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THE UNIVERSITY OF
TEXAS
—– AT AUSTIN –—
Conserved Gene Order and
Expanded Inverted Repeats Characterize
Plastid Genomes of Thalassiosirales
Anna Mengjie Yu
Theriot Lab
Keeling, 2004, Am. J. Bot. 9:1481
Introduction
• 15 diatom plastid genome sequenced
• Gene loss/ duplication/ transfer
• Variable plastid genome sizes
• Extensive genome rearrangement
Why Thalassiosirales?
• Reasonably dense phylogeny known
• Environmentally –driven petF transfer from plastid to nucleus reported
in T. oceanica (Lommer et al, 2010)
• 2 plastid genomes published
Cyclotella nana (formerly T. pseudonana) & T. oceanica
Gene content and genome size more similar within Thalassiosirales?
Gene order more conserved within Thalassiosirales?
Rhizosolenia imbricata
Chaetoceros simplex
Cerataulina daemon
Roundia cardiophora
Thalassiosira weissflogii
Cyclotella sp. L04_2
Cyclotella sp. WC03_2
Plastid Genome Assembly
Method
Genomic DNA Extraction
Illumina HiSeq 2000 PE
sequencing
Velvet v.1.2.08
de novo Assembly
Blast Plastid Contig
Bowtie2 mapping
Genome Finishing
Genome Annotation
( DOGMA, tRNAscan-SE 1.21)
Sanger Sequencing
Results
• General Features of Plastid Genome of Thalassiosirales and
Other Three Sequenced Diatoms
• Gene Loss/Gain/Pseudonization and Functional Gene Transfer
from Plastid to Nucleus
• Expanded IR and Conserved IR boundary in Thalassiosirales
• Conserved Gene Order Within Thalassiosirales Compared to
Other Three Sequenced Diatoms
• Circular, 116-129k bp
• Compact and lack introns
• Four overlapping genes :
psbC – psbD : 53bp
sufC – sufB: 1bp
atpD – atpF: 4bp
( 1bp in Rh. imbricata )
rpl4 – rpl23:
8bp
(17 bp in Cy. sp.L04_2 and Cy. sp.WC03_2)
Results
• General Features of Plastid Genome of Thalassiosirales and
Other Three Sequenced Diatoms
• Gene Loss/Gain/Pseudonization and Functional Gene Transfer
from Plastid to Nucleus
• Expanded IR and Conserved IR boundary in Thalassiosirales
• Conserved Gene Order Within Thalassiosirales Compared to
Other Three Sequenced Diatoms
Maximum Likelihood Tree
of Thalassiosirales and
other diatom species
based on 20 plastid genes
Phylogenetic
Distribution of acpP
(acyl carrier protein)
acpP1 lost in
Thalassiosirales
Schematic structure of nuclear-encoded plastid-targeted
diatom protein precursor
SPase: Signal peptidase
SPP: Stromal processing peptidase
Huesgen et al. 2013 PLOS One
Over 84% identity
Plastid
acpP
Nucleus
Phylogenetic
distribution of syfB
(Phe tRNA synthase)
syfB lost in
Thalassiosirales
Loss of
tufA
(translation elongation factor Tu)
and psaE,I,M
(photosystem I protein )
in Rhizosolenia
Gene loss due to
endosymbiont bacterium
Richelia intracellularis?
Phylogenetic
Distribution of gene
loss/gain across
diatom plastid genomes
More similar gene
content within
Thalassiosirales
Results
• General Features of Plastid Genome of Thalassiosirales and
Other Three Sequenced Diatoms
• Gene Loss/Gain/Pseudonization and Functional Gene Transfer
from Plastid to Nucleus
• Expanded IR and Conserved IR boundary in Thalassiosirales
• Conserved Gene Order Within Thalassiosirales Compared to
Other Three Sequenced Diatoms
Thalassiosirales
Comparison of inverted repeat boundaries in Thalassiosirales and other three sequenced diatoms
Results
• General Features of Plastid Genome of Thalassiosirales and
Other Three Sequenced Diatoms
• Gene Loss/Gain/Pseudonization and Functional Gene Transfer
from Plastid to Nucleus
• Conserved IR boundary and Expanded IR in Thalassiosirales
• Conserved Gene Order Within Thalasisosirales Compared to
Other Three Sequenced Diatoms
Gene order comparison of Thalassiosirales and other three sequenced diatoms using mauveAligner
Conclusion
•
Gene content more conserved within the Thalassiosirales plastid genomes
•
Gene order within Thalassiosirales highly conserved, except for extensive
genome rearrangement in T.oceanica.
•
Cy. nana, T. weissflogii and Ro. cardiophora share an identical gene order,
which is inferred to be the ancestral order for the Thalassiosirales
•
The larger size of the Thalassiosirales plastid genome is largely due to
expansion of inverted repeat.
•
Missing of psaE, psaI, psaM represents first documented instance of the
loss of photosynthetic genes in diatom plastid genome
Comparison of nucleotide substitution rates
Cp
Mt
Land plant
3
:
1
Green algae
1
:
1
Red algae
1
:
3
Comparison of nucleotide substitution rates
Cp
Mt
Land plant
3
:
1
Green algae
1
:
1
Red algae
1
:
3
Diatoms
?
Acknowledgement
All Theriot and Jansen Lab members
Society Student Travel Grant Sponsor
2014 23rd International Diatom Symposium Student Grant
2013 International Phycological Society Paul C. Silva Travel Award
2013 10th International Phycological Congress Financial Support
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