Previously, we generated raw sequence data for Valencia orange (S, sensitive), Ruby Red grapefruit (S), Clementine mandarin (S), LB8-9 Sugar Belle® mandarin hybrid (T, tolerant), and Lisbon lemon (T) and preliminary assemblies and analyses were carried out. Because of reduced sequencing costs, we were able to enter additional important genomes into the pipeline beyond those originally proposed, including Carrizo citrange, sour orange, and Shekwasha (an important breeding parent for HLB tolerance); these also have now been sequenced and assembled. Now, we have completed Hi-C sequencing of two genomes, and by incorporating these data with PacBio sequence assembly from two of our target genomes we have produced improved chromosome scale assemblies and have phased the two parental chromosomes of the target genomes using Illumina short reads from citrons, pummelos and mandarins. Minor assembly errors in repetitive DNA regions have been repaired, by genome alignment and comparison to the Poncirus assembly we recently published, resulting in polished assemblies of these two accessions. Initial preliminary characterizations of the presence/absence variations among the four phased haploid genomes have been made. Notable variations among these four involve transposable elements including MITES with characteristic sizes. A genome graph-based approach is being pursued, with the goal of building a genome graph containing the different types of structural variations that are now being identified. The availability of high-quality assemblies for the 3 basic species (C. medica, reticulata, and maxima) will allow thorough and complete characterization of large-scale structural variations (SVs: deletions, insertions, etc.) in our target genomes of commercial interest. SVs are a driving force for phenotypic diversity especially among somatic mutants (e.g., different oranges, grapefruits, etc.), and this type of information will become more important as we test different sweet orange mutants exhibiting enhanced tolerance of HLB and attempt to determine the underlying causes of such tolerance. Currently, we are developing this approach using 27 previously published whole genome shotgun sequences of a particular citrus species and aligning them to our high-quality assembly of the same species. We have found several distinct basic genome types, with varying admixture patterns; a detailed characterization is in progress. We now have the transcriptome data for two of our target genomes, using both Illumina and PacBio sequencing platforms, and genome annotation (i.e., identify all the genes within the genome) is in progress. Samples have been prepared and collected, and plans are in place to proceed with Hi-C sequencing of the target genomes not yet completed and polished, as well as to generate the transcriptome data required for genome annotation, and further characterization of large-scale structural variations within and among the genomes upon which we are focused.