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. 2016 Sep 13:6:28199.
doi: 10.1038/srep28199.

De novo sequencing, assembly and analysis of eight different transcriptomes from the Malayan pangolin

Aini Mohamed Yusoff  1   2 , Tze King Tan  1   2 , Ranjeev Hari  1   2 , Klaus-Peter Koepfli  3 , Wei Yee Wee  1   2 , Agostinho Antunes  4   5 , Frankie Thomas Sitam  6 , Jeffrine Japning Rovie-Ryan  6 , Kayal Vizi Karuppannan  6 , Guat Jah Wong  1 , Leonard Lipovich  7   8 , Wesley C Warren  9 , Stephen J O'Brien  10   11 , Siew Woh Choo  1   2
Affiliations

De novo sequencing, assembly and analysis of eight different transcriptomes from the Malayan pangolin

Aini Mohamed Yusoff et al. Sci Rep. .

Abstract

Pangolins are scale-covered mammals, containing eight endangered species. Maintaining pangolins in captivity is a significant challenge, in part because little is known about their genetics. Here we provide the first large-scale sequencing of the critically endangered Manis javanica transcriptomes from eight different organs using Illumina HiSeq technology, yielding ~75 Giga bases and 89,754 unigenes. We found some unigenes involved in the insect hormone biosynthesis pathway and also 747 lipids metabolism-related unigenes that may be insightful to understand the lipid metabolism system in pangolins. Comparative analysis between M. javanica and other mammals revealed many pangolin-specific genes significantly over-represented in stress-related processes, cell proliferation and external stimulus, probably reflecting the traits and adaptations of the analyzed pregnant female M. javanica. Our study provides an invaluable resource for future functional works that may be highly relevant for the conservation of pangolins.

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Figures

Figure 1
Figure 1. Assembly strategies to produce M. javanica transcriptome using three different assembly methods.
The final M. javanica transcriptome was represented by unigenes, which are consensus assembled transcripts from three different assembly methods.
Figure 2
Figure 2. Validation of unigenes using PCR.
The size of the PCR products of the validated unigenes meets well with the expected size. “N” is a negative control.
Figure 3
Figure 3. Phosphatidylinositol signaling pathway in the M. javanica transcriptome.
Figure 4
Figure 4. Comparative analysis.
(A) Venn diagram showing comparison between the genes of pangolin and other mammals. (B) Functional enrichment analysis of pangolin-specific genes. Significant functional categories were shown. GO terms highlighted in light red are biological processes, whereas GO terms highlighted in yellow are molecular functions.
Figure 5
Figure 5. Correlation between any two organs resulting from pairwise comparison using expression values in log10 (FPKM+1) quantified by RSEM.
See this image and copyright information in PMC

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