Abstract:

The dataset consists of whole genome DNA sequences, generated from invertebrate species from the Gulf of Mexico during the Benthic Invertebrate Taxonomy, Metagenomics, and Bioinformatics Workshop (BITMaB) in 2017 in Corpus Christi, Texas, USA. All genomic data sets were deposited in and distributed by GenBank (NCBI), the European Nucleotide Archive (ENA)- European Bioinformatics Institute (EMBL-EBI), DNA Data Bank of Japan, NemATOL, the Global Genome Initiative, and Ocean Genome Legacy.

Suggested Citation:

Joseph Sevigny, Francesca Leasi, Kelley Thomas, Michael Reuscher, Holly Bik, Paul Montagna and Krystalynne Morris. 2020. Whole genome DNA sequences of Gulf of Mexico invertebrates. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-pchj-dh15

Purpose:

The purpose of this project is to develop methodologies and infrastructure to characterize the taxonomic composition of benthic communities via metagenomics. This dataset provides sequencing data for representative meiofauna collected from the Gulf of Mexico. These sequences will be pivotal for the development and implementation of high-throughput sequencing workflows for analyzing meiofaunal communities.

Data Parameters and Units:

The headers are- Sample_Name, NCBI BioProject Accession, NCBI BioSample accession, NCBI SRA accession, Sequencing Project ID, Phylum, Family, Species, #SampleID, Phylum/Class/Order, FamilyID, SpeciesID, Taxonomist Notes, Taxonomist, Sample Site, Geo_Loc_Name, Estimated Coordinates, Date,ProbeDepth, WaterTemp, Conductivity, Salinity, DO, DO_mgL, pH, and Description

Methods:

Sample collection, identification, and preservation of benthic organisms for DNA sequencing was completed at the Harte Research Institute for Gulf of Mexico Studies at Texas A&M University - Corpus Christi during the context of the two BITMaB workshops in 2017 and 2018. After identification, the worms were placed into individual collection tubes containing ethanol 98%. DNA from each single individual was extracted with the Autogen Prep 956 Extractor at the Smithsonian National Museum of Natural History (NMNH) in Washington, D.C. Half of the DNA is stored at the NMNH biorepository, the other half is available for genetic and genomic investigations. Genomic sequencing libraries were constructed following the dilute nextera protocol and whole genome shotgun sequencing was completed using the Illumina HiSeq 2500 instrument for 250 bp paired-end reads at the Hubbard Center for Genome Studies. After demultiplexing the reads were quality checked with FastQC and adapter and low-quality bases were trimmed using Trimmomatic. An initial assembly was constructed from the trimmed reads using SPAdes software program. After assembly Blobtools and CONCOCT were used to identify and remove potential contaminates (bacteria and unwanted non-target Eukaryotes) from the genome assembly. The final assembly was then assessed for quality using the program QUAST (structure and continuity) and the program BUSCO (completeness).

Instruments:

Illumina HiSeq 2500; SPAdes software program; QUAST software program; BUSCO software program

Individual Files: