Applied Genomics Techniques Used to Understand Orangutans
Orangutans are the largest tree-climber mammals in the world. Due to their dependency on the forest habitat, orangutans are especially affected by deforestation activities that are often carried out for economic reasons within the areas they proliferate. To promote conservation efforts, and better understand their phylogenetic relationship with other primates, two species of orangutans were sequenced. Using these genomic sequences as a reference, conservation scientists are now able to monitor, in real time, how the orangutan populations in the wild are changing over a period, and decide whether decisive actions are required to prevent any further decline.
Because of deforestation, hunting and disease, almost 150,000 orangutans have disappeared from Borneo since 1999. All three species of orangutans have experienced sharp population declines and are characterized as endangered or critically endangered.
Recent research by Kronenberg and others, used long-read sequencing along with full-length complementary DNA sequencing and a multiplatform scaffolding approach to develop high quality contiguous ape genome assemblies without requiring a human genome scaffold. Their research provides the most comprehensive view to date of intermediate-size structural variation and highlights genes associated with structural variation and brain-expression differences between humans and apes. The ability to develop high-resolution assemblies like these will improve evolutionary analyses. – Kronenberg, Z. N., et al. (2018) High-resolution comparative analysis of great ape genomes. Science. 360:6393. DOI: 10.1126/science.aar6343.
“Gardeners of the Forest”
Orangutans eat hundreds of different types of fruit, and spread the seeds throughout the forest in their dung. They also make a new nest to sleep in every evening, breaking branches and allowing light through the thick canopy onto the forest floor, helping young plants to thrive and grow.
Automating Long-Read Sequencing
PerkinElmer has created an efficient workflow to automate the 10x Genomics® long-read sequencing technology which includes high molecular weight gDNA extraction, sample QC, and sample prep, providing Linked-Reads sequencing capabilities for a variety of sample types including saliva, dried blood spots, blood, and plasma.