Time Lapse. A glimpse into prehistoric genomics. DK Griffin University of Kent CoGen 2018 No conflict of interest

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1 Time Lapse A glimpse into prehistoric genomics DK Griffin University of Kent CoGen 2018 No conflict of interest

2 This is not a talk about time lapse imaging

3 Karyomapping

4 So, where do we start? Karyomapping works because We have characterized the human genome properly Every sequence mapped in order on each chromosome Chromosome level assembly

5 Cow-ryomapping Parental chromosomes Euploid (Chr 6) Monosomy (Chr 22) Trisomy (Chr 16)

6 Overview Every good genome needs a map assembling genomes Reconstructing ancestral karyotypes Dinosaurs Conclusions on a weird karyotype Will there be a "real" Jurassic Park? Parting thoughts

7 Overview Every good genome needs a map assembling genomes Reconstructing ancestral karyotypes Dinosaurs Conclusions on a weird karyotype Will there be a "real" Jurassic Park? Parting thoughts

8 Every good genome needs a map (Harris Lewin) Each sequence assigned to a specific locus on a chromosome Ultimate aim of any de-novo genome assembly is a representation of all the sequences, correctly ordered contiguously Study genome-phenome relationships, particularly of complex (e.g. quantitative) traits Mapping of Mendelian disorders Accurate identification of (e.g. cryptic) chromosome translocations Discovery and mapping of quantitative trait nucleotides (QTNs), expression quantitative trait loci (eqtls) Study of long-range regulatory interactions Significant economical impact, more efficient food production and improved global food security Agricultural species Relevance to conservation Understanding and preserving biodiversity Animals as models for human disease Retrace gross structural evolutionary changes across (extinct) species Dinosaurs!

falcons) Many more genomes to come Bird 10k project all species by 2020 Only 5 avian genomes initially

9 Genome assembly In 2014 ~45 newly sequenced avian genomes - produced using Next Generation Sequencing (NGS) Around another (e.g. falcons) Many more genomes to come Bird 10k project all species by 2020 Only 5 avian genomes initially assembled to chromosomal level: Chicken Turkey Duck Zebra Finch Collared Flycatcher sub-sub- Usually we are left with chromosomal scaffolds Evolution Highway - interactive browser

10 Mapping Genomes + Bioinformatic methods = NGS scaffolds Predicted Chromosome Fragments + FISH = Assembled genome

11 Cross-Species Probe Development CH O22 CH261-50C15 CH K1 CH N3 CH N6 CH C19 CH C5 CH261-72A10 CH261-69D20 CH261-49P24 CH H14 TGMCBa-205N19 CH261-4M5 TGMCBa-342P15 CH261-95H20 Hybridisation Success: CH261-40G6 Based on degree of sequence conservation, repeat content and GC content CH J5 TGMCBa-305E19 Bioinformatic approach to identify highly conserved sequence elements in all birds Peregrine Pigeon Zebra Finch Chicken Turkey Universal BACs Scaffolds PCFs Zebra Finch Chicken selected 93%Chicken 92% 91% 100% 100% Chicken non-selected 47% 26% 21% 100% 89% GGA2 GGA28 GGA14 GGA12

12 Application of Selected Bird Probes Probes worked across all birds and both reptiles million Chicken Peregrine Falcon Budgerigar Anolis Lizard Turtle

Chicken Zebra Finch PCFs Peregrine Chromosome 5 GGA2 Scaffolds Universal BACs Combined Mapping Approach CH261-123O22 CH261-50C15

CH261-49P24 CH261-122H14 TGMCBa-205N19 CH261-4M5 TGMCBa-342P15 CH261-95H20 Now mapped: Peregrine falcon Saker falcon Budgerigar

(2018) Chromosome-level assembly reveals extensive rearrangement in saker falcon, budgerigar but not ostrich genomes.

