Supplementary Figure 1 Taxonomy of the family Camelidae. The graph shows the six. species of extant camelids distributed among three genera.

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1 Supplementary Figure 1 Taxonomy of the family Camelidae. The graph shows the six species of extant camelids distributed among three genera. 1

2 a b 2

3 c Supplementary Figure 2 17 bp-mer estimation of the genome size. (a) 17 bp-mer estimation of the genome size of Bactrian camel. (b) 17 bp-mer estimation of the genome size of dromedary. (c) 17 bp-mer estimation of the genome size of alpaca. The X-axis represents the sequencing depth. The Y-axis represents the proportion of a K-mer count in total K-mer counts at a given sequencing depth. The estimated genome size for Bactrian camel, dromedary and alpaca are 2.4Gb, 2.5Gb and 2.6Gb respectively. 3

4 Supplementary Figure 3 GC content distribution for the three camelids genomes. The x-axis shows the GC content and the y-axis represents the ratio of the bin number divided by the total windows. These three organisms have a similar GC content distribution. 4

5 A B Supplementary Figure 4 Error types of genome assemble. (A) type I error of genome assembly which only single reads from PE can map to the region. (B) type II error of genome assembly which PE reads cannot map to the region. 5

6 Supplementary Figure 5 Comparison of the distribution of several features in the final gene set for the four mammals. Window refers to the length of every point. No obvious unexpected differences exists among these four organisms, indicating the high quality of gene structure annotation. 6

7 Supplementary Figure 6 Protein identity among the gene sets of the three camelids. Bactrian camel and dromedary shared 94.93% average amino acid identity among 14,071 1:1 orthologs, Bactrian camel and alpaca had an identity of 91.55% for 16,145 orthologs, and dromedary and alpaca had 90.8% for 15,167 orthologs. The results showed a high similarity for the three organisms. 7

8 Supplementary Figure 7 Distributions of Ka/Ks among the gene sets of the three camelids. These single copy orthologs are 1:1 Bactrian camel-dromedary, 1:1 Bactrian camel-alpaca and 1:1 dromedary-alpaca. 8

9 Supplementary Figure 8 Orthologous protein composition inferred for ten genomes. The ten species are opossum (Monodelphis domestica), horse (Equus caballus), human (Homo sapiens), dog (Canis lupus familiaris), panda (Ailuropoda melanoleuca), Bactrian camel (Camelus bactrianus), cow (Bos taurus), dromedary (Camelus dromedarius), mouse (Mus musculus) and alpaca (Vicugna pacos). 9

10 Supplementary Figure 9 Phylogenetic tree based on four-fold degenerated sites in 7,398 single-copy orthologous genes by using the maximum likehood method. Single-copy orthologous genes were from the selected genomes, including opossum (Monodelphis domestica), human (Homo sapiens), mouse (Mus musculus), dromedary (Camelus dromedarius), Bactrian camel (Camelus bactrianus), alpaca (Vicugna pacos), cow (Bos taurus), horse (Equus caballus), dog (Canis lupus familiaris) and panda (Ailuropoda melanoleuca). Branch lengths represent the neutral divergence rates. Blue numbers on the branches represent a LRT values, which illustrate the reliability of branches calculated by PhyML. 10

11 Supplementary Figure 10 Estimation of divergence time. The numbers on the nodes represent the divergence times from present (million years ago, Mya). The red dots in four internal nodes indicate fossil calibration times for Homo sapiens-mus musculus divergence ( Mya) 1, Canis lupus familiaris-equus caballus divergence ( Mya) 1, Bos taurus-homo sapiens divergence ( Mya) 1, and Homo sapiens-monodelphis domestica divergence ( Mya) ( were used in the analysis. The graph showed the estimated divergence times with their 95% confidence intervals. 11

12 Supplementary Figure 11 Branch specific ω values by using the dataset of 7,398 single-copy orthologs. Different ω values showed different nature selected pressures among the evolutionary process. The ω values for Bactrian camel and dromedary are higher than other species, indicating an accelerated evolution. 12

13 Supplementary Figure 12 Heterozygous SNP density of genomes of the three camelids. The blue, red and green lines represent the genomic SNP densities of Bactrian camel, dromedary and alpaca, respectively. Heterozygous SNPs of each individual genome were annotated, then non-overlapping 50 kb windows were chosen and heterozygous density in each window was calculated. 13

14 Supplementary Figure 13 Hierarchical clustering of over-represented GO categories for expanded gene families in Bactrian camel genome. The over-represented GO categories ( molecular function group only) were clustered hierarchically using the method of Kosiol et al

15 Supplementary Figure 14 Hierarchical clustering of over-represented GO categories for expanded gene families in dromedary genome. The over-represented GO categories ( molecular function group only) were clustered hierarchically using the method of Kosiol et al

16 Supplementary Figure 15 Hierarchical clustering of over-represented GO categories for expanded gene families in alpaca genome. The over-represented GO categories ( molecular function group only) were clustered hierarchically using the method of Kosiol et al

17 Supplementary Figure 16 Hierarchical clustering of over-represented GO categories for unique amino acid residues changed genes in Bactrian camel genome. The over-represented GO categories ( molecular function group only) were clustered hierarchically using the method of Kosiol et al

18 Supplementary Figure 17 Hierarchical clustering of over-represented GO categories for unique amino acid residues changed genes in dromedary genome. The over-represented GO categories ( molecular function group only) were clustered hierarchically using the method of Kosiol et al

