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    MUC7 belongs to the secretory calcium-binding phosphoprotein (SCPP) family, which likely evolved after the divergence of bony and cartilaginous fish6. Other than its syntenic relationship with the SCPP gene family and the functional similarity to other mucins, the evolut">6<">6. Other than its syntenic relationship with the SCPP gene family and the functional similarity to other mucins, the evoluti">6"">6<">66">">6<">66">">6<">66">">6<">66">">6<">6. Other than its syntenic relationship with the SCPP gene fami">6<">6. Other than its syntenic relationship">6">">6<">6. Other than its syntenic relationship with the SCPP gene family and the functional similarity to ot">6"">6<">66">">6<">6. Other than its syntenic relationship with the SCPP gene">6<">6. Other than its syntenic relationship with the SCPP gene family and the functional similarity to other mucins, the evolution of MUC7">6<">6. Other than its syntenic relationship with the SCPP ge">6<">66. Other than its synt">6. Other than its syntenic relationship with t">66. Other than its syntenic ">6<">6<">6. Other than its syntenic relationship with the SCPP gene family">66. Other than rst-last">rst-lastrst-last">MUC7 is evolutionarily related to SCPP gene family througrst-lrsrst-rst-last">MUC7 is evolutionarily related to SCPP gerst-lastrst-last">MUC7 is evolutionarily related to SCPP gene family through gene duplicationMUC7 is evolutionarrst-lastrst-last">MUC7 is evolutionarily related to SCPP gene family through gene duplicatiorst-lastrst-last">MUC7 is evolutionarily related trst-lrsrst-rst-last">MUC7 is evolutionarily related to SCPP gene family through gene duplrst-last"rst-last">MUC7 rst-lrsrst-rst-last">MUC7 is evolutionarily related to SCPP gene frst-lastrst-last">MUC7 is evorst-lrsrst-rst-last">MUC7 is evolutionarily related to SCPP gene family through gene duplicationMUC7 is evolutionarily relaterst-last"rst-last">MUC7 is evolutionarily related to SCPP genrst-lastrst-last">MUC7 is evolutionarily related to SCPP gene family rst-last">MUrst-lastrst-last">MUC7 is evolutionarily related to SCPP gene family through gene duplicationd=d="bd="b15. It is therefore possible that this gene has evolved convergently, filling the adaptive niche for a salivary-specific small mucin in rodents after lineage specific deletion of . It is . It is therefore possible that this gene has evolved convergently, filling the adaptive niche for a salivary-specific small mucin. It is t. It is therefore possible that this gene ha. It is . It is therefore possible that this gene has evolved convergently, filling the adaptive niche for a salivary-specific small mucin in rodents after lineage specific deletion of MUC7. There are some caveats in our analyses. First, I. It is . It is therefore possible that this gene has evolved convergently, filling the adaptive niche for a salivary-specific small mucin in rodents after lineage specific deletion of . It is t. It is therefore possible that this gene has evolved convergently, filling the adaptive niche for a salivary. It is . It is therefore possible that this gene has evolved convergently, filling the adaptive niche for a salivary-specific small m. It is . It is therefore possible that this gene has e. It. It i. It is therefore possible th. It is therefore . It is . It is therefore possible that this gene has evolved converg. It . It is therefore possible that this gene has evolved co. It is . It is therefore possible that this gene has evolved convergently, filling the adaptive niche for a salivary-specific small mucin in rodents after lineage specific deletion of . . It. It i. It i. . It. It is therefore possible that this gene has evolved convergently, filling the adaptiv repeats repe rep repeats6, where T and S clusters provide targets for O-gl repe r rep repeatsMUC1, MUng MUCng MUng MUC1, MUC4, and MUC6,ngng ngng ngng MUC1, MUC4, and MUC6, have intact PTS-repeats in mouseng ngng MUC1, MUC4, and MUC6, have intact PTS-repeats in mousengng ng MUC1, MUC4, and MUC6, have intact PTS-repeats in mouse33,SCPPem>SCPP gene fem>SCPP gem>SCPP gene family (e.g., MUC7 T and S percentage isem>SCPPSCPP gene family (e.g., MUC7 T and S percentage is significantlyem>SCPP geem>SCPP gene family (e.g., Mem>SCem>SCPP gene family (e.g., MUC7 T and S percentage is significem>SCPPSCPP gene family (e.g., MUCem>SCPPSCPP gene family (e.g., MUC7 T and S percentem>SCPPSCPP gene family (e.g., MUCem>SCPPSCPP gene famem>SCPPSCPP gene family (e.g., MUC7 T and S percentage is sigem>SCem>SCPP gene family (e.g., MUC7 T and S em>SCPPSCPP gene family (e.g., MUC7 T and S percentage isem>Sem>SCPem>SCPP gene family (SCPP gene family (e.em>SCPPSCPP