13 Chicken Zebra Finch PCFs Peregrine Chromosome 5 GGA2 Scaffolds Universal BACs Combined Mapping Approach CH O22 CH261-50C15 CH261-40G6 GGA2 CH J5 CH K1 CH N3 CH N6 CH C19 CH C5 CH261-72A10 GGA28 CH261-69D20 GGA14 CH261-49P24 CH H14 TGMCBa-205N19 CH261-4M5 TGMCBa-342P15 CH261-95H20 Now mapped: Peregrine falcon Saker falcon Budgerigar Ostrich Pigeon GGA12 TGMCBa-305E19 (a) (b) (c) (d) O Connor R.E. et al. (2018) Chromosome-level assembly reveals extensive rearrangement in saker falcon, budgerigar but not ostrich genomes. Genome Biology. 19:171. Damas J., O Connor R.E. et al. (2017). Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set. Genome Research, pp.gr

14 Reconstructing scaffold-based genomes Chicken/turkey EBR Chicken EBR 8a Chicken/turkey EBR crow/mgfinch/finch/woodpecker EBR

16 Overview Every good genome needs a map assembling genomes Reconstructing ancestral karyotypes Dinosaurs Conclusions on a weird karyotype Will there be a "real" Jurassic Park? Parting thoughts

Chromosome changes in animals In patients Polyploidization Pregnancy loss Partial hyatidiform moles Translocation Infertility Inversion Infertility Aneuploidy Insertions and deletions CNVs In

17 Chromosome changes in animals In patients Polyploidization Pregnancy loss Partial hyatidiform moles Translocation Infertility Inversion Infertility Aneuploidy Insertions and deletions CNVs In evolution Polyploidization More common in plants Some fish e.g. trout Translocation Species barrier Inversion Species barrier Fission and fusion Indels CNVs Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky

Turkey Chick ZF Turkey HSB Homologous synteny block EBR Evolutionary breakpoint region HSB HSB HSB HSB EBR EBR EBR Lithgow PE*, O'Connor R*, Smith D, Fonseka G, Al Mutery A, Rathje C, Frodsham R,

18 Turkey Chick ZF Turkey HSB Homologous synteny block EBR Evolutionary breakpoint region HSB HSB HSB HSB EBR EBR EBR Lithgow PE*, O'Connor R*, Smith D, Fonseka G, Al Mutery A, Rathje C, Frodsham R, O'Brien P, Kasai F, Ferguson-Smith MA, Skinner BM, Griffin DK (2014). Novel tools for characterising inter and intra chromosomal rearrangements in avian microchromosomes. Chromosome Res (1):85-97

22 ANCESTOR derived from MGRA Chicken Chromosome 5 Turkey Chromosome 5 Duck Chromosome 5 Zebra finch Chromosome 5 Ostrich Chromosome 5 (4 scaffolds) Budgerigar Chromosome 4q (9 scaffolds) Green Anole Lizard Chromosomes 1&2 (GGA 5 orthologue)

23 Multiple Genome Rearrangements and Ancestors reconstruction tools MGRA: Max Alekseyev and Pavel Pevzner (Genome Res May;19(5):943-57) MGRA2: Pavel Avdeyev, Shuai Jiang, Sergey Aganezov, Fei Hu, and Max Alekseyev

24 Romanov et al 2014

25 Overview Every good genome needs a map assembling genomes Reconstructing ancestral karyotypes Dinosaurs Conclusions on a weird karyotype Will there be a "real" Jurassic Park? Parting thoughts

26 Eulicosaurus regina Dinosaurs Captured the imagination of Scientists Creative arts General public Since earliest fossil discoveries Michael Crichton novel/ Steven Spielberg movie Jurassic Park And sequels Most recently in 2018 Not just the animals but also their genomics

