Transcriptome analysis of a wild bird reveals physiological responses to the urban environment

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1 Supplementary Information ppendix S1 Transcriptome analysis of a wild bird reveals physiological responses to the urban environment Hannah Watson 1*, Elin Videvall 1, Martin N. ndersson 1 and Caroline Isaksson 1 1 Department of iology, Lund University, SE Lund, Sweden *Corresponding author: hannah.watson@biol.lu.se Contents Supplementary Table S1. The top 20 most significant genes that were differentially expressed between urban (n = 6) and rural (n = 6) great tits Parus major from liver transcriptomes. Supplementary Table S2. The top 20 most significant genes that were differentially expressed between urban (n = 6) and rural (n = 5) great tits Parus major from whole blood transcriptomes. Supplementary Figure S1. Principal Components nalysis (PC) plots illustrating clustering within habitats among transcriptomes from () liver and () whole blood from urban and rural great tits Parus major. Supplementary Figure S2. Venn diagrams showing overlap of significant () differentiallyexpressed genes and () overrepresented gene ontology terms between whole blood (n = 11) and liver (n = 12) transcriptomes from urban and rural great tits Parus major. Supplementary Figure S3. erial photographs indicating the location of sampling sites (yellow pins) and surrounding habitat for the () urban and () rural great tit Parus major study populations in southern Sweden. Supplementary Figure S4. Plots illustrating the dissimilarity of an outlying sample (R2) from a transcriptome analysis of great tits Parus major from an urban (U1-U6) and a rural (R1-R6) environment. 1

2 Supplementary Table S1. The top 20 most significant annotated genes that were differentially expressed between urban (n = 6) and rural (n = 6) great tits Parus major from liver transcriptomes. Reads were mapped to the zebra finch Taeniopygia guttata genome. Gene names and descriptions are derived from UniProtK. positive log 2 -fold change indicates higher expression in urban, relative to rural, birds and vice-versa. Gene ID Gene name Gene description q-value Log 2 fold change ENSTGUG G2T6_TEGU putative metallothionein II 2.15E variant 2 ENSTGUG MTR 5-methyltetrahydrofolatehomocysteine 7.50E methyltransferase ENSTGUG MT4 metallothionein E ENSTGUG IL22R2 interleukin 22 receptor, alpha E ENSTGUG PTTG1 pituitary tumourtransforming 1.86E ENSTGUG CFHR5 complement factor H-related 5.58E ENSTGUG RRP1 ribosome binding protein E ENSTGUG IL4I1 interleukin 4 induced E ENSTGUG SMC4 structural maintenance of 3.22E chromosomes 4 ENSTGUG SL1 serum amyloid -like E ENSTGUG KP13 kinase (PRK) anchor 6.93E protein 13 ENSTGUG CSF3 colony stimulating factor 3 (granulocyte) 8.58E ENSTGUG MLKL mixed lineage kinase 1.10E domain-like ENSTGUG RHGP25 Rho GTPase activating 1.59E protein 25 ENSTGUG IL1RP interleukin 1 receptor 1.60E accessory protein ENSTGUG CD3D CD3d molecule, delta (CD3-1.67E TCR complex) ENSTGUG CSMD1 CU and Sushi multiple 1.67E domains 1 ENSTGUG RPL22L1-1 uncharacterised gene 1.81E ENSTGUG PL2R1 phospholipase 2 receptor 1, 180kDa 1.83E ENSTGUG COLL1 cordon-bleu WH2 repeat 2.17E protein-like 1 2

3 Supplementary Table S2. The top 20 most significant annotated genes that were differentially expressed between urban (n = 6) and rural (n = 5) great tits Parus major from whole blood transcriptomes. Reads were mapped to the genome of the zebra finch Taeniopygia guttata genome. Gene names and descriptions are derived from UniProtK. positive log 2 -fold change indicates higher expression in urban, relative to rural, birds and vice-versa. Gene ID Gene name Gene description q-value Log 2 fold change ENSTGUG DOCK2 dedicator of cytokinesis E ENSTGUG PCTP phosphatidylcholine transfer protein 1.10E ENSTGUG NK1-2 uncharacterised gene 3.76E ENSTGUG CD79 CD79b molecule, immunoglobulinassociated 4.27E beta ENSTGUG SYK spleen tyrosine kinase 5.61E ENSTGUG PXYLP1 2-phosphoxylose phosphatase E ENSTGUG CDH23 cadherin-related E ENSTGUG SCN4 sodium channel, voltage gated, type 2.04E IV alpha subunit ENSTGUG SWP70 SWP switching -cell complex 70kDa subunit 4.51E ENSTGUG PRP8 poly (DP-ribose) polymerase 7.16E family, member 8 ENSTGUG LPTM4 lysosomal protein transmembrane 4 beta 1.47E ENSTGUG NFKID nuclear factor of kappa light 1.47E polypeptide gene enhancer in - cells inhibitor, delta ENSTGUG NK1-1 uncharacterised gene 1.47E ENSTGUG MME membrane metallo-endopeptidase 2.35E ENSTGUG FS Fas cell surface death receptor 2.42E ENSTGUG GPR18 G protein-coupled receptor E ENSTGUG RHGP15 Rho GTPase activating protein E ENSTGUG SFRP2 secreted frizzled-related protein E ENSTGUG SLC615 solute carrier family 6 (neutral 2.42E amino acid transporter), member 15 ENSTGUG CRD11 caspase recruitment domain family, member E

4 Supplementary Figure S1. Principal Components nalysis (PC) plots illustrating clustering within habitats among transcriptomes from () liver and () whole blood from urban (blue; denoted U1-U6) and rural (red; denoted R1-R6, excluding R2) great tits Parus major. The variance associated with each of PC1 and PC2 is shown. 4

5 Supplementary Figure S2. Venn diagrams showing overlap of significant () differentiallyexpressed genes and () overrepresented gene ontology terms between whole blood (n = 11) and liver (n =12) transcriptomes from urban and rural great tits Parus major. 5

6 Supplementary Figure S3. erial photographs indicating the location of sampling sites (yellow pins) and surrounding habitat for the () urban and () rural great tit Parus major study populations in southern Sweden. The urban site is a city park located in Malmö (55 35 N E) and the rural site is a forest in Vomb (55 39 N E), which is located 35 km northeast of Malmö. The satellite images were taken from Google Earth (2015) and are reproduced at identical scales for direct comparison. 6

7 Supplementary Figure S4. Plots illustrating the dissimilarity of an outlying sample (R2) from a transcriptome analysis of great tits Parus major from an urban (U1-U6) and a rural (R1-R6) environment. The () scatterplot, generated from Principal Components 1 and 2, indicates the high dissimilarity of the blood transcriptome of R2 in relation to the transcriptomes of all other individuals; and, () heatmap illustrates Euclidean distance between the blood transcriptomes. lighter colour indicates a shorter distance, while a darker colour indicates a greater distance to other transcriptomes. The variance associated with each of PC1 and PC2 is shown in (). Due to the high dissimilarity of R2 to all other samples, it was removed from the main analyses of blood transcriptomes in the accompanying paper. 40 R1 U6 PC2: 15% variance 0 40 R2 U5 R3 R4 R5 R6 U3 U2 U4 80 U PC1: 50% variance Count Value U4 U2 U3 R4 R6 R5 R3 U5 U1 R1 U6 R2 R2 U6 R1 U1 U5 R3 R5 R6 R4 U3 U2 U4 7