gene family (e.g., MUC7 T anem>SCem>SCPP gene family (e.g., Mem>SCPPSCPP gene family (e.g., MUC7 T and S percentage is sigem>SCPPSCPP gene family (e.g., MUC7 em>SCemem>Sem>SCPP gene family (e.g., MUC7 T and S percentage is significantly higher em>SCPPSCPP gene family (e.g., MUC7 T and S percentage is significantly higher than the adjacent PROL1 among mammals, P-value = 1.123 × 10−9, one-tailed Student’s t-test). We also coem>SCeem>Sem>SCPem>SCPemem>Sem>SCPP gene family (e.g., MUC7 T anem>SCPPSCPP gene family (e.g., MUC7 T and S percentaem>SCPPSCPP gene family (e.g., MUC7 T and S percentem>SCp"p" ip" id="_p" id="_p" id="__tag_553522946">38 (Table S1). Briefly, we compared the expression in minor salivary gland (the only salivarynominal P-value for saliva-specific expression for all genes across the genome. This analysis showed there is an unexpectedly high number of genes with saliva-specific expression adjacent to nominal nominal P-value for saliva-specific expression for all genes across the genome. This analysis showed there is an unexpectedly high numbernominal P-value nominal nominal P-valuenominalnominal P-value for saliva-specific expression for all genominal nominal P-value for saliva-specific expression for all genes across the genome. This analysis showed there is an unexpectedly high number of genes with saliva-snominal Pnominnominominal P-valunominal P-value for salivanominal P-value for saliva-specific expression for all genes across the genome. This analFigure 2nominominal P-value for saliva-specific expnominnominal nominominanominal P-value fnominnominanominal P-value fnominal P-vanominal nominal P-value for saliva-specific expression for all genes across the genome. This analysis showed therenominal Pnominalnominanominanominanominanominal P-value for saliva-spnominal nominal P-value for nominal P-value for saliva-specific expression for all genes across the genome. This analysis showed there inominnominal P-value for saliva-specific expression for all genes across the genome. This analysis showed there is an unexpectedly high number of genes with saliva-specific expression adjacent to MUC7 when compared to the rest of the genome (Wilcoxon rank-sum test, nominal P-valnomin<4, which characterized su4, which characterized subexonic repeat content in 4, which characterized subexonic repeat content in dozens of different eukaryotic genomes. According to their analysis, MUC7 PTS-repeats were in the upper 0.4% and 17% for subexonic repeat cross-species divergence in nucleotide and copy number divergence, respectively (<Figure 3iv civ class="fig iconblock ten_col whole_riv cliv classiv civ claiv class="fig icoiv cliv claiv class="fig icoiv class="fig iconbliv classiv class="fig iconblock ten_col whole_rhythm iv class=iv clasiv claiv claiv claiv class="fig iconblock ten_col whole_rhythm clearfix" id="f3" co-legend-rid="lgiv cliv class="fig iconblock ten_col whole_rhythm clearfix" id="f3" co-legend-rid="lgnd_f3">iv class="figiv clasiv claiv classiv class="fig iconblock ten_col whole_rhythm clearfix" id="f3" co-legend-ridiv claiv class="fig iconblock ten_col whole_rhythm cleiv claiv class="fig iconblock ten_col whole_rhythm clearfix" id="f3" co-legend-rid="lgnd_f3">e of clusterie of cle of clustering of T and S content than expected by chance. Indeed, the number of nonsynonymous differences from the pairwise comparison of individual repe of ce of clustering of T and S contente of clusterie of cle of clustering of T and S content than expected by chance. Indeed, the number of nonsynonymous differences from the paire ofe of clustering of T and S content than expected by chance. Indeed, the number of nonsynonymous differences from the pairwise comparison of individual repeats within and between species strongly correlate with the nue of e e ofe of clustering of T and S content than expected by chance. Indeed, the number of nonsynonymous differences from the pairwise comparison of individual repeats within and between species strongly correlate wie of cluse of clustering of T and S content than expected by chance. Indeed, the number of nonsynone of e e ofe of clustering of T and S content than expected by chance. Indeed, the number of nonsynonymous differences from the pairwise comparison of individual repeats within and between species strongly correlate with the number of synonye of e e ofe of clustering of T and S conmong primates (mong primmong primates (Figure S6). Overall, our findings show that both the number of T and S amino acids as well as their context within individual PTS repeat domains remain highly conserved. This points to O-glymongmong pmong primates (To further understand the adaptive forces that have shaped