19 Supplementary Figure 18 Volcano plot of expression levels in renal cortex of Bactrian camel. The negative log 10 P-values (y-axis) are plotted against the log 2 fold changes (x-axis) in gene expression for comparison of control group with water-restricted conditions. Based on the normalized expression values, genes matching false discovery rate (FDR) 0.01 and log2(fold change) 1 were defined as differentially expressed genes (DEGs) in different conditions. The plot indicates the up-regulated genes (red), down-regulated genes (green), or not DEG (blue) in the renal cortex of Bactrian camels under WR. 19

20 Supplementary Figure 19 Volcano plot of expression levels in renal medulla of Bactrian camel. The negative log 10 P-values (y-axis) are plotted against the log 2 fold changes (x-axis) in gene expression for comparison of control group with water-restricted conditions. Based on the normalized expression values, genes matching false discovery rate (FDR) 0.01 and log2(fold change) 1 were defined as differentially expressed genes (DEGs) in different conditions. The plot indicates the up-regulated genes (red), down-regulated genes (green), or not DEG (blue) in the renal medulla of Bactrian camels under WR. 20

21 Supplementary Figure 20 Distribution of expression levels in renal cortex of Bactrian camel. The log 10 (RPKM of water-restricted condition) (y-axis) are plotted against the log 10 (normalized gene expression values of control group condition) (x-axis) in gene expression. Based on the normalized expression values, genes matching false discovery rate (FDR) 0.01 and log2(fold change) 1 were defined as differentially expressed genes (DEGs) in different conditions. The plot indicates the up-regulated genes (red), down-regulated genes (green), or not DEG (blue) in the renal cortex of Bactrian camels under WR. RPKM: reads per kilobase per million mapped reads. 21

22 Supplementary Figure 21 Distribution of expression levels in renal medulla of Bactrian camel. The log 10 (RPKM of water-restricted condition) (y-axis) are plotted against the log 10 (normalized gene expression values of control group condition) (x-axis) in gene expression. Based on the normalized expression values, genes matching false discovery rate (FDR) 0.01 and log2(fold change) 1 were defined as differentially expressed genes (DEGs) in different conditions. The plot indicates the up-regulated genes (red), down-regulated genes (green), or not DEG (blue) in the renal medulla of Bactrian camels during WR. RPKM: reads per kilobase per million mapped reads. 22

23 Supplementary Figure 22 GO classification of significantly up regulation of genes expression in renal cortex of Bactrian camel under water restriction condition. The enriched GO were shown mainly in three categories: biological process, cellular component and molecular function. 23

Supplementary Figure 23 GO classification of significantly down regulation of genes expression in renal cortex of Bactrian camel under water

24 Supplementary Figure 23 GO classification of significantly down regulation of genes expression in renal cortex of Bactrian camel under water restriction condition. The enriched GO were shown mainly in three categories: biological process, cellular component and molecular function. 24

25 Supplementary Figure 24 GO classification of significantly up regulation of genes expression in renal medulla of Bactrian camel under water restriction condition. The enriched GO were shown mainly in three categories: biological process, cellular component and molecular function. 25

Supplementary Figure 25 GO classification of significantly down regulation of genes expression in renal medulla of Bactrian camel under water

26 Supplementary Figure 25 GO classification of significantly down regulation of genes expression in renal medulla of Bactrian camel under water restriction condition. The enriched GO were shown mainly in three categories: biological process, cellular component and molecular function. 26

27 Supplementary Figure 26 A heat map of the expression patterns of AQP family. The heat map was generated based on hierarchical cluster analysis of expression of AQP family in renal cortex and renal medulla for control group and water restriction. 27

28 Supplementary Figure 27 Bactrian camels unique amino acid changes in the AQP4 gene. Red rectangle indicates Bactrian camel s unique amino acid change with R261C. 28

29 Supplementary Table 1 Statistics of raw data for the Bactrian camel genome*. Pair-end Libraries Solexa Reads Insert Size Average Reads Length (bp) Total Data (Gb) Sequence Coverage (X) Physical Coverage (X) 170 bp bp bp kb kb kb kb Total * The genome size is estimated to be 2.4 Gb for Bactrian camel genome (see Supplementary Table 7). 29

30 Supplementary Table 2 Statistics of raw data for the dromedary genome*. Pair-end Libraries Solexa Reads Insert Size Average Reads Length (bp) Total Data (Gb) Sequence Coverage (X) Physical Coverage (X) 170 bp bp bp kb kb kb Total * The genome size is estimated to be 2.3 Gb for dromedary genome (see Supplementary Table 7). 30

31 Supplementary Table 3 Statistics of raw data for the alpaca genome*. Pair-end Libraries Insert Size Average Reads Length (bp) Total Data (Gb) Sequence Coverage (X) Physical Coverage (X) 170 bp bp Solexa 800 bp Reads 2 kb kb kb Total * The genome size is estimated to be 2.6 Gb for alpaca genome (see Supplementary Table 7). 31

32 Supplementary Table 4 Statistics after error correction for the Bactrian camel genome*. Pair-end Libraries Solexa Reads Insert Size Total Data (Gb) Average Reads Length (bp) Sequence Coverage (X) Physical Coverage (X) 170 bp bp bp kb kb kb kb Total * The genome size is estimated to be 2.4 Gb for Bactrian camel genome (see Supplementary Table 7). 32

33 Supplementary Table 5 Statistics after error correction for the dromedary genome*. Pair-end Libraries Solexa Reads Insert Size Average Reads Length (bp) Total Data (Gb) Sequence Coverage (X) Physical Coverage (X) 170 bp bp bp kb kb kb Total * The genome size is estimated to be 2.3 Gb for dromedary genome (see Supplementary Table 7). 33

