Conserved Gene Order and Expanded Inverted Repeats Characterize Plastid Genomes of Thalassiosirales Anna Mengjie Yu THE UNIVERSITY OF TEXAS —– AT AUSTIN.

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Conserved Gene Order and Expanded Inverted Repeats Characterize Plastid Genomes of Thalassiosirales Anna Mengjie Yu THE UNIVERSITY OF TEXAS —– AT AUSTIN –— 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 Roundia cardiophora Cerataulina daemon Chaetoceros simplex Thalassiosira weissflogii Cyclotella sp. WC03_2 Cyclotella sp. L04_2

Method Genomic DNA Extraction Illumina HiSeq 2000 PE sequencing Velvet v de novo Assembly Blast Plastid Contig Genome Annotation ( DOGMA, tRNAscan-SE 1.21) Plastid Genome Assembly Genome Finishing Sanger SequencingBowtie2 mapping

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, k 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

Phylogenetic Distribution of acpP (acyl carrier protein) Maximum Likelihood Tree of Thalassiosirales and other diatom species based on 20 plastid genes acpP1 lost in Thalassiosirales

Schematic structure of nuclear-encoded plastid-targeted diatom protein precursor SPase: Signal peptidase SPP: Stromal processing peptidase Huesgen et al PLOS One

Over 84% identity Plastid Nucleus acpP

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?

More similar gene content within Thalassiosirales Phylogenetic Distribution of gene loss/gain across diatom plastid genomes

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

Land plant 3 : 1 Green algae 1 : 1 Red algae 1 : 3 Cp Mt Comparison of nucleotide substitution rates

Land plant 3 : 1 Green algae 1 : 1 Red algae 1 : 3 Diatoms ? Cp Mt Comparison of nucleotide substitution rates

Acknowledgement All Theriot and Jansen Lab members Society Student Travel Grant Sponsor rd International Diatom Symposium Student Grant 2013 International Phycological Society Paul C. Silva Travel Award th International Phycological Congress Financial Support

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