RPAN2: Rice Pan-genome Browser 2

Rice is one of the most important food crops globally. In 2017, we created the Rice Pangenome Browser (RPAN) to present a linear pangenome based on approximately 3K rice genomes collected using short-read sequencing, providing a vital resource for rice research and breeding programs. Recent advancements in long-read (also known as third-generation) sequencing technologies have enabled the production of a growing number of high-quality individual genomes. These advancements enable the assembly of more complete and accurate pangenomes. Here, we introduce RPAN2 - an upgraded version of RPAN that retains all previous short-read data while integrating new pangenomes constructed from long-read data. This new version features both a linear and a graph-based pangenome, supported by enhanced visualization methods.

This database provides three pangenomes:

• 3K-RG: A linear rice pangenome constructed from short-read sequencing data of the 3K Rice Genome Project (3K-RGP), containing ~ 260 Mbp novel sequences and 15,362 novel genes.
• 111TGS-RG: A linear rice pangenome derived from third-generation sequencing (TGS) data of 111 rice accessions with 113 samples, comprising 879 Mb novel sequences and 19,319 novel genes.
• 326TGS-RG: A graph-based rice pangenome built from reference genome and 263 high-quality rice genomes assembled from long reads from three previous studies and additional publicly available resources.