    To further understand the adaptive forces that have shaped MUC7 PTS-repeat copy number variation

    To further unders

    To further understand the adaptive forces that have shaped MUC7 PTS-repeat copy number variation in primates, we documented copy number variation of MUC7 PTS-repeats within and across primates, using polymerase chain reaction (PCR)-based genotyping across 10 non-human primate species (Fig. 4A, To fur

    To further understand the adaptive forces that have shaped MUC7 PTS-repeat copy number variation in primates, we documented copy number variation of MUC7 PTS-repeats within and across primates, using polymerase chain reaction (PCR)-based genotyp

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    gegenigenic pgenigenic pressures, as suggested by the Red Queen hypothesis53.

    Our results draw an initial picture of the evolution of MUC7 at three levels corresponding to three functional roles of the protein. At the first level, the signal peptide has evolved under negative selection, maintaining the extracellular activity of the protein. At the second level, the histatin-like domain has evolved under directional selection in the primate lineage, possibly to counteract a particular fungal pressure. At the third level, the copy number of PTgenic prgenicgenicgegenigenic genic gegenigenic pgenigenic pressures, as suggested bgenic prgenic pressures, as suggested by the Red Queen hypothesis53.

    Our results draw an initial picture genicggenigenic pressures, as suggested by the Red Queen hypothesis53.

    Our results draw an initial picture of the evolution of MUC7 at thgenicgegenigenic genic gegenigenic pressures, as suggested by the Red Queen hypothesisgegenigenic pressures, as suggested by the Red Queen hypothesis53e e vae variations. Therefore, directional positive selection can le vare e vae variationse variate variations. Therefore, directional positive selection can lead to rapid increase or contraction of subexonic repeats in a species-specific manner. Examples of such rapid evolution of copy number variation of subexonic repeats in humans were demonstrated for the dopamine receptor gene a als also affect the copy number variable cysteine-rich domains (CYS), which are functionally important in some mu also af also affect the copy number variable cysteine-rich domains (CYS), which are functionally als also also affect the copy number varia also affect the copy number variable cysteine-rich domain also also affect the copy number variable cysteine-rich domains (CYS), which are functionally important in some mucin genes but apparently absent in MUC7 also af also affect the copy number variable cysteine-rich domains (CYS), which are functiona also af also affect the copy number variable cysteine-rich domains (CYS), which are functionally important in some mucin genes but apparently absent in MUC7 also affect th also als also affect the copy number v also affect the c also also affect the copy number variable cysteine-rich domains (CYS), which are functionally important in some mucin genes but apparently absent in MUC7 also af.a>...

    Bioinformatic and evolutionary analysis

    To determine the presence of subexonic repeats across mammalian MUC7 orthologs, we used (ia>.

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    .titip"tip" id="__tag_553522932">64 under JTT with freq. (+F) model, and gamma distributed with invariant sites (G+I)tip" id="tip" itip"tip" itip" id="__tag_553522932">646tip" tip" id="__tag_553522932">64 under JTT with freq. (+F) model, and gamma distributed with invariant sites (G+I) with 500 bootstrap replicates (Figure S7).

    Copy number simulations

    We simulated the copy number changes for Great apes (Human, Chimpanzee, Gorilla and Orangutan) under different copy number gain-loss rate (0.5/1.0/1.5/2.0 copies per million year). Based on the species phylogeny of these four great ape species, we assumed that the original copy number state for the common ancestor of Great apes was 5 copierom Gorilla and they started the copy number gain and loss simulation separately. The same simulation continues to 5 million years ago that Human and Chimpanzee separated from each other, and start their copy number gain/loss process independently until present. We simulated this process 1,000 times for 4 different copy-number-change rates (0.5/1.0/1.5/2.0 copies per million year), and for each simulation, calculated the variation of final state of simulated copy numbers for Human, Chimpanzee, Gorilla and Orangutan. The observed copy number state in present is Human 5 or 6 copies, Chimpanzee 5 copies, Gorilla 4 or 5 copies, and Orangutan 6 or 7 copies. The variations of observed copy number state in present are significantly less than variations simulated under neutrality (wilcoxon rank-sum test, P-value < 0.01).rom rom Gorilla and they started the copy number gain and loss simulation separaterom Gorilla and they started the copy number gain and loss simulation seprom Gorilla and they started the copy number gain and loss simulation seprom Grom Gorilla and they started the copy number gain and loss simulation separately. The same simulation continues to 5 million years ago that Human and Chimpanzrom Gorom Gorilla and they started the rom Grom Gorirom Gorom Gorilla and they starrom Grom Gorilla and they started the copy number grom Gorom Gorilla and they started the copy number gain and loss simulation seprom Grom Gorilla and they started the copy number gain and loss simulation separately. The same simulation continues to 5 million years ago that Human and Chimpanzee sepe%7CBody&TO=Extee%7CBody&TO=External%7CLink%7CURI&rendering-type=normal" target="pmc_ext">http://www.ucsc.edu/)e%7CBoe%7CBody&TO=External%7CLink%7CURI&rendering-type%7CBoe%7CBody&TO=External%7CLink%7CURI&re%7CBoe%7CBody&TO=External%7CLink%7CURI&rendering-type=normal" target="pmc_ext">http://www.ucsc.edu/) and used it as e%7CBoe%7CBe%7CBe%e%7Ce%7CBody&TO=External%7CLink%7CURI&rendering-tye%7CBoe%7CBody&TO=External%7CLink%7CURI&rendering-type=normal" target="pmc_ext">http://www.ucsc.edu/) and used it as a reference tree for the simulations. We assumed that the effective population size (Ne) is constant for each primate species and that Ne for Chimpanzees is twice the human Ne. Given a reference tree, and population parameters, CoMuS generates polymorphic samples similar to Hudson’s mspprimprimatprimatprprimprimateprimprimatprimates. It is important to nprimates. It is important to note that our results regaprimaprimates. It is important to note that our results regarding the adaptive constraintprimaprprimprimates. It is important to note that our results regarding the adaptive constraints on the PTS-repeats are partially dependent on the mutation rate of subexonic repeats, which have been shown to vary widely4,65.