27 Extinction events & climate change Permo-Triassic mass extinction event (PTME) ~251 mya Massive volcanic eruptions in Siberian Trapps prolonged global warming, anoxic conditions devastated synapsid species increasingly arid conditions Followed by period of extraordinary ecological change. ~10-15 my before ocean reefs, forests and vertebrate numbers were re-established Dinosaurs first appeared mya Low in biodiversity and abundance for ~30 million years by mid Jurassic, increase vastly in abundance, geographical spread, body size Dominant vertebrates and extraordinary biodiversity Dinosaurs survived Carnian-Norian Extinction event (CNEE) 228 mya Saw end of the rhynchosaurs and dicynodonts Dinosaurs survived End-Triassic mass extinction event (ETME) 201 mya Devastated the crocodilian ancestors leaving only 23 extant species. Steady increase in dinosaur biodiversity and abundance after this time Now >1000 dinosaur species in fossil record ~30 more being identified each year Cretaceous-Paleogene (K-Pg) extinction event 66 mya Chicxulub impactor meteor strike Extreme reduction in temperature and daylight Wiped out all but one therapod lineage Emerged again as modern birds, with over 10,000 biodiverse representatives

28 Theropod Dinosaur Lineage Diapsid Ancestor Lepidosauromorpha Archelosauria Squamates (Snakes & Lizards) Sphenodontia (Tuatara) Testudines (Turtles) Archosauria Crurotarsi (Crocodiles) Avemetarsalia Pterosauria DINOSAURIA Saurischia Ornithoscelida Ornithischia Theropoda Maniraptora Avialae Aves 275mya 260mya 250mya 245mya 235mya 230mya 175mya 165mya Permian Triassic Jurassic

29 Some questions Can we reconstruct ancestral dinosaur genomes (karyotypes) by inference? Did dinosaurs have bird like karyotypes? Does this explain, in part, their biodiversity and resistance to climate change?

30 Dinosaur Genome Reconstruction Adapted bioinformatic approach taken by Romanov et al. (2014) to reconstruct avian ancestor Combined previous karyotype and chromosome painting data Highly conserved avian FISH probes tested on: Anole lizard (Anolis carolinensis) Red eared slider turtle (Trachemys scripta) Spiny soft-shelled turtle (Apalone spinifera) (Matsuda et al. 2005)

31 Chicken FISH in reptiles Chicken chromosome 26 - Protomicrochromosome - ancestral macrochromosome region that split in avian lineage to form a microchromosome Lizard Turtle

32 Crocs are bad Atypical reptilian karyotype 2n=44 ish No microchromosomes ~23 species that underwent wholesale chromosome fusion A shame because it might have given us Archosaurian ancestor ~240MYA

33 Diapsid Ancestor 275mya Archelosaur Ancestor 255mya Gallus gallus Diapsid Ancestor 275 mya Archelosaur Ancestor 255 mya Gallus gallus Z W a Ancestor to Avian Genome

34 Overview Every good genome needs a map assembling genomes Reconstructing ancestral karyotypes Dinosaurs Conclusions on a weird karyotype Will there be a "real" Jurassic Park? Parting thoughts

Conclusions 1 All aspects of avian cytogenetics combine to gain picture of Avian evolution (from avian ancestor) Dinosaur evolution (from the Diapsid ancestor to avian ancestor) Basic pattern of 2n =

35 Conclusions 1 All aspects of avian cytogenetics combine to gain picture of Avian evolution (from avian ancestor) Dinosaur evolution (from the Diapsid ancestor to avian ancestor) Basic pattern of 2n = 80 (~30 pairs of microchromosomes) became fixed about the time the dinosaurs emerged 240mya Evolutionary advantage to retaining this configuration or lack of opportunity for change? Genome is constrained by size (related to flight?) Opportunity for interchromosomal change is reduced Doesn t preclude fission or intrachromosomal (e.g. inversion) Crocs not constrained by genome size Possible advantages of multiple chromosomes in a karyotype Generates BIODIVERSITY, the driver of natural selection. More chromosomes lead to more combinations of gametes Increase in recombination rate (at least one obligatory chiasma per chromosome) Configuration is successful AND absence of positive selection for change

