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. Author manuscript; available in PMC: 2022 May 10.
Published in final edited form as: Curr Biol. 2021 Mar 2;31(9):1836–1849.e12. doi: 10.1016/j.cub.2021.01.104
REAGENT or RESOURCE SOURCE IDENTIFIER
Biological Samples
Hormaphis cornu This study N/A, Methods S1
Hormaphis hamamelidis This study N/A, Methods S1
Hamamelis virginiana This study N/A, Methods S1
Chemicals
Calcofluor White Sigma-Aldrich F3543
Congo Red Sigma-Aldrich C6767
Escin Sigma-Aldrich E1378
Collagenase/Dispase Roche 10269638001
Hyaluronidase Sigma-Aldrich H3884
Methyl salicylate Sigma-Aldrich M6752
Phenol:Chloroform:Isoamyl alcohol Thermo Fisher AM9730
Proteinase K Sigma-Aldrich 03115887001
RNasin® Ribonuclease Inhibitor Lucigen 30281
Hexadecyltrimethylammonium bromide Sigma-Aldrich 52365
Polyvinylpyrrolidone Sigma-Aldrich PVP40
β-mercaptoethanol Sigma-Aldrich M6250
EDTA Sigma-Aldrich 324506
Malvidin 3,5-diglucoside chloride Sigma-Aldrich PHL89727
Peonidin-3,5-diglucoside chloride Carbosynth FP65437
Critical Commercial Assays
Zymo ZR-96 Quick gDNA kit Zymo Research D3012
Nextera XT DNA Library Preparation Kit Illumina FC-131–1096
Quick-RNA Plant Miniprep Kit Zymo Research R2024
PicoPure RNA Isolation Kit Thermo Fisher KIT0204
MyBaits Arbor Bioscience
Deposited Data
Raw and analyzed data This paper Methods S1A–J
Oligonucleotides
WGB library sequencing primers
WGB_RTr1:TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN
WGB_PCRr1:TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
WGB_PCRr2:GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
WGB_TSOr2:/5Biosg/GTCTCGTGGGCTCGGAGATGTGTATAAGAGACArGrGrG		 84 IDT, Methods S1K
H. cornu genotyping qPCR probes
gwas-1
VIC: CTTTTATCGAGGGTCAATT
FAM: TCTTTTATCGAGAGTCAATT
context_sequence: GCTTCTAGGTTAATCTTTTATCGAG[G/A]GTCAATTCTAAGTATTTAACAGTGC
FWD: TGGATCTTATGAGCTGCTTCTAGGT
VIC: CCTATACCACCATCTGCACTGTTAA
gwas-7
VIC: TTCCTATCTGATGGACCTAA
FAM: TCCTATCTGATGAACCTAA
context_sequence: TTCGCTTAGTCATTCCTATCTGATG[G/A]ACCTAATGGTATATCGGTTTGCTGT
FWD:CCATCTCCTTGATTCGCTTAGTCA
REV: ATGGTGACAATTATACAAACAGCAAACC
gwas-8
VIC: ACGCTTTATTTTAAAATATT
FAM: CGCTTTATTTTACAATATT
context_sequence: TTTGTAAAGTATACGCTTTATTTTA[A/C]AATATTTAATTTTTCATTCAAAATA
FWD:TGTATACTATAAAAGACTAAAAGATAAAAATGTTTGGTTT
REV: TGGAAAACGTTATGTTCTAGTTTATTTTGAATGAAA
gwas-9
VIC: AACATGTACCAAATTTAA
FAM: AACATGTACCTAATTTAA
context sequence: TATGACCAATATCCGAACATGTACC[A/T]AATTTAAACAACTAAACATAAATAT
FWD:CCTAAAAATTTTGAAAGGTATGACCAATATCCG
REV: AAAATTTCGGAAATCCGTTGTCACAA
gwas-other
VIC: ACACATTCTCTTTTTTTC
FAM: ACACATTCTTATTTTTTC
context_sequence: TTAGCTATGGCTTGGTGGAAAAAA[AG/TA]AGAATGTGTGTATNCGAGGGAAAAG
FWD: ACAGGAGTAAGAAGTCATCCATTAGCT
REV: CGACGTCATTTAAACAGGAGATGGT		 This paper Thermo Fisher, Methods S1L
H. cornu amplicon sequencing primers This paper IDT, Methods S1M
Software and Algorithms
FIJI 53 https://imagej.net/Fiji
Chicago and HiC genome scaffolding Dovetail Genomics https://dovetailgenomics.com/ga_tech_overview/
Supernova version 2.1.1 54 https://support.10xgenomics.com/de-novo-assembly/software/pipelines/latest/using/running
RepeatMasker version 4.0.9 91 http://www.repeatmasker.org
BUSCO 56 https://busco.ezlab.org
gVolante web interface 57 https://gvolante.riken.jp
BRAKER version 2.1.4 61,62 https://github.com/Gaius-Augustus/BRAKER
UTRme 66 https://github.com/sradiouy/UTRme
APOLLO 67 https://genomearchitect.readthedocs.io/en/latest/
Integrative Genomics Reviewer 68,69 http://software.broadinstitute.org/software/igv/
BWA version 0.7.17-r1188 63 https://github.com/lh3/bwa
SAMtools version 0.1.19 / 1.3 / 1.7 71 http://www.htslib.org/download/
BCFtools version 0.1.19 / 1.7 / 1.9 72 http://www.htslib.org/download/
VCFtools version 0.1.15 / 0.1.16 73 https://vcftools.github.io
R version 3.6.1 85 https://www.r-project.org
SNPRelate version 1.20.1 (R package) 74 https://bioconductor.org/packages/release/bioc/html/SNPRelate.html
Picard version 2.18.0 Broad Institute http://broadinstitute.github.io/picard/
GATK version 3.4 75 https://gatk.broadinstitute.org/hc/en-us
PLINK version 1.90 76 http://zzz.bwh.harvard.edu/plink/
Sushi version 1.24.0 (R package) 77 https://github.com/dphansti/Sushi
BEDtools version 2.29.2 78 https://bedtools.readthedocs.io/en/latest/
vcfR version 1.10.0 (R package) 79 https://github.com/knausb/vcfR
snpStats version 1.36.0 (R package) 80 http://bioconductor.org/packages/release/bioc/html/snpStats.html
LDheatmap version 0.99.8 (R package) 81 https://sfustatgen.github.io/LDheatmap/index.html
Trim Galore! version 0.6.5 82 http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
cutadapt version 2.7 82 https://cutadapt.readthedocs.io/en/stable/
RepBase 83 https://www.girinst.org/repbase/
PseudoreferencePipeline Reilly, P. F. (unpublished) https://github.com/YourePrettyGood/PseudoreferencePipeline
HISAT version 2.1.0 86 http://daehwankimlab.github.io/hisat2/
HTSeq version 0.12.4 87 https://htseq.readthedocs.io/en/master/
Glimma version 1.14.0 (R package) 88 https://bioconductor.org/packages/release/bioc/html/Glimma.html
edgeR version 3.28.1 (R package) 89 http://bioconductor.org/packages/release/bioc/html/edgeR.html
EnhancedVolcano version 1.4.0 (R package) 90 https://github.com/kevinblighe/EnhancedVolcano
BLAST version 2.7.1 58,60 https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download
HMMER version 3.1b2 99 http://hmmer.org
ReSpect database 96 https://rdrr.io/github/WMBEdmands/compMS2Miner/man/ReSpect.html
UniProt/Swiss-Prot database 97 https://www.uniprot.org
WebGestalt 2019 98 http://www.webgestalt.org
PFAM database 100 http://pfam.xfam.org
SignalP-5.0 101 http://www.cbs.dtu.dk/services/SignalP/abstract.php
tmhmm version 2.0 102 http://www.cbs.dtu.dk/services/TMHMM/
MAFFT version 7.419 103, 104 https://mafft.cbrc.jp/alignment/software/
stats (R package) 85 https://www.rdocumentation.org/packages/stats/versions/3.6.2
trimAI version 1.4 105 http://trimal.cgenomics.org/downloads
Seqinr version 3.6–1 (R package) 106 http://seqinr.r-forge.r-project.org
Ggseqlogo version 0.1 (R package) 107 https://github.com/omarwagih/ggseqlogo
seqtk version 1.3 Li, H. (unpublished) https://github.com/lh3/seqtk
FastTree version 2.1.11 111 http://www.microbesonline.org/fasttree/
ggtree version 2.2.2 (R package) 112 https://bioconductor.org/packages/release/bioc/html/ggtree.html
PAML version 4.9j 113 http://abacus.gene.ucl.ac.uk/software/paml.html
Polymorphorama version 6 114 https://ib.berkeley.edu/labs/bachtrog/data/polyMORPHOrama/polyMORPHOrama.html
SweeD-P version 3.1 51 https://cme.h-its.org/exelixis/web/software/sweed/
MaCS version 0.4f 118 https://github.com/gchen98/macs
Other
H. cornu RNA sequencing This paper Methods S1B
H. cornu red-green GWAS This paper Methods S1C
Red-green targeted resequencing This paper Methods S1D
H. hamamelidis genome resequencing This paper Methods S1E
H. hamamelidis targeted resequencing This paper Methods S1F
H. cornu salivary gland red-green RNA seq This paper Methods S1G
H. virginiana gall-leaf RNA seq This paper Methods S1H
H. virginiana red-green galls RNA seq This paper Methods S1I
FigShare resources: genomes, annotations, protein sequences and analysis scripts This paper Methods S1J