Comparative Genome Maps in Pacific Salmon

1. Comparative Genome Maps in Pacific Salmon Ruth B. Phillips

2. Why make genetic and genome maps for Pacific salmon? • To assist in mapping QTLs for important traits • To identify genes under selection • To correlate Pacific salmon maps with the maps/genome sequences of Atlantic salmon and rainbow trout • Genetic maps of trout and Atlantic salmon have been correlated with those of sequenced teleosts—so specific genes linked to many SNPs and microsatellites are known

3. Phylogeny of the North American Subfamily Salmoninae Oncorhynchus (Pacific salmon and trout) Salmoninae Salvelinus ( Lake, brook, bull trout and Arctic and Dolly Varden char) Salmo Atlantic salmon, brown trout Coregoninae Coregonus (whitefish) Oakley & Phillips, 1999; Crespi & Fulton, 2004—based on nuclear and mitochondrial data; Koop et al., 2008 (EST data)

4. Phylogeny of Pacific Salmon and Trout 2N= 52 2N=74 2N=57, 58 2N=68 2N=60 2N=64-68 2N=58-64 Tree based on combined nuclear and mitochondrial DNA: analysis done by Crespi and Fulton, 2004 Although diploid chromosome numbers vary widely, all species have 50 chromosome arms suggesting multiple fusions/fissions have occurred

5. The Major SD gene (SEX) is on a different chromosome in each species of Pacific Salmon Pacific salmon and trout share the OmyY1 male specific marker shown in green—so they must share the SD gene Pacific salmon share male specific OtY2 and GH-Y (sockeye lacks GH-Y) Sockeye is unusual in that males have 57 chromosomes and females 58 chromosomes R. Phillips et al., 2008 Phylogeny based on nuclear and Mitochondrial data

6. OmyY1 haplotypes correspond in general to inland and coastal trout OmyY1 Haplotype* Network *Based on 969bp of OmyY1 Sequence-Brunelli et al., 2010 Geographic distribution of OmyY1 Haplotypes

7. Coastal Populations have mainly 2N=60, and Interior Populations 2N=58 Phillips et al, 2005: Chromosome fusion of Pair #25 and Pair #29 from the Coastal fish gives 2N=58 found in the Interior fish. Map from GH Thorgaard, 1983: 29 populations were Sampled All had 52 chromosome arms (which I have condensed to 50 when the 2 very small metacentrics are considered one arm)

8. Chromosome Rearrangements Accompanied Speciation • Salmonids have a large # of transposons • Chromosome arms are conserved, but are rearranged in each species (Phillips et al., 2009 and current research) The sex chromosome corresponds to a different chromosome arm in each species Conclusion: massive release of transposons resulted in chromosome rearrangements and new sex chromosomes in each species

9. SNP maps completed for rainbow trout and Atlantic salmon • Atlantic salmon: • Lien et al. 2011--over 5600 SNPs mapped and correlated map with stickleback genome • Rainbow trout: • Miller et al., 2012—over 4500 SNPs mapped + 2 microsats/linkage group • Pacific Salmon • Everett et al., 2012—over 1000 SNPs in sockeye • Naish et al: mapping several thousand SNPs in coho & chinook crosses scored for microsatellite loci

10. Linking Chromosomes to the Genetic maps • Microsatellites and SNPs isolated from BAC “end sequences” have been placed on the genetic maps • BACs containing markers on the genetic maps are used as probes in FISH experiments • If the same BACs are used on chromosomes of different species—comparative maps can be obtained • Most of the rainbow trout BACs work on chinook chromosomes

11. Rainbow Trout Chromosome Map, 2009 Chromosome Omy1=LG6 If 20 & 22 are considered as one chromosome arm, then NF=100 or 50 pairs of chrom. arms Markers added so at least 1/chrom. arm All of the Pacific salmon have 50 pairs of chrom. arms

12. Localization of BAC containing FGF6 (Omy1q) to chromosome 7 in Chinook

13. Localization of Omy7INRA (Omy15q) to sex chromosome pair in Chinook

14. Localization of Tcrbeta to chrom. 9 in Chinook (found in inland rainbow trout)

15. Salmonid fishes: two rounds of polyploidy • Whole genome duplication in ancestor of teleosts (about 15% of genes in zebrafish retain duplicates) • Second whole genome duplication in ancestor of salmonids • Speciation involved different chromosome rearrangements in each salmonid species • most species have 50 pairs of chromosome arms

