Abstract:

Different DNA preservation methods were tested for the next generation whole genome sequencing of Gulf of Mexico invertebrates. The abundant spionid polychaete Streblospio from Rincon Bayou, collected in spring 2016, was used as the model organisms. The goal of this pilot study was to assess the optimal preservation strategy for samples of the C-Image project. All genomic data sets were deposited in and distributed by GenBank (NCBI), the European Nucleotide Archive, DNA Data Bank of Japan, NemATOL, the Global Genome Initiative, and Ocean Genome Legacy.

Suggested Citation:

Joseph Sevigny, Francesca Leasi, Michael Reuscher, Anja Schulze , Holly Bik, Paul Montagna, Kelley W. Thomas.. 2020. Whole genome DNA sequences of the spionid polychaete Streblospio collected from Oso Bay and Palmetto Park, Corpus Christi on 2017-01-01. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-d9rb-x333

Purpose:

Comparison of the genomes from individuals belonging to both morphotypes (S. gynobranchiata and S. benedicti) living in sympatry in the Gulf of Mexico was done in order to assess if reproductive isolation is due to phylogenetic or vicariant constraints.

Data Parameters and Units:

Sample Name, Project, NCBI BioProject Accession (PRJNA483473), NCBI BioSample Accession (SAMN14404818; SAMN14404819), NCBI Short read archive accession (SRR11356412; SRR11356411), Sequencing Read Counts, Phylum (Annelida), Family (Spionidae), Genus_species (Streblospio_benedictii; Streblospio_gynobranchiata), DNA_concentration, Taxonomy-well, Taxonomist, Sample Site (Palmetto Park and Oso Bay Bridge, Corpus Christi), Longitude-Latitude (Decimal degrees), Date (YYYY-MM-DD), SamplingTime, ProbeDepth (water depth in m), WaterTemp (Water Temperature in degree C), Conductivity (µS/cm), Salinity, DO (Dissolved Oxygen), DO_mgL, pH, and Description.

Methods:

Two Polychaeta individuals of the genus Streblospio were collected from the Gulf of Mexico (Corpus Christi, TX) during the annual BitMaB workshop on January 01, 2017. Specifically, S. gynobranchiata was collected from Oso Bay and S. benedictii from the Palmetto and respectively identified by Drs. Michael Reuscher and Anja Schulze (Texas A&M). After identification, the worms were placed into individual collection tubes containing ethanol 98%. DNA from every single individual was extracted with the Autogen Prep 956 Extractor at the Smithsonian National Museum of Natural History (Washington, D.C.). Half of the DNA is stored at the NMNH biorepository, the other half is available for genetic and genomic investigations. Prior to genome sequencing, the 18S ribosomal gene from each sample was amplified and sequenced to confirm the identification of the animal in the sample. The resulting sequences from both samples were found to contain a single dominant sequence variant (greater than 99% of reads) that matched at 98.46 % identity to the Spionida, Polydora ciliate (same family and the closest related species in SILVA). 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. 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. After assembly Blobtools and CONCOCT were used to identify and remove potential contaminants (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.

Provenance and Historical References:

Rice, Stanley A.; Levin, Lisa A. (1998). Streblospio gynobranchiata, a new spionid polychaete species (Annelida: Polychaeta) from Florida and the Gulf of Mexico with an analysis of phylogenetic relationships within the genus Streblospio. Proceedings of the Biological Society of Washington. 111(3): 694-707.

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