Uncovering the underlying mechanisms of the complex phenotype formation and evolution is the key problem in life sciences. Two major steps are included in this process. One is the accurate and complete genome assembly, and another is genetics and epigenetics functional pattern discovery from the high-dimensional multi-omics data. I have achieved a series of original achievements in the genome assembly and functional pattern discovering. 1) Proposed a sequence graph model based on sequential k-mer patterns to address the accuracy assembly of high repetitive sequence, such as telomere and centromere, and obtain the accurate and complete reference genome. 2) Developed efficient graph pattern mining methods based on the proposed multi-omics dimensionality reduction approaches to discover the genetics and epigenetics functional patterns. 3) By applying the developed methods on three Papaver species, the applicant obtained high-quality genome for each species and revealed punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway. The applicant has published 20 papers as first/corresponding author (including the co-first/corresponding) in Nature, Science, Nature Communications, Fundamental Research, Molecular Biology and Evolution, Genome Biology, Briefings in Bioinformatics, Bioinformatics，Genomics Proteomics & Bioinformatics (the total IF is 200). The total citation of my paper is over 1000 times, and my h-index is 16.