Sago Palm Genome Size Estimation via Real-Time Quantitative PCR
Article Sidebar
Main Article Content
Abstract
Sago palm, Metroxylon sagu Rottb., is an underutilized indigenous food crop that can be found mainly in the South East Asia and Pacific regions. It is a main starch producer and socioeconomically important crop in the South East Asia region including Malaysia. The sago starch provides foronsiderable potential to food security in the places where it is grown. However, not many molecular works have been reported thus far. In the post genomic era, sago plant genome sequencing is very important for sustainable starch development in these regions. Therefore, determination of the genome size is prerequisite to full genome sequencing and assembly. Here we report on the use of real-time quantitative polymerase chain reaction (qPCR) in determining the genome size. For this work, we calculated the genome size, G (bp) of M. sagu based on qPCR-derived copy number of two single copy genes. Pichia pastorisas a control to estimate sago palm genome size. With this technique, the genome size of M. sagu was calculated to be 1.87 Gbp. This genome size information would be beneficial for subsequent molecular work including genome sequencing and analysis on this economically important crop plant.
Keywords: Genome size; Metroxylon sagu; real-time PCR; copy number; Pichia pastoris
*Corresponding author: Tel.: +60 82 58 3038 Fax: +60 82 58 3160
E-mail: hairulroslan@hotmail.com
Article Details
Copyright Transfer Statement
The copyright of this article is transferred to Current Applied Science and Technology journal with effect if and when the article is accepted for publication. The copyright transfer covers the exclusive right to reproduce and distribute the article, including reprints, translations, photographic reproductions, electronic form (offline, online) or any other reproductions of similar nature.
The author warrants that this contribution is original and that he/she has full power to make this grant. The author signs for and accepts responsibility for releasing this material on behalf of any and all co-authors.
Here is the link for download: Copyright transfer form.pdf
References
[2] Hare, E.E. and Johnston, J.S., 2011. Genome size determination using flow cytometry of propidium iodide-stained nuclei. Methods in Molecular Biology, 772, 3-12.
[3] Zhang, J.Z. and Fan M.Y., 2002. Determination of genome size and restriction fragment length polymorphism of four Chinese rickettsial isolates by pulsed-field gel electrophoresis. Acta Virologica, 46, 25-30.
[4] D’Hondt, L., Hofte, M., Van Bockstaele, E. and Leus, L., 2011. Applications of flow cytometry in plant pathology for genome size determination, detection and physiological status. Molecular Plant Pathology, 12, 815-828.
[5] Mounsey, K.E., Willis, C., Burgess, S.T.G., Holt, D.C., McCarthy, J. and Fischer, K., 2012. Quantitative PCR-based genome size estimation of the astigmatid mites Sarcoptes scabiei, Psoroptes ovis and Dermatophagoides pteronyssinus. Parasites & Vectors, 5, 3. https://doi.org/10.1186/1756-3305-5-3.
[6] Henk, D.A. and Fisher, M.C., 2012. The gut fungus Basidiobolus ranarum has a large genome and different copy numbers of putatively functionally redundant elongation factor genes. Plos One; 7 (2), e31268. https://doi.org/10.1371/journal.pone.0031268
[7] Armaleo, D. and May, S., 2009. Sizing the fungal and algal genomes of the lichen Cladonia grayi through quantitative PCR. Symbiosis, 49, 43. https://doi.org/10.1007/s13199-009-0012-3
[8] Gao, J. and Scott, J.G., 2006. Use of quantitative real-time polymerase chain reaction to estimate the size of the house-fly Musca domestica genome. Insect Molecular Biology, 15, 835-837.
[9] Tsoumani, K.T. and Mathiopoulos, K.D., 2012. Genome size estimation with quantitative real-time PCR in two Tephritidae species: Ceratitis capitata and Bactrocera oleae. Journal of Applied Entomology, 136, 626-631.