34 Supplementary Table 6 Statistics after error correction for the alpaca genome*. Pair-end Libraries Solexa Reads Insert Size Average Reads Length (bp) Total Data (Gb) Sequence Coverage (X) Physical Coverage (X) 170 bp bp bp kb kb kb Total * The genome size is estimated to be 2.6 Gb for alpaca genome (see Supplementary Table 7). 34

35 Supplementary Table 7 17-mer statistics for the genomes of three species. Species K number K depth (X) Genome Size (bp) Used Base (bp) Used Read Physical coverage (X) C.bactrianus 51,384,018, ,446,858,035 62,606,245, ,389, C.dromedarius 45,493,835, ,274,691,798 59,913,535, ,231, V.pacos 92,057,544, ,630,215, ,039,540,270 1,123,874,

36 Supplementary Table 8 Statistics of the Bactrian camel genome assembly. Contig Scaffold Size (bp) Number Size (bp) Number N90 6,585 82,329 1,733, N80 11,069 59,395 3,388, N70 15,392 44,207 4,768, N60 19,894 32,837 6, N50 24,909 23,893 8,760, Longest 203, ,538, Total Size 1,992,031, ,005,902, Total Number (>100 bp) , ,480 Total Number (>2 kb) , ,067 36

37 Supplementary Table 9 Statistics of the dromedary genome assembly. Contig Scaffold Size (bp) Number Size (bp) Number N90 11,564 40, , N80 21,141 27,746 1,275, N70 30,944 19,994 2,122, N60 41,675 14,457 2,976, N50 54,135 10,265 4,123, Longest 539,544 23,736,781 Total Size 1,992,183,914 2,014,928,193 Total Number (>100 bp) 203, ,723 Total Number (>2 kb) 67,075 3,395 37

38 Supplementary Table 10 Statistics of the alpaca genome assembly. Contig Scaffold Size (bp) Number Size (bp) Number N90 13,519 33, , N80 26,079 22,965 1,948, N70 38,461 16,564 2,898, N60 51,492 11,988 3,985, N50 66,333 8,491 5,130, Longest 678, ,394, Total Size 2,036,384, ,049,118, Total Number ( 100 bp) , ,453 Total Number ( 2 kb) -- 53, ,314 38

39 Supplementary Table 11 Assessment of genome coverage by assembled transcripts of Bactrian camel. Dataset Number Total Length (bp) Covered by Assembly With >90% Sequence in one Scaffold Number With >50% Sequence in one Scaffold Percent(%) Number Percent(%) All >200bp >500bp >1000bp

40 Supplementary Table 12 Assessment of wild Bactrian camel genome* coverage by assembled transcripts of Bactrian camel. Dataset Number Total Length (bp) Covered by Assembly With >90% Sequence in one Scaffold Number With >50% Sequence in one Scaffold Percent(%) Number Percent(%) All >200bp >500bp >1000bp * The wild Bactrian camel genome was derived from the previous research 3. 40

41 Supplementary Table 13 Statistics of the aligned genomes. Genome # scaffolds/chr Genome size (Gb, with N) Genome Size (Gb, without N) Genome Size (Mb, masked) %masked V.pacos 319, C.bactrianus 140, C.dromedarius 117, H.sapiens , B.taurus 12, , Note: The genomes were masked with Ns in repeat sequence regions prior to LASTZ alignment. 41

42 Supplementary Table 14 Genome alignment statistics. Species vs Species Aligned Length(Gb) Target Genome Coverage Rate Query Genome Coverage Rate V.pacos vs H.sapiens % 88.85% V.pacos vs C.bactrianus % 88.81% V.pacos vs C.dromedarius % 83.64% C.bactrianus vs B.taurus % 95.44% C.dromedarius vs B.taurus % 86.55% C.dromedarius vs C.bactrianus % 90.63% 42

43 Supplementary Table 15 Segmental duplications in the three camelids genomes. Cutoff (kb) Number of Median size Genome SDs (bp) coverage (bp) >1 7,444 1,774 26,686,484 Bactrian camel > ,589 13,453,011 > ,133 7,525,705 > , ,532 >1 10,604 1,628 26,087,631 Dromedary > ,803 10,325,058 > ,554 4,356,878 > >1 24,295 2,124 36,422,148 Alpaca >5 3,823 7,152 19,304,290 > ,543 9,940,988 > , ,636 The segmental duplications in these three organisms were detected with different cutoff size (1 kb, 5 kb, 10 kb and 50 kb). 43

44 Supplementary Table 16 Statistics of the predicted protein coding genes for alpaca genome. De novo Homolog Gene set Number Average transcript length (bp) Average CDS length (bp) Average exon per gene Average exon length (bp) Average intron length (bp) AUGUSTUS 21,781 44,725 1, ,503 GENSCAN 45,949 30,335 1, ,201 H.sapiens 19,148 24,163 1, ,961 C.familiaris 20,254 21,856 1, ,752 S.scrofa 18,836 18,652 1, ,708 A.melanoleuca 19,703 22,209 1, ,840 C.bactrianus 22,356 23,511 1, B.taurus 19,737 22,012 1, ,761 GLEAN 20,864 24,788 1, ,147 Final set 20,864 24,788 1, ,147 44

