

“…For each dataset (Primates, Rodents, Pecora, and Combined), we used the SISRS pipeline to identify putative orthologs and phylogenetically informative sites (Schwartz et al 2015) . SISRS identifies orthologous loci by assembling a "composite genome" from a subsample of reads pooled across all species.…”

“…In the absence of reference genomes or annotation information, the SISRS bioinformatics pipeline (Schwartz et al 2015) facilitates genome-wide ortholog comparison directly from unannotated whole-genome sequencing (WGS) reads, enabling genome-scale informativeness comparisons among locus types. Using WGS data from focal sets of primates, rodents, and pecora, we identify millions of potentially informative sites in the absence of reference information.…”

A Primer on Infectious Disease Bacterial Genomics

“…The software package kSNP (178,179) takes a reference-free approach to identifying SNVs by breaking up each genomic data set into k-mers and comparing these k-mers. Another software package, SISRS (180), assembles a composite genome from the sequencing data and uses this assembled composite as a reference for variant calling.…”

sppIDer: a species identification tool to investigate hybrid genomes with high-throughput sequencing

“…The number of reference genomes available has rapidly increased, but it is not complete 41 in most clades. To avoid the drawbacks of limited reference genomes, several new phylogenetic 42 approaches have been developed that do not require sequence alignments or whole-genome 43 assemblies, such as phylogeny-building approaches using kmers (Fan et al 2015), de novo 44 identification of phylogenetically informative regions (Schwartz et al 2015), and local 45 assemblies of target genes (Allen et al 2015;Johnson et al 2016). These methods can accurately 46 reconstruct known and simulated phylogenies of pure lineages.…”

“…Alignment and assembly (AA)-free phylogeny-building methods are gaining popularity, 308 but they have not previously been applied to hybrid data. Therefore, we also tested how AA-free 309 phylogenetic methods, such as AAF (Fan et al 2015) or SISRS (Schwartz et al 2015), 310 performed in detecting and visualizing hybrids compared to sppIDer. We found that these 311 methods performed well when given only pure lineages, but when hybrids were included, they 312 either failed completely or produced incorrect phylogenies.…”