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Heteroplasmy, Length, and Sequence Characterization of the Mitochondrial Control Region in Tomistoma schlegelii

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Abstract

This study describes the organization of the repetitive pattern in the mtDNA control region of Tomistoma schlegelii. Using newly designed primers, we detected length variations of approximately 50–100 bp among individuals, and only one individual showed a heteroplasmic band. Sequencing the region after CSB III revealed two main patterns: a repeat motif and a variable number tandem repeat (VNTR) pattern. The VNTR region, with a core unit of 104 bp, consisting of four motifs and a short AT chain, is implicated in the length variation seen among individuals of Tomistoma. A conserved motif seen in a family unit indicated that the repeat pattern was stably inherited from the maternal parent to all offspring. A combination of VNTR patterns specific to different crocodilians was seen in Tomistoma, and the overall secondary structure was shown to be similar to that in Crocodylus and Gavialis.

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Acknowledgments

We would like to thank the directors general Dato Abdul Rasid Samsudin of the Department of Wildlife and National Parks, Peninsular Malaysia (Perhilitan), and Dato Haji Len Talif Salleh of the Forest Department of Sarawak and Sarawak Forestry Corporation (SFC) for permits and permission to carry out this work. We extend our appreciation to the officers of these government bodies: Dr. Sandie Choong, Dr. Abraham Matthews, and Mr. Rauf Kadir (Perhilitan); Mr. Shahbudin Sabki (Forest Department Sarawak); Mr. Engkamat Lading (SFC); and all their staff who assisted with sample collection. We also thank Zoo Negara, Melaka Zoo, Taiping Zoo, Temerloh Mini Zoo, the crocodile farms in Kuching and Miri, Sarawak, and their personnel for assisting with sample collection. This work was funded by Universiti Tunku Abdul Rahman (UTAR); SOS Rhino, Sabah, Malaysia; the Zoological Society for the Conservation of Species and Population (Zoologische Gesellschaft für Arten- und Populationsschutz, ZGAP); and BOH Plantations Sdn. Bhd.

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Authors and Affiliations

  1. Universiti Tunku Abdul Rahman, Kuala Lumpur, Wilayah Persekutuan, Malaysia

    Taranjeet Kaur & Alan H. K. Ong

  2. Department of Pre-Clinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Lot PT 21144, Jalan Sungai Long, Bandar Sungai Long, Cheras, 43000, Kajang, Selangor, Malaysia

    Alan H. K. Ong

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  1. Taranjeet Kaur
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  2. Alan H. K. Ong
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Correspondence to Alan H. K. Ong.

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Supplementary Fig. 1

Sequence alignment of the repetitive region generated after CSB III using primer L15790. The 3’ portion of CSB III is indicated. Motifs R1 and R2 in the motif region are indicated in bold. The VNTR sequence is shaded, and the motifs in the tandem repeats are in bold. The first 6 individuals are members of a family unit, with TK008 being the maternal parent. The heteroplasmic bands of TK011 are indicated as “short” for the 2.8 kb band and “long” for the 3.0 kb band. TK006 is a homoplasmic individual possessing the same VNTR sequence as the heteroplasmic individual, TK011. (DOC 41 kb)

Supplementary material 2 (DOC 30 kb)

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Kaur, T., Ong, A.H.K. Heteroplasmy, Length, and Sequence Characterization of the Mitochondrial Control Region in Tomistoma schlegelii . Biochem Genet 49, 562–575 (2011). https://doi.org/10.1007/s10528-011-9431-y

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