45 Supplementary Table 17 Statistics of the predicted protein coding genes for Bactrian camel genome. Gene set Number Average transcript length (bp) Average CDS length (bp) Average exons per gene Average exon length (bp) Average intron length (bp) De novo AUGUSTUS 19,062 51,245 1, ,662 GENSCAN 39,581 34,865 1, ,357 B.taurus 30,670 24,738 1, ,915 Homolog C.familiaris 19,302 22,516 1, ,697 H.sapiens 31,506 16,391 1, ,580 S.scrofa 50,642 9, ,143 GLEAN 16,758 44,844 1, ,642 C.familiaris 17,323 26,634 1, ,901 Synteny H.sapiens 17,211 32,467 1, ,571 S.scrofa 15,107 21,527 1, ,779 Synteny-nr* 17,477 31,688 1, ,450 Final set 20,251 32,103 1, ,804 *Synteny-nr: Synteny non-redundancy. The synteny non-redundancy gene sets are predicted by LASTZ based on the C.familiaris, H.sapiens and S.scrofa. 45

46 Supplementary Table 18 Evaluation of completeness of the Bactrian camel genome assembly using core eukaryotic gene mapping approach. Parameter Number Percent (%) Total KOGs One KOG align one gene One KOG align several genes One KOG align no gene Note: KOG is mammal s orthologous gene found in the genome. 46

47 Supplementary Table 19 Evaluation of completeness of the dromedary genome assembly using core eukaryotic gene mapping approach. Parameter Number Percent (%) Total KOGs One KOG align one gene One KOG align several genes One KOG align no gene Note: KOG is mammal s orthologous gene found in the genome. 47

48 Supplementary Table 20 Evaluation of completeness of the alpaca genome assembly using core eukaryotic gene mapping approach. Parameter Number Percent (%) Total KOGs One KOG align one gene One KOG align several genes One KOG align no gene Note: KOG is mammal s orthologous gene found in the genome. 48

49 Supplementary Table 21 The number of genes with homology or functional classification using each annotation method for Bactrian camel genome. Number Percent (%) Total 20, % Annotated 19, SwissProt 18, Annotated TrEMBL 19, InterPro 16, KEGG 14, GO 13, Unannotated 1,

50 Supplementary Table 22 The number of genes with homology or functional classification using each annotation method for dromedary genome. Number Percent (%) Total 20, % Annotated InterPro 17, GO 14, KEGG 15, Swissprot 20, TrEMBL 18, Unannotated

51 Supplementary Table 23 The number of genes with homology or functional classification using each annotation method for alpaca genome. Number Percent (%) Total 20, % Annotated InterPro 16, GO 13, KEGG 14, Swissprot TrEMBL Unannotated 1,

52 Supplementary Table 24 Statistics of the repeats for Bactrian camel genome. RepBase TEs TE proteins De novo Combined TEs Length (bp) % in genome Length (bp) % in genome Length (bp) % in genome Length (bp) % in genome DNA 64,835, ,974, ,472, ,366, LINE 343,627, ,766, ,876, ,420, LTR 115,311, ,536, ,557, ,544, SINE 52,747, ,959, ,099, Other 9, , Unknown 1,003, ,648, ,649, Total 573,690, ,255, ,253, ,144, Repbase TEs: results of RepeatMasker analysis using Repbase; TE proteins: results of RepeatProteinMask analysis using Repbase; De novo: results of RepeatMasker analysis using the library predicted by the de novo method; Combined: the combined results for Repbase TEs, TE proteins, and the de novo method. 52

53 Supplementary Table 25 Statistics of the repeats for dromedary genome. RepBase TEs TE Proteins De novo Combined TEs Length (Mb) %in Genome Length (Mb) % in Genome Length (Mb) % in Genome Length (Mb) % in Genome DNA LINE LTR SINE Other Unknown Total Repbase TEs: results of RepeatMasker analysis using Repbase; TE proteins: results of RepeatProteinMask analysis using Repbase; De novo: results of RepeatMasker analysis using the library predicted by the de novo method; Combined: the combined results for Repbase TEs, TE proteins, and the de novo method. 53

54 Supplementary Table 26 Statistics of the repeats for alpaca genome. RepBase TEs TE Proteins De novo Combined TEs Length (bp) %in Genome Length (bp) % in Genome Length (bp) % in Genome Length (bp) % in Genome DNA 64,297, ,987, ,294, ,344, LINE 366,454, ,134, ,524, ,933, LTR 122,782, ,636, ,878, ,861, SINE 45,617, ,121, ,497, Other 6, , Unknown ,437, ,437, Total 595,690, ,738, ,070, ,532, Repbase TEs: results of RepeatMasker analysis using Repbase; TE proteins: results of RepeatProteinMask analysis using Repbase; De novo: results of RepeatMasker analysis using the library predicted by the de novo method; Combined: the combined results for Repbase TEs, TE proteins, and the de novo method. 54

55 Supplementary Table 27 Repeats comparison in five species genomes. Bactrian camel Alpaca Dromedary Cattle Human Length (Mb) % in genome Length (Mb) % in genome Length (Mb) % in genome Length (Mb) % in genome Length (Mb) % in genome DNA LINE LTR SINE Other Unknown Total 609,

56 Supplementary Table 28 Non-coding RNA genes in the Bactrian camel genome. Type Copy # Average length (bp) Total length (bp) % of genome mirna , trna , rrna snrna rrna , S , S , S S , snrna 1, , CD-box , HACA-box , splicing , Total ,

57 Supplementary Table 29 Non-coding RNA genes in the dromedary genome. Type Copy # Average length (bp) Total length (bp) % of genome trna , rrna , mirna , snrna CD-box , H-ACA box , scarna , Spliceosomal RNA , Total 2, ,

