Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Biological samples | ||
| Canis Familiaris | Various veterinary referral hospitals | N/A |
| Three Canid bone paleontological remains | This paper | Botai (sample ID: AL2350); Pietrele (sample ID: AL3185); Eliseevichi (sample ID: AL2657). |
| Chemicals, peptides, and recombinant proteins | ||
| Trizol | Life Technologies | 15596026 |
| RNAlater | Life Technologies | AM7020M |
| Critical commercial assays | ||
| TruSeq DNA nano kit | Illumina | FC-121-4001 |
| TruSeq Stranded mRNA library Prep Kit High Throughput | Illumina | RS-122-2103 |
| Illumina TruSeq Nano DNA library prep HT | Illumina | 20000903 |
| TruSeq® Stranded mRNA LT-Set A | Illumina | RS-122-2101 |
| NextSeq High Output v2.5 75 cycle kit | Illumina | 20024906 |
| Deposited data | ||
| DNA sequencing data | This paper | SRA:PRJNA685036 ncbi.nlm.nih.gov/sra |
| RNA sequencing data | This paper | SRA:PRJNA690861 ncbi.nlm.nih.gov/sra |
| Three ancient wolf DNA sequencing data | This paper | ENA: PRJEB42199 http://www.ebi.ac.uk/ena |
| Dog genome reference (CanFam3.1, ENSEMBL release-85) | ENSEMBL | http://www.ensembl.org/index.html |
| Dog genome Annotation (CanFam3.1-plus) | 66 | http://tools.genouest.org/data/tderrien/canFam3.1p/annotation/trackhub/canfam3.1ptrackhub/hub.txt |
| Oligonucleotides | ||
| gDNA targeted primer: IGF1 Forward:CACTGATCCAGAAGAATCCAACT | 9 | N/A |
| gDNA targeted primer: IGF1 Reverse: CAAAGAACCATGTAAGCCTATTTGT | 9 | N/A |
| gDNA targeted primer:IGF1-AS mutation Forward:GTGGGCTTGTCTGTGCAAAT | This paper | N/A |
| gDNA targeted primer:IGF1-AS mutation Reverse:CCTGAGCATAAAAACTAGGCAGA | This paper | N/A |
| gDNA targeted primer:IGF1-SINE Forward:CACTGATCCAGAAGAATCCAACT | This paper | N/A |
| gDNA targeted primer:IGF1-SINE Reverse:CAAAGAACCATGTAAGCCTATTTGT | This paper | N/A |
| cDNA targeted primer:IGF1-AS short isoform Forward:AGCTGGTCATCAATTTGCCCC | This paper | N/A |
| cDNA targeted primer:IGF1-AS short isoform Reverse:AAGGAAAGACTCAGTTTGGGTGT | This paper | N/A |
| cDNA targeted primer:IGF1-AS long isoform Forward:TGGAAACCACTGGATCTGAGCT | This paper | N/A |
| cDNA targeted primer:IGF1-AS long isoform Reverse:AAGGAAAGACTCAGTTTGGGTGT | This paper | N/A |
| cDNA targeted primer:IGF1-AS last exon RPA Forward:GCACCACAGAGGAAGGATGAT | This paper | N/A |
| cDNA targeted primer:IGF1-AS last exon RPA Reverse:TGGGATGTGTAGGTTGACCAG | This paper | N/A |
| cDNA targeted primer:IGF1 RPA Forward:TGCTCTCAACATCTCCCATCTCT | This paper | N/A |
| cDNA targeted primer:IGF1 RPA Reverse:ACCGTTTTGGCCAGACTCTTT | This paper | N/A |
| cDNA targeted primer:IGF1-AS/IGF1 exon 3 RPA Forward:CCTTGGGCATGTCAGTGTGG | This paper | N/A |
| cDNA targeted primer:IGF1-AS/IGF1 exon 3 RPA Reverse:GACAGGCATCGTGGATGAGTG | This paper | N/A |
| cDNA targeted primer:GAPDH qRT-PCR Forward:AAGCAGGGATGATGTTCTGG | This paper | N/A |
| cDNA targeted primer:GAPDH qRT-PCR Reverse:CCTCATGACCACCGTCCA | This paper | N/A |
