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CONTENTS OF SUPPLEMENTARY TABLES:
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For each table the column heading and explanation of column contents are given.



Table S1 - probes used for library reduction	

nr. ESTs	number of ESTs in contig already sequenced at least 4 times
Sequence 5’ to 3’	probe sequence against that contig

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Table S2 - intensity of spots on subtraction filter

seq.name	sequence name with info on library origin (3 letter code before first _underscore), PCR plate where EST was amplified (two numbers between _underscores_), and well location on that plate (A01-P24)
library.id	library where amplicon came from
plate.nr	PCR plate number (which determines a particular position on filter)
intensity.6andup.filter1	spot intensity from hybridization of filter 1 with pooled probes against contigs repeated 6 or more times in first ~2000 sequences
intensity.PCR103.filter1	spot intensity from hybridization of filter 1 with control probe against shared sequence in all amplicons
intensity.4and5.filter2	spot intensity from hybridization of filter 1 with pooled probes against contigs repeated 4-5 times in first ~2000 sequences
intensity.PCR103.filter2	spot intensity from hybridization of filter 2 with control probe against shared sequence in all amplicons

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Table S3 - Bicyclus anynana ESTs

EST.nr	indexing identity number for each EST
EST.name	"name of EST with info on library origin (3 letter code before first _), PCR plate where EST was amplified (two numbers between ""underscores""), and well location on that plate (A01-P24)"
library	library where EST came from
EST.incontig	contig (Table S4) to which the EST was assembled
EST.sequence	nucleotidic sequence of EST (sentence case for bases with Phred<20 and capitals for >=20)
EST.length	length of EST sequence
OK.contig	0/1 code ESTs belonging to contigs that have been excluded/included in the analysis based on complexity scores (Table S4)

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Table S4 - Bicyclus anynana contigs

