The Artemis Comparison Tool ACT

Comparative Genomics It might be expected that if two organisms diverged from a common ancestor, they should share: - similar gene content - similar gene organization However, genome evolution is a highly dynamic process: - gene acquisition and gene loss will change genome content - gene rearrangements will change the order of genes. Comparative genomics tell us about common and unique features between different organisms at the genome level. Identification of similarities and differences between genomes may allow us to understand: - How two organisms evolved - Why certain organisms cause diseases while others do not

Region sharing similarity Representing sequence similarity/identity MQALL… …RHP Region sharing similarity (BlastP) MAVV… …RHP

ACT- Artemis Comparison Tool

Orthologue of E. coli b0170 Orthologue of E. coli b0169 Orthologue of E. coli b0171

Genome 1 Genome 2 Region of Synteny

Genome 1 Genome 2 Rearrangements

Genome 1 Genome 2 Insertion or deletion

Whole genomes Chromosomal rearrangements Pathogenicity islands/prophages Gene acquisition and loss Gene rearrangements Pseudogenes Phase variation Single nucleotides

Prokaryotic examples

Whole genomes: S. typhi vs. E. coli SPI-2 SPI-9 SPI-1 SPI-10 SPI-7 Vi S. typhi DNA matches E. coli

Multiple genomes B. pertussis IS elements B. bronchiseptica prophage B. parapertussis IS elements

Whole genomes: S. aureus Mu50 vs. N315

Multiple genomes Mu50 N315 MRSA252 MW2 MSSA476

Pathogenicity islands/prophages tRNA-Phe type IV pilus sopE Vi antigen S. typhi E. coli

Gene acquisition and loss Insect toxin Y. pestis Y. enterocolitica

Small rearrangements

Pseudogenes secreted effector protein (type-III) S. typhi S. typhimurium

ACT Eukaryotic examples

Synteny:T.annulata and T. parva (Chr2) BlastN & TBlastX T. annulata T. parva

Synteny: TA & TP ACT comparison

T. annulata & T. parva comparison (Chr 3) Synteny Genus-specific expansion Species-specific expansion Species-specific genes

P. falciparum vs P. knowlesi: break in synteny Chrl3 P. knowlesi

Improving gene prediction with ACT P. falciparum chr13 P. knowlesi Comparison between orthologous genes in P. falciparum and P. knowlesi

ACT comparison: 3 malaria species P. yoelii P. falciparum P. knowlesi

“species-specific” genes at interruptuions in synteny Plasmodium falciparum Plasmodium knowlesi Plasmodium yoelii

ACT comparison of qut gene cluster

Generating ACT comparison files ACT supports three different comparison file formats: 1) BLAST version 2.2.2 output: The blastall command must be run with the -m 8 flag which generates one line of information per HSP. 2) MEGABLAST output: ACT can also read the output of MEGABLAST, which is part of the NCBI blast distribution. 3) MSPcrunch output: MSPcrunch is program for UNIX and GNU/Linux systems which can post-process BLAST version 1 output into an easier to read format. ACT can only read MSPcrunch output with the -d flag. Here is an example of an ACT readable comparison file generated by MSPcrunch -d. 1399 97.00 940 2539 sequence1.dna 1 1596 AF140550.seq 1033 93.00 9041 10501 sequence1.dna 9420 10880 AF140550.seq 828 95.00 6823 7890 sequence1.dna 7211 8276 AF140550.seq 773 94.00 2837 3841 sequence1.dna 2338 3342 AF140550.seq The columns have the following meanings (in order): score, percent identity, match start in the query sequence, match end in the query sequence, query sequence name, subject sequence start, subject sequence end, subject sequence name. The columns should be separated by single spaces.