Masaaki Taniguchi
Principal Investigator
NARO
David Gamarra
Principal Investigator
NARO
Project Overview
Our main objective is to construct a reference genome for Japanese wild boar (Sus scrofa leucomystax) and Ryukyu wild boar (Sus scrofa riukiuanus). Therefore, we first extracted high molecular weight genomic DNA (HMW-DNA) from existing biological tissue samples held by NARO during this year. However, the samples were collected in 2014 and storage conditions did not allow to obtain best quality HMW-DNA for long-read sequencing analyses. Therefore, we started collecting new Japanese wild boar samples from skeletal muscle from a male from Yamanashi Prefecture (May 2024), two males from Saga Prefecture (December 2024), and two males from Nagasaki Prefecture (January 2025). First, HMW-DNA was extracted from the skeletal muscle of the individual from Yamanashi Prefecture. The quality control analyses confirmed that this sample was suitable for Long-read sequencing analysis. Therefore, Long-read sequencing was performed using PromethION (Oxford Nanopore Technologies).
The analysis of sequence data obtained from the HMW-DNA extracted from the skeletal muscle samples from Yamanashi Prefecture has the potential to construct the first Japanese wild boar reference genome, both in terms of quality and quantity, and we are currently continuing the assembly work (connecting sequence fragment data). In addition, we performed long-read sequencing analysis on Japanese wild boar from Nagasaki Prefecture (from NARO collection) and Ryukyu wild boars from Okinawa Prefecture. However, HMW-DNA from Ryukyu wild boars seems to be not as good as Yamanashi sample in terms of DNA fragment length. In summary, the detection rate of known ortholog genes, which is one of the evaluation indicators of assembly data, was ~98.4% for the Yamanashi and Nagasaki samples, but 94.3% for the Ryukyu wild boar samples. At first instance, lower HMW-DNA quality samples might be insufficient for constructing a reference genome. However, we are improving our assembly pipelines for these samples and considering mapping of genomic data to the Japanese wild boar reference genome that will be completed in a near future.
