What is comparative genomics?

1. Assembly of Mmu16

• Total size: 99Mbp
• Not one contiguous sequence (contig)
• 8,635 contigs on 20 “scaffolds”
• Average scaffold size: 10Mbp
• Number of gaps: 8615
• Total size of gaps: ~6Mbp
• Total coverage: ~93Mbp

Q: Why are there so many gaps?

Q: Is there a great danger of missing genes that might be in the gaps?

2. Identify genes in Mmu16

• Scaffolds of >10kbp were examined (scaffolds larger than 1Mbp were chopped)
• Regions with repeat motifs were ignored using RepeatMasker
• Several gene prediction engines use (GenScan, Grail, Fgenes)
• Amino acid sequences from open reading frames searched against nr protein db (NCBI)
• Nucleotide searchers (using DNA from across scaffolds) performed against:
• Celera’s gene clusters
• Mmu, Rno, & Hsa EST db’s
• NCBI’s RefSeq mRNA db
• Celera’s dog genomic db
• Public pufferfish genomic db

Q: Why dog and pufferfish? Why not just rat/mouse/human?

Q: Why not just use DNA from the predicted genes for the db searches?

Q: Why were only regions >10kbp used?

2. Identify genes in Mmu16

• 1055 genes with high & medium confidence were predicted
• Other efforts have identified 1142 genes
• After visual annotation inspection, psuedogenes and annotation errors removed, leaving 731 homologues genes
• The genes found were mostly orthologues because they were reciprocal best matches by BLAST searches.

Q: Why did they find fewer than 1142 genes?

Q: Why did they visually inspect the results?

Q: Does their “reciprocal best match” test ensure they they are dealing with orthologues? How else can they provide evidence for orthology?

3. Identify regions of conserved synteny between Mmu16 and Hsa

• Regions of conserved synteny predicted by sequence similarity and by protein comparisons
• Synteny based on sequence comparisons:
• Syntenic anchors were located - regions with high (80%) similarity over short distances (~200bp or more).
• Average distance between anchors is 8kbp, but there are gaps as large as 707kbp in the mouse and 3.4Mbp in the human