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Figure S1. 17-Mer Distribution in the Yangtze Finless Porpoise Genome

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Figure S1. 17-Mer Distribution in the Yangtze Finless Porpoise Genome Figure S1. 17-mer distribution in the Yangtze finless porpoise genome. The x-axis is 17-mer depth (X); the y-axis is the number of sequencing reads at that depth. Figure S2. Sequence depth distribution of the assembly data. The x-axis shows the sequencing depth (X) and the y-axis shows the number of bases at a given depth. The results demonstrate that 99% of bases sequencing depth is more than 20. Figure S3. Comparison of gene structure characteristics of Yangtze finless porpoise and other cetaceans. The x-axis represents the length of corresponding genetic element of exon number and the y-axis represents gene density. Figure S4. Phylogeny relationships between the Yangtze finless porpoise and other mammals reconstructed by RAxML with the GTR+G+I model. Table S1. Summary of sequenced reads Raw Reads Qualified Reads1 Total Read Sequence Physical Total Read Sequence Physical Library SRA Data Length Coverage2 Coverage2 Data Length Coverage2 Coverage2 Insert Size (bp) Number (Gb) (bp) (×) (×) (Gb) (bp) (×) (×) 289 58.94 150.00 23.67 22.80 57.84 149.75 23.23 22.41 SRR6923836 462 71.33 150.00 28.65 44.12 70.12 149.74 28.16 43.44 SRR6923837 624 67.47 150.00 27.10 56.36 63.90 149.67 25.66 53.50 SRR6923834 791 57.58 150.00 23.12 60.97 55.39 149.67 22.24 58.78 SRR6923835 4,000 108.73 150.00 43.67 582.22 70.74 150.00 28.41 378.80 SRR6923832 7,000 115.4 150.00 46.35 1,081.39 84.76 150.00 34.04 794.27 SRR6923833 11,000 107.37 150.00 43.12 1,581.08 79.78 150.00 32.04 1,174.81 SRR6923830 18,000 127.46 150.00 51.19 3,071.33 97.75 150.00 39.26 2,355.42 SRR6923831 Total 714.28 - 286.87 6,500.27 580.28 - 233.04 4,881.43 - 1Raw reads in mate-paired libraries were filtered to remove duplicates and reads with low quality and/or adapter contamination, raw reads in paired-end libraries were filtered in the same manner then subjected to k-mer-based correction. 2Coverage was calculated using an estimated Yangtze finless porpoise genome size of 2.5 Gb. Sequence coverage refers to the total length of generated reads, and physical coverage refers to the total cloned DNA used for the paired reads. Table S2. 17-mer depth distribution. K-mer K-mer_Num Peak_Depth Genome Size Used Bases Used Reads Depth(x) value 17 211,733,348,694 85 2,490,980,572 240,621,642,121 1,616,373,163 95.24 Table S3. Statistics for the final assemblies of the Yangtze finless porpoise genome Contig Scaffold Size (bp) Number Size (bp) Number N90 13,158 49,727 405,799 1,478 N80 21,552 36,306 692,029 1,042 N70 29,550 27,239 996,516 763 N60 37,733 20,364 1,337,316 562 N50 46,692 14,892 1,704,448 407 Longest 367,721 8,041,833 Total Size 2,297,280,777 2,324,302,892 Average length 21,911.42 95,897.00 Table S4. Summary of BUSCO analysis of matches to the 4,104 mammalian BUSCOs Count Ratio Complete BUSCOs 3,838 93.60% Complete and single-copy BUSCOs 3,807 92.80% Complete and duplicated BUSCOs 31 0.80% Fragmented BUSCOs 132 3.20% Missing BUSCOs 165 4.10% Table S5. Prediction of repetitive elements in the assembled Yangtze finless porpoise genome Type Repeat Size (bp) % of genome TRF 36,679,712 1.65 RepeatMasker 41,255,099 1.86 RepeatProteinMask 285,727,584 12.87 De novo 824,692,743 37.15 Total 887,629,810 39.98 Table S6. Summary statistics of interspersed repeat regions Repbase TEs TE proteins De novo Combined TEs % in % in % in % in Type Length (bp) Length (bp) Length (bp) Length (bp) genome genome genome genome DNA 13,030,245 0.59 5,742,922 0.26 58,599,942 2.64 70,751,802 3.19 LINE 14,122,460 0.64 274,740,639 12.38 551,867,994 24.86 607,756,082 27.38 SINE 5,488 0.00 0 0 106,612,802 4.80 106,617,381 4.80 LTR 2,395,432 0.11 5,257,279 0.24 90,096,068 4.06 94,925,729 4.28 Other 14,148,952 0.64 699 0.00 27,594,115 1.24 37,361,001 1.68 Unknown 362,336 0.02 0 0 3,922,485 0.18 4,284,821 0.19 Total 41,255,099 1.86 285,727,584 12.87 824,692,743 37.15 850,996,764 38.33 Table S7. Data on all species used during the genome analysis Species Latin name Version Source Cow Bos taurus UMD_3.1.1 Ensembl Pig Sus scrofa Sscrofa10.2 Ensembl Opossum Monodelphis domestica MonDom5 Ensembl Horse Equus caballus EquCab2 Ensembl Human Homo sapiens GRCh38 Ensembl Yangtze River dolphin Lipotes vexillifer Lipotes_vexillifer_v1 NCBI Bottlenose dolphin Tursiops truncatus NIST Tur_tru v1 NCBI Killer whale Orcinus orca Oorc_1.1 NCBI Common minke whale Balaenoptera acutorostrata BalAcu1.0 NCBI Sperm whale Physeter catodon Physeter_macrocephalus-2.0.2 