The impact of sequencing depth and relatedness of the reference genome in population genomic studies: a case study with two caddisfly species (Trichoptera, Rhyacophilidae, Himalopsyche)

README <br> ##Repeatmodeler libraries: #Commands used: module load repeatmodeler/2.0 BuildDatabase -name hk1 -engine ncbi HK1_ge_500_ordered.fasta.masked &amp;&amp; RepeatModeler -engine ncbi -pa 8 -database hk1 BuildDatabase -name himjap -engine ncbi Him_jap_ge_500_ordered.fasta &amp;&amp; RepeatModeler -engine ncbi -pa 8 -database himjap BuildDatabase -name himjap -engine ncbi Him_HT1_ge_500_ordered.fasta &amp;&amp; RepeatModeler -engine ncbi -pa 8 -database himht1 <br> #Files generated: HK1_consensi.fa.classified - Custom repeat libraries of Himalospyche kuldschensis generated using RepeatModeler2 Him_jap1_consensi.fa.classified - Custom repeat libraries of Himalospyche japonica generated using RepeatModeler2 Him_HT1_consensi.fa.classified - Custom repeat libraries of Himalospyche tibetana generated using RepeatModeler2 <br> ##Repeatmasker results #Commands used: RepeatMasker -pa 6 -lib HK1_consensi.fa.classified -e ncbi -s -xsmall HK1_ge_500_ordered.fasta RepeatMasker -pa 6 -lib Him_jap1_consensi.fa.classified -dir ./himjap1 -e ncbi -s -xsmall Him_jap_ge_500_ordered.fasta RepeatMasker -pa 6 -lib Him_HT1_consensi.fa.classified -dir ./himjap1 -e ncbi -s -xsmall Him_HT1_ge_500_ordered.fasta <br> #Files generated: HK1_ge_500_ordered.fasta.masked - Masked assembly of Himalopsyche kuldschensis obtained from RepeatMasker 4.1.0 analysis Him_jap_ge_500_ordered.fasta.masked - Masked assembly of Himalopsyche japonica obtained from RepeatMasker 4.1.0 analysis Him_HT1_ge_500_ordered.fasta.masked - Masked assembly of Himalopsyche tibetana obtained from RepeatMasker 4.1.0 analysis HK1_ge_500_ordered.fasta.tbl - Annotated repeats in the Himalopsyche kuldschensis assembly obtained from RepeatMasker 4.1.0 analysis using custom repeat database generated using RepeatModeler2. Him_jap_ge_500_ordered.fasta.tbl - Annotated repeats in the Himalospyche japonica assembly obtained from RepeatMasker 4.1.0 analysis using custom repeat database generated using RepeatModeler2. Him_HT1_ge_500_ordered.fasta.tbl - Annotated repeats in the Himalopsyche tibetana assembly obtained from RepeatMasker 4.1.0 analysis using custom repeat database generated using RepeatModeler2. <br> ##Annotations using GEMOMA #Input files used from previous annotated genomes (see https://doi.org/10.1093/gigascience/giac011) himphry.gff - Himalopsyche phryganeae annotation gff file used for GEMOME annotation himphry.fasta -Himalopsyche phryganeae annotation fasta file used for GEMOME annotation rhybru.gff - Rhyacophila brunneae annotation gff file used for GEMOME annotation rhybru.fasta - Rhyacophila brunneae annotation fasta file used for GEMOME annotation <br> #Commands used conda activate gemoma GeMoMa -Xmx50G GeMoMaPipeline threads=$SLURM_NPROCS outdir=himhk1 GeMoMa.Score=ReAlign AnnotationFinalizer.r=NO o=true t=HK1_ge_500_ordered.fasta.masked s=own i=himphry a=himphry.gff g=himphry.fasta s=own i=rhybru a=rhybru.gff g=rhybru.fasta GeMoMa -Xmx50G GeMoMaPipeline threads=$SLURM_NPROCS outdir=himjap1 GeMoMa.Score=ReAlign AnnotationFinalizer.r=NO o=true t=Him_jap_ge_500_ordered.fasta.masked s=own i=himphry a=himphry.gff g=himphry.fasta s=own i=rhybru a=rhybru.gff g=rhybru.fasta GeMoMa -Xmx50G GeMoMaPipeline threads=$SLURM_NPROCS outdir=himht1 GeMoMa.Score=ReAlign AnnotationFinalizer.r=NO o=true t=Him_HT1_ge_500_ordered.fasta.masked s=own i=himphry a=himphry.gff g=himphry.fasta s=own i=rhybru a=rhybru.gff g=rhybru.fasta <br> #Files generated: HimHK1predicted_proteins.fasta - Predicted proteins from GEMOMA annotation of Himalopsyche kuldschensis Himjappredicted_proteins.fasta - Predicted proteins from GEMOMA annotation of Himalopsyche japonica Him_HT1predicted_proteins.fasta - Predicted proteins from GEMOMA annotation of Himalopsyche tibetana <br> Him_HT1final_annotation.gff - Gff file from GEMOMA annotation of Himalopsyche tibetana HimHK1final_annotation.gff - Gff file from GEMOMA annotation of Himalopsyche kuldschensis Himjap_annotation.gff - Gff file from GEMOMA annotation of Himalopsyche japonica <br> ##BUSCOS #commands used module load busco/4.1.4 busco -i genome HK1_ge_500_ordered.fasta-l endopterygota -o HK1 -m genome --long busco -i genome Him_HT1_ge_500_ordered -l endopterygota -o Him_HT1 -m genome --long busco -i genome Him_jap_ge_500_ordered.fasta -l endopterygota -o Him_jap1 -m genome --long <br> #Files generated HK1_single_buscos.faa - BUSCO amino acids HK1_single_buscos.fna - BUSCO genes Him_phry1_single_buscos.faa - BUSCO amino acids Him_phry1_single_buscos.fna - BUSCO genes Him_HT1_single_buscos.faa - BUSCO amino acids Him_HT1_single_buscos.fna - BUSCO genes Him_jap1_single_buscos.faa - BUSCO amino acids Him_jap1_single_buscos.fna - BUSCO genes <br> #BUSCOS from previous studies (see https://doi.org/10.1093/gigascience/giac011) Rhy_bru_single_buscos.faa - BUSCO amino acids Rhy_bru_single_buscos.fna - BUSCO genes G1_single_buscos.faa G1_single_buscos.fna <br> #Proteins were blasted against ncbi nr database #command: blastp -query ../fa/${P} -db blast/nr/nr -outfmt 5 -max_target_seqs 10 -evalue 1e-4 -out ../xml/${P}.xml #Results:Him_jap_blastp_all.xml - Blastp results of Himalopsyche japonica Him_HT1_blastp_all.xml - Blastp results of Himalopsyche tibetana Him_HK1_blastp_all.xml - Blastp results of Himalopsyche kuldschensis <br> #Rhyacophila brunneae reference genome used for SNP calling in this study Rhyacophila_bru_ge_500_ordered - Rhyacohila brunnea genome assembly used in this study