Deeply conserved synteny resolves early events in vertebrate evolution

Articles https://doi.org/10.1038/s41559-020-1156-z Deeply conserved synteny resolves early events in vertebrate evolution Oleg Simakov 1,2,13 ✉, Ferdinand Marlétaz 1,11,13, Jia-Xing Yue 3,12, Brendan O’Connell 4, Jerry Jenkins 5, Alexander Brandt6, Robert Calef7, Che-Huang Tung8, Tzu-Kai Huang8, Jeremy Schmutz 5, Nori Satoh 9, Jr-Kai Yu 8, Nicholas H. Putnam 7, Richard E. Green4 and Daniel S. Rokhsar 1,6,10 ✉ Although it is widely believed that early vertebrate evolution was shaped by ancient whole-genome duplications, the number, timing and mechanism of these events remain elusive. Here, we infer the history of vertebrates through genomic comparisons with a new chromosome-scale sequence of the invertebrate chordate amphioxus. We show how the karyotypes of amphioxus and diverse vertebrates are derived from 17 ancestral chordate linkage groups (and 19 ancestral bilaterian groups) by fusion, rearrangement and duplication. We resolve two distinct ancient duplications based on patterns of chromosomal conserved synteny. All extant vertebrates share the first duplication, which occurred in the mid/late Cambrian by autotetraploidization (that is, direct genome doubling). In contrast, the second duplication is found only in jawed vertebrates and occurred in the mid–late Ordovician by allotetraploidization (that is, genome duplication following interspecific hybridization) from two now-extinct progenitors. This complex genomic history parallels the diversification of vertebrate lineages in the fossil record. I n the 1970s, Ohno1 proposed that vertebrates arose through a process involving one or more genome-wide duplications. This hypothesis received early support from the discovery of multiple vertebrate Hox clusters compared with one invertebrate cluster2 and the finding of numerous vertebrate gene families with members distributed across multiple chromosomes3,4. Further evidence came from the discovery of paralogous (that is, duplicated) blocks of linked genes on multiple chromosomes within the human genome5–8, culminating in the discovery of widespread quadruply conserved synteny of the human genome9,10. These studies support the so-called ‘2R’ scenario of two rounds of whole-genome duplication during vertebrate evolution. However, the number, timing and mechanism of these duplication events are still debated3,10–14. Alternatives to the 2R hypothesis include the recent proposal of a single whole-genome duplication with “additional large paralogy regions being the product of rare segmental duplications occurring both before and after”, based on comparative analyses of the sea lamprey genome13,15. Others have suggested a series of large segmental duplications without any genome-wide events16,17, although this is a minority view. Contributing to this uncertainty are discrepancies in the inferred chromosomal organization of the proto-vertebrate ancestor. By analysing gene linkages within and among selected bony vertebrate genomes (Euteleostomi), some authors have suggested the existence of 10–13 proto-vertebrate (that is, before any duplications) chromosomes13,15,18–20, although other studies10,14,21 have inferred 17 ancestral chromosomes. Results and discussion Amphioxus chromosomes reflect ancestral chordate linkages. As an invertebrate chordate whose lineage diverged before the emergence of vertebrates, amphioxus species have often served as a proxy for the ancestral proto-vertebrate condition22, and provide a critical outgroup for analysing vertebrate-specific gene duplications2–4,10 and the evolution of vertebrate gene regulation23. To robustly infer the proto-vertebrate karyotype and the genomic changes that accompanied the invertebrate-to-vertebrate transition, we produced a chromosome-scale genome assembly of amphioxus (the Florida lancelet Branchiostoma floridae). We combined existing shotgun data10 with new in vitro24 and in vivo25 chromatin conformation capture sequences that enable megabase-scale scaffolds to be accurately linked together to reconstruct chromosomes24,25 (Methods, Supplementary Notes 1 and 2 and Extended Data Fig. 1a). The resulting chromosome-scale assembly of B. floridae represents a substantial improvement over the original draft genome sequence, which achieved only megabase-scale scaffolds10, and megabase-scale assemblies of other amphioxus species23,26. Our assembly assigns 94.5% of genes to the 19 B. floridae chromosomes BFL1–19. We validated the chromosome-scale accuracy of the new B. floridae assembly by generating a dense meiotic linkage map made from the F1 progeny of two wild parents (Supplementary Note 3 and Extended Data Fig. 1b)10,22. To examine the conservation of syntenic relationships, we constructed Oxford dot plots comparing the chromosomal positions of orthologous genes between genomes of amphioxus and multiple Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan. 2Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria. 3Université Côte d’Azur, CNRS, INSERM, IRCAN, Nice, France. 4Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA. 5HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA. 6Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA. 7Dovetail Genomics, Scotts Valley, CA, USA. 8Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan. 9Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan. 10Chan Zuckerberg Biohub, San Francisco, CA, USA. 11Present address: Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK. 12Present address: State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China. 13These authors contributed equally: Oleg Simakov, Ferdinand Marlétaz. ✉e-mail: ; 1 820 Nature Ecology & Evolution | VOL 4 | June 2020 | 820–830 | www.nature.com/natecolevol Articles NATurE ECOlOgy & EvOluTIOn BFL15 BFL16 BFL17 BFL18 BFL19 BFL14 BFL13 BFL12 BFL11 BFL9 BFL10 BFL8 BFL7 BFL6 BFL5 BFL4 BFL3 BFL1 a BFL2 between distinct patterns of conserved synteny across the chicken (chromosome code: GGA), gar (chromosome code: LOC), human (chromosome code: HSA), frog (chromosome code: XTR), sea lamprey and scallop (vertical dashed lines Fig. 1 and Extended Data Figs. 2 and 3). BFL2 exhibits an alternating block pattern of CLGJ LOC28 LOC27 LOC26 LOC25 LOC24 LOC23 LOC22 LOC21 LOC20 LOC19 LOC18 LOC17 LOC16 LOC15 LOC14 LOC13 LOC12 6,000 Spotted gar 5,000 LOC11 4,000 LOC10 LOC9 3,000 LOC8 LOC6 2,000 LOC5 LOC4 LOC3 1,000 LOC2 LOC1 A JCJ C Q O I E D F H K B G N M CLGB CLGC GGAZ GGA33 GGA28 GGA27 GGA26 GGA25 GGA24 GGA23 GGA22 GGA21 GGA20 GGA19 GGA18 GGA17 GGA15 GGA14 GGA13 GGA12 G (...truncated)