Upgrading Citrus Genome Sequence Resources: Providing the Most Complete Tools Necessary for Genome Editing Strategies to Create HLB Resistant Cultivars

Upgrading Citrus Genome Sequence Resources: Providing the Most Complete Tools Necessary for Genome Editing Strategies to Create HLB Resistant Cultivars

Report Date: 10/22/2022
Project: 18-010   Year: 2022
Category: Plant Improvement
Author: Fred Gmitter
Sponsor: Citrus Research and Development Foundation

This is the final quarterly report for the project. We were lacking sufficient PacBio long read coverage for Ruby Red grapefruit and Shiikuwasha, to complete the series of seven commercially important citrus for which we aimed to provide the highest possible quality genome assemblies to a chromosome scale and with the greatest accuracy and contiguity technically possible. New HMW DNA preparations were made from the last two selections, and PacBio sequencing has begun. To provide the best possible annotation of the genomes, we required broader collections of tissue types to maximize the number of expressed genes we can find for annotation of the assemblies. We collected samples of tender flush, mature leaves, flowers, young and nearly mature fruit, bark, and for some accessions leaf tissue with and without symptoms of CLas infection and citrus canker. RNA samples were prepared and for two of the seven genomes, we have completed pooled sample RNAseq using the PacBio Seq IIe platform to have full-length transcript reads, and tissue-specific barcoded samples Illumina short reads, to enable tissue specific gene expression studies as well. Five of the seven genomes have been assembled using both the PacBio and Hi-C sequencing and assembly using Hi-Rise; preliminary assemblies of the last two listed above will be completed once the new PacBio reads are available. We have focused on finalizing two of the seven genomes that are most near to full completion, while continuing to generate genome and transcriptome data for the remaining five These two have had their chromosomes properly phased, multiple previous unanchored sequence contigs have now been integrated, centromeric regions have been defined, telomeric regions have been polished, and we have resolved nearly all highly repetitive sequences in these regions on a scale unmatched by any other citrus genome assembly. We are confident that these two are the most perfect and accurate citrus genome assemblies possible with current sequencing technologies and assembly tools. The RNAseq data for these two, mentioned above, are being used currently to complete the annotation of the assembly, a manuscript is being written, and we anticipate making these two assemblies public in the near future. The same steps applied to these two as described above, will be implemented with the remaining five genomes, and we will take these all to the same level of completeness and perfection.     


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