SyMAP is a synteny mapping and analysis program that compares genomes of different species to understand gene function and evolutionary history. It finds synteny blocks between a physical map (e.g. FPC map) and a sequenced genome using anchors like markers and BAC end sequences. The algorithm uses a directed acyclic graph and dynamic programming to order anchors into synteny chains while allowing for errors and rearrangements. SyMAP displays synteny results through interactive views and aids in tasks like correcting BAC clone end assignments. It has been applied to several plant genome projects.

1. SyMAP Synteny Mapping and Analysis Program Austin Shoemaker

2. SyMAP Team Dr. Cari Soderlund Dr. Will Nelson Austin Shoemaker Interactive SyMAP views Sytry Testing environment for synteny finding algorithms Worked with the team on: The synteny finding algorithm MySQL database schema

3. Background Comparative Genomics Physical Map Computing Synteny Properties of FPC to Genome Synteny

4. Comparative Genomics Compare genomes of different species Knowledge of one helps understand the other Gene Function Organism O 1 has a gene G 1 Organism O 2 has a gene G 2 with a sequence similar to G 1 G 1 and G 2 may have similar functions Evolutionary History Genome rearrangements

5. Genome Rearrangements Rearrangement Scenario Result Inversion Duplication Insertion Deletion A BCD E A DCB E A B C AC AB A C B A B CD A B B CD A B C A B C B , A BB C AB AB AB

6. Whole-Genome Duplication mya (million years ago) Last Common Ancestor rice maize diverged 50-70 mya 70 mya duplication 11 mya duplication

7. Synteny At least two pairs of genes with similar structure and function on the same chromosome Order does not need to be conserved Often found using sequenced genomes We use a physical map and a genomic sequence Genome A c d e f g c d e f g Genome B

8. Physical Map Expensive to sequence large genomes A physical map provides partial ordering of pieces of DNA and pieces of genes

9. FPC Map FingerPrinted Contigs Soderlund et al. 1997 Type of physical map Made up of clones Snippets of DNA We use BAC clones Bacterial artificial chromosome clones Stored in clone libraries

10. Making a BAC Clone Library Take thousands of copies of a genome Cut it up into overlapping pieces (~150,000 base pairs) Restriction enzymes Proteins that cut at specific DNA sequences Partial digestion Restriction enzymes not allowed to cut at all possible locations so that the clones overlap

11. Clones Each clone is stored in a well on a microtiter plate Do not know the order of the clones, or where each clone is on the chromosome

12. Clone Fingerprinting Clone fingerprints are found to gather more information on a clone Fully digest a clone using restriction enzymes If two clones share many fragments, they may overlap

13. Clone Fingerprinting Fragments are run on a gel Shorter fragments migrate faster Measure migration rate False positives and false negatives

14. FPC Assembles fingerprinted clones into contigs Contig -> contiguous overlapping clones Assembles into many contigs instead of one large contig Unclonable regions Uneven distribution

15. Markers Markers are pieces of DNA ~ 300 base pairs Hybridization A marker hybridizes to a clone when the clone contains the marker

16. BESs Expensive to sequence entire clones BAC End Sequences BESs are sequences from the ends of BAC clones ~800 base pairs Do not know which end the sequence comes from There are errors in the sequence

17. Anchors Locations of two genomes found to be similar through a comparison of DNA sequences We use marker sequences and BESs searched against a known genome sequence Maize has an FPC map with markers and BESs The rice genome is sequenced G G C C G T G G T G C T C T T T G C A A T G G G G G C T G T G G T G C T C T T C G C A A T G G G

18. Component Summary

19. Finding Chains

20. Key Synteny Finding Algorithms Vandepoele et al. (2002) – ADHoRe Variable gap size Coefficient of determination to determine the quality of a synteny block Haas et al. (2004) – DAGchainer Directed acyclic graph Dynamic programming Gap penalty

21. Other Synteny Finding Algorithms Key characteristics for us: Dynamic programming Ordering the anchors to form a DAG Gap penalty Variable gap size Not appropriate for finding synteny using an FPC map Do not consider the error conditions that arise

22. FPC to Genome Synteny Properties associated with FPC FPC maps do not cover the entire genome False+ and False- hybridized markers FPC coordinates are approximate Which end of the parent clone a BES belongs to is unknown

23. FPC Synteny Properties 1 x 2 o 3 x 4 x 5 o 6 8 # x 9 x a x b x c x 7 x 1 2 3 4 5 6 7 8 9 a b c Genome A (FPC map) Genome B (sequenced genome)

