Abstract:

Individuals from eight Cnidarian species were shotgun sequenced using 454 GS-FLX Titanium technology. These species include Leiopathes glaberrima, Tanacetipathes sp, Corynactis californica, Amplexidiscus fenestrafer, Eunicea flexuosa, Plumarella sp, Metridium senile and Millepora alcicornis. Genomic libraries were prepared from the double-stranded DNA using Nextera DNA Sample Prep Kit (Epicentre Biotechnologies, Madison WI) and shotgun sequenced on a 454 GS-FLX sequencer using the Titanium Sequencing Kit (Roche Diagnostics Corporation, Indianapolis, IN). From this data, microsatellite coverage and GC content were calculated for each species and compared across samples. Sequences are available at the NCBI Sequence Read Archive: SRX323262, SRX327567, SRX326898, SRX326897, SRX326758, SRX326761, SRX327565, SRX323169.

Suggested Citation:

Iliana Baums. 2017. Genomic Sequences and Microsatellite abundance across the Anthozoa and Hydrozoa in the phylum Cnidaria. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7XG9P43

Publications:

Ruiz-Ramos, D. V., & Baums, I. B. (2014). Microsatellite abundance across the Anthozoa and Hydrozoa in the phylum Cnidaria. BMC Genomics, 15(1), 939. doi:10.1186/1471-2164-15-939

Purpose:

The objectives of this work were: 1) to describe the microsatellite abundance and composition in different members of the Cnidaria with focus on the Anthozoa and Hydrozoa, 2) to detect a phylogenetic signal in microsatellite abundance and composition and to 3) correlate the mitochondrial genome mutation rates and the presence of intra-cellular symbionts to microsatellite abundance and composition. This work provides resources for the design of microsatellite primers for future studies of cnidarian populations.

Data Parameters and Units:

Species; Symbodium present (Y,N); Total sequences; Mean raw sequence length (bp, basepairs); Sequences with msats (Sequences with microsatellites); % Sequences with msats (Percentage of sequences with microsatellites); % Sequences with msats (after bootstrapped mean) (Percentage of sequences with microsatellites after bootstrapped mean); Bootstrapped mean of total msat (Bootstrapped mean of total microsatellites); Bca CI (95%), (Bias corrected confidence interval calculated from 10000 bootstraps); Total msat (microsatellites count/Mbp); SRA Accession; NCBI Assembly; Bias (difference between the arithmetic mean and the bootstrapped sample); BootMean (the bootstrapped mean of the sample based on 10000 bootstraps); Mono- (number of mononucleotide microsatellites); Di-(number of dinucleotide microsatellites); Tri- (number of trinucleotide microsatellites); Tetra- (number of tetranucleotide microsatellites); Penta- (number of pentanucleotide microsatellites); Hexa- (number of hexanucleotide microsatellites); Genus; Coverage (counts/Mbp)

Methods:

Phylogenetic data were generated from multiple sequences available from NCBI GenBank and do not have a relevant spatial and temporal extent.

Instruments:

454 GS-FLX DNA sequencer

Provenance and Historical References:

NCBI Assembly information given for those species that were included in this analysis, but not sequenced as a part of this effort.

Individual Files: