Download M2009Mapping_of_recomb_breakpoints--Poulter

Mapping of recombination breakpoints in a chytrid fungus
Russell Poulter and Margi Butler
Russell Poulter
Department of Biochemistry
Otago University
[email protected]
Batrachochytrium dendrobatidis (Bd) is the only chytrid known to
infect vertebrates
-causes chytridiomycosis in frogs and other amphibians
-chytridiomycosis is a potentially fatal epidermal infection of
amphibians
-has caused mass mortality, population declines and extinctions
-mechanistic/proximate cause of mortality is unknown, but may
relate to osmotic imbalance/loss of electrolytes
-symptoms include include abnormal posture, lethargy, loss of
righting reflex
Archey’s Frog
Leiopelma archeyi
Photo: Phil Bishop, Zoology
Chytrids have been
isolated from NZ frogs
Maximum-likehood tree of B.atrachochytrium dendrobatidis among the eukaryotes
Phylogeny of B. d. based
on rDNA operon.
(James et al., 2006)
Southern Corroboree frog, Pseudophryne corroboree, one
of the endangered Australian amphibian species.
Bd has caused the species to become extinct in the wild
Litoria ewingii (Brown Tree frog) infected with Batrachochytrium
B. dendrobatidis occurs on all continents
except Antarctica
1961
1938
Effect of Bd on amphibians, varies with host
species and climate
-Bd is a generalist pathogen known to infect over 90 amphibian
species on five continents
-a continuum exists in the host response to Bd
-several species are known to carry infection without any
recognised pathogenic effects
-other species suffer up to 100 % mortality, rapid species declines
and in some cases, extinction
First described by Joyce Longcore in 1997 who was
sent samples from dendrobatid (poison dart) frogs
kept at the National Zoo (Washington)
Zoospore of Bd is ~ 5 µm dia
Discharge papillae form and contents cleave into zoospores.
Only very low levels of genetic variation have been found in
global surveys of Batrachochytrium isolates
Morehouse et al., . Mol Ecol. 12:395-403 (2003)
Only five variable
nucleotide
positions were
detected among 10
loci (5918 bp)
This suggests that Bd
might be a recently
emerged clone that
has spread rapidly
across the world.
The alternative is that
Bd has a very stable
genome, that there
are very few new
mutations and that the
heterozygosities are
ancient and stable.
http://www.broad.mit.edu/annotation/genome/batrachochytrium_dendrobatidis
Strain sequenced = JEL423
http://genome.jgi-psf.org/Batde5/Batde5.home.html
BLASTN search using part of a Broad contig as the query
Query= supercont1.1 of Batrachochytrium dendrobatidis [DNA] 16000001610000
Searching not the assembled data but the raw(ish)
sequence reads (the ‘traces’)
Region with homozygous
sites in both strains
Region with heterozygous sites in both strains
Region with sites polymorphic
between two strains
Supercontig 5: Haplotype data generated from examination of the Trace Data
from the two whole Bd genome projects. Supercontig 5 is 1.7Mb.
JEL423
JAM081
Haplotype A
Haplotype B
Repetitious Elements
Supercontig 5: recombination breakpoints occur where there is a boundary
between heterozygous and homozygous sequence. Six strains share a common
breakpoint and must have a shared, common ancestor.
original ancestral heterozygous supercontig 5
JEL229
JEL197
JAM081
*
JEL423, JEL225, JEL308, RTP1-4
*
JEL253
*
P16
Supercontig 1: Five strains share a common breakpoint and must
have a shared, common ancestor. These strains were also clustered in the
supercontig 5 analysis, together with JEL 253.
original ancestral heterozygous supercontig 1
JEL404
JEL229
JEL197
JAM081
JEL423
JEL225, P16
*
*
*
RTP1-4
JEL253
*
JEL308
Sequence chromatograms showing heterozygous sites
supercontig 5 (position~ 600,000)
JEL 197
JEL225
JEL253
JEL308
P16
Data: Cynthia Huang, MSc student
Acknowledgments:
University of Otago Research Committee
Joyce Longcore, University of Maine
The Broad Institute, MIT/Harvard
Joint Genome Institute (JGI), University of California/Dept. of Energy, USA
University of Otago
New Zealand