58 Supplementary Table 30 Non-coding RNA genes in the alpaca genome. Type Copy # Average length (bp) Total length (bp) % of genome mirna , trna , rrna snrna 18S ,, S , S S , CD-box , HACA-box , splicing , Total ,

59 Supplementary Table 31 Statistics for the orthologous gene families of these ten species genomes. Species Genes number Unclustered genes Family number Unique families Average genes per family Bactrian camel 20, , Dromedary 20, , Alpaca 20,864 1,867 15, Cattle 21, , Horse 20, , Dog 19, , Panda 19, , Human 21,642 1,195 15, Mouse 22,843 1,851 15, Opossum 19,448 1,195 15, Note: Unclustered genes refer to those specific to the current species; unique families refer to those specific to the current species. 59

60 Supplementary Table 32 Branch specific ω values of ten species. Species Mean ω 95% confidence interval of ω Low Opossum Human Mouse Dromedary Bactrian camel Alpaca Cattle Horse Dog Panda Up 60

61 Supplementary Table 33 Statistics of identified SNPs for Bactrian camel genome. Type Analyzed regions Heterozygote Heterozygote rate ( 10-3 ) Genome 1,976,686,993 2,289, Autosomes 1,883,590,687 2,237, Chr.X* 93,096,306 52, CDS 30,798,739 21, Autosomes 29,713,812 20, Chr.X* 1,084, *The X-chromosome-derived scaffolds were identified by LASTZ alignment to the cattle X chromosome. 61

62 Supplementary Table 34 Statistics of identified SNPs for dromedary genome. Type Analyzed regions Heterozygote Heterozygote rate ( 10-3 ) Genome 1,976,042,088 1,462, Autosomes 1,884,026,699 1,443, Chr.X* 92,015,389 18, CDS 30,874,565 13, Autosomes 29,788,584 13, Chr.X* 1,085, *The X-chromosome-derived scaffolds were identified by LASTZ alignment to the cattle X chromosome. 62

63 Supplementary Table 35 Statistics of identified SNPs for alpaca genome. Type Analyzed regions Heterozygote Heterozygote rate ( 10-3 ) Genome 2,006,396,020 5,346, Autosomes 1,907,527,860 5,237, Chr.X* 98,868, , CDS 42,584,726 81, Autosomes 40,525,019 79, Chr.X* 2,059,707 1, *The X-chromosome-derived scaffolds were identified by LASTZ alignment to the cattle X chromosome. 63

64 Supplementary Table 36 GO enrichment analysis for expanded gene families in Bactrian camel genome. GO ID Description Taxonomy P-value Number of genes GO: olfactory receptor activity MF 1.45e GO: G-protein coupled receptor activity MF 1.29e GO: G-protein coupled receptor protein BP 1.04e signaling pathway GO: cellular component organization or BP 1.4e biogenesis at cellular level GO: receptor activity MF 4.4e GO: cellular macromolecular complex BP 1.3e assembly GO: cellular component biogenesis BP 1.5e GO: intracellular non-membrane-bounded CC 6.0e organelle GO: integral to membrane CC 9.6e GO: signal transduction BP 6.2e GO: nucleosome CC 2.3e GO: nucleosome assembly BP 6.7e GO: intracellular organelle part CC 1.8e GO: GTP binding MF 4.6e GO: macromolecular complex CC 6.1e GO: GTPase activity MF 1.4e GO: microtubule CC 4.6e GO: protein polymerization BP 1.3e GO: biological regulation BP 1.5e GO: regulation of cellular process BP 4.3e GO: structural molecule activity MF 8.1e GO: cell part CC 2.3e GO: odorant binding MF 2.1e-11 6 GO: cellular process BP 2.8e GO: microtubule-based movement BP 4.2e GO: membrane CC 4.9e GO: intracellular organelle CC 2.8e GO: nucleus CC 2.1e GO: pheromone binding MF 4.6e-06 3 GO: cysteine-type endopeptidase inhibitor MF 9.0e-06 5 activity GO: ferric iron binding MF 3.3e-05 5 GO: endopeptidase inhibitor activity MF 4.5e-05 9 GO: cellular iron ion homeostasis BP 5.1e-05 5 GO: DNA binding MF GO: sulfotransferase activity MF GO: viral reproduction BP GO: structural constituent of ribosome MF GO: ribosome CC GO: ribosome biogenesis BP GO: protein catabolic process BP GO: serine-type endopeptidase inhibitor MF activity GO: metalloendopeptidase activity MF P-values were adjusted by Benjimini-Hochberg false discovery rate method 4. 64

