The Cuon Enigma: Genome survey and comparative genomics of the endangered Dhole (Cuon alpinus)

Abstract

35The Asiatic wild dog is an endangered monophyletic canid restricted to Asia; facing threats 36 from habitat fragmentation and other anthropogenic factors. Dholes have unique adaptations 37 as compared to other wolf-like canids for large litter size (larger number of mammae) and 38 hypercarnivory making it evolutionarily notable. Over evolutionary time, dhole and the 39 subsequent divergent wild canids have lost coat patterns found in African wild dog. Here we 40 report the first high coverage genome survey of Asiatic wild dog and mapped it with African 41 wild dog, dingo and domestic dog to assess the structural variants. We generated a total of 42 124.8 Gb data from 416140921 raw read pairs and retained 398659457 reads with 52X 43 coverage and mapped 99.16% of the clean reads to the three reference genomes. We 44 identified ~13553269 SNV's, ~2858184 InDels, ~41000 SVs, ~1854109 SSRs and about 45 1000 CNVs. We compared the annotated genome of dingo and domestic dog with dhole 46 genome sequence to understand the role of genes responsible in pelage pattern, dentition and 47 mammary glands. Positively selected genes for these phenotypes were looked for SNP 48 variants and top ranked genes for coat pattern, dentition and mammary glands were found to 49 play a role in signalling and developmental pathways. Mitochondrial genome assembly 50 predicted 35 genes, 11 CDS and 24 tRNA. This genome information will help in 51 understanding the divergence of two monophlyletic canids, Cuon and Lycaon, and the 52 evolutionary adaptations of dholes with respect to other canids. 53 54 55 56 57 58 59The Asiatic wild dog (Cuon alpinus) or dhole is monotypic canid belonging to the genus 60 Cuon. Dholes were widely distributed across the continents of North America, Europe and 61

Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog (Cuon alpinus)

“…However, future studies should also consider additional markers those are tested as part canid forensic studies (for example see Van Asch et al, 2009; Berger et al, 2014; Hellmann et al, 2006; Eichmann, Berger & Parson, 2004) on dholes. In addition, already available dhole genome information (Campana et al, 2016; Habib et al, 2018) also can be used to develop a suitable SNP panel for in depth analyses of dhole population and demographic parameters.…”

Not a cakewalk: Insights into movement of large carnivores in human‐dominated landscapes in India

“…In India, dholes share habitat with large carnivores like the tiger and leopard. Previous studies on dholes have focused on the intraguild competition, behavioral ecology, and genetics (Acharya, 2007; Ghaskadbi et al., 2016; Habib, Ghaskadbi, et al, 2018; Hayward et al., 2014; Johnsingh, 1980; Modi et al., 2018) but information on their movement ecology is limited.…”

Peer Review #1 of "Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog (Cuon alpinus) (v0.4)"

“…However, future studies should also consider additional markers those are tested as part canid forensic studies (for example see van Asch et al, 2009;Berger et al, 2004;Hellmann et al, 2006;Eichmann, Berger PeerJ reviewing PDF | (2018:10:32285:4:0:NEW 7 Jul 2019) Manuscript to be reviewed & Parson, 2004) on dholes. In addition, already available dhole genome information (Campana et al, 2016;Habib et al, 2018) also can be used to develop a suitable SNP panel for in depth analyses of dhole population and demographic parameters.…”