[10] Kim, J.H., Roh, J.Y., Kwon, D.H., Kim, Y.H., Yoon, K.A., Yoo, S., Noh, S.J., Park, J.H., Shin, E.H., Park, M.Y. and Lee, S.H., 2014. Estimation of the genome sizes of the chigger mites Leptotrombidium pallidum and Leptotrombidium scutellare based on quantitative PCR and k-mer analysis. Parasites & Vectors, 7, 279. https://doi.org/10.1186/1756-3305-7-279
[11] Park, B. and Kim, Y., 2012. Genome size estimation of an endoparasitoid wasp, Cotesia plutellae, using quantitative real-time polymerase chain reaction. Journal of Asia-Pacific Entomology, 15, 349-353.
[12] Kaewkong, W., Imtawil, K., Maleewong, W., Intapan, P.M., Sri-Aroon, P., Wongkham, S. and Wongkham, C., 2012. Genome size estimation of liver fluke Opisthorchis viverrini by real-time polymerase chain reaction based method. Parasitology International, 61, 77-80.
[13] Jensen, M.K., Vogt, J.K., Bressendorff, S., Seguin-Orlando, A., Petersen, M., Sicheritz-Pontén, T. and Mundy, J., 2015. Transcriptome and genome size analysis of the Venus flytrap. Plos One, 10: e0123887. https://doi.org/10.1371/journal.pone.0123887
[14] Wilhelm, J., Pingoud, A. and Hahn, M., 2003. Real-time PCR-based method for the estimation of genome sizes. Nucleic Acids Research, 31: e56. https://doi.org/10.1093/ nar/gng056
[15] Dolezel, J., Bartos, J., Voglmayr, H. and Greilhuber, J., 2003. Nuclear DNA content and genome size of trout and human. Cytometry. Part A , 51, 127-8.
[16] De Schutter, K., Lin, Y-C., Tiels, P., Van Hecke, A., Glinka, S., Weber-Lehmann, J., Rouzé, P., Van de Peer, Y. and Callewaert, N., 2009. Genome sequence of the recombinant protein production host Pichia pastoris. Nature Biotechnology, 27, 561-566.
[17] Siti Suhaila, A.R., Mohd Saleh, N., Norwati, M., Mahani, M.C., Namasivayam, P. and Kandasamy, K.I., 2018. DNA content and genome size of highly valued malaysian agarwood, Aquilaria malaccensis LAMK. Malaysian Applied Biology, 47, 13-21.
[18] Tang, C., Yang, M., Fang, Y., Luo, Y., Gao, S., Xiao, X., An, Z., Zhou, B., Zhang, B.,
Tan, X., Yeang, H.Y., Qin, Y., Yang, J., Lin, Q., Mei, H., Montoro, P., Long, X., Qi, J.,
Hua, Y., He, Z., Sun, M., Li, W., Zeng, X., Cheng, H., Liu, Y., Yang, J., Tian, W.,
Zhuang, N., Zeng, R., Li, D., He, P., Li, Z., Zou, Z., Li, S., Li, C., Wang, J., Wei, D., Lai,
C.Q., Luo, W., Yu, J., Hu, S., Huang, H., 2016. The rubber tree genome reveals new
insights into rubber production and species adaptation. Nature Plants, 2, 16073. https://doi:
10.1038/nplants.2016.73.
[19] Singh, R., Ong-Abdullah, M., Low, E-L., Manaf, M.A., Rosli, R., Nookiah, R., Ooi, L.C.,
Ooi, S.E., Chan, K.L., Halim, M.A., Azizi, N., Nagappan, J., Bacher, B., Lakey, N., Smith,
S.W., He, D., Hogan, M., Budiman, M.A., Lee, E.K., DeSalle, R., Kudrna, D., Goicoechea,
J.L., Wing, R.A., Wilson, R.K., Fulton, R.S., Ordway, J.M., Martienssen,
R.A., Sambanthamurthi, R., 2013. Oil palm genome sequence reveals divergence of
interfertile species in Old and New worlds. Nature, 500, 335-339.
[20] Pellicer, J., Fay, M.F. and Leitch, I.J., 2010. The largest eukaryotic genome of them all? Botanical Journal of the Linnean Society 164, 10-15.
[21] Zonneveld, B.J.M., 2010. New record holders for maximum genome sizes for monocots and eudicots. Journal of Botany, 2010, article ID 527357. https://doi.org/ 10.1155/2010/527357.