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SUPPLEMENTARY INFORMATION
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Figure S1 Quality improvement of a co-dominant AFLP. mCCeACC171-
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175 was a co-dominant AFLP marker with two distinct alleles of 171 and 175
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bp, but with a pattern that is somewhat ambiguous. The original AFLP traces to
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the left of the vertical black bar were generated with the Mse+CC primer,
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whereas the traces to the right of the bar are for the same individuals amplified
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with Mse+CCAA, which was used to generate a reliable genotype
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(mCCAAeACC171-175 marker on LG25).
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Figure S2
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extension. The bottom trace shows a region of the original Hha+GA trace with
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18 peaks, including a 222 bp peak that was selected for sequencing. The four
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traces above have alternative 3-base (GAN) extensions. The original peaks
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separate into the four groups, except for the peak indicated with the blue line,
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which is an overlapping peak in the +2 trace (size homoplasy), and splits into
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two peaks in the +3 profiles. The +3 peaks are higher (vertical scales are not
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identical) and more isolated.
Separation of a complex AFLP trace by selective primer
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Figure S3 Basic cytogenetic characteristics of Biston betularia. (a) DAPI-
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stained mitotic spermatogonial metaphase showing 2n = 62 chromosomes; (b)
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YOYO-1 stained spermatocyte complement showing n = 31 meiotic metaphase
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I bivalents (individual bivalents are arbitrarily numbered to facilitate their
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distinction); (c) DAPI-stained male pachytene complement showing n = 31
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meiotic bivalents (chromomere pattern is not seen due to the pretreatment in
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hypotonic solution); (d) DAPI-stained female pachytene complement (n = 31)
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showing chromomere patterns; note the WZ bivalent is easily identified from
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the DAPI-highlighted heterochromatic thread of the W chromosome; (e)
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Orcein-stained polyploid nucleus of the female Malpighian tubule cell showing
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a large spherical sex-chromatin body (arrow), representing multiple copies of
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the heterochromatic W chromosome; (f) orcein-stained polyploid nucleus of the
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male Malpighian tubule cell without sex chromatin. Scale bars indicate 5 μm in
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(a, b), 10 μm in (c, d), and 20 μm in (e, f).
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Figure S4 Gene order rearrangements between B. betularia and B. mori.
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Gene order rearrangements were detected between B. betularia and B. mori in
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five linkage groups. Two of these are shown in this figure, the others are
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included in Figure 3 (LG11 and LG29) and in Figure 4 (Z). The B. mori
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chromosomes are scaled according to scaffold sizes in SilkDB using estimated
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gap sizes, which differ slightly from the fixed gap sizes in Kaikobase.
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Figure S5 Reconstruction of Z chromosome rearrangements between
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Biston betularia and Bombyx mori. Hypothetical scheme of rearrangements,
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which could explain the different gene order that differentiated the Z
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chromosomes of Bombyx mori (left) and Biston betularia (right) from a common
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ancestor. Double-headed arrows indicate inversions, single-headed arrows
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transpositions; colour of arrows corresponds to colour of repositioned genes.
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For simplicity, unidirectional alterations from B. mori to B. betularia (from left to
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right) are illustrated; however, as the ancestral structure of the Z chromosome
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is unknown, reverse unidirectional alterations (from right to left) or bidirectional
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alterations from any intermediate structure are equally possible.
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Table S1 Blast results and primers for the mapped genes. Details of the
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genes included in the linkage map: gene identity, GenBank accession number,
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NCBI and SilkDB blast results and primers used to isolate and genotype the
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genes. The SilkDB blast results present the best blastx hit, unless tblastx
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produced a better hit that was not annotated. The tblastx hits have no Bombyx
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gene identifier.
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Table S2 Paternal segregation pattern of mapping family (‘16’) offspring.
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The alleles have been translated from SNP nucleotides, indel large/small, or
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AFLP present/absent into a binary 1 or 0 code representing the chromosomal
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origin of the allele. "md" stands for missing data. Conditional formatting is used
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to demonstrate the recombination breakpoints per individual (vertical
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orientation) by means of a green/white change. For example, individual 1 does
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not have any recombination over the full length of LG1, while individual 2
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recombined between 6-PGD and tpi.
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Table S3
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Bombyx mori). Gene names are listed in the first column with alternative
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identifiers or frequently used abbreviations in brackets. Methods used to
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confirm Z-linkage are abbreviated as: FISH (fluorescence in situ hybridization);
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South (Southern hybridization); LM (linkage mapping); Inh (hemizygous
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inheritance). References are numbered in square brackets and listed in full
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below the table; all B. betularia data originate from this study. Only confirmed
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Z-linked genes are given in O. nubilalis and only the two genes specifically
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mentioned in the text are included for P. xylostella since only uniref90 best hits
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are available for this species. All except two genes (31/33) are also Z-linked in
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B. mori. MYST histone acetyltransferase (BGIBMGA006995) is located on
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chromosome 17 in B. mori and the identity of Papilio spp. acid phosphatase is
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unclear; however no acid phosphatase homologues occur on the Z-
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chromosome scaffolds of B. mori.
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List of published lepidopteran Z-linked genes (excluding