2019-10_18-010_Gmitter PR – 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: 12/30/2019
Project: 18-010   Year: 2019
Category: Plant Improvement
Author: Fred Gmitter
Sponsor: Citrus Research and Development Foundation, Inc.

The project has been proceeding well and mostly is on track to achieve the first year’s objectives, to generate PacBio genome sequence data, to begin assembly of the genomes as data are generated, and to prepare plant materials for the next phases of the project (which will include Omni-C library construction and sequencing for chromosome scale assemblies, and for transcriptome sequencing to inform annotation. Using optimized protocols for DNA purification, we have produced the quantity of HMW DNA, and quality of the preps required for PacBio long read sequencing. Samples were sent to the UC Berkeley Genome Sequencing Laboratory, and sequencing libraries were constructed there. Contractual issues between UF and UCB/LBNL, based on language in the UF-CRDF contract, delayed the start of the sequencing runs. Sequencing runs were finally authorized in mid-September, despite the lack of resolution of the contractual issues. The first genomes were finished running in late October. Preliminary output from the first genome run showed that >250 Gbp of sequence were produced, yielding potentially > 83X coverage of the genome, very near our target of 85X coverage; the remaining genomes are in queue and should be completed in November-December. Plant materials are being prepared for samples to be used for Omni-C sequencing, and for RNA isolations and sequencing to enable annotation of assembled sequences.


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