Dataset: Rockfish microhaplotype sequences

Name: Rockfish microhaplotype sequence accessions from samples near Carmel and Monterey Bays, CA, 2013-2016 (Larval Dispersal in Kelp Rockfish project)
Published: 2018-02-27
Keywords: biota, oceans

Cite This Dataset

Spatial Extent: N:36.6405 E:-121.8946 S:36.3977 W:-121.9825

Temporal Extent: 2013-07-19 - 2015-10-01

Project:

Integrative evaluation of larval dispersal and delivery in kelp rockfish using inter-generational genetic tagging, demography and oceanography (Larval Dispersal in Kelp Rockfish)

Program:

Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO)

Principal Investigator:

Mark Carr (University of California-Santa Cruz, UCSC)

Co-Principal Investigator:

Christopher Edwards

Dr John Carlos Garza (University of California-Santa Cruz, UCSC)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2018-02-27

Restricted:

Validated:

Current State:

Final no updates expected

Rockfish microhaplotype sequence accessions from samples near Carmel and Monterey Bays, CA, 2013-2016 (Larval Dispersal in Kelp Rockfish project)

Abstract:

This dataset contains NCBI accessions and collection metadata for samples collected in September 2010 along the coast of Monterey and Carmel, California.

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Description

2018-02-21: The data are currently stored in the Dryad repository as the following two packages. The files may also be accessed here via the 'Get Data' button (above).

Dryad package: Kelp-rockfish genotypes, DOI: 10.5061/dryad.6cp14g8
Data from: "Larval dispersal connects marine reserves and replenishes fished populations along the central California coast." Baetscher DS, Anderson EC, Saarman E, Malone D, Carr MH, Garza JC (2018?) Molecular Ecology (in press).
NOTE: not all files are publicly available until the associated publication is published.

This data repository contains the following: Genotypes for 96 microhaplotypes - this file contains the genotypes for 6,108 kelp rockfish sequenced at 96 amplicon loci using paired-end Illumina sequencing. Genotypes were filtered for read depth (minimum 20 reads total per locus/individual) and allele balance (0.4 ratio of read depth for allele 1:allele 2 in a heterozygote). Samples with missing data at more than 10 percent of loci were excluded from this data set. Variant call format file generated using Freebayes software from 2,293 rockfish samples sequenced at 96 microhaplotype loci. Samples include four species of rockfishes: kelp (Sebastes atrovirens), copper (S. caurinus), black-and-yellow (S. chrysomelas), and gopher (S. carnatus). This file contains 1,495 variant sites across the 96 loci.

Dryad package: Rockfish microhaplotype sequences, DOI: 10.5061/dryad.5863d
Data from: Baetscher DS, Clemento AJ, Ng TC, Anderson EC, Garza JC (2017) Microhaplotypes provide increased power from short-read DNA sequences for relationship inference. Molecular Ecology Resources, https://doi.org/10.1111/1755-0998.12737
Consensus sequences and primer information for 192 targeted amplicons, the Binary Alignment/Map (BAM) files and variant call format (VCF) files for all retained regions genotype files for 144 kelp rockfish species and an R Notebook documenting all statistical analyses.

Methods & Sampling

Haplotype data from 150bp amplicon sequencing on an Illumina MiSeq. All loci used in the generation of haplotype sequence data will be submitted to GenBank (National Center for Biotechnology Information).

Genotype data are generated with high-throughput DNA sequencing on an Illumina MiSeq instrument. Amplicons are prepared through polymerase chain reaction with primers designed from either expressed sequence tags in publicly available databases (e.g., Cyverse) or from sequences generated by double digest Restriction-Site Associated DNA (RAD) sequencing. Amplicon sequencing is using the procedure described in Campbell et al. 2015 (Molecular Ecology Resources 15: 855-867) termed genotyping in thousands by sequencing (GT-seq). Data are filtered by quality score and genotypes called for all locus by individual combinations with read depth ≥20. Genotyping accuracy is evaluated by confirmation of Mendelian segregation in known families. Haplotypes are called from constituent SNPs using FreeBayes software.

Data Processing Description

Standard filtering for quality scores and read depth have been applied to the raw instrument output to call haplotypes.

BCO-DMO Processing Notes:
- created table of files downloaded from Dryad
- added conventional header with dataset name, PI name, version date

Data Files

File
Dryad package: Kelp-rockfish genotypes, DOI: 10.5061/dryad.6cp14g8 filename: doi_10.5061_dryad.vq3rg55__v1.zip (ZIP Archive (ZIP), 47.55 MB) MD5:d90e22185e4542e088f59b2e1c564799 Zip file containing two files: Genotype data (CSV) and the variant call format (VCF) file used to generate genotypes for all kelp rockfish.
rockfish_microhaplotype_dryad.csv (Comma Separated Values (.csv), 4.40 KB) MD5:ed4a92f7c1bcff4f6a6e0421030bf8e2 Primary data file for dataset ID 684944

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1260693

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
Carr_1999		1999-09-22	Long Marine Lab UCSC	Mark Carr (Principal Investigator)	data info

Instruments

Automated DNA Sequencer

Supplied Name: Illumina MiSeq

Supplied Description:

Used to sequence genomes

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Thermal Cycler

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Thermal Cycler

Generic Description:

A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
file_link	hyperlink to downloadable file	unitless	file_link
file_size	file size	kilobytes to gigabytes	file_size
publication	publication that used the data	unitless	reference_paper
Dryad_DOI	dryad.org DOI	unitless	no_bcodmo_term
description	description of file contents	unitless	brief_desc
file_name	file name	unitless	file_name

Status message

Database

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Dataset: Rockfish microhaplotype sequences