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Elephant Genomes Reveal Insights Into Differences in Disease Defense

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Elephant Genomes Reveal Insights Into Differences in Disease Defense Elephant Genomes Reveal Insights into Differences in Disease Defense Mechanisms between Species SUPPLEMENTARY MATERIALS Supplementary Figure 1. Synteny analyses between the Hi-C and loxAfr4.0 African bush elephant assemblies. (a) Jupiter plot showing correspondence between assemblies considering the total length of both reference and query assemblies. (b) Dot plot of the percent identity and mapping positions between scaffolds in the two assemblies from minimap. Supplementary Figure 2. Semantic clustering of significantly enriched Gene Ontology terms for biological processes found near common elephant accelerated regions. Rectangle size reflects corrected p-values. REVIGO Gene Ontology treemap glycogen positive regulation nuclear of NF−kappaB envelope metabolic transcription organization factor activity process positive regulationsister chromatid biorientation glycogen cellular metabolism response to cisplatin vitamin E isopentenyl epoxygenase diphosphate negative metabolic P450 of NF−kappaB metabolic regulation pathway process of process interleukin−13 dimethylallyl secretion cell diphosphate phospholipid biosynthetic process catabolic monoacylglycerol prostate division process catabolic process gland development monocarboxylic protein transcription nucleosome acid assembly localization monocarboxylictransport protein acid oligomerization transport protein regulation ubiquitin−dependent localization of cell differentiation to endocannabinoid involved in embryonic endocytosis placenta development signaling microtubule regulation of pathway phagocytosis, mitotic cellular transcription from response engulfment chromosome cellular response to DNA hydrostatic factor activity to pressure RNA polymerase II response to G−quadruplex regulation starvation movement response to mesenchymal establishmentlymphotoxin cell ribosomal mitochondrial cell towards estrogen DNA of T cell RNA 3' of mitotic A protein double−strand adhesion proliferation promoter break repair spindle biosynthetic import into via homologous recombination stimulus unwinding uridylation nucleus repair spindle pole stimulus anergy localization process Supplementary Figure 3. Semantic clustering of significantly enriched Gene Ontology terms for biological processes found near Asian elephant-specific accelerated regions. Rectangle size reflects corrected p-values. abslog10pvalue regulation of leukotriene innate detection of cellular lysobisphosphatidic voltage−gated B4 acid chemical stimulus calcium channel response to pressure metabolic ubiquitin−dependent involved in catabolic process activity immune natriuresis endocytosis sensory perception estrogen processleukotriene response of smell stimulus ubiquitin−dependent positiveendocytosispositive B4 regulation regulation innate positive regulation of of viral secretion by of lipid lung epithelial biosynthetic process icosanoid entry into cell involved in vitamin lung growth positive regulation very of extracellular long−chain host cell E fatty acid secretion matrix organization catabolismacylglycerol positive metabolic process negative metabolic catabolic regulation of kinase glial cell regulation process process activity apoptotic process negative immune establishment mitotic of protein homophilic cell of chromosome deubiquitinationregulation adhesion via mitotic movement of plasma membrane spindle towards protein adhesion localization spindle pole deubiquitination molecules synapse regulation CD8−positive, alpha−beta of RNA splicing T cell activation positive response responsemitochondrial double−strand regulation to signal break repair of cellular organic via homologous mitotic response drug negative transduction recombination senescence substance drug negative regulation of branching organization lymphotoxin to metabolicmetabolism involved in salivary protein protein astral cell cycle immune system regulation gland morphogenesis by sister stimulus process regulation of chromatid A glucocorticoid long cellular mesenchymal−epithelial microtubule oligomerization biorientation response signaling trimerization of natural term organizationcheckpoint process interleukin−5 biosynthetic mediated to regulation killer cell synaptic peptidoglycan intermediate filament mesenchymal cell process signaling of mitotic depression bundle assembly production degranulation pathway recombination proliferation Supplementary Figure 4. Semantic clustering of significantly enriched Gene Ontology terms for biological processes found near African bush elephant-specific accelerated regions. Rectangle size reflects corrected p-values. abslog10pvalue steroid cellular carboxylic detection of cellular G−quadruplex sphingolipid hormone nuclear