65 Supplementary Table 37 GO enrichment analysis for expanded gene families in dromedary genome. GO ID Description Taxonomy P-value Number of genes GO: RNA-directed DNA polymerase MF activity GO: RNA-dependent DNA replication BP GO: nucleotidyltransferase activity MF GO: RNA binding MF 1.5e GO: structural constituent of ribosome MF 2.6e GO: ribosome CC 2.6e GO: cellular macromolecule biosynthetic BP 9.7e process GO: translation BP 6.1e GO: cellular biosynthetic process BP 5.7e GO: structural molecule activity MF 2.7e GO: intracellular CC 2.1e non-membrane-bounded organelle GO: cytoplasmic part CC 1.87e GO: transferase activity, transferring MF 4.63e phosphorus-containing groups GO: cellular macromolecule metabolic BP 5.7e process GO: cytoplasm CC 7.2e GO: macromolecule metabolic process BP 6.8e GO: macromolecular complex CC 7.7e GO: cellular metabolic process BP 1.5e GO: nucleic acid binding MF 4.1e GO: primary metabolic process BP 4.5e GO: transferase activity MF 2.5e GO: nucleic acid metabolic process BP 7.2e GO: cellular process BP 1.0e GO: pheromone receptor activity MF 2.3e GO: nucleobase, nucleoside, nucleotide BP 3.2e and nucleic acid metabolic process GO: metabolic process BP 1.8e GO: cellular protein metabolic process BP 3.5e GO: intracellular organelle CC 2.2e GO: gene expression BP 2.77e GO: intracellular part CC 4.37e GO: protein metabolic process BP 3.68e GO: iron ion binding MF 2.09e GO: G-protein coupled receptor activity MF 5.8e GO: ferric iron binding MF 1.6e GO: iron ion transport BP 3.7e GO: cellular iron ion homeostasis BP 3.7e GO: transmembrane receptor activity MF 1.24e GO: receptor activity MF 1.4e GO: large ribosomal subunit CC 3.6e GO: olfactory receptor activity MF 1.0e GO: cytochrome-c oxidase activity MF 5.8e GO: rrna binding MF 7.14e GO: G-protein coupled receptor protein signaling pathway BP 4.56e

66 GO: intracellular CC 1.68e GO: chromosomal part CC 2.13e GO: keratin filament CC 4.84e GO: cell surface receptor linked BP 5.57e signaling pathway GO: heme binding MF 6.58e GO: hydrogen ion transmembrane MF 3.63e transporter activity GO: chromosome, centromeric region CC 5.45e-06 9 GO: monooxygenase activity MF 1.32e GO: mitochondrion CC 2.3e GO: dutp metabolic process BP 7.8e-05 5 GO: protein folding BP 9.3e GO: chromatin CC GO: intracellular organelle part CC GO: small ribosomal subunit CC GO: translational elongation BP GO: catalytic activity MF GO: aspartic-type endopeptidase activity MF GO: MHC class I protein complex CC GO: cell part CC GO: MHC protein complex CC GO: nucleosome CC GO: antigen processing and presentation BP GO: nucleosome assembly BP GO: prefoldin complex CC GO: homophilic cell adhesion BP P-values were adjusted by Benjimini-Hochberg false discovery rate method 4. 66

67 Supplementary Table 38 GO enrichment analysis for expanded gene families in alpaca genome. GO ID Description Taxonomy P-value Number of genes GO: structural constituent of ribosome MF 3.98e GO: ribosome CC 3.98e GO: translation BP 7.89e GO: structural molecule activity MF 5.898e GO: gene expression BP 2.22e GO: cellular macromolecule BP 5.096e biosynthetic process GO: intracellular CC 5.18e non-membrane-bounded organelle GO: macromolecule metabolic process BP 7.45e GO: cellular macromolecule metabolic BP 3.2e process GO: macromolecular complex CC 2.3e GO: regulation of transcription, BP 4.3e DNA-dependent GO: transition metal ion binding MF 5.5e GO: intracellular CC 1.68e GO: ferric iron binding MF 6.3e GO: primary metabolic process BP 1.1e GO: iron ion transport BP 1.5e GO: metal ion binding MF 2.3e GO: cellular iron ion homeostasis BP 3.45e GO: protein metabolic process BP 6.49e GO: small ribosomal subunit CC 6.98e GO: cellular protein metabolic process BP 8.19e GO: zinc ion binding MF 2.56e GO: cellular process BP 4.32e GO: cell part CC 8.7e GO: intracellular organelle CC 5.55e GO: biological regulation BP 3.9e GO: gamete generation BP 5.1e-10 7 GO: homophilic cell adhesion BP 2.9e GO: nucleic acid binding MF 2.01e GO: regulation of cellular process BP 5.79e GO: cell adhesion BP 6.42e GO: ephrin receptor activity MF 3.58e-05 5 GO: olfactory receptor activity MF GO: defense response BP GO: plasma membrane CC GO: microtubule CC GO: protein polymerization BP GO: transmembrane receptor protein BP tyrosine kinase signaling pathway GO: protein catabolic process BP GO: microtubule-based movement BP GO: metalloendopeptidase activity MF P-values were adjusted by Benjimini-Hochberg false discovery rate method 4. 67

68 Supplementary Table 39 GO enrichment of unique amino acid residues changed gene in Bactrian camel genome. GO ID Description Taxonomy P-value Number of genes GO: protein phosphorylation BP 3.6e GO: protein kinase activity MF 1.18e GO: catalytic activity MF 1.62e GO: transferase activity, transferring MF 2.7e phosphorus-containing groups GO: transferase activity MF 3.15e GO: phosphotransferase activity, MF 4.8e alcohol group as acceptor GO: protein serine/threonine kinase MF 5.33e activity GO: kinase activity MF 6.3e GO: ATP binding MF GO: phosphate-containing compound BP metabolic process GO: macromolecule modification BP GO: protein modification process BP GO: vacuolar proton-transporting CC V-type ATPase, V1 domain GO: small molecule binding MF P-values were adjusted by Benjimini-Hochberg false discovery rate method 4. 68

69 Supplementary Table 40 GO enrichment of unique amino acid residues changed gene in dromedary genome. GO ID Description Taxonomy P-value Number of genes GO: peptidyl-histidine modification BP GO: protein kinase activity MF GO: protein phosphorylation BP GO: ATP binding MF GO: catalytic activity MF GO: protein serine/threonine kinase MF activity GO: phosphate-containing compound BP metabolic process GO: small molecule binding MF GO: small molecule metabolic BP process GO: phosphotransferase activity, MF alcohol group as acceptor GO: protein tyrosine kinase activity MF GO: peptidyl-amino acid modification BP GO: purine ribonucleoside MF triphosphate binding GO: nucleotide binding MF P-values were adjusted by Benjimini-Hochberg false discovery rate method 4. 69

