biostudies-literatureZhang Fthethe Agricultural Science and Technology Innovation Program and the Cooperation and Innovation Missionthe CAAS Innovative Team Awardthe National High-level Personnel of Special Support ProgramNatural Science Foundation of Shanghaithe Hainan Yazhou Bay Seed Lab ProjectNational Natural Science Foundation of Chinathe Hainan Provincial Joint Project of Sanya Yazhou Bay Science and Technology CitySJTU JiRLMDS Joint Research Fund853-863https://www.ebi.ac.uk/biostudies/studies/S-EPMC9104699biostudies-literatureUnknown32(5)The concept of pan-genome, which is the collection of all genomes from a population, has shown a great potential in genomics study, especially for crop sciences. The rice pan-genome constructed from the second-generation sequencing (SGS) data is about 270 Mb larger than <i>Nipponbare</i>, the rice reference genome (NipRG), but it is still disadvantaged by incompleteness and loss of genomic contexts. The third-generation sequencing (TGS) with long reads can help to construct better pan-genomes. In this paper, we report a high-quality rice pan-genome construction method by introducing a series of new steps to deal with the long-read data, including unmapped sequence block filtering, redundancy removing, and sequence block elongating. Compared to NipRG, the long-read sequencing-based pan-genome constructed from 105 rice accessions, which contains 604 Mb novel sequences, is much more comprehensive than the one constructed from ∼3000 rice genomes sequenced with short reads. The repetitive sequences are the main components of novel sequences, which partially explain the differences between the pan-genomes based on TGS and SGS. Adding six wild rice accessions, there are about 879 Mb novel sequences and 19,000 novel genes in the rice pan-genome in total. In addition, we have created high-quality reference genomes for all representative rice populations, including five gapless reference genomes. This study has made significant progress in our understanding of the rice pan-genome, and this pan-genome construction method for long-read data can be applied to accelerate a broad range of genomics studies.Genome researchLong-read sequencing of 111 rice genomes reveals significantly larger pan-genomes.PMC9104699MDS-JF-2019A07B21HJ022320ZR14282003217064331971928B21HJ0508U21A20214CAAS-ZDXT202001B21HJ0215320LH044Zhang FZheng XLi ZDong XWei CWang WXue HLi MXu JfalseLong-read sequencing of 111 rice genomes reveals significantly larger pan-genomes.The concept of pan-genome, which is the collection of all genomes from a population, has shown a great potential in genomics study, especially for crop sciences. The rice pan-genome constructed from the second-generation sequencing (SGS) data is about 270 Mb larger than <i>Nipponbare</i>, the rice reference genome (NipRG), but it is still disadvantaged by incompleteness and loss of genomic contexts. The third-generation sequencing (TGS) with long reads can help to construct better pan-genomes. In this paper, we report a high-quality rice pan-genome construction method by introducing a series of new steps to deal with the long-read data, including unmapped sequence block filtering, redundancy removing, and sequence block elongating. Compared to NipRG, the long-read sequencing-based pan-genome constructed from 105 rice accessions, which contains 604 Mb novel sequences, is much more comprehensive than the one constructed from ∼3000 rice genomes sequenced with short reads. The repetitive sequences are the main components of novel sequences, which partially explain the differences between the pan-genomes based on TGS and SGS. Adding six wild rice accessions, there are about 879 Mb novel sequences and 19,000 novel genes in the rice pan-genome in total. In addition, we have created high-quality reference genomes for all representative rice populations, including five gapless reference genomes. This study has made significant progress in our understanding of the rice pan-genome, and this pan-genome construction method for long-read data can be applied to accelerate a broad range of genomics studies.2022-01-01T00:00:00Z2022 May2025-04-19T04:22:00.469Z2025-04-19T04:22:00.469ZS-EPMC91046993539627510.1101/gr.276015.121