endosymbiont working group: wolbachia genome analysis

Advancing Science with DNA Sequence

Endosymbiont Working group: Wolbachia genome analysis

Initial research interest:

•Gene content differences between Wolbachia genomes•Functional category comparison between Wolbachia genomes •Comparative analysis between Wolbachia genomes and Anaplasma (closely related genus) genomes•Comparative analysis between Wolbachia genomes and host associated [arthropods] metagenome in IMG


Introduction to Wolbachia

• Gram-negative bacteria

• Produce intracellular inherited infections in many invertebrates

• Extremely common with 20-75% of all insects being infected

• Infection of numerous non-insect invertebrates including nematodes, mites and spiders

• Diverse phenotypes from infection, from endosymbiosis to reproductive parasitism as characterized by their ability to override chromosomal sex determination, induce partenogenesis, selectively kill males, influence sperm competition and generate cytoplasmic incompatibility in early embryos


Wolbachia induced phenotypes

Werren et al., 2008, Nature Reviews


Wolbachia genome projects

Werren et al., 2008, Nature Reviews


Finished Wolbachia genomes in IMG

Wolbachia endosymbiont TRS of Brugia malayi

Wolbachia endosymbiont of Culex quinquefasciatus Pel

Wolbachia endosymbiont of Drosophila melanogaster

Wolbachia sp. wRi


Taxon_OID Status Genome Name Host Name GC % Genome Size

Gene Count

CDS Count

RNA Count

tRNA Count

Pseudo Count

COG Count

Pfam Count

KEGG Count

IMG Pathway

Count

637000340 FWolbachia

endosymbiont TRS of Brugia malayi

Brugia malayi .34 1080084 940 900 40 34 95 598 646 389 134

642555168 FWolbachia

endosymbiont of Culex quinquefasciatus Pel

Culex quinquefasciatus .34 1482455 1312 1275 37 34 813 901 403 137

637000339 F

Wolbachia endosymbiont of

Drosophila melanogaster

Drosophila melanogaster .35 1267782 1312 1268 44 34 73 753 832 405 151

643692055 F Wolbachia sp. wRi Drosophila simulans .35 1445873 1187 1150 37 34 821 882 409 137

Genome statistics


Function category comparison


Wolbachia pan(COG)


•RNase P protein component

•ATPases of the AAA+ class•Predicted Fe-S oxidoreductases

•Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains

•Nitrate/nitrite transporter•AAA ATPase containing von Willebrand factor type A (vWA) domain

•Phage-related terminase

Strain-specific COGs

Wolbachia (Brugia malayi)

Wolbachia (Drosophila melanogaster)


•Predicted aminoglycoside phosphotransferase•ABC-type transport system involved in cytochrome c biogenesis, permease component•Endoglucanase•Pseudouridine synthase•Short-chain dehydrogenases of various substrate specificities•Mannose-6-phosphate isomerase•Predicted N-acetylglucosaminyl transferase•Transposase and inactivated derivatives•Predicted protease with the C-terminal PDZ domain

Wolbachia (Culex quinquefasciatus_Pel)

•Dipeptide/tripeptide permease

•Predicted ATPase (AAA+ superfamily)•ABC-type amino acid transport/signal transduction systems, periplasmic component/domain•ABC-type amino acid transport system, permease component•Fucose permease•5'-3' exonuclease (including N-terminal domain of PolI)

Wolbachia (wRi)

Strain-specific COGs


Wolbachia, endosymbiont of Drosophila melanogaster – no homologs in other

Wolbachia genomes


Wolbachia endosymbiont of B. malayi – no homologs in other Wolbachia genomes


Wolbachia endosymbiont of Culex quinquefasciatus – no homologs in other

Wolbachia genomes


Wolbachia sp. wRi – no homologs in other Wolbachia genomes


Wolbachia, endosymbiont of Drosophila melanogaster – with homologs in other Wolbachia

genomes


Phylogenetic distribution of Wolbachia COGs

Anaplasmataceae

Rickettsiaceae


Introduction to Anaplasma

• Gram-negative bacteria

• Reside in host red blood cells and lead to the disease anaplasmosis, most commonly in tropical areas of the world

• Requires intermediate tick hosts for maturation, and flies may act as mechanical vectors

• Species of veterinary interest are found in cattle, sheep and goats


Finished Anaplasma genomes in IMG

Anaplasma centrale str. Israel

Anaplasma marginale Florida

Anaplasma marginale St. Maries

Anaplasma phagocytophilum HZ


COGs tree


16S tree


Whole genome comparison between Anaplasma and Wolbachia

Comparison between complete genome of Wolbachia TRS Brugia malayi and Anaplasma phagocytophilum.


Correlation matrix COG


PCA analysis based on COG

PCA analysis of complete genomes of Wolbachia and Anasplasma species

Wolbachia TRS Brugia malayi

Anaplasma phagocytophilum

HZ

Advancing Science with DNA SequenceComparative analysis between Wolbachia

TRS Brugia Malayi and Anaplasma phagocytophilum HZ


COGs in common between Anaplasma spp. and Wolbachia TRS


Correlation based on KO


Pfams of Wolbachia genomes in their family of Anaplasmataceae


Pfams of Wolbachia genomes in their family of Anaplasmataceae

ankyrin repeat transposasehelix-turn-helix


PCA of Wolbachia genomes

Wolbachia endosymbiont of Culex quinquefasciatus

Wolbachia endosymbiont of Drosophila melanogaster

Wolbachia sp. wRi

Wolbachia endosymbiont of TRS of Brugia malayi


Comparative analysis between Wolbachia genomes and Host-associated [arthropod]

metagenomes


Wolbachia sequences in metagenome dataset

• Compared sequenced Wolbachia genomes to Host-associated (arthropod) metagenomes

• In the adult Ambrosia beetle metagenome sample from Bern, Switzerland– 36% of the genome from a Culex

quinquefasciatus host (mosquito) had hits to the metagenome of ≥90% ID


Horizontal gene transfer

• Viruses:– Caudovirales

• Eshcherichia phage D108 (Wolbachia TRS)• Kelbsiella phage KP34 (Anaplasma

phagocytophilum).– Geminiviridae

• Helicobasidium mompa endovirus1– Secoviridae

• Eukaryota– Nematode

• Rhaditidae: caenorhabditis elegans bristol

47%


panCOG Gang

Mariana, Cristina, Parag, Betsy, Alex, Ananda

endosymbiont working group: wolbachia genome analysis

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