Corresponding author: Kuo-Hsiang Hung (
Academic editor: Ricardo Moratelli
The Chinese pangolin
This work was funded by The Ministry of Science and Technology of Taiwan under Grant [109-2628-B-020 -002].
No potential conflict of interest was reported by the author(s).
Pangolins (
The Chinese pangolin
Three subspecies of the Chinese pangolin have been identified in some reports based on morphological traits (
An increase in pangolin numbers has been documented in many areas throughout Taiwan (
The sample of
Before genome sequencing, the quality/quantity of DNA samples were assessed using the Agilent Genomic DNA ScreenTape assay in conjunction with the 4200 TapeStation system (Agilent Technologies). The 10 ug of total DNA was sonicated using a Covaris M220 Focused-ultrasonicator to a size ranging from 400 to 500 bp. Subsequently, genomic DNA was used for library preparation using the Illumina Truseq DNA Sample Preparation Kit (Illumina, San Diego, USA), following the manufacturers’ preparation protocol. Genome sequencing was performed using the Illumina HiSeq platform for PE 2 × 150 bp sequencing. The raw sequences were filtered to obtain qualified reads using FASTP v.0.20 (
The assembled mitochondrial genome was annotated using the MITOS2 web server to predict the location of protein-coding genes (PCGs), transfer RNAs (tRNAs), ribosomal RNAs (rRNAs) and putative secondary structures of tRNAs (
Phylogenetic relationships were constructed based on the full mitogenome and 13 PCG sequences of
The mitogenome sequence of
The sequence length of 13 PCGs was 11,396 bp with base compositions of 31.84%, 29.35%, 13.28% and 25.53% for A, C, G and T, respectively (Table
All PCGs started with a typical ATN codon: four (ND1, ND2, COX1, COX2, ATP8, ATP6, COX3, ND4L, ND4, ND6 and CYTB) with ATG and two (ND3 and ND5) with ATA. The complete stop codons, TAA and AGA, were found in six genes (ND1, COX2, ATP8, ATP6, ND4L and ND5) and three genes (COX1, ND6 and CYTB), while the remaining five genes terminated with a single base T (ND2, COX3, ND4) or one base TA (ND3) (Table
The sequence lengths of 12S and 16S rRNA were 960 bp and 1,566 bp, respectively. The base composition of both rRNAs was 37.92% A, 21.54% C, 17.74% G and 22.80% T and the A + T content was 60.72%. The 22 tRNAs were interspersed in the whole mitochondrial genome, varying from 59 (tRNA-Ser(GCU)) to 73 nucleotides (tRNA-Gln and tRNA-Asn). The A + T content of these tRNAs was 63.68% and positive AT skew and negative GC skew were found (Table
The topology of phylogenetic trees, based on full mitogenome sequences, illustrated that Asian and African pangolin species were separated into two distinct monophyletic clades, consistent with previous studies (
The complete mitochondrial genome of
The genome sequence data are available in GenBank (
Nick Ching-Min Sun, Chi-Chun Huang, Tulshi Laxmi Suwal, Meng-Jou Chi, Nian-Hong Jang-Liaw and Kuo-Hsiang Hung designed the experiments. Nick Ching-Min Sun, Tulshi Laxmi Suwal and Meng-Jou Chi collected materials. Chi-Chun Huang and Yu-Wei Tseng performed the experiments. Nick Ching-Min Sun, Chi-Chun Huang, Yu-Wei Tseng and Kuo-Hsiang Hung analysed the data. Nick Ching-Min Sun, Chi-Chun Huang and Kuo-Hsiang Hung drafted the manuscript.
No potential conflict of interest was reported by the author(s).
Complete mitochondrial genome map of
Putative secondary structure of the 22 tRNAs of
Maximum Likelihood (ML) phylogenetic tree of
Characteristics of the mitochondrial genome of
Gene | Position | Length (bp) | Anticodon | Codon | Intergenic nucleotides* | Strand | ||
From | To | Start | Stop | |||||
tRNA-Phe | 1 | 68 | 68 | GAA | 0 | H | ||
