Tuesday March 30
Parallel session 1: Phylogeny and Fungal Tree of Life
PS1.1
Joseph Spatafora[1] Barbara Robbertse[1] Francesc Lopez[2]
Jeffrey Townsend[2]
spatafoj@science.oregonstate.edu
The Assembling the Fungal Tree of Life (AFTOL)
project is a large multi-laboratory collaboration that is focused on analyzing
large amounts of genomic sequence data to infer phylogenetic relationships
within the Kingdom Fungi. Our current research has identified a set of
pan-orthologs that are distributed throughout the Fungi and are of suitable
length and variability for phylogenetic analyses. In addition to standard
phylogenetic analyses, we have tested the phylogenetic informativeness of these
loci and compared them to markers traditionally used in phylogenetic analyses.
Major findings from these analyses reveal that there exist numerous orthologous
markers that are significantly more informative than standard loci currently in
use in molecular phylogenetics and that individual markers vary in their level
of informativeness based on the node or region of the phylogenetic tree in
question. To expand this sampling to lineages for which genomes have not
been sequenced, we are developing high throughput sequencing strategies and
bioinformatic tools for mining heterogeneous genomic data for the AFTOL
pan-orthologs and their inclusion in phylogenetic analyses. We will
outline our bioinformatics pipeline, and present some preliminary data and
findings concerning the evolution of plant-associated fungal lineages and major
evolutionary trends in the Ascomycota.
PS1.2
AspGD comparative genomics pipelines and visualization tools
Jennifer Russo Wortman1, Jonathan Crabtree1, Marcus C. Chibucos1,
Joshua Orvis1,
Martha B. Arnaud2, Maria C. Costanzo2, Diane O. Inglis2,
Prachi Shah2, Marek S. Skrzypek2, and Gavin Sherlock2
1Institute
for Genome Sciences,
2Department of Genetics,
jwortman@som.umaryland.edu
The Aspergillus Genome
Database (http://www.aspgd.org/) is an online genomic resource for
Aspergillus genomics and molecular biology, with information curated from
the literature and web-based research tools for exploration and analysis of
these data. With ten annotated
genome sequences from eight Aspergillus species publicly available, and
more on the way, our goals include leveraging comparative genomics for
annotation improvement, and providing sophisticated querying and visualization
tools to maximize the utility of these data.
The Aspergillus genomes were
annotated at different institutions using diverse methods over an extended time
frame, during which available tools and datasets have evolved. Common annotation
inconsistencies include missed gene calls, gene truncations, failure to predict
small exons, and inappropriate gene merges.
We are developing a standard, optimized pipeline across all
Aspergillus genomes, comprehensively incorporating new data as it becomes
available and leveraging comparative genomics analyses to improve protein-coding
gene prediction. Resulting
annotations will be integrated into AspGD, along with ortholog and synteny data
linking knowledge across the Aspergilli.
Otholog and synteny data are currently available at the AspGD website
through data downloads as well as interactively through the Sybil software
infrastructure. Sybil is an open
source, web-based software package for visualizing and mining comparative
genomics data (http://sybil.sf.net). Powered by a Chado relational
database (http://www.gmod.org/schema), Sybil provides an extensive set of
interfaces for interrogating multi-genome comparisons at varying levels of
resolution from the whole genome scale to individual loci.
Sybil allows users to search for genes, clusters or genomic regions and
visualize the results in a comparative genomic context, along with syntenic
relationships and annotated features of interest.
Configurable reports are available through the web interface, supporting
the identification of core and accessory genes from all or a subset of available
genomes. Reports and displays are
interactive and linked, allowing seamless navigation from a chromosome view, to
a cluster report, to an individual protein page.
All of the data in AspGD are freely available to the public from
http://www.aspgd.org/. AspGD is
supported by grant RO1 AI077599 from the NIAID at the NIH.
PS1.3
The evolution of pathways and gene functions:
lessons from phylogenomics in fungi
Berend Snel
Theoretical Biology and Bioinformatics,
Department of Biology, Science Faculty
Utrecht University
b.snel@uu.nl
The ever increasing amount of sequenced genomes potentially allows
unprecedented insight into pathway evolution. However precise analyzes are
hindered by incomplete knowledge on protein interactions and genome dynamics
that obfuscate precise orthology. These processes include gene duplications,
genome duplications, domain re-arrangements and gene loss. Small scale manual
analyzes and careful large scale computational analyzes nevertheless allow for
the elucidation of some fascinating evolutionary stories. In this talk I will
present two stories that were uncovered using phylogenomic analysis of fungal
genome sequences.
Firstly I will discuss the evolution of the pathway surrounding the small
GTPase Ras. The genome sequences of primitive fungi show that in contrast to
what was previously thought many features of this pathway are not animal
specific but were present in the ancestor of the Fungi/Metazoa group. The
phylogenetic profiles of individual orthologous groups in this pathway do not
match well, but they do match near perfectly on the family level, providing a
new twist to the phylogenetic profile method for function prediction and our
understanding of the evolutionary forces constraining the co-evolution of
interacting proteins. Secondly I will discuss the evolutionary implications of
single gene duplications versus genome duplications in the evolution of protein
complexes in S. cerevisiae.