Ghost-tree: Creating hybrid-gene phylogenetic trees for diversity analyses

Jennifer Fouquier, Jai Ram Rideout, Evan Bolyen, John Chase, Arron Shiffer, Daniel McDonald, Rob Knight, James G Caporaso, Scott T. Kelley

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Background: Fungi play critical roles in many ecosystems, cause serious diseases in plants and animals, and pose significant threats to human health and structural integrity problems in built environments. While most fungal diversity remains unknown, the development of PCR primers for the internal transcribed spacer (ITS) combined with next-generation sequencing has substantially improved our ability to profile fungal microbial diversity. Although the high sequence variability in the ITS region facilitates more accurate species identification, it also makes multiple sequence alignment and phylogenetic analysis unreliable across evolutionarily distant fungi because the sequences are hard to align accurately. To address this issue, we created ghost-tree, a bioinformatics tool that integrates sequence data from two genetic markers into a single phylogenetic tree that can be used for diversity analyses. Our approach starts with a "foundation" phylogeny based on one genetic marker whose sequences can be aligned across organisms spanning divergent taxonomic groups (e.g., fungal families). Then, "extension" phylogenies are built for more closely related organisms (e.g., fungal species or strains) using a second more rapidly evolving genetic marker. These smaller phylogenies are then grafted onto the foundation tree by mapping taxonomic names such that each corresponding foundation-tree tip would branch into its new "extension tree" child. Results: We applied ghost-tree to graft fungal extension phylogenies derived from ITS sequences onto a foundation phylogeny derived from fungal 18S sequences. Our analysis of simulated and real fungal ITS data sets found that phylogenetic distances between fungal communities computed using ghost-tree phylogenies explained significantly more variance than non-phylogenetic distances. The phylogenetic metrics also improved our ability to distinguish small differences (effect sizes) between microbial communities, though results were similar to non-phylogenetic methods for larger effect sizes. Conclusions: The Silva/UNITE-based ghost tree presented here can be easily integrated into existing fungal analysis pipelines to enhance the resolution of fungal community differences and improve understanding of these communities in built environments. The ghost-tree software package can also be used to develop phylogenetic trees for other marker gene sets that afford different taxonomic resolution, or for bridging genome trees with amplicon trees.

Original languageEnglish (US)
Article number11
JournalMicrobiome
Volume4
DOIs
StatePublished - 2016

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Phylogeny
Genes
Genetic Markers
Aptitude
Fungi
Plant Diseases
Animal Diseases
Sequence Alignment
Computational Biology
Names
Ecosystem
Software
Genome
Transplants
Polymerase Chain Reaction
Health

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)

Cite this

Fouquier, J., Rideout, J. R., Bolyen, E., Chase, J., Shiffer, A., McDonald, D., ... Kelley, S. T. (2016). Ghost-tree: Creating hybrid-gene phylogenetic trees for diversity analyses. Microbiome, 4, [11]. https://doi.org/10.1186/s40168-016-0153-6

Ghost-tree : Creating hybrid-gene phylogenetic trees for diversity analyses. / Fouquier, Jennifer; Rideout, Jai Ram; Bolyen, Evan; Chase, John; Shiffer, Arron; McDonald, Daniel; Knight, Rob; Caporaso, James G; Kelley, Scott T.

In: Microbiome, Vol. 4, 11, 2016.

Research output: Contribution to journalArticle

Fouquier, J, Rideout, JR, Bolyen, E, Chase, J, Shiffer, A, McDonald, D, Knight, R, Caporaso, JG & Kelley, ST 2016, 'Ghost-tree: Creating hybrid-gene phylogenetic trees for diversity analyses', Microbiome, vol. 4, 11. https://doi.org/10.1186/s40168-016-0153-6
Fouquier J, Rideout JR, Bolyen E, Chase J, Shiffer A, McDonald D et al. Ghost-tree: Creating hybrid-gene phylogenetic trees for diversity analyses. Microbiome. 2016;4. 11. https://doi.org/10.1186/s40168-016-0153-6
Fouquier, Jennifer ; Rideout, Jai Ram ; Bolyen, Evan ; Chase, John ; Shiffer, Arron ; McDonald, Daniel ; Knight, Rob ; Caporaso, James G ; Kelley, Scott T. / Ghost-tree : Creating hybrid-gene phylogenetic trees for diversity analyses. In: Microbiome. 2016 ; Vol. 4.
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