70 Supplementary Table 41 The top 10 GO terms of the gained genes in the Bactrian camel genome. GO term GO description P-value GO: sensory perception of smell 0.00 GO: olfactory receptor activity 0.00 GO: immune response 0.00 GO: chemokine activity 2.69E-13 GO: cytokine receptor binding 4.40E-13 GO: G-protein coupled receptor protein signaling pathway 2.80E-12 GO: negative regulation of megakaryocyte differentiation 4.84E-12 GO: zinc ion binding 2.35E-11 GO: antigen processing and presentation 3.02E-11 GO: sensory perception of taste 1.07E-06 P-values were adjusted by Benjimini-Hochberg false discovery rate method 4. 70

71 Supplementary Table 42 The top 10 GO terms of the gained genes in the dromedary genome. GO term GO description P-value GO: sensory perception of smell 0.00 GO: olfactory receptor activity 0.00 GO: Sequestering of actin monomers 1.51e-05 GO: Response to pheromone 3.32e-05 GO: Pheromone receptor activity 3.32e-05 GO: Homophilic cell adhesion 3.49e-05 GO: Cytochrome-c oxidase activity 1.14E-04 GO: Antigen binding 3.00E-04 GO: Cellular response to reactive oxygen species 3.16E-04 GO: NEDD8 ligase activity 3.16E-04 P-values were adjusted by Benjimini-Hochberg false discovery rate method 4. 71

72 Supplementary Table 43 Rapidly evolving GO categories associated with fat and energy in the Bactrian camel and dromedary genomes compared with alpaca genome. GO ID Bactrian camel dn/ds Bactrian camel versus alpaca Alpaca dn/ds P-value Dromedary dn/ds Dromedary versus alpaca Alpaca dn/ds P-value GO description GO: ATP catabolic process GO: E-05 ATPase activity ATPase activity coupled to GO: E E-16 transmembrane movement of substances GO: E E-07 mitochondrion GO: E-07 mitochondrial matrix GO: E lipid transport GO: E-05 response to insulin stimulus 72

73 Supplementary Table 44 Rapidly evolving GO categories associated with fat and energy in the Bactrian camel genome compared with dromedary genome. GO ID Bactrian camel dn/ds Dromedary dn/ds GO description P-value GO: fatty acid metabolic process GO: cellular lipid metabolic process GO: triglyceride biosynthetic process GO: lipid catabolic process GO: cholesterol homeostasis 2.31E-12 GO: cholesterol metabolic process GO: glycerophospholipid biosynthetic process GO: fat cell differentiation 2.54E-09 GO: carbohydrate metabolic process 8.06E-05 GO: generation of precursor metabolites and energy 1.61E-06 GO: cellular response to insulin stimulus 4.44E-10 GO: insulin receptor signaling pathway 7.54E-05 73

74 Supplementary Table 45 Transcriptome sequenced data statistics for control group and water restriction. Total reads (M) Total base (Gb) Map reads (M) Map ratio (%) Renal cortex (CG) Renal medulla (CG) Renal cortex (WR) Renal medulla (WR)

75 Supplementary Table 46 Transcriptomic representation of genes of the aldosterone-regulated sodium reabsorption in renal cortex for control group and water restriction. Gene ID Gene Name RPKM of CG RPKM of WR Log2 Ratio (WR/CG) Up-Down-Regulation (WR/CG) P-value (WR/CG) FDR (WR/CG) Ala_bactrian_19666 ATP1A Up 0 0 Ala_bactrian_09473 ATP1A Up 2.41E E-35 Ala_bactrian_02829 ATP1A Up 8.57E E-01 Ala_bactrian_15986 ATP1B Up 0 0 Ala_bactrian_03560 ATP1B Up 1.81E E-04 Ala_bactrian_17974 ATP1B Up 4.49E E-18 Ala_bactrian_06438 ATP1B Up Ala_bactrian_10566 FXYD Down 0 0 Ala_bactrian_14226 HSD11B Up 6.75E E-01 Ala_bactrian_10747 IGF Up Ala_bactrian_04915 INSR Up 0 0 Ala_bactrian_08579 IRS Up 8.59E E-105 Ala_bactrian_15617 IRS Up 5.27E E-01 Ala_bactrian_19183 KCNJ Up 8.70E E-80 Ala_bactrian_11246 KRAS Down 4.42E E-07 Ala_bactrian_03613 MAPK Up 1.94E E-170 Ala_bactrian_14091 MAPK Up 1.31E E-28 Ala_bactrian_12234 NEDD4L Up 5.05E E-100 Ala_bactrian_02710 NR3C Up 1.52E E-25 Ala_bactrian_09741 NR3C Up 4.83E E-37 Ala_bactrian_10426 PDPK Up 7.60E E-38 Ala_bactrian_03414 PIK3CA Up 8.09E E-01 75

