Supplementary Information - BioMedSearch

Supplementary Information Viral Adaptation to Host: A proteome based analysis of codon usage and amino acid preferences Iris Bahir1, Menachem Fromer2, Yosef Prat2 and Michal Linial1,3, * 1

Department of Biological Chemistry, Institute of Life Sciences, School of Computer Sciences and Engineering, 3 The Sudarsky Center for Computational Biology, The Hebrew University of Jerusalem, 91904, Israel 2

The following supplementary information is available with the online version of this paper. Supplementary Table S1 includes detailed information for all 121 known viruses that infect human. Data source for Figure 1B. Supplementary Table S2 includes the detailed table for the viruses and the hosts that are analyzed in this study. Supplementary data S1 shows the distance matrix for the similarity in amino acid distribution and codon usage between viruses and hosts mapped by their broad taxonomy by the 6 taxonomical groups: human, mammals - excluding human, vertebrate - excluding mammals, plants, insects, and bacteria. Data extension - Figure 4. Supplementary Table S3 contains the GC content for the pairs of 30 viruses and their unique hosts (IDs are according to Table 1 and supplementary Table S2). Data source for Figure 6A. Supplementary data S2 shows the complete distance matrix for the similarity in codon usage between pairs of 30 viruses and 30 hosts. Data extension - Figure 6B. Supplementary Table S4 contains the data compiled for the partition of human infecting virus proteins to functional groups. Data source for Figure 7.

Supplementary Table S2 A list of 30 hosts and their organism ID according to NCBI taxonomy. The number of representative viruses that infect the specific hosts are listed (# Vir) as well as the sum of their proteins (# Pr). The statistical information includes the commutative number of the amino acids (# aa), the number of associated open reading frames (# ORF), the total number of the respective codons (# codons) and the average length of the viral proteins and the average number of codons for an ORF. The data only cover full length representative viruses from ViralZone (supported by SwissProt/UniProtKB). The data was used as a source for data in Figures 3-6.

HUM SQUM MAC RAT MOUS PIG BOVN SHP HORS CAT DOG CHK MOSQ COMO CHIL AMMO ARAB LET RICE TOM BACI CHLM ENCO LACO MYBC MYPL PSDO SALM STRP ECOL total

NCBI TaxID

Viral hosts

Host name

Human Squirrel monkey Macaque Rat Mouse Pig Bovine Sheep Horse Cat Dog Chicken Tiger mosquito Codling moth Rice stem borer Noctuid moth Arabidopsis Lettuce Rice Tomato Bacillus subtilis Chlamydia psittaci Enterococcus faecalis Lactococcus Mycobacteria Mycoplasma Pseudomonas syringae Salmonella typhimurim Streptomyces coelicolor Escherichia coli

H. sapiens

9606

Saimiri Macaca Rattus M. musculus S. scrofa B. bovis O. aries E. caballus F. domesticus C. canis G. gallus A. Albopictus C. Pomonella C. suppressalis S. Frugiperda C. Hayek L. sativa O. sativa S. lycopersicum

9520 9539 10116 10090 9823 9913 9940 9788 9685 9615 9031 7160 82600 168631 7108 3701 4236 4530 4081 1423

# Vir

# Pr

# Codons

aa / Protein

Codon / ORF

23 1

1104 75

471751 33202

2027 137

793917 58837

427

392

1 1 1 3 5 1 1 1 1 3 1 1 1 1 1 1 2 4 1 1

7 7 7 295 36 28 7 2 7 103 3 143 468 122 5 6 6 16 27 8

1704 5023 2754 93628 14567 8976 1136 774 2357 46673 1532 36936 77552 37391 1624 3857 1436 3840 6064 1648

16 29 13 405 61 28 24 2 14 532 3 145 468 136 5 13 6 21 32 12

2335 17393 3556 125470 23234 9004 2385 776 5113 189090 1543 37370 78020 43519 1629 8186 1235 4993 6374 2268

443 243 718 393 317 405 321 162 387 337 453 511 258 166 306 325 643 239 240 225

429 146 600 274 310 381 322 99 388 365 355 514 258 167 320 326 630 206 238 199

1

206

189

221

42234

126

14526

1 1 1 1

39 85 14 5

6900 15251 3272 866

40 86 14 5

7181 15669 3287 871

191 177 179 234

115 180 182 235

173

174

1

56

10207

174

31106 182

179

1

53

12454

67

15392

1 64

708 3663

154167 1099776

1375 6016

273272 1777551

235 218 310

230 199 287

# aa

# ORF

83554 1351 1357 1763 2093 317 602 1902 562

Supplementary Table S3 GC content (in percentage) for the pairs of 30 viruses and their hosts is shown. The abbreviate names refer to the list in Additional data file 2 and Table I.

ID 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30

HUM SQUM MAC RAT MOUS PIG BOVN SHP HORS CAT DOG CHK MOSQ COMO CHIL AMMO ARAB LET RICE TOM BACI CHLM ENCO LACO MYBC MYPL PSDO SALM STRP ECOL

GC - Host 0.5066 0.5047 0.4977 0.5119 0.5200 0.5254 0.5315 0.5167 0.5102 0.5246 0.5103 0.5208 0.4862 0.4594 0.3999 0.5075 0.4471 0.4024 0.5414 0.4197 0.3958 0.4141 0.3781 0.3632 0.6683 0.2984 0.5957 0.5297 0.7193 0.5149

GC-Virus 0.5574 0.3555 0.4194 0.4689 0.4233 0.3523 0.4180 0.3405 0.4759 0.4372 0.4332 0.4399 0.3969 0.4679 0.2985 0.5137 0.3976 0.4385 0.4607 0.4165 0.4016 0.3673 0.3575 0.3673 0.625 0.3208 0.5694 0.4823 0.6391 0.3993

Supplementary data S1 Illustration for the L2 distance values between human and mammalian viruses (excluding human) and 6 tested hosts groups as indicated (A). Note that a smaller L2 value indicates high resemblance. The analysis was performed for all pairwise distances and the results were scaled according to the colored ruler (B). (see Materials and Methods and details in legend of Figure 4).

A Human 1.4

Mammals (no H)

Vir x Ho

L2 distance - score L2

1.2 1 0.8 0.6 0.4 0.2 0

Ins Pla B Ma Hu V ma e ma erte nts acte bra cts ria n ls (no tes (no H) M)

H

B

M

V

I

P

B

H

M

V

I

P

B

Host x Host

Human Mammals (no H) Vertebrates (no M) Insects Plants Bacteria

amino-acids

codon usage

Virus x Virus


Virus x Host



Supplementary data S2 A distance matrix based on the L2 measure for the similarity in codon usage between 30 pairs of viruses and hosts. For details see legend of Figure 6. The abbreviation of the hosts (X-axis) and their viruses (Y-axis) are listed in Additional data file 2 and Table I. The colors used in the abbreviate names are as appears in legend of Figure 6A.
