Supplementary information

Sequencing and Comparison of Yeasts to Identify Genes and Regulatory Elements

S1. Sequences and Alignments

S1a	Assembly	S. paradoxus	Spar_contigs	(fasta, 12 Mb)	Spar_scaffolds	(txt, 23 kb)
		S. mikatae	Smik_contigs	(fasta, 12 Mb)	Smik_scaffolds	(txt, 23 kb)
		S. bayanus	Sbay_contigs	(fasta, 12 Mb)	Sbay_scaffolds	(txt, 23 kb)
S1b	ORFs	Listing	Table of ORFs with unamibuguous correspondence
		S. cerevisiae	Scer_extended	(fasta.gz, 4.0 Mb)	Fasta file containing each ORF (uppercase) and flaking intergenic regions (lowercase)
		S. paradoxus	Spar_extended	(fasta.gz, 4.0 Mb)
		S. mikatae	Smik_extended	(fasta.gz, 3.6 Mb)
		S. bayanus	Sbay_extended	(fasta.gz, 3.6 Mb)
S1c	Alignments	Nucleotide	all_alignments	(tar.gz, 23 Mb)	Aligned ORFs and flanking sequences
			Browse	by chromosome
		Protein	All protein alignments available at the SGD site

S2. Annotation

S2a	ORF annotation	Forward	S.paradoxus	S.mikatae	S.bayanus	The best match of every predicted ORF
		Forward full	S.paradoxus	S.mikatae	S.bayanus	All matches for every predicted ORF
		Reverse	S.paradoxus	S.mikatae	S.bayanus	The best match of every S. cerevisiae ORF
		Reverse full	S.paradoxus	S.mikatae	S.bayanus	All matches for every S. cerevisiae ORF
S2b	Synteny	Synteny blocks	S.paradoxus	S.mikatae	S.bayanus	Blocks of conserved gene order (synteny)
S2c	Correspondence	Homology Groups	S.paradoxus	S.mikatae	S.bayanus	Genes of ambiguous correspondence (large families)
S2c	Correspondence	Homology Groups	S.paradoxus	S.mikatae	S.bayanus	Genes of ambiguous correspondence (small families)
S2d	Features	tRNA	S.paradoxus	S.mikatae	S.bayanus	Predicted tRNA genes (and usage)
		Transposons	S.paradoxus	S.mikatae	S.bayanus	Transposable elements (best match)
		Transposons full	S.paradoxus	S.mikatae	S.bayanus	Transposable elements (all matches)
S2e	Alignments	Aligned features	tRNA/RNA	CEN	ARS	LTR	Orthologous alignments of S. cerevisiae features

S3. Visualization of gene correspondence

S3a	Dotplots	S.paradoxus	S.mikatae	S.bayanus	Dotplots of gene correspondence
S3b	Tiling	Example	Figure 1 showing S. cerevisiae Chromosome VII
		Visualization	250 files tiling the S.cerevisiae genome (jpg/ps/matlab)
S3c	Interactive	Synteny viewer	Interactive synteny viewer can be found at the SGD site

S4. Mutation Counts

S4a	MutationCounts	(xls)	68 kb	Overall counts of transitions, transversions, insertions, deletions along phylogenetic tree
S4b	KaKs_average	(xls)	435 kb	Ka/Ks rate for uninterrupted S. cerevisiae ORFs
S4b	KaKs_details	(xls)	834 kb	Ka/Ks rate for uninterrupted S. cerevisiae ORFs (all pairwise comparisons)

S5. Rearrangements

S5a	Sparadoxus_walking	(txt)	444 kb	Distances between consecutive ORFS in each species and S. cerevisiae
	Smikatae_walking	(txt)	457 kb
	Sbayanus_walking	(txt)	446 kb
S5b	Rearrangements	(xls)	24 kb	Table of genomic rearrangements for each species (translocations, inversions, segmental duplications)
	Rearrangements_figure	(xls)	24 kb
S5c	All_insertions	(xls)	58 kb	Table of all insertions/deletions of al least 2kb between consecutive syntenic ORFs
	Ambiguity_clusters	(xls)	23 kb	Clusters of ORFs with ambiguous correspondence define regions of rapid change

S6. RFC test

S6a	orf_decisions	(txt)	365 kb	Test outcome for every ORF as kept, rejected or no_call
S6b	RFC	(xls)	1,445 kb	RFC score for every ORF across each species and S. cerevisiae
	RFC_Intergenic	(xls)	63 kb
S6c	window_based_named	(txt)	2,900 kb	Window-based RFC analysis for each species and S. cerevisiae
	window_based_unnamed	(txt)	1,007 kb
	window_based_suspicious8	(txt)	540 kb
S6d	SmallORFs	(doc)	40 kb	Correlation of RFC test with length of open frame for short ORFs of varying lengths
	SmallORFs3	(doc)	40 kb

S7. Revisiting S. cerevisiae annotation

S7a	Change_Start	(xls)	434 kb	Table of proposed start codon changes
	Change_Stop	(xls)	434 kb	Table of proposed stop codon changes in S. cerevisiae
	Merged_ORFs	(xls)	434 kb	Table of proposed merges between consecutive S. cerevisiae ORFs
S7b	Change_Start_End_alignments	(txt)	1,362 kb	Alignment of proposed start/end boundary changes
S7c	Frameshifts	(txt)	1,014 kb	Alignment of apparent single-species frame-shift mutations
S7d	Resequencing	(xls)	20 kb	Results of resequencing proposed frame-shifts in S. cerevisiae
S7e	PCR_resequenced_regions	(txt)	412 kb	Alignment of resequenced regions
	SEQ1000	(fasta)	48 kb	Primers used
S7f	Intron_table	(xls)	30 kb	Table of proposed novel introns and proposed changed introns
S7g	introns_known	(txt)	1,771 kb	Alignments of known, changed and proposed novel introns
	introns_known_bad	(txt)	276 kb
	introns_known_v3	(txt)	2,967 kb
	novel_noSGD_noARES	(txt)	4,110 kb
	novel_noSGD_yesARES	(txt)	290 kb

S8. Genome-wide motifs

S8a	TopMinis	(txt)	164 kb	Table of mini-motifs with CC1, CC2, CC3 score, extension and conservation counts
	AllMinis	(txt)	335 kb
S8b	CC1_collapsing	(txt)	179 kb	Sequence-based motif collapsing for each test
	CC2_collapsing	(txt)	137 kb
	CC3_collapsing	(txt)	167 kb
S8c	MegaRecollapsing	(xls)	313 kb	Co-occurence-based collapsing of grouped consensi
S8d	GenesHit	(txt)	1.5 Mb	Genes containing each genome-wide motif (upstream)
	GenesHit_down	(txt)	1.5 Mb	Genes containing each genome-wide motif (downstream)

S9. Category-based motif discovery

S9a	Increased_Enrichment	(xls)	25 kb	Increased enrichment of known motifs by using multiple genomes
S9b	Comparison_with_MEME	(xls)	24 kb	Comparison of our category-based motif discovery and MEME for known motifs
S9c	Category_Based_Novel	(xls)	48 kb	All category-based motifs discovered, clustered by sequence similarity