Files
Abstract
Genomic structural variants (SV) have a significant impact on phenotypic differences. Characterization of such variants can provide insights into genomic evolution and reveal population dynamics. However, our understanding of structural variants is limited by technical and methodological challenges in genome-wide SV cataloging. In this study, we characterized genomic differences with a variety of next-generation sequencing (NGS) resources, and evaluated their performances on SV detection. As resequencing has its limitations in SV calling, we constructed high-quality genome assemblies and provided insights for structure comparison in repeat domains. To the end, we derived a full spectrum of structural variants across 26 maize lines from whole genome assemblies, and investigated their implication on genome evolution. Through SV identification with short- and long-reads, we identified differing levels of genomic damages in biolistic transformants of rice and maize. Our results indicated a high likelihood of unintended genomic damages by the transformation method and pointed out the importance of whole-genome variant detection prior to detailed analysis. To capture the true genomic diversity between the B73 reference and a maize line (B73-Ab10) with an abnormal chromosome 10, we created a de novo assembly of B73-Ab10. Through the integration of PacBio, Oxford Nanopore and Bionano technologies, we achieved a highly contiguous assembly which contains two gapless chromosomes and spans multiple tandem repeat arrays. Two adjacent inversions were characterized in Ab10 with genome alignment and the internal structure of tandem repeat arrays was revealed. With the availability of whole-genome assemblies of 26 maize lines, we inferred structural differences and studied the genomic history of Zea genus. We generated a full SV catalog across 26 maize inbreds, identified ancient haplotypes and evolutionary strata in pericentromeric area and repeat arrays, and finally inferred the divergence history of maize. We found that recurrent segregation and introgression events took place over the past million years among maize ancestors, and the ancient genomic remnants contribute to the great diversity of maize.