    Analysis for gene with salivary-specific expression

    The dataset from gene-expression database, GTExprimates. It isprimateprimatprimprimatprimates. It is important to note that primatesprimaprimates. It is important to note that our results regarding the adaptive constraints on the PTS-repeats are partially primaprprimprimates. It is important to note that our te model A (allowing ω values to vary both among site and across branches), and compared with null model with fix ω = 1. Each branch in the phylogeny was tested separately. The difference of the -lnL values were compared by Chi-square test, and alpha-value = 0.05 (if P-value < 0.05 we reject the null hypothesis). The data can be found in te modelte mote mte modte modte model A (allowing ω valute model A (allowing ω values to vary both among site and across bte mote model A (allowing ω valueste model A (allowing ω vte model A (allowite model te model A (allowing ω values to vary both ate model A (ate modte model te model A (allowing ω values to vary bote mte modte model A (allowing ωte mte model A (allowing ω values to vary both among site and acrte mote model A (allowing �te model A (allowing ω valueste model A (allowte model A (allowing ω valte model te model A (allowing ω vate model A (allowinte mte model A (allote modte modte modte model A (allowing ω valueste model A (allowte model A (allowing ω te model te model A (allowing ω vate model A (allowinte mte model A (allte modte modte modte model A (allowing ω valueste model A (allowte model A (allowing ω te model te model A (allowing ω vate model A (allowinte mte model A (allte modte modte modte model A (allowing ω valueste model A (allowte model A (allowing ω te model te model A (allowing ω vate model A (allowinte mte model A (allote modte modte modte model A (allowing ω valueste model A (allowte model A (allowing Table S4: Table S4 Table S4:

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  • human huma human human huma human carcin human carcinoma-associated transmembrane mucins, MUC1, MUC4 AND MUC16. human huma human human huma human carcin human carcinoma-associated transmembrane mucins, MUC1, MUC4 AND MUC16. Gene. Gene human carcinoma huma human ca human carcinoma-associated trans human huma human human huma human carcin human carcinoma-associated transmembrane mucins, MUC1, MUC4 AN human carcinoma-associated transmembrane mucins, MUC1, MUC4 AND MUC16. Gene 100SA SA SA 1SA 100, 4060&#xSA 100, 4060–4065 (2003). [PMC free article] SA 100SA 100 1SA 100, 4060SA 100, 4060–4065 (2003)SASA 100 1SA SA SA 1SA 100, 4060–4065 (2003). 100, 4060–4065 (2003). 100, SA 4103–41 4103 4103� 4103–4117 (2002). 4103& 4103 4103&# 4103&# 4103 4103– 4103–4117 (2002). [[[PMC free article] [, 25362–25370 (1999)274, 25362–253d">[d">[[[[[[[[[[[d">[[[[d">[[[[[[[[[[[[[[[[[[[[[[ ref pmc">[[ ref p ref ref pm ref pm ref ref pmc">[[PMC free article] [[ ref p ref ref pm ref pm ref ref pmc">[[PMC free article] ref pmc" ref pmc">[[[[[, 433–436 (2003). pan>, 433–436 (2003). pan>, pan>,pan>, 4pan>, 4pan>,pan>, 433�pan>, 433–436 (2003). [, 43pan>, 433–436 (2pan>, 433–436 (2003). , 433–436 (2003). pan>, 433ȁpan>,pan>, 433pan>, 433–436 (2003). pan>, pan>,pan>, 4pan>, 4pan>,pan>, 433�pan>, 433–436 (2003). [[, 433pan>, 433–436 (2003). pan>, 433ȁpan>,pan>, 433pan>, 433–436 (2003). pan>, pan>,pan>, 4pan>, 4pan>,pan>, 433�pan>, 433–436 (2003). [, 433pan>, 433–436 (2003). , 43pan>, 433–436 (2pan>, 433–436 (2003). , 433–436 (2003). pan>, 433ȁpan>,pan>, 433pan>, 433–p ref pubmed">[p ref p refp ref pp ref pp refp ref pubmed"p ref pubmed">[[[[[[[

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