76 Ala_bactrian_10548 PIK3CB Up 9.41E E-68 Ala_bactrian_14406 PIK3CD Up 5.21E E-60 Ala_bactrian_00530 PIK3CG Up 3.28E E-02 Ala_bactrian_02487 PIK3R Up 1.73E E-26 Ala_bactrian_08669 PIK3R Up 9.32E E-70 Ala_bactrian_18999 PIK3R Up 6.84E E-18 Ala_bactrian_00529 PIK3R Up 1.75E E-11 Ala_bactrian_11097 PRKCA Up 2.08E E-134 Ala_bactrian_01079 PRKCB Down 8.31E E-01 Ala_bactrian_02418 PRKCG Up 7.24E E-01 Ala_bactrian_09164 SCNN1A Up 0 0 Ala_bactrian_16445 SCNN1B Up 2.12E E-34 Ala_bactrian_00164 SCNN1G Up 1.07E E-109 Ala_bactrian_15032 SFN Down 6.89E E-16 Ala_bactrian_10043 SGK Up 6.75E E-216 Ala_bactrian_13495 SLC9A3R Up 5.68E E-05 The genes showed in this table belong to the KEGG pathway (map04960). 76

77 Supplementary Table 47 Transcriptomic representation of genes of the aldosterone-regulated sodium reabsorption in renal medulla for control group and water restriction. Gene ID Gene Name RPKM of CG RPKM of WR Log2 Ratio (WR/CG) Up-Down-Regulation (WR/CG) P-value (WR/CG) FDR (WR/CG) Ala_bactrian_19666 ATP1A Up 0 0 Ala_bactrian_09473 ATP1A Down 1.87E E-11 Ala_bactrian_02829 ATP1A Up 2.66E E-01 Ala_bactrian_18032 ATP1A Up 3.53E E-02 Ala_bactrian_15986 ATP1B Up 8.26E E-85 Ala_bactrian_03560 ATP1B Down 5.16E E-01 Ala_bactrian_17974 ATP1B Up 1.81E E-06 Ala_bactrian_06438 ATP1B Down 4.80E E-01 Ala_bactrian_10566 FXYD Up 1.77E E-210 Ala_bactrian_14226 HSD11B Up 0 0 Ala_bactrian_10747 IGF Down 1.41E E-01 Ala_bactrian_04915 INSR Down 1.54E E-72 Ala_bactrian_08579 IRS Down 7.44E E-01 Ala_bactrian_15617 IRS Down 9.99E E-73 Ala_bactrian_19183 KCNJ Up 2.16E E-10 Ala_bactrian_11246 KRAS Down 3.17E E-24 Ala_bactrian_03613 MAPK Down 9.59E E-17 Ala_bactrian_14091 MAPK Up 7.05E E-56 Ala_bactrian_12234 NEDD4L Down 4.65E E-84 Ala_bactrian_02710 NR3C Down 9.71E E-14 Ala_bactrian_09741 NR3C Down 8.92E E-40 Ala_bactrian_10426 PDPK Down 1.24E E-51 77

78 Ala_bactrian_03414 PIK3CA Down 4.74E E-92 Ala_bactrian_10548 PIK3CB Down 2.30E E-76 Ala_bactrian_14406 PIK3CD Down 2.31E E-18 Ala_bactrian_00530 PIK3CG Down 5.68E E-10 Ala_bactrian_02487 PIK3R Down 9.66E E-01 Ala_bactrian_08669 PIK3R Up 6.54E E-23 Ala_bactrian_18999 PIK3R Down 1.91E E-15 Ala_bactrian_00529 PIK3R Down 9.12E E-06 Ala_bactrian_11097 PRKCA Down 2.46E E-98 Ala_bactrian_01079 PRKCB Down 1.09E E-09 Ala_bactrian_02418 PRKCG Down 3.09E E-01 Ala_bactrian_09164 SCNN1A Up 1.03E E-99 Ala_bactrian_16445 SCNN1B Up 1.71E E-113 Ala_bactrian_00164 SCNN1G Up 2.29E E-72 Ala_bactrian_15032 SFN Up 5.10E E-04 Ala_bactrian_10043 SGK Down 8.68E E-03 Ala_bactrian_13495 SLC9A3R Up 1.55E E-90 The genes showed in this table belong to the KEGG pathway (map04960). 78

79 Supplementary Table 48 Transcriptomic representation of genes of the aquaporins family in renal cortex for control group and water restriction. Gene ID Gene Name RPKM of CG RPKM of WR Log2 Ratio (WR/CG) Up-Down-Regulation (WR/CG) P-value (WR/CG) FDR (WR/CG) Ala_bactrian_10657 AQP Up 0 0 Ala_bactrian_17951 AQP Up 0 0 Ala_bactrian_00286 AQP Up E E-251 Ala_bactrian_10592 AQP Down E-02 Ala_bactrian_13653 AQP Up E E-67 Ala_bactrian_10970 AQP Down Ala_bactrian_01284 AQP Up

80 Supplementary Table 49 Transcriptomic representation of genes of the aquaporins family in renal medulla for control group and water restriction. Gene ID Gene Name RPKM of CG RPKM of WR Log2 Ratio (WR/CG) Up-Down-Regulation (WR/CG) P-value (WR/CG) FDR (WR/CG) Ala_bactrian_10657 AQP Up 0 0 Ala_bactrian_17951 AQP Up 0 0 Ala_bactrian_00286 AQP Up 0 0 Ala_bactrian_10592 AQP Up 1.53E E-04 Ala_bactrian_13653 AQP Up 2.37E E-20 Ala_bactrian_10970 AQP Down Ala_bactrian_17742 AQP Up Ala_bactrian_01284 AQP Up

Molecular Cell Biology - Problem Drill 01: Introduction to Molecular Cell Biology

Molecular Cell Biology - Problem Drill 01: Introduction to Molecular Cell Biology Question No. 1 of 10 1. Which statement describes how an organism is organized from most simple to most complex? Question