36 Conclusions 2 Avian ancestor was probably a bipedal, feathered dinosaur Reconstruction of (mostly intra-chromosomal) rearrangements may give clues to evolution of phenotypic traits Dinosaurs DID NOT GO EXTINCT (BIRDS ARE DINOSAURS!!) On the contrary They survived 3-4 extinction events WITH INCREDIBCLE CLIMATE CHANGE Re-emerging more diverse each time (most recently as birds) Perhaps in part because of their amazing karyotype

37 THIS NOT ONLY LEADS TO THIS

38 BUT ALSO THIS

39 Overview Every good genome needs a map assembling genomes Reconstructing ancestral karyotypes Dinosaurs Conclusions on a weird karyotype Will there be a "real" Jurassic Park? Parting thoughts

Why there will be no Jurassic Park DNA will not survive that long This is a well described field Neanderthal men and wooly mammoths, yes Cave bears are particularly well studied The DNA would be

41 Why there will be no Jurassic Park DNA will not survive that long This is a well described field Neanderthal men and wooly mammoths, yes Cave bears are particularly well studied The DNA would be fragmented Unclear of organization or gaps Developmental biology don t work like that Recreating the molecular cues that the eggs gives the developing embryo would be nigh on impossible Theoretical possibility for recreating recently extinct species Some gene function studies looking at dino genes by manipulating chick embryos

42 Overview Every good genome needs a map assembling genomes Reconstructing ancestral karyotypes Dinosaurs Conclusions on a weird karyotype Will there be a "real" Jurassic Park? Parting thoughts

Extinction events & climate change Permo-Triassic mass extinction event (PTME) ~251 mya Volcanoes in the Siberian Trapps Dinosaurs first appeared 245-240 mya They have been biodiverse almost from the

43 Extinction events & climate change Permo-Triassic mass extinction event (PTME) ~251 mya Volcanoes in the Siberian Trapps Dinosaurs first appeared mya They have been biodiverse almost from the outset Perhaps because of their karyotype Dinosaurs survived Carnian-Norian Extinction event (CNEE) 228 mya Dinosaurs survived End-Triassic mass extinction event (ETME) 201 mya Cretaceous-Paleogene (K-Pg) extinction event 66 mya Chicxulub impactor meteor strike WE ARE THE METEOR We are living a great extinction event and we caused it And dinosaurs (birds) will probably survive it Perhaps because of their chromosomes But we might not

44 For the first time in 66 million years The karyotype of a Velociraptor

45 Acknowledgments Digital Scientific UK Griffin lab (University of Kent past and present) Becky O Connor, Mike Romanov, Ben Skinner, Claudia Rathje, Gothami Fonseka, Katie Fowler, Becca Jennings, Lucas Kiazim, Kat Sanders, Giuseppe Silvestri, RVC London. Denis Larkin, Marta Farre, Joana Damas Kornsorn Srikulnath, Worrapong Singchat, Bal-Jing Ballsackz - Thailand Michael Schmid lab, Ferguson-Smith Lab Dave Burt, Roslin Institute Peter Houde NMSU Yoichi Matsuda, Shibusawa - Hokkaido, Japan BBSRC, Cytocell Martin Lawrie, John Anson Central Veterinary Research Laboratory Dubai (CVRL) Ullrich Wernery, Suntiha Joseph, Abdullah Al Mutery Nicole Valenzuela Iowa 45 genome consortium Tom Gilbert, Erich Jarvis, Guojie Zhang Paul Barrett - Natural History Museum Digital Scientific UK Michael Ellis

The Triassic Transition

The Triassic Transition The Age of Reptiles Begins As the Paleozoic drew to a close through the Carboniferous and Permian several important processes were at work. Assembly of Pangea Evolutionary radiation