Ordospora Colligata Mitosporidium Daphniae

Enough of streamlining: vertical transmission allows microsporidia to evolve unorthodox genomic features and become ecologically successful

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. Karen Luisa Haag (UFRGS-Brazil) Jean-François Pombert (IIT-USA) Dieter Ebert (UniBasel-Switzerland)

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. 2018 © 48th European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

3-Layered spore wall 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. 2018 © 48th EuropeanHaag et alContact 2014 PNAS Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

GAINS Polar filament Schizogony

Mitosporidium daphniae

M. daphniae FISK171 NOV7 GBEP1 OC4 Origin Switzerland Finland Norway UK UK

Assembly 5.63 Mb 2.26 Mb 2.32 Mb 2.30 Mb 2.29 Mb

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. 2018 © 48th EuropeanPombert etContact al 2015 MBio Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

Mitosporidium daphniae

M. daphniae FISK171 NOV7 GBEP1 OC4 Origin Switzerland Finland Norway UK UK

Assembly 5.63 Mb 2.26 Mb 2.32 Mb 2.30 Mb 2.29 Mb

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. # Proteins 3,330 1,849 1,862 1,857 1,879 Protein length 382 aa 355 aa 356 aa 356 aa 355 aa

Mitosporidium daphniae

M. daphniae FISK171 NOV7 GBEP1 OC4 Origin Switzerland Finland Norway UK UK

Assembly 5.63 Mb 2.26 Mb 2.32 Mb 2.30 Mb 2.29 Mb

Mitosporidium daphniae

M. daphniae FISK171 NOV7 GBEP1 OC4 Origin Switzerland Finland Norway UK UK

Assembly 5.63 Mb 2.26 Mb 2.32 Mb 2.30 Mb 2.29 Mb

2018GC © contentII Joint Congress on Evolutionary42.80 Biology 2018. % All rights reserved38.51 - Any reproduction % even in part is38.39 prohibited. % 38.44 % 38.52 % # Proteins 3,330 1,849 1,862 1,857 1,879 Protein length 382 aa 355 aa 356 aa 356 aa 355 aa # Introns 4,209 30 30 30 30 Intron length 80 kb 31 kb 31 kb 31 kb 31 kb

Mitosporidium daphniae

M. daphniae FISK171 NOV7 GBEP1 OC4 Origin Switzerland Finland Norway UK UK Transmission Horizontal Horizontal Horizontal Horizontal Horizontal Assembly 5.63 Mb 2.26 Mb 2.32 Mb 2.30 Mb 2.29 Mb

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . Paths to genome reduction in bacteria At high Ne (e.g. symbionts that have free-living phases with large populations) • Natural selection • Stable core metabolic repertoire of genes • Pseudogenes are rare • Minimized intergenic regions • Reduced amount of TEs

At low Ne (e.g. symbionts relying on vertically transmission) 2018 © II Joint• CongressGenetic on Evolutionary drift Biology 2018. All rights reserved - Any reproduction even in part is prohibited. • Reduction of the core metabolic repertoire of genes • Pseudogenes and duplications are frequent • TE accumulation • AT-bias derived from the relaxation of purifying selection due to drift and a mutational bias towards AT 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. 2018 © 48th European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

Mitosporidium daphniae

H. tvaerminnensis H. magnivora M. daphniae FIOER33 ILG3 BEOM2 ILBN2 Origin Switzerland Finland Israel Belgium Israel Transmission Horizontal Mixed Mixed Mixed Mixed

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. 2018 ©Corradi 48thet al 2009 European Genome Biology; Haag et al 2011Contact Parasitology Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . Ordospora colligata (streamlined genomes) Hamiltosporidium spp. (inflated genomes) Mitosporidium daphniae

H. tvaerminnensis H. magnivora M. daphniae FIOER33 ILG3 BEOM2 ILBN2 Origin Switzerland Finland Israel Belgium Israel Transmission Horizontal Mixed Mixed Mixed Mixed Assembly 5.63 Mb 18.34 Mb 25.20 Mb 20.73 Mb 17.18 Mb

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. # Proteins 3,330 4,121 6,203 4,658 4,180 Protein length 382 aa 364 aa 355 aa 350 aa 340 aa

2018GC © IIcontent Joint Congress on Evolutionary 42.80Biology 2018. % All rights reserved - Any25.82 reproduction % even in part is prohibited.26.14 % 25.80 % 25.74 % # Proteins 3,330 4,121 6,203 4,658 4,180 Protein length 382 aa 364 aa 355 aa 350 aa 340 aa # Introns 4,209 890 5,708 1,891 1,491 Intron length 80 kb 302 kb 195 kb 310 kb 264 kb

H. tvaerminnensis H. magnivora

FIOER33 ILG3 BEOM2 ILBN2 Assembly 18.34 Mb 25.20 Mb 20.73 Mb 17.18 Mb Repeated Elements 4.77 Mb 8.18 Mb 6.06 Mb 4.84 Mb (26 %) (32 %) (29 %) (28 %) Retrotransposons 7.5 % 11.3 % 9.1% 8.5 % DNA transposons 3.7 % 3.5 % 4.1 % 3.2 %

H. tvaerminnensis H. magnivora

Segmental2018 © II Joint Congress duplications on Evolutionary Biology 2018. All rights reserved4.28 - Any Mb reproduction even in part10.18 is prohibited. Mb 14.65 Mb 4.55 Mb (23 %) (40 %) (70 %) (26 %) Multi-copy gene families 448 1172 646 360 # copies largest family 180 555 245 184

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited.

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . Genomes of H-transmitted Genomes of H&V-transmitted microsporidia microsporidia (dataset 1; n=12) (dataset 2; n=7) Orthology analysis (Ortho Finder)

Splitting single- and multi-copy genes

mRNA alignment of single-copy genes (MACSE)

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. 112,055 pairwise 8,846 pairwise comparisons comparisons for dataset 1 for dataset 2

Calculating dN/dS (SNAP) 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. 2018 © 48th European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

Splitting single- and multi-copy genes

mRNA alignment of single-copy mRNA alignment of multi-copy genes (MACSE) genes (MACSE)

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. 112,055 pairwise 8,846 pairwise 7,790 pairwise comparisons comparisons comparisons for dataset 1 for dataset 2 (dataset 1) + 64,437 pairwise comparisons Calculating dN/dS (dataset 2) (SNAP) 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. 2018 © 48th European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

Genetic drift • Repetitive elements • Non coding sequences • Duplications • Mildly deleterious mutations

fin

FIOER33 ILG3 BEOM2 ILBN2 Assembly 18.34 Mb 25.20 Mb 20.73 Mb 17.18 Mb Mean sequencing depth 390 X 645 X 26 X 18 X Segmental duplications 4.28 Mb 10.18 Mb 14.65 Mb 4.55 Mb 23 % 40 % 70 % 26 %

Longest2018 © II Joint Congress duplicated on Evolutionary Biologyregion 2018. All rights reserved41.8 - Any reproduction kb even in part68.9 is prohibited. kb 43 kb 52.3 kb N50 duplicated contigs 12 kb 18 kb 15 kb 15 kb

FIOER33 ILG3 BEOM2 ILBN2 Assembly 18.34 Mb 25.20 Mb 20.73 Mb 17.18 Mb Mean sequencing depth 390 X 645 X 26 X 18 X Segmental duplications 4.28 Mb 10.18 Mb 14.65 Mb 4.55 Mb 23 % 40 % 70 % 26 %

FIOER33 n Mean SD Variance p Non duplicated contigs 2204 1.04549 0.64448 0.41535 < 0.001 Duplicated contigs 711 0.73068 0.49026 0.24036

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. ILG3 n Mean SD Variance p Non duplicated contigs 1668 1.11631 0.70648 0.49911 < 0.001 Duplicated contigs 1070 0.80481 0.58575 0.34311