Pangolin genomes and the evolution of mammalian scales and immunity Siew Who Choo et al. 2017. Genome Research

Manis sp.

Manis sp.

Rationale Only mammal who’s skin is covered by large and overlapping keratinized scales. Origin of this unique trait is unknown…Perhaps defense armor against predators? Most poached and trafficked mammal in the world…meat as delicacy and scales for use in traditional medicine. Malayian and Chinese pangolins are listed as critically endagered by the IUCN. Whole-genome sequence to provide knowledge for further research in the biology and conservation of pangolins.

Sequencing and Assembly Strategy Female pangolins (Malaysian and Chinese spp) using Ilumina sequencing platform to ~145x and ~54x respectively. Assembled using CLC Assembly Cell 4.10, SGA 0.10.10, and SOAPdenovo2 (Malayan) or SOAPdenovo1.0.5 (Chinese) Short-read and mate-pair libraries ranging from ~180 bp to 8 kbp OrthoMCL used to identify homologous protein sequences among the pangolins, cat, dog, and giant panda.

Sequencing and Assembly Strategy RNA-seq expression using their Malayan pangolin transcriptome data. Cerebellum, cerebrum, lung, hearth, kidney, liver, spleen, and thymus. Protein encoding reads were mapped to the genome assembly using TopHat 2.0.11. Calculated the expression of the genes and generated heat maps of pangolin-specific genes across organs.

Assembly Statistics Malayan Chinese Transposable elements accounted for ~28 - 30% of the genome < other carnivores. Low proportions of intronics repeats (SINEs, LINEs, and LTRs). Malayan Chinese Length of ~2.5 Gbp N50 scaffold = 204,525 bp 23,446 protein-coding genes Length of ~2.7 Gbp N50 scaffold = 157,892 bp 20,298 protein-coding genes

Major Results and Conclusions Malayan pangolin has 3x heterozygosity rate than Chinese. Result of founder effect and smaller effective population size. Pseudogenized genes (presumably loss of function) that could account for unique traits such as teeth loss and poor vision. Edentolous: out of 107 genes Poor vision: out of 217

Major Results and Conclusions 8,325 ancestral gene families shared with cat, dog, and panda, out of which 4,958 and 3,465 are unique to Malayan or Chinese spp respectively. 1,152 pangolin-specific gene families. 18 families contracted: out of the 10 interferon genes (immunity), only 3 and 2 were found. 147 families expanded: genes for olfactory receptors, cathepsin and septin genes (deterioration of microbal pathogens). Positive selection: hair formation, energy storage, metabolism, robust muscular system, nervous system, and disease response. Edentolous: out of 107 genes ENAM, AMELX, and AMBN. Poor vision: out of 217 genes BFSP2

Major Results and Conclusions Pseudogenization of the IFNE gene suggests a compromised innate immunity, which can increase the probability of infection of the skin or mucose-protected organs. Scales might be an morphological innovation to compensate for the decrease in protection that skin will usually provide. Studies are needed on the relationships between IFNE, skin healing, and scale development genes. Edentolous: out of 107 genes ENAM, AMELX, and AMBN. Poor vision: out of 217 genes BFSP2

Questions What environmental conditions could promote selection for a decrease in the immune capacity that doesn’t drive the animal to extinction but instead promotes the evolution of a unique trait? Is it possible for the decrease in the immune capacity of the skin to be a result of the appearance of scales?