Abstract
This data article presents the first complete mitochondrial genome (mitogenome) of an endangered slow loris subspecies, Nycticebus coucang insularis Robinson, 1917 from Tioman Island, Pahang. Once considered as extinct, an individual of the subspecies was captured alive from the island during the 2016 Biodiversity Inventory Programme as highlighted in the related research article entitled “Rediscovery of Nycticebus coucang insularis Robinson, 1917 (Primates: Lorisidae) at Tioman Island and its mitochondrial genetic assessment” Rovie-Ryan et al., 2018. Using MiSeq™ sequencing system, the entire mitogenome recovered is 16,765 bp in length, made up of 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region. The mitogenome has been deposited at DDBJ/EMBL/GenBank under the accession number NC_040292.1/MG515246.
Keywords: Nycticebus coucang insularis, Mitogenome, Tioman island
Specifications table
| Subject area | Genomics |
| More specific subject area | Mitogenomics |
| Type of data | Morphological measurements, tables, mitogenome sequence data in FASTA file format, photographs in JPEG image file format, figures in PNG image file format |
| How data was acquired | Buccal swab DNA sampling, DNA was extracted using QIAamp® DNA Mini Kit (Qiagen, Germany), Hardware used for analysis includes M220 Focused-ultrasonicator (Covaris, USA) and MiSeq™ Benchtop Sequencer (Illumina, USA), NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) was used for sequencing, Softwares for analyses includes BOWTIE2, GENEIOUS v10.1.3, MITOS annotation web service, and MEGA v7 |
| Data format | Raw, semi-analyzed, and analyzed |
| Experimental factors | Assembly of short read sequences to construct complete mitogenome sequence, phylogenetic analysis, bootstrap test |
| Experimental features | Genomic DNA was extracted from the buccal swab sample. The complete mitogenome was sequenced and assembled by using BOWTIE2 as a plugin in GENEIOUS v10.1.3. Phylomitogenomics relationship was constructed using MEGA v7 |
| Data source location | The individual was caught at Kampung Sungai Asah, Tioman Island, State of Pahang, Malaysia (Latitude: 2°43′16.32″N Longitude: 104°11′40.93″E) |
| Data accessibility | Voucher specimen of the specimen is kept at the Wildlife Genetic Resource Bank (WGRB) of PERHILITAN (voucher number = NC37). The mitogenome data is available at DDBJ/ENA/GenBank under the accession number NC_040292/MG515246. https://www.ncbi.nlm.nih.gov/nuccore/MG515246.1https://www.ncbi.nlm.nih.gov/nuccore/NC_040292.1 |
| Related research article | Rovie-Ryan, J.J., Gani, M., Gan, H.M., Bolongon, G.G., Cheng, T.C., Razak, N., Rosli, N., Aziz, M.A. & Matkasim, K. (2018). Rediscovery of Nycticebus coucang insularis Robinson, 1917 (Primates: Lorisidae) at Tioman Island and its Mitochondrial Genetic Assessment. Sains Malaysiana, 47 (10), 2533–2540 [1]. |
Value of the data
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1. Data
Nycticebus coucang insularis Robinson, 1917 was speculated to have extinct in Tioman Island (State of Pahang, Malaysia) [2] until the rediscovery of an individual during the 2016 Biodiversity Inventory Programme [1]. Morphological measurements of the individual (total length = 279 mm, head body = 263 mm, tail = 16 mm, ear = 18 mm, hind foot = 45 mm and weight = 500 g) and photographs were taken (Fig. 1). Here, we present the mitogenome of the specimen which was caught at Kampung Sungai (Sg.) Asah, Tioman Island (Latitude: 2°43′16.32″ Longitude: 104°11′40.93″). We provided a table (Table 1) and figure (Fig. 2) of the gene organization of the mitogenome and calculated the genetic distances among the Nycticebus mitogenomes (Table 2). We also provided the phylomitogenomic tree construction of among the available mitogenomes of Nycticebus (Fig. 3).
Fig. 1.
Photographs of the individual (Nycticebus coucang insularis) caught at Kampung Sg. Asah, Tioman Island during the recent 2016 Biodiversity Inventory Programme (photographed by Cheng T.C.).
Table 1.
The mitochondrial genome organization of N. coucang insularis.