contig.nr	indexing identity number for each contig
contig.name	name of contig (starting with C_ for contigs of alignment depth >= 2, and S_ for singletons)
consensus.seq	"majority rule"" consensus sequence (with N masking regions of low complexity)
consensus.length	length of consensus
nr.ESTs	number of ESTs in contig (= alignment depth)
list.ESTs	list of all individual EST names in contig (EST data in Table S3)
alignment.ESTs	file with alignment for contigs of depth >=2
peptide.sequence	predicted peptide sequence using ESTscan
complexity	complexity score calculated with algorithm "complex" as described in Methods
OK.complex	0/1 code respectively for excluded and included contigs in ms analysis
blastx.Dmel.pro	output of best hit from BLASTX analysis to Drosophila melanogaster peptides
CG.Dmel.pro	CG number of best hit from BLASTX analysis to Drosophila melanogaster peptides
uniqueid.Dmel.pro	FlyBase identification number of best hit from BLASTX analysis to Drosophila melanogaster peptides
genesymbol.Dmel.pro	gene name of best hit from BLASTX analysis to Drosophila melanogaster peptides
transcript.Dmel.pro	transcript of best hit from BLASTX analysis to Drosophila melanogaster peptides
Evalue.Dmel.pro	Evalue of best hit from BLASTX analysis to Drosophila melanogaster peptides
frame.Dmel.pro	reading frame of best hit from BLASTX analysis to Drosophila melanogaster peptides
link.Dmel.pro	URL to FlyBase page of best hit from BLASTX analysis to Drosophila melanogaster peptides
blastn.Dmel.nuc	output of best hit from BLASTN analysis to Drosophila melanogaster nucleotidic sequences
CG.Dmel.nuc	CG number of best hit from BLASTN analysis to Drosophila melanogaster nucleotidic sequences
uniqueid.Dmel.nuc	FlyBase identification number of best hit from BLASTN analysis to Drosophila melanogaster nucleotidic sequences
genesymbol.Dmel.nuc	gene name of best hit from BLASTN analysis to Drosophila melanogaster nucleotidic sequences
ranscript.Dmel.nuc	transcript of best hit from BLASTN analysis to Drosophila melanogaster nucleotidic sequences
Evalue.Dmel.nuc	Evalue of best hit from BLASTN analysis to Drosophila melanogaster nucleotidic sequences
link.Dmel.nuc	URL to FlyBase page of best hit from BLASTN analysis to Drosophila melanogaster nucleotidic sequences
blastx.Bmori.est.pro	output of best hit from BLASTX analysis to openSputnik's annotation of translated Bombyx mori ESTs
Evalue.Bmori.est.pro	Evalue of best hit from BLASTX analysis to openSputnik's annotation of translated Bombyx mori ESTs
frame.Bmori.est.pro	reading frame of best hit from BLASTX analysis to openSputnik's annotation of translated Bombyx mori ESTs
blastn.Bmori.nuc.est	output of best hit from BLASTN analysis to openSputnik's annotation of Bombyx mori ESTs
Evalue.Bmori.nuc.est	Evalue of best hit from BLASTN analysis to openSputnik's annotation of Bombyx mori ESTs
blastn.lep.nuc	output of best hit from BLASTN analysis to the Lepidopteran nucleotide collection from NCBI
id.lep.nuc	gene identification of best hit from BLASTN analysis to the Lepidopteran nucleotide collection from NCBI
Evalue.lep.nuc	Evalue of best hit from BLASTN analysis to the Lepidopteran nucleotide collection from NCBI
link.lep.nuc	URL to GenBank page of best hit from BLASTN analysis to the Lepidopteran nucleotide collection from NCBI
blastx.invert.pro	output of best hit from BLASTX analysis to Invertebrate protein collection from EMBL
id.invert.pro	gene identification of best hit from BLASTX analysis to Invertebrate protein collection from EMBL
Evalue.invert.pro	Evalue of best hit from BLASTX analysis to Invertebrate protein collection from EMBL
frame.invert.pro	reading frame of best hit from BLASTX analysis to Invertebrate protein collection from EMBL
link.invert.pro	URL to EMBL page of best hit from BLASTX analysis to Invertebrate protein collection from EMBL
blastx.NonRed.pro	output of best hit from BLASTX analysis to collection of all Non-redundant peptide sequences
id.NonRed.pro	gene identification of best hit from BLASTX analysis to collection of all Non-redundant peptide sequences
Evalue.NonRed.pro	Evalue of best hit from BLASTX analysis to collection of all Non-redundant peptide sequences
frame.NonRed.pro	reading frame of best hit from BLASTX analysis to collection of all Non-redundant peptide sequences
blastx.SwissP.pro	output of best hit from BLASTX analysis to collection of all SwissPro peptide sequences
id.SwissP.pro	gene identification of best hit from BLASTX analysis to collection of all SwissPro peptide sequences
Evalue.SwissP.pro	Evalue of best hit from BLASTX analysis to collection of all SwissPro peptide sequences
frame.SwissP.pro	reading frame of best hit from BLASTX analysis to collection of all SwissPro peptide sequences
blastn.organel.nuc	gene identification of best hit from BLASTN analysis to the organelle nucleotide collection from NCBI
id.organel.nuc	gene identification of best hit from BLASTN analysis to the organelle nucleotide collection from NCBI
Evalue.organel.nuc	Evalue of best hit from BLASTN analysis to the organelle nucleotide collection from NCBI
link.organel.nuc	URL to GenBank page of best hit from BLASTN analysis to the organelle nucleotide collection from NCBI
blastn.rfam.nuc	output of best hit from BLASTN analysis to the Rfam nucleotide collection from NCBI
id.rfam.nuc	gene identification of best hit from BLASTN analysis to the Rfam nucleotide collection from NCBI
Evalue.rfam.nuc	Evalue of best hit from BLASTN analysis to the Rfam nucleotide collection from NCBI
link.rfam.nuc	URL to GenBank page of best hit from BLASTN analysis to the Rfam nucleotide collection from NCBI
blastn.Ecoli.nuc	output of best hit from BLASTN analysis to the E. coli nucleotide collection from NCBI
id.Ecoli.nuc	gene identification of best hit from BLASTN analysis to the E. coli nucleotide collection from NCBI
Evalue.Ecoli.nuc	Evalue of best hit from BLASTN analysis to the E. coli nucleotide collection from NCBI
link.Ecoli.nuc	URL to GenBank page of best hit from BLASTN analysis to the E. coli nucleotide collection from NCBI
blastx.plant.pro	output of best hit from BLASTX analysis to plant protein collection from EMBL
id.plant.pro	gene identification of best hit from BLASTX analysis to plant protein collection from EMBL
Evalue.plant.pro	Evalue of best hit from BLASTX analysis against collection of plant proteins from EMBL
frame.plant.pro	reading frame of best hit from BLASTX analysis against collection of plant proteins from EMBL
link.plant.pro	URL to best hit from BLASTX analysis against collection of plant proteins from EMBL
blastn.Bmori.wgs.c	output of best hit from BLASTN analysis against nucleotide sequence collection from the Chinese whole genome shotgun sequence of Bombyx mori
id.Bmori.wgs.c	gene identification of best hit from BLASTN analysis against nucleotide sequence collection from the Chinese whole genome shotgun sequence of Bombyx mori
Evalue.Bmori.wgs.c	Evalue of best hit from BLASTN analysis against nucleotide sequence collection from the Chinese whole genome shotgun sequence of Bombyx mori
link.Bmori.wgs.c	URL to NCBI page of best hit from BLASTN analysis against nucleotide sequence collection from the Chinese whole genome shotgun sequence of Bombyx mori
blastn.Bmori.wgs.j	output of best hit from BLASTN analysis against nucleotide sequence collection from the Japanese whole genome shotgun sequence of Bombyx mori
id.Bmori.wgs.j	gene identification of best hit from BLASTN analysis against nucleotide sequence collection from the Japanese whole genome shotgun sequence of Bombyx mori
Evalue.Bmori.wgs.j	Evalue of best hit from BLASTN analysis against nucleotide sequence collection from the Japanese whole genome shotgun sequence of Bombyx mori
link.Bmori.wgs.j	URL to NCBI page of best hit from BLASTN analysis against nucleotide sequence collection from the Japanese whole genome shotgun sequence of Bombyx mori
blastn.Bmori.cds.nuc	output of best hit from BLASTN analysis against the collection of predicted coding sequence from the Chinese whole genome shotgun sequence of Bombyx mori
id.Bmori.cds.nuc	gene identification of best hit from BLASTN analysis against the collection of predicted coding sequence from the Chinese whole genome shotgun sequence of Bombyx mori
Evalue.Bmori.cds.nuc	Evalue of best hit from BLASTN analysis against the collection of predicted coding sequence from the Chinese whole genome shotgun sequence of Bombyx mori
blastx.Bmori.wgs.pro	output of best hit from BLASTX analysis against the collection of predicted peptides from the Chinese whole genome shotgun sequence of Bombyx mori
id.Bmori.wgs.pro	gene identification of best hit from BLASTX analysis against the collection of predicted peptides from the Chinese whole genome shotgun sequence of Bombyx mori
Evalue.Bmori.wgs.pro	Evalue of best hit from BLASTX analysis against the collection of predicted peptides from the Chinese whole genome shotgun sequence of Bombyx mori
frame.Bmori.wgs.pro	reading frame of best hit from BLASTN analysis against the collection of predicted coding sequence from the Chinese whole genome shotgun sequence of Bombyx mori

