UP, Silliman Achieve Genomic Milestone for Endangered Visayan Spotted Deer

By Francis Allan L. Angelo

The Philippines has reached a significant milestone in conservation genomics with the sequencing of the Visayan Spotted Deer’s genome, a move that strengthens ongoing efforts to preserve one of the world’s rarest deer species.

The breakthrough, led by researchers from the University of the Philippines (UP) and Silliman University (SU), is expected to enhance breeding programs and genetic diversity assessments crucial for the survival of the critically endangered species.

The Visayan Spotted Deer (Rusa alfredi), native to the Philippines, once thrived across Panay, Guimaras, Negros, Cebu, and Masbate. However, rampant deforestation and hunting have pushed the species to the brink, leaving only small populations in the mountainous areas of Panay and Negros.

In a collaborative effort, the Philippine Genome Center’s satellite facility at UP Visayas (PGC Visayas) partnered with Silliman University’s Center for Tropical Conservation Studies (CENTROP) to sequence the deer’s genome. CENTROP manages the world’s largest captive population of the Visayan Spotted Deer, with a long-term goal of reintroducing them into their natural habitat.

Genome Sequencing for Conservation

Using next-generation sequencing technology, PGC Visayas researchers successfully decoded and assembled the deer’s genome. Persie Mark Sienes, a lead researcher from SU’s Biology Department, highlighted the importance of this development in managing the species’ genetic health.

“The deer’s genome will be useful to design species-specific microsatellite markers, assess genetic diversity, and determine levels of inbreeding in captive populations,” Sienes said. “This will significantly improve current breeding efforts and mitigate the negative effects of breeding with small population sizes.”

With this first-ever draft genome of the Visayan Spotted Deer, the possibility of implementing scientifically guided breeding programs is now within reach.

Scientific Collaboration, National Pride

The successful sequencing effort reflects the increasing capacity of Filipino scientists to conduct world-class genomics research. Prof. Victor Marco Emmanuel Ferriols, Assistant to the Executive Director for PGC Visayas, underscored the importance of investing in local research talent and infrastructure.

“Boosting conservation efforts for the Visayan Spotted Deer highlights the homegrown talent and capabilities of our scientists and their ability to maximize investments in R&D infrastructure, especially those in the regions,” Ferriols said.

The sequencing project was led by Ma. Carmel F. Javier and Albert C. Noblezada of PGC Visayas, in collaboration with scientists from SU, UP Diliman’s Marine Science Institute, and UP Visayas’ National Institute of Molecular Biology and Biotechnology. Their work was published in GigaByte on February 24, 2025.

Challenges in Conservation Genomics

Despite the scientific breakthrough, the researchers faced significant challenges in obtaining permits to collect samples and securing sustained funding for genome sequencing.

Javier noted that while laboratory procedures were manageable, regulatory hurdles and financial constraints often slowed progress.

“The value of genomic studies may not be so obvious or fully recognized in the Philippines, but sequencing the genome of the Visayan Spotted Deer opens up more opportunities for research and collaboration in conservation,” she said.

Noblezada, who led the bioinformatics analysis, expressed hope that the project would inspire more genomic research partnerships for other endangered species.

The Visayan Spotted Deer’s genome is the first endangered endemic species to be sequenced and assembled entirely in the Philippines.

The research team believes this success sets a precedent for sequencing other endangered species found on the country’s new polymer banknotes, which were launched by the Bangko Sentral ng Pilipinas (BSP) in December 2024 to promote biodiversity conservation.

As part of the new polymer series, the 500-piso note features the Visayan Spotted Deer, while other denominations showcase similarly threatened species.

With the growing capabilities of PGC Visayas and other local research institutions, scientists are optimistic about sequencing more species to aid conservation efforts.

PGC Visayas, established in 2019 with support from UP and the Department of Science and Technology (DOST), acquired its sequencing technology in 2021 during the COVID-19 pandemic, thanks to funding from the Department of Health (DOH) and the Department of Budget and Management (DBM).

The center, which is located at Room 205, 2nd floor of the Regional Research Center Building of UP in Miagao campus, now serves as a hub for genomics research, bioinformatics analysis, and training programs for regional scientists.

For R&D collaboration in Omics research, email pgc.upvisayas@up.edu.ph or contact Cell Number 09178116643 or send a message to https://www.facebook.com/PGCVisayas.