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, Remarks: Deposited on IST Austria data repository
, Publicly available reference genomes and annotations
, All data were obtained at the WormBase Parasite database (https://parasite.wormbase.org/index.html)
, , p.16
, Genomic sequences: schistosoma_mansoni.PRJEA36577.WBPS9.genomic, p.17
, Annotation: schistosoma_mansoni, p.20
, Genomic sequences: schistosoma_japonicum.PRJEA34885.WBPS9.genomic.fa 21
, Annotation: schistosoma_japonicum
, Genomic sequences: schistosoma_haematobium.PRJNA78265.WBPS9.genomic, p.25
, Annotation: schistosoma_haematobium
, Orthology
, The same pipeline was applied to S. japonicum and S. haematobium. Example is shown here for the S
, Mapping of S. mansoni genes on the S. japonicum genome 33
, mansoni gene sequences were mapped to the S. japonicum genome using Blat (79) with a translated query and 34 database
, CDS_transcripts.fa The final coverage values are part of the Figure 1-source data 2 (S. mansoni), Figure 1-source data 3, p.36
, Figure 1-source data 4 (S. japonicum)
, Determination of Z-specific maximum coverage threshold for S. mansoni reference species 40
, The maximum value of log2(female:male) coverage for Z-specific assignment in S. mansoni was determined using the R 41 script Script5_Genomics_mansoni (Part I) with the input file InputFile1_Smansoni_SoapCov_By10kb_ForR, which contains 42 the SoapCov outputs for male (ERR562989_Depth) and female, 562990.
, shown in Appendix 1-figure 1): 45 A) When plotted, the log2(female:male) ratio of coverage shows a bimodal distribution. The highest peak is 46 distributed around 0 and corresponds to the windows that are localized on the known autosomes (Chromosomes 47 1 to 7) of the current version of the genome assembly, This involved the following steps PRJEA36577)
, female:male)=-0.26. 50 C) We use this value to exclude the pseudoautosomal windows (plotted in grey) of the ZW linkage group and 51 consider only the non-pseudoautosomal windows (plotted in orange) for the next step. 52 coverage value is not consistent with the adjacent windows: 5 consecutive 10kb windows with consistent 58 coverage were required to be considered either pseudoautosomal or Z-specific. For instance, yellow bands on the 59 graph highlight regions of more than one window but less than five, 48 B) If we consider only the unimodal distribution of autosomal window coverage They are tagged as " Excluded " in Figure 1- 60 source data 2, as are the two adjacent windows, pp.49-51
, We then applied this threshold value to all the genome, considering only scaffolds longer than 50kb for classification. The 63 final classification of each scaffold (as " Z " or " Autosome " ) is presented in Figure 1-source data 2. Used R script is, p.64
, Part II); and corresponding input file is, pp.1-10
, Autosome " depending on the window assignment. When a gene overlapped 66 with an excluded window, it was excluded as well, order to exclude these genes, the following script was used, p.67
, using as input a 3-column file (Chromosome ID, First base of window to exclude, Last base of 68 window to exclude)
, Determination of Z-specific maximum coverage threshold for S. japonicum
, female:male) coverage for Z-specific assignment in S. japonicum was determined using the R 72 script Script7_Genomics_japonicum (Part I) with the input file InputFile3_Sjaponicum_SoapCov_Bestloc_ForR, which 73 contains the SoapCov outputs for male (Depth_40640) and female (ERR562990_Depth), and the assignment to S, p.2
, shown in Appendix 1-figure 2): 77 A) When plotted, the log2(female:male) ratio of coverage shows a bimodal distribution. 78 B) As S. japonicum genome is only assembled at the scaffold level, This involved the following steps we used the log2, 2009.
, coverage of the scaffold mapping to S. mansoni autosomes to get the distribution of autosomal log2(female:male)
, female:male)=-0.4. 82 D) We use this value to classify scaffolds that mapped to the S. mansoni ZW linkage group as Z-specific or 83 pseudoautosomal (grey in Appendix 1-figure 2, panel D), and consider only the non-pseudoautosomal scaffolds 84 (plotted in orange) for the next step. 85 E) The non-pseudoautosomal scaffold (InputFile4_Sjaponicum_1pr100) coverage displays an unimodal distribution, 86 and the 95 th percentile has a value of log2(female:male)=-0.84. 87 F) When visualizing the log2(female:male) along the ZW linkage group, it appears that no single threshold value can 88 finely discriminate Z-specific and pseudoautosomal scaffolds. So we use the log2(female:male)=-0.84 threshold as 89 maximum value for Z-specific regions, 80 C) If we consider only the unimodal distribution of the autosome-assigned scaffold coverage, the 1 st percentile has a 81 log2 orange), and log2(female:male)=-0.4 threshold as minimum value for 90 pseudoautosomal regions Scaffolds with log2(female:male) between these two values were classified as 91 " ambiguous
, We then applied this threshold value to all the genome. Used R script is : Script7_Genomics_japonicum (Part II); and 94 corresponding input file is, pp.3-5
, Autosome " or " Ambiguous " assignment is shown in Figure 1-source data 4
, Determination of Z-specific maximum coverage threshold for S. haematobium
, Female) coverage for Z-specific assignment in S. haematobium was determined using the R 99 script Script8_Genomics_haematobium (Part I) with the input file InputFile5_Shaematobium_SoapCov_Bestloc_ForR, which 00 contains the SoapCov outputs for two female libraries, Depth_ERR037800, Depth_ERR036251), and the assignment to S. 01 mansoni chromosomes, p.2
, shown in Appendix 1-figure 3): 04 A) When plotted, the log2(Female) coverage shows a bimodal distribution. 05 B) As the S. haematobium genome is only assembled at the scaffold level (Young et al. 2012), we used the 06 log2(Female) coverage of the scaffold mapping to S, This involved the following steps
, 08 C) If we consider only the unimodal distribution of the autosome-assigned scaffold coverage, the 5 th percentile has a 09 log2(Female)=4
, 10 D) We use this value to classify scaffolds that mapped to the S. mansoni ZW linkage group as Z-specific or 11 pseudoautosomal (grey in Appendix 1-figure 3, panel D), and consider only the non-pseudoautosomal scaffolds 12 (plotted in orange) for the next step. 13 E) The non-pseudoautosomal scaffold, InputFile6_Shaematobium_5pr100) coverage displays a unimodal 14 distribution, and the 99 th percentile as a value log2(Female)=4.6
, Female) along the ZW linkage group, it appears no single threshold value cannot finely 16 discriminate between Z-specific and pseudoautosomal scaffolds. So we used the log2(Female)=4.6 threshold as We then applied this threshold value to all the genome. Used R script is: Script8_Genomics_haematobium (Part II); and 22 corresponding input file is, 15 G) When visualizing log2, pp.5-7
, Autosome " or " Ambiguous " assignment is shown in Figure 1-source data 3
, Definition of evolutionary strata 26
, Genes that were Z-specific in both S. mansoni and S. japonicum were assigned to stratum S0. Genes that were Z-specific 27 only in S. mansoni were assigned to stratum S1mans, and genes that were Z-specific in S
, The exhaustive classification is defined by the 30 comparison of " Z " or " Autosome " assignment, based on coverage (see 2.4 -2.6), between S. mansoni and S. japonicum 31 species. The stringent classification is a subset of the exhaustive classification: it only contains genes localized on the ZW 32 linkage map in S. mansoni and with a best location on the Z or PSA region in S. japonicum (see Figure 1-source data 1), This assignment was performed separately for two classifications
, Transcriptomics
, Raw read processing 38 Reads were first trimmed with Trimmomatic (v0, 81)), using the following commands, pp.39-40
, READS=~pathwaytoreads
,
, fastq`; do 47 echo ${i} 48 module load java 49 java -jar ~/tools/Trimmomatic-0, p.3010
, 51 HEADCROP:12 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN, p.36
, 52 done 53 54 (ii) S. japonicum
, READS=~pathwaytoreads
,
, fastq`; do 61 echo ${i} 62 module load java 63 java -jar ~/tools/Trimmomatic-0, p.3010
, 65 HEADCROP:12 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN, p.36
, Read mapping on reference genome 69 Reads were mapped to their respective reference genomes with TopHat2 (83), an alignment program for RNA-seq reads 70 which takes splice junctions into account
,
,
, Build the indexed genome for Bowtie2
, READS=~pathwaytoreads 58 OUF=~, p.59
, LIST=Input text file containing the library_ID and located in OUF
, cd ${READS} 62 63 while read i; do 64 mkdir ${OUF}
, {i} -b 100 --fr-stranded ${READS}/${i}_forward ${READS}
, Comparative analysis of gene expression 72
, We perform all the expression analyses in R (Script9_Transcriptomics) with the input files (i) InputFile7_Transcriptomics1 73 corresponding to the newly identified one-to-one orthologs (see 1.2); and (ii)
, In adults, a correlation analysis revealed an inconsistency between replicates, corresponding to the S. mansoni female and 77 male adults: ERR506076 and ERR506082. The corresponding heatmaps are shown in Appendix 1-figure 4, These two 78 libraries were excluded from further analyses
, Tables resulting from the Loess normalization are InputFile8_SuperTableNormalized_Transcriptomics1_RPKM, p.81
, InputFile9_SuperTableNormalized_Transcriptomics1_TPM, and 83 InputFile11_SuperTableNormalized_Transcriptomics2_RPKM
, They can be used directly in the script Script9_Transcriptomics at the step C
, Number of Protein-Protein Interactions (PPIs), vol.87
, The full set of known PPIs for S. mansoni was downloaded from StringDB: 88 https
, We kept only interactions supported by experimental evidence or text mining
, | awk '{print $1, $2}' | 93 perl -pi -e 's/6183\.//gi' | perl -pi -e 's/__mRNA//gi' | perl -pi -e 's/\
, We cleaned the coverage location, so that "Not analysed (Scaffold <40Kb)" was replaced by NA
, cat InputFile14_PPIs_woNA | perl -pi -e 's/Not analysed \(Scaffold \< 40kb\, pp.99-113
, Then counted the number of interactions present for each gene
, Output: 5 last columns of " InputFile8-2_SuperTableNormalized_LoessOnAll_Transcriptomics1_RPKM
, Proteomics vs microarrays correlation
, We performed all the expression analyses in R (Script10_Proteomics_Microarrays) with the input files (i), p.12
, InputFile12_Proteomics1_Microarrays for which a low value was imputed to undetected proteins*; and (ii)