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. We performed Hi-C sequencing with two genomes and incorporated these data with PacBio sequence of one of our target genomes resulting in an improved chromosome scale assembly. The two parental chromosomes of the target genome were phased/separated using Illumina short reads from citrons, pummelos and mandarins. By genome alignment and comparison to the Poncirus assembly (see below), minor assembly errors in repetitive regions have been fixed, resulting in a polished assembly; transcript sequencing for annotation (i.e., identify all the genes within the genome) currently is in progress. The availability of high-quality assemblies for the 3 basic species (C. medica, reticulata, and maxima) will allow a more thorough and complete characterization of large-scale structural variation (SVs: deletions, insertions, etc.) in genomes of commercial interest. These SVs are the driving force for phenotypic diversity especially among somatic mutants (e.g., different oranges, grapefruits), and this information will become more important as we test different sweet orange mutants exhibiting enhanced tolerance of HLB. A manuscript is in preparation on this work. As an example of the utility of these quality-improved new citrus genome assemblies, we have examined the polyembryonic allele associated with a MITE transposon insertion in the promoter of the CitRKD1 gene in the mandarin lineage, for sequence completeness. Previous reference assemblies either lacked this allele (the MITE insertion obviously is absent in the monoembryonic Clementine reference) or were missing important sequence in the promoter region of the gene (in the sweet orange reference assembly from China). Full knowledge of the polyembryony gene in citrus is important because it is the basis for rootstock propagation by nucellar seedlings, and it is an impediment to breeding by preventing the ability to make hybrids using polyembryonic seed parents. More importantly, this example demonstrates the quality of our assemblies; lacking promoter sequence for important HLB-resistance candidate genes could lead to CRISPR editing failures, which is exactly what we proposed to prevent through successful achievement of the objectives of this project. We completed and published on the first ever high-quality reference genome of Poncirus trifoliata using the same pipeline used for this project, and a manuscript was published in The Plant Journal (https://doi.org/10.1111/tpj.14993), and the sequence has been released to the global citrus research community through Phytozome and the Citrus Genome Database. By mining this new genome, we identified candidate genes within previously identified chromosomal regions for HLB tolerance, including a transcription factor gene and one disease resistance-like gene that are up-regulated by CLas and positively selected in trifoliate orange. These genes are promising candidate genes for further research and were highlighted in our published manuscript, so other researchers may also begin to explore their potential.