| Gene | Start | End | Orientation | Length (bp) |
|---|---|---|---|---|
| tRNA-Phe | 1 | 71 | forward | 71 |
| 12S rRNA | 72 | 1,042 | forward | 971 |
| tRNA-Val | 1,043 | 1,110 | forward | 68 |
| 16S rRNA | 1111 | 2699 | forward | 1,589 |
| tRNA-Leu | 2,700 | 2,775 | forward | 76 |
| ND1 gene | 2776 | 3730 | forward | 955 |
| tRNA-Ile | 3,731 | 3,799 | forward | 69 |
| tRNA-Gln | 3,797 | 3,868 | reverse | 72 |
| tRNA-Met | 3,872 | 3,940 | forward | 69 |
| ND2 gene | 3941 | 4982 | forward | 1,042 |
| tRNA-Trp | 4,983 | 5,049 | forward | 67 |
| tRNA-Ala | 5,059 | 5,126 | reverse | 68 |
| tRNA-Asn | 5,128 | 5,200 | reverse | 73 |
| rep origin | 5,201 | 5,233 | reverse | 33 |
| tRNA-Cys | 5,234 | 5,300 | reverse | 67 |
| tRNA-Tyr | 5,301 | 5,367 | reverse | 67 |
| COX1 gene | 5,380 | 6,921 | forward | 1,542 |
| tRNA-Ser | 6,923 | 6,990 | reverse | 68 |
| tRNA-Asp | 6,996 | 7,064 | forward | 69 |
| COX2 gene | 7,065 | 7,748 | forward | 684 |
| tRNA-Lys | 7,751 | 7,819 | forward | 69 |
| ATP8 gene | 7,820 | 8,023 | forward | 204 |
| ATP6 gene | 7,981 | 8,661 | forward | 681 |
| COX3 gene | 8,661 | 9,444 | forward | 784 |
| tRNA-Gly | 9,445 | 9,513 | forward | 69 |
| ND3 gene | 9,514 | 9,860 | forward | 347 |
| tRNA-Arg | 9,861 | 9,929 | forward | 69 |
| ND4L gene | 9,930 | 10,226 | forward | 297 |
| ND4 gene | 10,220 | 11,603 | forward | 1,384 |
| tRNA-His | 11,604 | 11,666 | forward | 63 |
| tRNA-Ser | 11,667 | 11,724 | forward | 58 |
| tRNA-Leu | 11,725 | 11,794 | forward | 70 |
| ND5 gene | 11,795 | 13,606 | forward | 1,812 |
| ND6 gene | 13,603 | 14,130 | reverse | 528 |
| tRNA-Glu | 14,131 | 14,199 | reverse | 69 |
| CYTB gene | 14,203 | 15,342 | forward | 1,140 |
| tRNA-Thr | 15,347 | 15,414 | forward | 68 |
| tRNA-Pro | 15,417 | 15,485 | reverse | 69 |
| D-loop | 15,486 | 16,765 | forward | 1,280 |
Fig. 2.
The complete mitogenome of N. coucang insularis.
Table 2.
Genetic distances (in percentage, %) calculated among the Nycticebus mitogenomes using the Kimura 2-parameter model as implemented in MEGA v7.
| Species/Subspecies | 1 | 2 | 3 | 4 | |
|---|---|---|---|---|---|
| 1. | N. coucang insularis | ||||
| 2. | N. coucang | 1.145 | |||
| 3. | N. bengalensis | 1.133 | 0.504 | ||
| 4. | N. pygmaeus | 11.387 | 11.402 | 11.387 |
Fig. 3.
Phylomitogenomic relationship of the genus Nycticebus as constructed using the neighbor-joining method. Illustrations of Nycticebus were taken from [9] with permission.
2. Experimental design, materials, and methods
Genomic DNA (gDNA) was extracted from the buccal swab sample using QIAamp® DNA Mini Kit (Qiagen, Germany). gDNA was later sheared using the M220 Focused-ultrasonicator (Covaris, USA) and the library was prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) according to the manufacturer's protocol and sequenced on the MiSeq™ Benchtop Sequencer (2 × 250 bp paired-end reads) (Illumina, USA). BOWTIE2 [3] as a plugin in GENEIOUS v10.1.3 [4] was used to assemble a total of 1,318,109 short read sequences to construct reliable mitogenome using a reference sequence of Nycticebus coucang (GenBank Accession number: NC_002765). The mitogenome was annotated using the MITOS annotation web service [5]. In summary, the entire mitogenome is 16,765 bp in length which are made up of 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region as summarized in Table 1 while Fig. 2 showed the gene organization. Genetic distances among Nycticebus were also calculated using the Kimura 2-parameter model [6] implemented in MEGA v7 [7] as shown in Table 2.
To construct the phylomitogenomic relationship within the genus Nycticebus, available mitogenomes of N. bengalensis (KC977312, KY436589, and NC_021958), N. coucang (NC_002765), and N. pygmaeus (NC_033381) were aligned using MUSCLE [8] as implemented in GENEIOUS v10.1.3. The neighbor-joining method was used for the phylomitogenomic tree construction (Fig. 3) as implemented in MEGA v7 with 2000 bootstrap replications and Kimura 2-parameter model.
Acknowledgments
The authors would like to thank the Small Mammals Inventory Team of PERHILITAN for their assistance during sampling, the Director General of PERHILITAN for the support and permission to conduct this study, and to Monash University Malaysia for providing the necessary facilities and equipment. Special thanks to Helga Schulze and Emeritus Prof. Colin Groves for permission to use the slow loris illustrations and Universiti Malaysia Terengganu for publication funding.
Footnotes
Transparency document associated with this article can be found in the online version at https://doi.org/10.1016/j.dib.2019.104058.
Transparency document
The following is the transparency document related to this article:
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