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Table S5 - SNPs

contig.nr	indexeding identity number for each contig
contig.name	name of contig (starting with C_ for contigs of alignment depth >= 2, and S_ for singletons)
IUBconsensus.length	length of consensus sequence generated using IUB codes for SNPs
nr.ESTs	number of ESTs in contig (= alignment depth)
single-hit SNPs	total number of SNPs (minor allele count of at least 1)
double-hit SNPs	number of SNPs with minor allele count of at least 2

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Table S6 - Bicyclus anynana contigs	

contig.nr	indexing identity number for each contig
contig.name	name of contig (starting with C_ for contigs of alignment depth >= 2, and S_ for singletons)
nr.ESTs	number of ESTs in contig (= alignment depth)
microsat.inseq.nr	number identifying microsatellite in respective contig (some contigs had more than one microsatellite)
nucs.in.repeat	number of nucleotides in microsatellite motif
repeat.sequence	nucleotide sequence of microsatellite motif
nr.repeats	number of times the motif is repeated in the consensus sequence of the contig
position.begin	nucleotide position in the consensus where microsatellite begins
position.end	nucleotide position in the consensus where microsatellite ends
depth.at.microsat	depth of alignment at microsatellite location
polymorphic	1/0 code for polymorphic and monomorphic microsatellites, respectively
nr.alleles	number of alleles or microsatellite observed in contig alignment

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Table S7 - GO miner summary table	

GO ID	identification number for Gene Ontology (GO) category
Dmel	number of D. melanogaster CG numbers (genes) for each GO category
Bany	number of identified B. anynana contigs with homology D. melanogaster CG numbers (genes) for each GO category
Term	GO description
Table 5	1/0 code respectively for the table entries where were and were not used in Table 5 of ms