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 preliminarily assembled. 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 continuing. Hi-C sequencing of the 7 remaining target genomes is underway; once completed these data will be integrated with the PacBio assembly, to produce improved chromosome scale assemblies. RNA samples of these 7 additional genomes have been prepared 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.In a related effort, our team recently compared 69 new east Asian genomes and other mainland Asian citrus to reveal a previously unrecognized wild sexual species native to Japan’s Ryukyu Islands: C. ryukyuensis, which hybridized with an ancient east Asian mandarin to produce Shekwasha (shiikuwasha) mandarin, a powerful source of HLB tolerance in rootstock breeding. Further, by studying the genomes of C. ryukyuensis-derived hybrids and other citrus. we traced the origin and spread of apomixis (nucellar embryony, a trait that is required for seed propagation of citrus rootstocks) from Mangshanyeju wild mandarins in China a few million years ago through most of the commonly known contemporary citrus types (orange, grapefruit, lemon, etc.). This work resulted in deeper understanding and new genome-based tools that can be exploited for two critically important traits in citrus genetic improvement, nucellar embryony and most importantly HLB tolerance; the research was published in Nature Communications in July 2021 (see https://doi.org/10.1038/s41467-021-24653-0). We used the PacBio Sequel platform to sequence full-length gene transcripts in the leaf tissues of sweet orange and trifoliate orange and reconstructed their leaf transcriptomes. We identified novel full-length transcripts that were not present in the published reference transcriptomes. We found that some NBS-encoding genes (nucleotide binding site genes, one typical class of disease resistance genes in plants) underwent alternative splicing. One alternatively spliced NBS transcript expressed in HLB symptomatic leaf and fruit of sweet orange, and another alternatively spliced NBS transcript was differentially expressed in CLas-infected trifoliate orange samples, suggesting that isoforms of some NBS-encoding genes may play an important role in HLB tolerance of trifoliate orange, or alternatively HLB susceptibility in sweet orange. The new transcriptomes will be useful to identify candidate genes for disease resistance that have been missed in the published citrus genomes and transcriptomes.