16. One comparison of the trout map with zebrafish map (Many trout linkage groups have synteny blocks with zebrafish Trout Omy12: Hsp70a GH1Hox BA1 Zebrafish #3 GH Hsp 70 HoxBA Trout Omy13: Hsp70b GH2 HoxBA2 Order of markers usually not conserved with zebrafish

17. Comparative Chromosome Mapping between Atlantic Salmon and Rainbow Trout • Linkage groups assigned to chromosomes • Genetic and chromosome maps have been correlated between the two species • Results confirm presence of 50 pairs of “chromosome arms” that have been totally rearranged between the two species • Phillips et al., BMC Genetics 2009

18. Centric Fusions vs Tandem Fusions Centric Fusions Tandem Fusions p q Both result in reduction of chromosome number, but # of arms is reduced only with tandem fusions Tandem fusions are found mainly in Atlantic Salmon

19. Rainbow Trout/Atlantic Salmon Summary • Whole chromosome “arms” are conserved between Atlantic salmon and rainbow trout • Gene order often conserved within the arms • Blocks of repetitive DNA on large Atlantic salmon chromosomes represent sites of tandem fusion-most fusions are “head to tail” • Effect of tandem fusions on genetic recombination: • Male genetic map is very condensed except at telomeres • All homeologous chromosome arms identified by Lien et al., 2012 using SNPs blasting data vs stickleback genome

20. Ideogram showing location of BACs on the Atlantic salmon chromosomes p qa qb NF=74 or 37 pairs qa qb 50 pairs of chrom. segments qc Phillips et al., 2009

21. Atlantic Karyotype with Homologous Chromosome Arms from Rainbow Trout

22. Rainbow Karyotype with Homologous Chromosome Arms from Atlantic Salmon

23. Comparative Chromosome Mapping • Need BAC clones which • Either work on both species OR • Are isolated from BAC libraries of each species • Rainbow trout BAC clones were used for hybridization to chinook chromosomes • Problem: • BAC clones from heterologous species may hybridize to duplicate loci or not work at all—currently a BAC library for chinook is being pooled

24. Chinook Chromosome Map-2012

25. Chinook-Rainbow Comparative Map Corresponding RT chrom. arms shown in color

26. Comparison between Chinook Salmon and Rainbow Trout Maps • Whole chromosome arms are conserved between chinook salmon and rainbow trout • One minor exception suggests that a reciprocal translocation occurred before the other chromosome rearrangements • Gene order on each arm is usually conserved • Although the ancestral trout karyotype (2N=58) could be converted to the chinook karyotype (2N=68) by five changes, only 1/3 of the chromosomes are conserved between these species

27. Rainbow Trout Chromosome Variation • Inland rainbow trout have 58 chromosomes • A major difference between inland and coastal chromosomes is fusion between chromosome pairs #25 and #29 of coastal trout in 2N=58 compared to 2N=60 • This same fusion is found in all Pacific salmon • Two other fusion chromosomes are found in all Pacific salmon

28. Comparison of chinook, coho, and sockeye with rainbow chromosome maps • Number of chromosomes in coho and sockeye is similar to that in rainbow trout • Whole chromosome arms are conserved, but less than 1/3 of the rainbow trout (RT) chromosomes are conserved in chinook and sockeye, and about half between coho and RT Only 20% of the chromosomes are the same in all 4 species. Each species has unique fusions

29. Summary • Only a few changes from the rainbow trout diploid chromosome number could yield the chromosome numbers in the other species • BUT • Chromosome fusions/fissions have been massive among these four species—so that less than 20% of the chromosomes have been conserved among all species

30. Questions for the Future • Are chromosome fusions just random, or is there a selective advantage to any of the rearrangements?? • In sockeye we have evidence that the fusion involved in producing the Y chromosome brought genes advantageous to male fitness next to the SEX gene (Sockeye has the XXY system) • If many rearrangments were produced at the time of speciation, perhaps selection was involved in production of sex chromosomes in other species