12S ribosomal RNA | 69 | 1028 | 960 | 0 | H | |||
tRNA-Val | 1028 | 1093 | 66 | UAC | -1 | H | ||
16S ribosomal RNA | 1094 | 2659 | 1566 | 0 | H | |||
tRNA-Leu (UAA) | 2660 | 2733 | 74 | UAA | 0 | H | ||
ND1 | 2737 | 3693 | 957 | ATG | TAA | 3 | H | |
tRNA-Ile | 3693 | 3761 | 69 | GAU | -1 | H | ||
tRNA-Gln | 3759 | 3831 | 73 | UUG | -3 | L | ||
tRNA-Met | 3833 | 3901 | 69 | CAU | 1 | H | ||
ND2 | 3875 | 4913 | 1039 | ATG | T-- | -27 | H | |
tRNA-Trp | 4941 | 5007 | 67 | UCA | 27 | H | ||
tRNA-Ala | 5011 | 5079 | 69 | UGC | 3 | L | ||
tRNA-Asn | 5081 | 5153 | 73 | GUU | 1 | L | ||
tRNA-Cys | 5186 | 5250 | 65 | GCA | 32 | L | ||
tRNA-Tyr | 5251 | 5317 | 67 | GUA | 0 | L | ||
COX1 | 5319 | 6869 | 1551 | ATG | AGA | 1 | H | |
tRNA-Ser(UGA) | 6865 | 6933 | 69 | UGA | -5 | L | ||
tRNA-Asp | 6941 | 7007 | 67 | GUC | 7 | H | ||
COX2 | 7008 | 7691 | 684 | ATG | TAA | 0 | H | |
tRNA-Lys | 7694 | 7757 | 64 | UUU | 2 | H | ||
ATP8 | 7759 | 7959 | 201 | ATG | TAA | 1 | H | |
ATP6 | 7920 | 8600 | 681 | ATG | TAA | -40 | H | |
COX3 | 8600 | 9383 | 784 | ATG | T-- | -1 | H | |
tRNA-Gly | 9384 | 9452 | 69 | UCC | 0 | H | ||
ND3 | 9453 | 9799 | 347 | ATA | TA- | 0 | H | |
tRNA-Arg | 9800 | 9866 | 67 | UCG | 0 | H | ||
ND4L | 9867 | 10163 | 297 | ATG | TAA | 0 | H | |
ND4 | 10157 | 11534 | 1378 | ATG | T-- | -7 | H | |
tRNA-His | 11535 | 11602 | 68 | GUG | 0 | H | ||
tRNA-Ser (GCU) | 11603 | 11661 | 59 | GCU | 0 | H | ||
tRNA-Leu (UAG) | 11663 | 11733 | 71 | UAG | 1 | H | ||
ND5 | 11743 | 13554 | 1812 | ATA | TAA | 9 | H | |
ND6 | 13538 | 14062 | 525 | ATG | AGA | -17 | L | |
tRNA-Glu | 14063 | 14131 | 69 | UUC | 0 | L | ||
CYTB | 14135 | 15274 | 1140 | ATG | AGA | 3 | H | |
tRNA-Thr | 15275 | 15341 | 67 | UGU | 0 | H | ||
tRNA-Pro | 15341 | 15407 | 67 | UGG | -1 | L | ||
D_loop | 15521 | 16570 | 1049 | 113 | H |
Notes: * The numbers of nucleotides between the given and its previous gene, negative values indicate an overlap; H indicated that the genes are transcribed on the heavy strand.
Nucleotide composition in two rRNA, 13 protein-coding genes and 22 tRNA of mitochondrial genome of
Adenine |
Cytosine |
Guanine |
Thymine |
A+T |
AT skew | GC skew | Length (bp) | |
|
37.92 | 21.54 | 17.74 | 22.80 | 60.72 | 0.2490 | -0.0967 | 2,526 |
12S ribosomal RNA | 36.87 | 22.92 | 17.92 | 22.29 | 59.16 | 0.2465 | -0.1224 | 960 |
16S ribosomal RNA | 38.57 | 20.69 | 17.62 | 23.12 | 61.69 | 0.2504 | -0.0801 | 1,566 |
|
31.84 | 29.35 | 13.28 | 25.53 | 57.37 | 0.1100 | -0.3770 | 11,396 |
ND1 | 33.02 | 29.99 | 12.23 | 24.76 | 57.78 | 0.1430 | -0.4207 | 957 |
ND2 | 37.63 | 30.80 | 9.14 | 22.43 | 60.06 | 0.2531 | -0.5423 | 1,039 |
COX1 | 28.43 | 27.21 | 15.51 | 27.85 | 56.28 | 0.0103 | -0.2739 | 1,551 |
COX2 | 32.16 | 28.95 | 13.74 | 25.15 | 57.31 | 0.1223 | -0.3563 | 684 |
ATP8 | 38.81 | 29.85 | 7.46 | 23.88 | 62.69 | 0.2382 | -0.6001 | 201 |
ATP6 | 33.33 | 32.89 | 10.72 | 23.06 | 56.39 | 0.1821 | -0.5084 | 681 |
COX3 | 26.79 | 30.99 | 16.33 | 25.89 | 52.68 | 0.0171 | -0.3098 | 784 |
ND3 | 34.29 | 31.70 | 10.95 | 23.06 | 57.35 | 0.1958 | -0.4865 | 347 |
ND4L | 31.98 | 29.97 | 11.45 | 26.60 | 58.58 | 0.0918 | -0.4471 | 297 |
ND4 | 33.67 | 31.57 | 11.25 | 23.51 | 57.18 | 0.1777 | -0.4745 | 1,378 |
ND5 | 34.93 | 30.41 | 9.88 | 24.78 | 59.71 | 0.1700 | -0.5096 | 1,812 |
ND6 | 16.38 | 8.57 | 32.57 | 42.48 | 58.86 | -0.4434 | 0.5834 | 525 |
CYTB | 30.53 | 31.67 | 13.86 | 23.94 | 54.47 | 0.1210 | -0.3912 | 1,140 |
|
36.46 | 20.94 | 15.38 | 27.22 | 63.68 | 0.1451 | -0.1531 | 1495 |
Mitochondrial genome characteristics
Table
Characteristics of the mitochondrial genome of pangolins used in this study.
File: oo_625289.pdf