Development of Microsatellites for the Philippine Eagle, Pithecophaga jefferyi, Using Next-generation Sequencing
Perry S. Ong1†, Vonette Joi B. Padilla1, Marco Philip B. Serafica1, Adrian U. Luczon1, Dennis Joseph I. Salvador2, Melizar V. Duya1, Ian Kendrich C. Fontanilla1, and Jonas P. Quilang1*
1Institute of Biology, University of the Philippines Diliman
Quezon City, Metro Manila 1101 Philippines
2Philippine Eagle Foundation, Davao City, Davao Del Sur 8000 Philippines
†Deceased 02 Mar 2019
The Philippine Eagle, Pithecophaga jefferyi, is a critically endangered bird of prey that is endemic to the dipterocarp forests of the Philippines. In this study, data from next-generation sequencing (NGS) were used for the development of microsatellites for the Philippine Eagle. A total of 49,965 microsatellite loci were predicted and 20,960 primer pairs were designed. Forty (40) of these pairs were synthesized and were tested on 20 captive individuals. Twenty (20) of these markers showed high amplification success rates and exhibited polymorphism. A maximum of 24 alleles was detected across the 20 markers with an average of 13.9 alleles, which is remarkably higher than other microsatellite studies in eagles. The resulting values for observed heterozygosity (Ho) ranged from 0 to 1.00 with an average of 0.290, while expected heterozygosities ranged from 0.791 to 0.968 with an average of 0.910.
The Philippine Eagle, Pithecophaga jefferyi Ogilvie-Grant 1896, occurs primarily in the steep terrains and heavy forests of the four islands in the Philippines: Luzon, Samar, Leyte, and Mindanao (Bueser et al. 2003). The Philippine Eagle has a small and rapidly decreasing population due to extensive deforestation and is classified as a critically endangered species. Owing to the increasing concern over the endangered status of the Philippine Eagle, studies have been initiated across the country to investigate the bird’s genetic background. DNA barcodes from 43 individuals of six species of captive Accipitrids, including 31 individuals of Philippine Eagle found in the Philippine Eagle Center (PEC), were reported by Ong et al. (2011). Luczon et al. (2014) determined the genetic diversity of 22 individuals of Philippine Eagle (19 of which came from the wild and 3 were captive-bred) using mitochondrial control region. However, a more thorough knowledge of its genetic diversity is needed to provide more insights into the management and conservation of the species. . . . read more
ABDELKRIM J, ROBERTSON BC, STANTON JAL, GEMMELL NJ. 2001. Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing. BioTechniques 46(3): 185–192.
BUESER GLL, BUESER KG, AFAN DS, SALVADOR DI, GRIER JW, KENNEDY RS, MIRANDA HC. 2003. Distribution and nesting density of the Philippine Eagle Pithecophaga jefferyi on Mindanao Island, Philippines: What do we know after 100 years? Ibis 145(1): 130–135.
GALBUSERA P, VAN DONGEN S, MATTHYSEN E. 2000. Cross-species amplification of microsatellite primers in passerine birds. Conserv Genet 1(2): 163–168.
KOFLER R, SCHLÖTTERER C, LELLEY T. 2007. SciRoKo: A new tool for whole genome microsatellite search and investigation. Bioinformatics 23(13): 1683–1685.
KOLPAKOV R, BANA G, KUCHEROV G. 2003. mreps: Efficient and flexible detection of tandem repeats in DNA. Nucleic Acids Res 31(13): 3672–3678.
LUCZON AU, FONTANILLA IKC, ONG PS, BASIAO ZU, SUMAYA AMT, QUILANG JP. 2014. Genetic diversity of the critically endangered Philippine Eagle Pithecophaga jefferyi (Aves: Accipitridae) and notes on its conservation. J Threat Taxa 6(10): 6335–6344.
ONG PS, LUCZON AU, QUILANG JP, SUMAYA AMT, IBANEZ JC, SALVADOR DJ, FONTANILLA IKC. 2011. DNA barcodes of Philippine accipitrids. Mol Ecol Resour 11(2): 245–254.
THIEL T, MICHALEK W, VARSHNEY R, GRANER A. 2003. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106(3): 411–422.
UNTERGASSER A, CUTCUTACHE I, KORESSAAR T, YE J, FAIRCLOTH BC, REMM M, ROZEN SG. 2012. Primer3 – New capabilities and interfaces. Nucleic Acids Res 40(15): e115.
YEH FC, YANG RC, BOYLE TBJ, YE ZH, MAO JX. 1999. POPGENE version 1.32, the user-friendly shareware for population genetic analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Canada. Retrieved from http://www.ualberta.ca/fyeh on 13 May 2018.