Research Project Presentation

Haila Schultz

Dataset

  • Washington Ocean Acidification Center Cruises
  • Paired zooplankton samples from net tows: morphology and metabarcoding
  • metabarcoding marker: mitochondrial cytochrome C oxidase subunit I (COI)

Number of Samples

Month 2019 2020 2020
April 7 7 7
July 7 7 7
Sept 7 7 7

Stations

Project Goals

  1. Taxonomically ID zooplankton communities using sequence reads

  2. Compare zooplankton communities among

  • years
  • seasons
  • locations

Methods to-date

  1. Download data
  2. Trim primers using cutadapt (in progress)

Trimming primers

#set file path
path <- "../data"
#make matched list of forward and reverse reads
fnFs <- sort(list.files(path, pattern = "_R1_001.fastq.gz", full.names = TRUE))
fnRs <- sort(list.files(path, pattern = "_R2_001.fastq.gz", full.names = TRUE))

#specify primer sequences
FWD <- "GGWACWGGWTGAACWGTWTAYCCYCC"  
REV <- "TAIACYTCIGGRTGICCRAARAAYCA"

Take a look at one file

cd ../data
zcat 2018APRP402ObB-COI-59samples_S191_L001_R1_001.fastq.gz | head -n 2
@M02815:67:000000000-KDDDG:1:1101:10445:1250 1:N:0:TAAGGCGA+ACTGCATA
GGAACTGGTTGAACTGTATATCCTCCTTTATCTGCAGGACTTGCACATGCTGGGGCTTCTGTAGATATAGGAATCTTTACACTACATATTGCTGGAGCCTCTTCTATTTTAGGAGCAGTTAATTTCATTACAACTGTATTTAATATGCGATCAGCAGGATTAACTATAGACAGTATCCCCTTATTCGTATGGTCTGTGTTTATTACAGCAATTTTATTTTTATTATCTCTACCAGTTTTAGCTGGAGCAATCACCATTCTTTTAACTGATAGTAATTTAAATACAACTTTCTTCGACCC

Methods for the next four weeks

  1. Filter reads based on quality using DADA2
  2. Merge forward and reverse reads
  3. Run BLASTn against the NCBI nt database as a reference
  4. Calculate diversity index for each sample
  5. Make NMDS plots colored by year, month, and location
  6. Make barplots to compare relative abundances of taxa among samples