To investigate the genetic and structural variations between Dan340 and other maize inbred lines, we used pbsv (Version 2.2.2) [1]. First, the PacBio reads of B73 and Mo17 were downloaded from MaizeGDB [2], and the PacBio reads of SK were obtained from the National Genomics Data Center [3]. Next, the subreads were aligned to the Dan340 reference genome assembled in this study using pbmm2 to generate a bam file. Then, samtools (Version 1.7, RRID:SCR_002105) [4] was used to identify and split the bam file based on chromosomes and scaffolds. Afterward, pbsv discover was used to generate svsig files for different chromosomes and scaffolds. The svsig files of multiple samples were then used together to perform the structural variations (SV) joint calling with “pbsv call”, thus generating the vcf files. The high-quality Dan340 reference genome allowed us to identify large SVs in different maize inbred lines. By mapping the PacBio long reads of B73 to the Dan340 genome, we identified 8,289 structural variations (longer than 500 bp) between the two representative maize genomes, including 1,653 insertions, 6,537 deletions, 36 inversions, and 63 duplications (Table 1). Furthermore, the structural variations presented in Mo17 and SK were also detected in this study (Tables 2 and 3). This dataset provides abundant variation resources for future molecular improvements and breeding in maize. [1] PBSV. https://github.com/PacificBiosciences/pbsv. Accessed 2021 Sep 11. [2] MaizeGDB. https://maizegdb.org/download. 52. Accessed 2021 Aug 8. [3] National Genomics Data Center. https://ngdc.cncb.ac.cn/search/?dbId=gsa&q=CRA001371. Accessed 2021 Aug 8. [4] 59.Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. Twelve years of SAMtools and BCFtools. Gigascience. 2021 Feb 16;10(2):giab008. doi: 10.1093/gigascience/giab008. Table 1 Structural variations between Dan340 and B73. Chr. Number Insertion Number Insertion Length (bp) Deletion Number Deletion Length (bp) Inversion Number Inversion Length (bp) Duplication Number Duplication Length (bp) 1 266 432,723 998 13,194,452 7 120,136 8 311,433 2 183 316,530 743 10,075,332 7 177,706 9 261,774 3 201 381,536 838 11,475,573 5 24,457 7 37,754 4 183 303,142 698 9,809,218 2 113,807 7 255,958 5 181 330,690 651 9,519,227 3 108,429 6 121,490 6 122 252,117 527 7,723,482 3 55,199 8 300,610 7 140 226,942 512 7,146,020 2 49,011 4 122,886 8 140 204,697 577 7,720,113 1 80,400 3 42,148 9 121 219,627 569 7,539,785 3 17,955 9 114,595 10 116 209,091 424 6,256,310 3 130,724 2 40,306 Table 2 Structural variations between Dan340 and Mo17. Chr. Number Insertion Number Insertion Length (bp) Deletion Number Deletion Length (bp) Inversion Number Inversion Length (bp) Duplication Number Duplication Length (bp) 1 171 226,204 1049 1,4591,535 10 223,256 6 157,653 2 102 164,536 668 9,437,198 4 40,341 5 149,456 3 121 196,809 767 11,363,033 0 0 4 26,512 4 96 146,230 628 8,996,741 3 50,713 10 169,360 5 102 147,883 660 9,449,523 3 190,422 7 85,046 6 75 101,725 567 8,423,089 3 130,693 3 20,573 7 84 119,614 521 7,784,957 4 159,203 6 275,006 8 83 123,397 603 8,751,739 2 30,781 5 214,099 9 61 83,589 529 7,194,721 1 10,328 3 55,228 10 75 126,350 497 6,832,836 5 227,243 4 159,642 Table 3 Structural variations between Dan340 and SK. Chr. Number Insertion Number Insertion Length (bp) Deletion Number Deletion Length (bp) Inversion Number Inversion Length (bp) Duplication Number Duplication Length (bp) 1 244 355,348 1,226 17,656,467 15 228,724 16 404,487 2 133 220,966 842 12,542,190 6 244,805 5 76,672 3 173 286,569 894 12,961,969 4 7657 6 96,601 4 211 338,458 1012 14,231,859 3 70,762 14 315,182 5 160 248,233 786 10,660,145 8 280,670 5 206,286 6 93 118,612 588 8,923,936 4 55,606 2 1760 7 115 175,971 622 8,865,791 1 30,856 9 233,675 8 143 210,185 685 10,443,437 2 3061 6 152,412 9 114 186,005 647 8,682,441 4 9595 7 37,664 10 109 159,668 559 8,726,188 4 132,337 4 95,237