NCBI Table S8. Prediction of protein-coding genes in the Yangtze finless porpoise Total Average Average Average Average Average Gene set Genes Gene CDS Exon per Exon Intron Predicted Length(bp) Length(bp) Gene Length(bp) Length(bp) Augustus 37,303 28,264.61 921.47 6.25 147.40 5,738.43 De novo GlimmerHMM 85,860 6,800.71 489.92 3.44 142.38 2,728.15 Geneid 134,560 9,110.22 526.35 4.11 128.03 2,876.60 Cow 27695.00 29558.89 1287.05 6.87 187.29 8,717.24 Killer whale 26942.00 32091.07 1356.77 7.37 184.21 7,706.16 Sperm whale 26836.00 26501.65 1271.89 7.04 180.71 7,912.74 Common 26332.00 30653.48 1318.68 7.35 179.52 7,995.26 Homolog minke whale Yangtze River 26007.00 31493.15 1344.52 7.37 182.39 7,865.01 dolphin Bottlenose 24622.00 31536.45 1266.24 6.79 186.47 8,077.46 dolphin Final set - 18479 36929.68 1687.41 10.17 165.89 3,842.38 Table S9. Summary statistics of comparative gene structure Gene set Numbers Average Average CDS Average Average Average Gene Length Length Exons per Exon Length Intron (bp) (bp) Gene (bp) Length (bp) Yangtze finless 18,479 36,929.68 1,687.41 10.17 165.89 3,842.38 porpoise Yangtze river 18,877 45,085.80 1,697.09 9.92 180.00 4,613.82 dolphin Killer whale 18,129 51,256.47 1,749.02 10.30 169.76 4,949.68 Sperm whale 18,626 37,852.40 1,603.08 9.67 165.74 3,794.73 Common 18,400 50,781.71 1,697.13 10.28 165.10 4,702.13 minke whale Table S10. Summary of the predicted pseudogenes Type Numbers % of genome Frame-shifted genes 2373 93.79 Prematurely terminated genes 2131 84.23 Frame-shifted and prematurely terminated genes 1974 78.02 Total 2530 100 Table S11. Functional annotation of predicted genes in the Yangtze finless porpoise genome Database Number % of genome Total 18,479 100 InterPro 17,507 94.74 GO 11,997 64.92 Annotated Swiss-Prot 15,807 85.54 TrEMBL 15,970 86.42 KEGG 8,529 46.16 Unannotated 102 0.55 Table S12. Summary statistics of gene families in 11 species Genes Maximum Total Genes in Non-clustered Unique Species Families per gene family genes families genes families family size Cow 19,981 18,197 1,784 17,157 114 1.06 15 Pig 22,410 18,891 3,519 17,512 179 1.08 21 Human 22,813 21,385 1,428 17,781 383 1.20 18 Opossum 21,313 14,262 7,051 12,248 479 1.16 27 Horse 20,431 17,884 2,547 16,700 192 1.07 18 Yangtze finless 18,479 14,072 4,407 13,911 44 1.01 5 porpoise Yangtze River 17,905 16,626 1,279 16,187 159 1.03 12 dolphin Common 17,525 16,340 1,185 16,071 25 1.02 8 minke whale Killer whale 17,283 16,658 625 16,493 5 1.01 4 Sperm whale 17,579 15,621 1,958 15,425 6 1.01 5 Bottlenose 16,531 13,400 3,131 13,337 6 1.00 7 dolphin Table S13. GO enrichment analysis of the unique gene families in the Yangtze finless porpoise lineage GO Type Function Adjust P-value GO:0001518 Cellular component voltage-gated sodium channel complex 0.012289 GO:0005248 Molecular function voltage-gated sodium channel activity 0.012437 GO:0005272 Molecular function sodium channel activity 0.016213 GO:0005787 Cellular component signal peptidase complex 0.008365 GO:0015081 Molecular function sodium ion transmembrane transporter activity 0.021554 GO:0034706 Cellular component sodium channel complex 0.012289 GO:0071205 Biological process protein localization to juxtaparanode region of axon 0.008439 GO:0099612 Biological process protein localization to axon 0.008439 Table S14. GO enrichment analysis of the expanded gene families in the Yangtze finless porpoise lineage GO Type Function Adjust P-value GO:0006325 biological process chromatin organization 0.000391 GO:0007155 biological process cell adhesion 0.002884 homophilic cell adhesion via plasma membrane adhesion GO:0007156 biological process 9.82E-09 molecules GO:0016192 biological process vesicle-mediated transport 0.012336 GO:0016337 biological process single organismal cell-cell adhesion 4.41E-07 GO:0022610 biological process biological adhesion 0.002884 GO:0051276 biological process chromosome organization 0.005419 GO:0000786 cellular component nucleosome 9.82E-09 GO:0005576 cellular component extracellular region 0.049732 GO:0005622 cellular component intracellular 0.000606 GO:0005886 cellular component plasma membrane 8.76E-07 GO:0032993 cellular component protein-DNA complex 1.21E-08 GO:0044427 cellular component chromosomal part 1.74E-08 GO:0003779 molecular function actin binding 0.002109 GO:0005488 molecular function binding 0.010055 GO:0005509 molecular function calcium ion binding 6.45E-07 GO:0005515 molecular function protein binding 0.005586 GO:0046982 molecular function protein heterodimerization activity 4.05E-05 GO:0046983 molecular function protein dimerization activity 0.048739 Table S15.
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