ubiquitin−dependent chemical stimulus envelope protein response response receptor DNA catabolic ubiquitin−dependent acid involved in catabolic organization process complex unwinding endocytosis sensory perception to to metabolic of smell process assembly bleomycin cisplatin sphingolipid process detection of ubiquitin−dependent endocytosis glycogen positive arginine chemical stimulus nucleolar negative catabolism regulation of catabolic protein metabolic targeting to regulation of mitochondrion copper ribosome nucleosome negative process process chromatin sister chromatid regulation of isopentenyl assembly assembly involved in diphosphate histone mRNA regulation SNARE complex catabolic of NLRP3 urea ion metabolic inflammasome cohesion assembly complex process assembly cycle organization process ribosomal sensory perception protein regulation of transport ribosomal large localization reactive oxygen small subunit regulation of androgen species negative biosynthetic subunit regulation mRNA stability rRNA export biogenesis embryo of smell regulation of positive process receptor of involved in chemokine (C−C biogenesis cell dopamine motif) ligand from nucleus implantation cellular signaling division secretion 4 production negative response to UV regulation of pathway adenylate cyclase regulation of activity regulation negative protein protein viral synaptic regulation regulation of ERBB2−ERBB3 regulation of of cellular transmission, calcineurin−NFAT signaling transcription process of signaling pathway peptidyl−prolyl folding from RNA pore formation in membrane cascade response to interleukin−17 dopaminergic polymerase II of other organism promoter isomerization secretion synaptic endodeoxyribonuclease presynapse heat cellular vesicle skeletal to response regulation of muscle nucleus to response immune adenylate 5−phosphoribose exocytosis hypertrophy signaling starvation chaperone−mediated 1−diphosphate eIF2 alpha cyclase−inhibiting to system pathway biosynthesis dopamine receptor negative regulation negative regulation protein stimulus process phosphorylation negative RNA signaling pathway of interleukin−13 of platelet−derived regulation of activity polyadenylation growth factor interleukin−6−mediated secretion signaling folding by dsRNA receptor−beta pathway signaling pathway Supplementary Figure 5.Tuberculosis (TB) rates in Asian and African elephants. In a study of captive elephants, Asian elephants tested positive for TB in significantly higher numbers than did African elephants (Greenwald et al. 2009). Supplementary Figure 6. Demographic models for three elephant species, implemented in Hudson’s ms. Width of grey bars represent population size changes over time. (a) Asian elephant (Elephas maximus): 14 100 -s 100000 -t 0.01 -G -1.24 -eN 1 17.5 -eG 2 0.14 -eG 4 - 0.096 -eN 37.5 25. (b) African bush elephant (Loxodonta Africana): 8 100 -s 100000 -t 10 -eN 4.8 352 -eG 29 .07. (c) African forest elephant (L. cyclotis): 4 100 -s 100000 -I 2 2 2 -n 2 4.0 -en 0.16 1 4.0 -en 0.33 2 13.4 -en 1.6 2 4.0 -ej 1.6 1 2 -en 6.45 2 13.4 -en 33.0 2 100.0. Supplementary Table 1. Genomic SeQuence Data Obtained for the Asian Elephant. Library insert size and type Read lengths Coverage 200 bp paired-end 2x125 bp 34x 3 kb mate-paired 2x100 bp 15x 5 kb mate-paired 2x100 bp 13.8x 8 kb mate-paired 2x100 bp 14.7x 10 kb mate-paired 2x100 bp 15.2x Total coverage: 94.4x Supplementary Table 2. Summary Statistics for the Asian Elephant Genome Assembly. Feature Contigs Scaffolds Assembly length 2.98Gb 3.13 Gb Longest 731 kb 14.6 Mb Number 90,662 6,954 N50 79.8 kb 2.77 Mb L50 10,736 336 Percent genome in gaps 0.09 4.88 BUSCO results C: 91.5% [D:0.4%], F:5.7%, M:2.8%, n:4,104 BUSCO: Benchmarking Universal Single Copy Orthologs; C: complete; D: duplicated; F: fragmented; M: missing Supplementary Table 3. Interspersed Repeat Content of the Asian Elephant Genome Assembly, Estimated with a Library of Known Mammalian Repeats (RepBase) and De Novo Repeat Identification (RepeatModeler). Repeat Type RepBase RepeatModeler Length (bp) % Genome Length (bp) % Genome (51.52% total) (46.11 total) SINEs 342,400,474 10.94 55,270,845 1.77 LINEs 872,332,896 27.88 1,031,262,873 32.96 LTR 241,033,286 7.70 195,360,272 6.24 DNA transposons 87,641,059 2.80 62,073,944 1.98 Unclassified 6,190 0.04 98,648,742 3.15 Supplementary Table 4. Comparison of Statistics for the African Savannah Elephant Genome Assemblies. loxAfr3 loxAfr4 Current study Feature Contigs Scaffolds Contigs Scaffolds Contigs Scaffolds Assembly length 3.1 Gb 3.2 Gb 3.1 Gb 3.3 Gb 3. 1 Gb 3.3 Gb Longest 567 kb 129 Mb 567 kb 225 Mb 567 kb 240 Mb Number 95,867 2,353 95,891 2,303 95,889 1,784 N50 69 kb 46 Mb 69 kb 94 Mb 69 kb 89 Mb L50 13,607 21 13,607 11 13,607 11 Percent genome 0 2.45 0 4.68 0 4.69 in gaps Supplementary Table 5. Demographics of elephants with and without records of neoplasia No record
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