Dataset: Cuvierina SRA

Please refer to the paper for methodological details. If you have further questions, please contact the corresponding author (Dr. Erica Goetze): egoetze[at]hawaii[dot]edu.

From the cruise report:

Sample collection. Plankton samples were collected with 0.71m diameter bongo nets (200, 333 µm), and with an RMT1 midwater trawl (333 µm) that has a nominal mouth area of 1m2. A total of 50 plankton tows were conducted along the cruise leg (Table 1), with 35 tows conducted using the bongo and 14 samples collected with the RMT net. The bongo tows were oblique tows that sampled from between 211 to 488 m depth and the surface (324m average maximum depth of tow). The bongo samples will be used for quantitative estimates of animal abundance along the cruise leg (target species only, tows conducted with timedepth-recorder and flowmeter). The RMT tows were also oblique tows that sampled between 62 to 216 m depth and the surface (153 m average maximum depth of tow). All tows except one (station 42) were conducted at night, in order to efficiently sample the migratory community.

Sample handling and preservation. All plankton from the 200 µm mesh bongo net was preserved immediately in 100% ethyl alcohol for use in molecular studies, including DNA sequencing and microsatellite genotyping (and possibly RAD tag sequencing), in addition to estimates of abundance of target species. Plankton material from the 333 µm mesh bongo net and the RMT net was sorted live immediately following collection, and animals were individually identified, and preserved in acetone, RNALater, cryopreserved, and in some cases used for live imaging prior to preservation. These animals will be used for molecular, genomic and transcriptomic analyses. Both RNA/DNA ratios and prosome length - dry weight relationships will be used as measures of animal condition in copepods. In total, over 17,000 animals from 40 target species were individually sorted and preserved for this panel of measurements. Following live sorting and imaging of the 333 µm samples, the remaining plankton was preserved either in 4% buffered formalin or 100% ethyl alcohol for morphological studies.

Illumina sequence files:

This submission consists of reduced representation genomic data for 26 individual pteropod specimens in the genus Cuvierina. Specimens were collected during the Atlantic Meridional Transect cruise in 2012 (AMT22) as well as a Mar-Eco cruise.  Our research goals were to examine genomic divergence and species boundaries in these morphologically and ecologically distinct pteropod populations in adjacent ocean regions of the subtropical and equatorial Atlantic. We are interested in local adaptation of these populations to distinct oceanographic habitats. 

Genetic data consists of 300 bp paired-end sequence reads generated using an Illumina MiSeq sequencer. Two MiSeq lanes were run; approximately 400mB to 1GB of data were generated for each library, with a mean of 700mB per individual. Libraries for individuals #1, 2, 3, 4, 9, 10, 11, 12, 16, 17, 18, 19, and 25 were run together on a single MiSeq lane, and libraries for individuals #5, 6, 7, 8, 13, 14, 15, 20, 21, 22, 23, 24, and 26 were run together on a second lane. 

The raw data was cleaned of adapters, trimmed of poor sequence, and filtered for non-specific sequencing. Cutadapt v. 1.9.1 was used to remove the Truseq Illumina Adapters (LT), using a 90% mismatch parameter (-e 0.10) and a minimum adapter match overlap of 12 bp (-O 12). Reads that did not contain an adapter (potentially non-specific sequencing) were removed from the dataset (--discard-trimmed). Read 1 and read 2 were paired using the custom python script, "fastqCombinePairedEnd.py", and read pairs were verified using the custom Perl script, "FastqPairedEndValidator.pl". Trimmed, cleaned, and paired reads were checked for sequence quality using FastQC. 

This post-sequence processing resulted in three files included for each individual library: *.R1.fq (All read 1s that paired with a read 2), *.R2.fq (All read 2s that paired with a read 1), and  *.R1.clean.fq_singles.fastq (unpaired reads), with the * representing each respective putative Cuvierina sp. individual.