The advent of single-molecule sequencing technology dramatically changed access to genomic resources for all species. PacBio Sequel II and Sequel IIe system delivers highly accurate reads (HiFi reads) that enables assembly of high-quality genomes and transcriptomes with a single SMRT Cell 8M. PacBio sequencing has been used to sequence the highly complex and repetitive genomes and transcriptomes such as California redwood, Norway spruce, Scots pine, to agriculturally important crops including maize, rice, barley, wheat, and quinoa. Continued technical advances have led to increasing outputs, lower cost, and greater access. Recently, HiFi reads have ushered in new assembly tools that enables directly phased genome assemblies. Using long reads, we now not only have the ability to sequence full-length transcripts for genome annotation, but also look at tissue- and allele-specific isoform expression, under different conditions, in many individuals. Furthermore, long reads can be applied to look at transcriptome at the single cell level, to monitor allele specific expression single cell level. In this workshop, we will cover applications of long read sequencing for the purpose of genome and transcriptome sequencing for plants and their associated microbiome.