Integrative Biology | Meyer Lab

General information about the workshops

Where: Wrigley Marine Science Center, Catalina Island, CA

When: Amplicon sequencing: Aug 11-15, 2bRAD genotyping: Aug 15-23 (2017).

Target audience: Our workshops are geared towards graduate students, postdoctoral scholars, and any researchers working in ecology, evolutionary biology, or related fields. Experience with molecular biology is a plus, but is not essential. No prior programming experience is required, although familiarity with the command line interface is always helpful.

What to bring: Participants will need to provide their own laptop, up to 10 high-quality DNA samples, and appropriate laboratory attire (closed-toe shoes, long pants) for the wet-lab activities.

The workshops cover:
    • Hands-on training in production of sequencing libraries
    • Logistics of preparing and analyzing 100s of samples in parallel
    • Working with command line tools for analysis of large datasets
    • Profiling genetic variation or microbial communities from high-throughput DNA sequence data

Costs: The cost of registration depends on duration of each workshop: $1,300 for amplicon sequencing, $1,900 for 2bRAD, or $3,000 for both). This fee covers accommodations (see photos from past workshops for a view of the accomodations), 3 meals a day with coffee and snacks, in addition to laboratory supplies, sequencing costs, and facility fees. The budget includes resources for each participant to prepare and sequence libraries from 10 of their own samples, in addition to samples prepared together as part of the group project. Participants are responsible for arranging their own travel to the site.

Contact us with any questions about details, or to confirm your participation. Email workshop coordinators Demian Willette (demian.willette@lmu.edu), Eli Meyer (eli.meyer@oregonstate.edu), or Carly Kenkel(carly.kenkel@gmail.com) with "2017 Workshops" in the subject line. Space is limited! To reserve your spot, please confirm your participation no later than May 31 and pay registration fee no later than June 30th, 2017.

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Genome-wide SNP genotyping with 2bRAD


An example of genomic analysis using SNP genotypes from 2bRAD. QTL analysis of growth in the Pacific oyster revealed several regions associated with growth (a); details of one example (LG7) are shown in (b). SNP genotypes for this analysis were produced entirely by participants in the 2015 workshop.

This workshop (Aug 15-23) focuses on a cost-effective and flexible approach for genome-wide SNP genotyping, 2bRAD. We cover both the wet-lab molecular procedures for library preparation, and computational analysis of the resulting DNA sequences. Participants will gain experience with each step of the process, beginning with genomic DNA and ending with a table of thousands of SNP genotypes.

Specific topics include:
    • Planning and budgeting 2bRAD experiments
    • Preparing 2bRAD genotyping libraries
    • Quantifying libraries for multiplex sequencing
    • Processing raw sequence data prior to analysis
    • de novo analysis for organisms without a sequenced genome
    • Alignment of reads to reference and genotype determination
    • Filtering out uninformative or low-confidence genotypes

During the workshop, each participant will prepare 2bRAD libraries from:
(1) ten samples of high-quality DNA provided by the participant for their species of interest. The workshop costs include library preparation and sequencing for those samples, providing pilot data for each participants' species of interest.
(2) An additional six samples will be provided to each participant during the workshop. Genetic data from these samples will be used for a group project, to be described in a joint publication including all workshop participants.

The group project for our 2017 workshop will focus on samples of the invasive seagrass Halophila stipulacea (a) from Caribbean and Mediterranean sites where it is invasive, and from its native range in India, Africa, and the Red Sea (b).

Group project For this project we'll profile genetic variation in the invasive seagrass Halophilia stiplucea. We'll analyze a set of samples collected by Demian Willette and Kelcie Chiquillo, from Caribbean and African sites. We'll use 2bRAD to analyze genetic variation among these samples, asking:
    • What's the source of the Caribbean invasive populations?
    • Have there been multiple introductions or a single event?
    • Are invasives spreading through sexual or asexual reproduction?

Examples of publications featuring 2bRAD
Howells, et al. (2016) Global Change Biology
Pecoraro et al. (2016) Marine Genomics
Dixon et al. (2015) Science
Fu et al. (2014) DNA Research
Fletcher et al. (2013) BMC Genomics
Wang et al. (2012) Nature Methods

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High-throughput amplicon sequencing


Example of data on symbiont diversity collected using this method in a variety of Scleractinian corals.

This workshop (Aug 11-15) focuses on a straightforward and cost-effective approach for profiling community diversity using amplicon sequencing. Coursework will be focused on coral-associated Symbiodinium community diversity profiled using ITS2 and microbial community diversity profiled with 16S, though the method is applicable to any locus of appropriate length. We cover both the wet-lab molecular procedures for library preparation, and computational analysis of the resulting DNA sequences. Participants will gain experience with each step of the process, beginning with DNA samples and ending with quantitative descriptions of sequence diversity in each sample.

Specific topics include:
    • Preparing amplicon sequencing libraries
    • Pooling and barcoding libraries for multiplex sequencing
    • Processing raw sequence data prior to analysis
    • Clustering methods to identify OTUs and oligotypes
    • Statistical analysis of OTU and oligotype diversity

Each participant will prepare amplicon sequencing libraries from:
(1) ten samples of high-quality DNA provided by the participant for their species of interest. Workshop fees cover library preparation and sequencing for those samples, providing pilot data for each participants' species of interest.
(2) An additional six samples will be provided to each participant during the workshop. Sequence data from these samples will be used for a group project, to be described in a joint publication including all workshop participants.

The group project for our 2017 workshop will focus on samples of the Mountainous Star Coral Orbicella faveolata from the Flower Garden Banks (a). We sampled transects across massive colonies (b), collecting replicate samples from different regions of each colony (c).

Group project We'll profile diversity in algal symbionts and microbial communities in massive colonies of Orbicella faveolata, sampled from the Flower Garden Banks, Gulf of Mexico by Eli Meyer and Carly Kenkel. To study variation across microhabitats, and among colonies, we collected tissue samples in 3-6 m transects across massive colonies of Orbicella faveolata, and individual samples from an additional 20 colonies. In the workshop, we'll analyze variation ITS2 and 16S variation to ask:
    • How do symbiont communities vary with local microhabitat?
    • Are microbial communities correlated with algal symbionts on this scale?
    • How does variation in symbiont and microbial communities within colonies compare to variation among colonies?

Examples of publications featuring deep amplicon sequencing
Wright et al. (2016) bioRxiv
Klepac et al. (2015) Marine Ecology Progress Series
Quigley et al. (2014) PLoS ONE
Green et al. (2014) PeerJ
Kenkel et al. (2013) Molecular Ecology


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