Abstract:

This dataset contains anglerfish mitochondrial DNA and symbiont genomes isolated from Illumina whole-genome sequencing efforts. The dataset also includes symbiont chemotaxis protein cheA found while sampling free-living bacteria at discrete depths. The samples were collected during DEEPEND consortium cruises (D01-D04) in the Gulf of Mexico from 2015-05-01 to 2016-08-18.

Suggested Citation:

Tory Hendry, Lindsay Freed, Cole Easson, Jose Lopez. 2019. Anglerfish mitochondrial DNA and symbiont genomes isolated from Illumina whole-genome sequencing efforts, 2015-05-01 to 2016-08-18. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-bzj0-fa78

Purpose:

To deduce possible methods of symbiont transmission in deep-sea anglerfish.

Data Parameters and Units:

Genetic sequences (base pairs).

Methods:

Anglerfish samples collected by the DEEPEND Consortium were extracted using the DNeasy Blood and Tissue Kit (Qiagen) as is described in Hendry et al., 2018. Paired-end 250 base pair Illumina sequence libraries were prepared using the NexteraXT kit (Illumina, San Diego, CA) and sequenced using HiSeq2500 at the Cornell University Institute of Biotechnology Resource Center Genomics Facility. Contigs were assembled using DISCOVAR de novo and binned and assessed for quality using checkM. Binned genomes and sequences mapped to the reference genomes (GCA_002381345.1 and GCA_002300443.1) and submitted to NCBI. Anglerfish mitochondrial sequences were identified using a local BLAST search of the unbinned DISCOVAR genomic assemblies and deposited in Genbank (accession numbers MK118159-MK118174). We performed PCR assays on DNA extracted from environmental bacteria in 52 samples taken concurrently with anglerfish collections during DEEPEND consortium cruises (D01-D04) in the Gulf of Mexico. Primers for cheA specific to each symbiont were designed by importing symbiont and closely related sequences found using the BLAST genome searches into DECIPHER (Wright et al., 2012). Sequences were amplified using nested PCR primers and the New England Biolabs standard Taq polymerase kit (NE Biolabs, Ipswich, MA, USA) using the recommended protocol for amplification under 500 base pairs. Reactions were prepared in a UV sterilized biosafety cabinet with surface-sterilized implements. Negative controls prepared with sterile water were included in each round of PCR. No negative controls resulted in visible amplification. Amplifications were gel extracted using the Qiaquick gel extraction kit (Qiagen, Venlo, Netherlands) and Sanger Sequenced (Genewiz, New Jersey, USA).

Provenance and Historical References:

Hendry, T. A., Freed, L. L., Fader, D., Fenolio, D., Sutton, T. T., & Lopez, J. V. (2018). Ongoing Transposon-Mediated Genome Reduction in the Luminous Bacterial Symbionts of Deep-Sea Ceratioid Anglerfishes. mBio, 9(3). doi:10.1128/mbio.01033-18 Wright, E. S., Yilmaz, L. S., & Noguera, D. R. (2011). DECIPHER, a Search-Based Approach to Chimera Identification for 16S rRNA Sequences. Applied and Environmental Microbiology, 78(3), 717–725. doi:10.1128/aem.06516-11

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