24. Noise

25. SyMAP Algorithm Anchor (a k , b l ) a k is the location on the FPC map of genome G A b l is the location on the genomic sequence of G B Directed Acyclic Graph E = {u, v | |a k -a i |  M A and 0  b l -b j  M B } where u = (a i , b j ), v = (a k , b l ) are anchors Allows edges decreasing along G A Catch off-diagonal anchors Some inversions

26. SyMAP Algorithm Manhattan distance function with scaling D(v, w) =  |a k - a i | / t A + |b l - b j | / t B  Average distance between anchors may be different Dynamic Programming Node(v) = 1 + Max(0, Max u  P(v) (Node(u) - D(u,v))) P(v) is the set of edges (u,v)  E 1 is the score given to an individual anchor Plus the maximum path score for a previous node Penalized by the distance between the nodes

27. SyMAP Algorithm Chains must satisfy constraints Number of anchors Strength of line Pearson correlation coefficient Required to be more precisely linear the closer they are to the minimal number of anchors Exception for small and dense chains Lower correlation due to errors in the assignment of BES ends or clone ordering within a contig

28. Sytry Tool for testing synteny finding algorithms Allows for modifying the parameters of an algorithm and rerunning Results are shown as a dot plot Need to visually confirm results, as correct Correct is what looks right to the user

29. Automated Parameter Setting Difficult to set parameters (e.g., t A and t B ) Effects of changes can be unclear Dependent on average distance between anchors and noise Optimal values vary between regions Have the algorithm set the gap parameters Attempt to optimize t x for each chain

30. Sub-Chains Overall orientation of a synteny chain may not be accurate for sub-chains

31. Sub-Chain Finder Use only anchors that are part of a chain Define distance between anchors in terms of the number of anchors that fall between the anchors A significant gap signals the start of a possible inversion

32. Sub-Chains Evolutionary history e.g., total number of inversions Assigning an accurate orientation to all anchors in a chain Beneficial for fixing the clone end assignment of BES

33. BES Clone End Assignments BESs are arbitrarily assigned to clone ends Algorithm takes this into account However, the synteny when viewing can be distorted Orientation can be used to correct BES assignments

34. BES Clone End Assignments positive orientation -> lines should not cross 2 x 3 o 4 5 6 o 7 x 8 x 1 2 3 4 5 6 7 8 A B 1 x B A 2 3 4 5 6 7 8 2 3 4 5 6 7 8 1 1

35. BES Clone End Assignments negative orientation -> lines should cross 7 x 6 o 5 4 3 o 2 x 1 x 1 2 3 4 5 6 7 8 A 8 x B B A 1 2 3 4 5 6 7 1 2 3 4 5 6 7 8 8

36. SyMAP Views Accessible through a web browser Static views All synteny blocks ↔ sequenced chromosomes Synteny blocks ↔ sequenced chromosome Interactive views Dot plot view Genome to genome Chromosome to chromosome Alignment view FPC ↔ sequenced chromosome FPC ↔ FPC FPC ↔ sequenced chromosome ↔ FPC Close-up view FPC ↔ sequenced chromosome

37. All Blocks ↔ Sequenced Chromosomes

38. Blocks ↔ Sequenced Chromosome

39. Genome ↔ Genome Dot Plot

40. Chromosome ↔ Chromosome Dot Plot

41. Block ↔ Sequenced Chromosome

42. Subset Flipped

43. Contig ↔ Sequenced Chromosome

44. Filters and Controls

45. FPC ↔ Sequenced Chromosome ↔ FPC

46. FPC ↔ FPC

47. Close-up of Gene

48. SyMAP Implementation Caching is needed: Downloads large amounts of data from remote database History feature Navigating back and forth between the same views Soft References Remain alive as long as the memory is available Data objects Hold data in a compact form Converted to view objects when needed

49. Results www.agcol.arizona.edu/symap Maize and sorghum aligned to rice Maize FPC aligned to sorghum FPC Used in editing the maize FPC maps based on its alignment to rice (Wei et al., in preparation) Alignment of maize to rice chromosome 3 Buell et al. (2005) Used in OMAP project Aligning 12 species of rice to the sequenced genome of rice (Wing et al., in preparation)

50. Acknowledgements Thesis Committee Dr. Cari Soderlund, thesis advisor Dr. Peter Downey Dr. Kobus Bernard This work is funded in part by NSF DBI #0115903 www.agcol.arizona.edu/symap