TY - JOUR T1 - Genome assembly of the maize inbred line A188 provides a new reference genome for functional genomics JF - bioRxiv DO - 10.1101/2021.03.15.435372 SP - 2021.03.15.435372 AU - Fei Ge AU - Jingtao Qu AU - Peng Liu AU - Lang Pan AU - Chaoying Zou AU - Guangsheng Yuan AU - Cong Yang AU - Shibin Gao AU - Guangtang Pan AU - Jianwei Huang AU - Langlang Ma AU - Yaou Shen Y1 - 2021/01/01 UR - http://biorxiv.org/content/early/2021/03/16/2021.03.15.435372.abstract N2 - Heretofore, little is known about the mechanism underlying the genotype-dependence of embryonic callus (EC) induction, which has severely inhibited the development of maize genetic engineering. Here, we report the genome sequence and annotation of a maize inbred line with high EC induction ratio, A188, which is assembled from single-molecule sequencing and optical genome mapping. We assembled a 2,210 Mb genome with a scaffold N50 size of 11.61 million bases (Mb), compared to those of 9.73 Mb for B73 and 10.2 Mb for Mo17. Comparative analysis revealed that ∼30% of the predicted A188 genes had large structural variations to B73, Mo17 and W22 genomes, which caused considerable protein divergence and might lead to phenotypic variations between the four inbred lines. Combining our new A188 genome, previously reported QTLs and RNA sequencing data, we reveal 8 large structural variation genes and 4 differentially expressed genes playing potential roles in EC induction.Highlight Our manuscript presents a high-quality reference genome of the inbred line A188, and provides new insights into candidate genes underlying maize embryonic callus induction and other maize agronomic traits.Competing Interest StatementThe authors have declared no competing interest. ER -