1. General Guidelines

Number and Target Species of Reference Genomes

  • CCGP will provide a reference genome for one species in each project genus. For projects that include several closely related congeneric species, we suggest that you choose either the species with the widest California distribution, or one that will be most useful for your taxonomic group and community. Please contact Brad Shaffer (brad.shaffer@ucla.edu), if you are unsure of which species you should choose.

  • Estimated genome sizes of target species should be less than 5Gb. Please contact Brad or Erin (etoff@ucla.edu) for special considerations.

Overview of Sample Requirements

Sample Splitting Strategy

  • Reference genome library components will be completed on separate UC campuses.

  1. UC Davis (PacBio HiFi, required)

  2. Dovetail Omni-C (UCSC, required)

  3. Transcriptome (UCLA, optional but encouraged)

  4. Archival samples of both DNA tissue and RNA tissue in case of shipping/library failures (UCLA, required)

  • Please prepare three separate sets of DNA tissue PLUS two sets of each RNA tissue type.

    • When possible, DNA samples should come from the same individual.

    • RNA tissues should come from multiple tissues and when possible, multiple life stages.

    • For most taxa, this means that you will prepare at minimum 6 tubes of tissue for HMW DNA extractions (two each sent to UCSC, UC Davis, and UCLA) and at minimum 4 tubes per tissue type for RNA extractions (2 for RNA extraction, 2 for archive, sent to UCLA).

    • Providing more aliquots of sample in pre-dissected amounts will increase our chances of success in extraction.

    Please contact both UCDavis (Ruta Sahasrabudhe, rmsaha@ucdavis.edu) and UCSC (Sam Sacco, ssacco@ucsc.edu) at least a week in advance to set up an appointment if you plan to ship fresh samples with overnight shipping.

Very small species

This includes most insects: If you feel a single individual does not contain enough tissue to split between at least UC Davis and UC Santa Cruz, please submit multiple individuals to each shipping destination. It is better to send different whole animals to each lab (rather than splitting e.g. each of two specimens in half and sending half of each to two labs).