Microsatellite abundance across the Anthozoa and Hydrozoa in the phylum Cnidaria

Dannise V. Ruiz-Ramos, Iliana Brigitta Baums

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Background: Microsatellite loci have high mutation rates and thus are indicative of mutational processes within the genome. By concentrating on the symbiotic and aposymbiotic cnidarians, we investigated if microsatellite abundances follow a phylogenetic or ecological pattern. Individuals from eight species were shotgun sequenced using 454 GS-FLX Titanium technology. Sequences from the three available cnidarian genomes (Nematostella vectensis, Hydra magnipapillata and Acropora digitifera) were added to the analysis for a total of eleven species representing two classes, three subclasses and eight orders within the phylum Cnidaria. Results: Trinucleotide and tetranucleotide repeats were the most abundant motifs, followed by hexa- and dinucleotides. Pentanucleotides were the least abundant motif in the data set. Hierarchical clustering and log likelihood ratio tests revealed a weak relationship between phylogeny and microsatellite content. Further, comparisons between cnidaria harboring intracellular dinoflagellates and those that do not, show microsatellite coverage is higher in the latter group. Conclusions: Our results support previous studies that found tri- and tetranucleotides to be the most abundant motifs in invertebrates. Differences in microsatellite coverage and composition between symbiotic and non-symbiotic cnidaria suggest the presence/absence of dinoflagellates might place restrictions on the host genome.

Original languageEnglish (US)
Article number939
JournalBMC genomics
Volume15
Issue number1
DOIs
StatePublished - Jan 1 2014

Fingerprint

Hydrozoa
Cnidaria
Anthozoa
Microsatellite Repeats
Dinoflagellida
Genome
Hydra
Trinucleotide Repeats
Firearms
Mutation Rate
Invertebrates
Phylogeny
Titanium
Cluster Analysis
Technology

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Genetics

Cite this

@article{2d9e4730d86249118189297271588de6,
title = "Microsatellite abundance across the Anthozoa and Hydrozoa in the phylum Cnidaria",
abstract = "Background: Microsatellite loci have high mutation rates and thus are indicative of mutational processes within the genome. By concentrating on the symbiotic and aposymbiotic cnidarians, we investigated if microsatellite abundances follow a phylogenetic or ecological pattern. Individuals from eight species were shotgun sequenced using 454 GS-FLX Titanium technology. Sequences from the three available cnidarian genomes (Nematostella vectensis, Hydra magnipapillata and Acropora digitifera) were added to the analysis for a total of eleven species representing two classes, three subclasses and eight orders within the phylum Cnidaria. Results: Trinucleotide and tetranucleotide repeats were the most abundant motifs, followed by hexa- and dinucleotides. Pentanucleotides were the least abundant motif in the data set. Hierarchical clustering and log likelihood ratio tests revealed a weak relationship between phylogeny and microsatellite content. Further, comparisons between cnidaria harboring intracellular dinoflagellates and those that do not, show microsatellite coverage is higher in the latter group. Conclusions: Our results support previous studies that found tri- and tetranucleotides to be the most abundant motifs in invertebrates. Differences in microsatellite coverage and composition between symbiotic and non-symbiotic cnidaria suggest the presence/absence of dinoflagellates might place restrictions on the host genome.",
author = "Ruiz-Ramos, {Dannise V.} and Baums, {Iliana Brigitta}",
year = "2014",
month = "1",
day = "1",
doi = "10.1186/1471-2164-15-939",
language = "English (US)",
volume = "15",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "BioMed Central",
number = "1",

}

Microsatellite abundance across the Anthozoa and Hydrozoa in the phylum Cnidaria. / Ruiz-Ramos, Dannise V.; Baums, Iliana Brigitta.

In: BMC genomics, Vol. 15, No. 1, 939, 01.01.2014.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Microsatellite abundance across the Anthozoa and Hydrozoa in the phylum Cnidaria

AU - Ruiz-Ramos, Dannise V.

AU - Baums, Iliana Brigitta

PY - 2014/1/1

Y1 - 2014/1/1

N2 - Background: Microsatellite loci have high mutation rates and thus are indicative of mutational processes within the genome. By concentrating on the symbiotic and aposymbiotic cnidarians, we investigated if microsatellite abundances follow a phylogenetic or ecological pattern. Individuals from eight species were shotgun sequenced using 454 GS-FLX Titanium technology. Sequences from the three available cnidarian genomes (Nematostella vectensis, Hydra magnipapillata and Acropora digitifera) were added to the analysis for a total of eleven species representing two classes, three subclasses and eight orders within the phylum Cnidaria. Results: Trinucleotide and tetranucleotide repeats were the most abundant motifs, followed by hexa- and dinucleotides. Pentanucleotides were the least abundant motif in the data set. Hierarchical clustering and log likelihood ratio tests revealed a weak relationship between phylogeny and microsatellite content. Further, comparisons between cnidaria harboring intracellular dinoflagellates and those that do not, show microsatellite coverage is higher in the latter group. Conclusions: Our results support previous studies that found tri- and tetranucleotides to be the most abundant motifs in invertebrates. Differences in microsatellite coverage and composition between symbiotic and non-symbiotic cnidaria suggest the presence/absence of dinoflagellates might place restrictions on the host genome.

AB - Background: Microsatellite loci have high mutation rates and thus are indicative of mutational processes within the genome. By concentrating on the symbiotic and aposymbiotic cnidarians, we investigated if microsatellite abundances follow a phylogenetic or ecological pattern. Individuals from eight species were shotgun sequenced using 454 GS-FLX Titanium technology. Sequences from the three available cnidarian genomes (Nematostella vectensis, Hydra magnipapillata and Acropora digitifera) were added to the analysis for a total of eleven species representing two classes, three subclasses and eight orders within the phylum Cnidaria. Results: Trinucleotide and tetranucleotide repeats were the most abundant motifs, followed by hexa- and dinucleotides. Pentanucleotides were the least abundant motif in the data set. Hierarchical clustering and log likelihood ratio tests revealed a weak relationship between phylogeny and microsatellite content. Further, comparisons between cnidaria harboring intracellular dinoflagellates and those that do not, show microsatellite coverage is higher in the latter group. Conclusions: Our results support previous studies that found tri- and tetranucleotides to be the most abundant motifs in invertebrates. Differences in microsatellite coverage and composition between symbiotic and non-symbiotic cnidaria suggest the presence/absence of dinoflagellates might place restrictions on the host genome.

UR - http://www.scopus.com/inward/record.url?scp=84937206656&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84937206656&partnerID=8YFLogxK

U2 - 10.1186/1471-2164-15-939

DO - 10.1186/1471-2164-15-939

M3 - Article

C2 - 25346285

AN - SCOPUS:84937206656

VL - 15

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 1

M1 - 939

ER -