| cDNA targeted primer:IGF1 qRT-PCR Forward:CCTGCACTCCCTCTACTTGC | This paper | N/A |
| cDNA targeted primer:IGF1 qRT-PCR Reverse:CTCAAGCCTGCCAAGTCTG | This paper | N/A |
| cDNA targeted primer:IGF1-AS qRT-PCR Forward:TGAAGCTTCCCCAACAATTC | This paper | N/A |
| cDNA targeted primer:IGF1-AS qRT-PCR Reverse:TGGGTGTAGACGAGATCCTTG | This paper | N/A |
| Software and algorithms | ||
| Read alignment: bwa v0.7.17 | 42 | https://sourceforge.net/projects/bio-bwa/files/ |
| Samtools 1.6 | 43 | http://samtools.sourceforge.net/ |
| Variant caller: GATK v4.1.4.0 | 44,45 | http://gatkforums.broadinstitute.org/gatk |
| PicardTools 2.9.2 | http://broadinstitute.github.io/picard | http://github.com/broadinstitute/picard |
| Vcftools v0.1.16 | 74 | http://vcftools.sourceforge.net/ |
| Linear mixed model: GEMMA v0.94.1 | 75 | http://www.xzlab.org/software.html |
| Utility: PLINK v1.9 | 76 | http://zzz.bwh.harvard.edu/plink/ |
| Graphics and data analysis: R v3.3.0 | The Comprehensive R Archive Network (CRAN) | https://cran.r-project.org |
| Phred/Phrap/Consed package | 50–52 | http://www.phrap.org/phredphrapconsed.html |
| AdapterRemoval2 | 82 | https://github.com/MikkelSchubert/adapterremoval |
| RSeQC | 69 | https://github.com/MonashBioinformaticsPlatform/RSeQC |
| MapDamage v2.58 | 19 | https://github.com/ginolhac/mapDamage |
| FilterUniqSamCons | 84 | |
| ANGSD 0.614 | 85 | https://github.com/ANGSD/angsd |
| MultiQC tool | 65 | https://multiqc.info/ |
| STAR | 67 | https://github.com/alexdobin/STAR |
| Stringtie | 68 | https://ccb.jhu.edu/software/stringtie/ |
| RSEM v1.3 | 91 | https://github.com/deweylab/RSEM |
| Data visualization: Integrative Genomics Viewer: I.G.V 2.8.2 | 70 | http://software.broadinstitute.org/software/igv/ |
| Beagle v4.1 | 88 | http://faculty.washington.edu/browning/beagle/beagle.html |
| PHYLIP | 90 | https://evolution.genetics.washington.edu/phylip.html |
| FigTree v1.4.4 | Graphical viewer of phylogenetic trees | http://tree.bio.ed.ac.uk/software/figtree/ |
| Other | ||
| KOD Xtreme HotStart Polymerase | Merck | 71975-3 |
| ExoSap-ItTM reaction | Thermo Fisher Scientific | 78201.1.ML |
| BigDye Terminator v3.1 | Thermo Fisher Scientific | 4337458 |
| RecoverAllTM Total Nucleic Acid Isolation Kit | Thermo Fisher Scientific | A26135 |
| High-Capacity cDNA Reverse Transcription kit | Thermo Fisher Scientific | 4368814 |
| TURBODNase | Thermo Fisher Scientific | AM2238 |
| RNAse A/T1 Mix | Thermo Fisher Scientific | EN0551 |
| NucleoSpin RNAclean-up kit | Macherey-Nagel | 740948.50 |
| SYBR™ Safe | Thermo Fisher Scientific | S33102 |
| Ancient DNA genotyping determination and all statistical analyses related to the paper | This paper | Dataverse :doi: 10.7910/DVN/JBXYZD https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/JBXYZD |
| The two VCF files built for this work (one containing 1,156 dogs and one containing 86 wild canids) are publically available on the dog genome project website | This paper | https://research.nhgri.nih.gov/dog_genome/data_release/index.shtml |