Article

DNA sequence variation of mitochondrial large-subunit rRNA provides support for a two-subclass organization of the Anthozoa (Cnidaria)

Department of Zoology, University of New Hampshire, Durham 03824, USA.
Molecular marine biology and biotechnology 04/1996; 5(1):15-28.
Source: PubMed

ABSTRACT We have sequenced a portion of the mitochondrial 16S rRNA gene from 29 species of Anthozoa, representing six orders of the subclasses Ceriantipatharia, Hexacorallia, and Octocorallia, with the focus on deep-seamount corals (> 500-m depth). We have detected significant length variation in the gene, with homologous gene fragments ranging from 545 bp in a shallow-water scleractinian coral to 911 bp in a deep-sea antipatharian black coral. The aligned sequences were divided into five regions: three high-identity sequence blocks (HSBs) and two highly variable blocks of insertions/deletions (INDELs). Most of the length variation among species occurred as varying numbers of nucleotides in the two INDELs. Little or no intraspecific sequence variation was detected over spatial scales of up to approximately 150 km. Interspecific sequence variation was lowest among the octocorals and greatest among the ceriantipatharians. Our data indicate that the orders Ceriantharia and Antipatharia are highly divergent, and a phylogenetic reconstruction provides support for the two-subclass system of the class Anthozoa (Hexacorallia and Octocorallia).

Download full-text

Full-text

Available from: Thomas Kocher, Feb 05, 2015
0 Followers
 · 
341 Views
  • Source
    • "Although Reimer et al. (2004) and Sinniger et al. (2008) have shown that some species of the hexacorallian order Zoantharia can be distinguished by analyses of COI, generally for octocorals, COI sequences have low variability among species and genera, and this marker is considered more suitable for investigating higher-level (genus and higher) phylogenies. Msh1 is a mitochondrial region specific to octocorals and is considered to be a homolog of the prokaryote MutS gene (France et al., 1996; Berntson et al., 1999). Msh1 shows much more variability than COI, and is appropriate for more detailed phylogenetic investigations in many groups of octocorals (Sánchez et al., 2003b; Wirshing et al., 2005; McFadden et al., 2006b). "
    [Show abstract] [Hide abstract]
    ABSTRACT: The primary problem hindering the study of octocorals is the disordered situation regarding their taxonomy, chiefly caused by insufficient knowledge of valid morphological taxonomic characters. Briareum is an octocoral genus found in the Atlantic and Pacific in shallow tropical and subtropical waters, and occurs in both encrusting and branching colony forms. Their simple morphology and morphological plasticity have hindered taxonomic understanding of this genus. In this study three morphologically distinct types (= type-1, -2, and -3) of Briareum from the Ryukyu Archipelago and their genetic diversity were examined. Colony, anthostele morphology, and sclerite length were examined for each type. Four molecular markers (mitochondrial cytochrome c oxidase subunit 1, mitochondrial mismatch repair gene, nuclear 18S ribosomal DNA, internal transcribed spacer 2 (ITS2)) were used to evaluate molecular phylogenetic status of these variations. Although one morphological type ("deep" small colonies, = type-3) showed small differences in nuclear ITS2 sequences compared to the other two types, the remaining types had identical sequences for all molecular markers examined. The results suggest extremely low genetic diversity despite highly variable morphology of Briareum species in Okinawa. Nevertheless, considering the distribution patterns and discontinuous morphology of type-3 compared to the other two morphotypes, genetic isolation of type-3 is plausible. In Briareum, small variances in nuclear ITS2 sequences of type-3 may have much more importance than in molecular phylogenies of other octocorals. Further phylogenetic investigations and comparison with Briareum specimens from other regions are necessary to conclusively taxonomically identify the three types.
    ZOOLOGICAL SCIENCE 10/2014; 31(10). DOI:10.2108/zs130171 · 0.88 Impact Factor
  • Source
    • "ertions and / or deletions suggesting that this region may have good phylogenetic information . Even though we did find this variable region within the 16S alignment , it is very small ( 38 bp ) , and an independent phylogenetic analysis for this small region only supports 2 clades ( support values >0 . 8 for BI ) . Using a larger sample size than France et al . ( 1996 ) , and obtaining specimens from different genera and different localities , mainly around New Zealand but also including the North Pacific , Chile , the Atlantic and the Mediterranean , we expected to see larger variable regions within the 16S alignment that showed genetic and geographic var - iation , but we did not . Higher variation"
    [Show abstract] [Hide abstract]
    ABSTRACT: Bamboo corals belong to a species rich and abundant group of octocorals that occur throughout the world's oceans, primarily in the deep-sea. Their study through morphological, ecological and evolutionary approaches has been problematic because of the extreme environments many of them inhabit and therefore the difficulty of obtaining good quality samples. However, new undescribed species have been commonly collected as part of invertebrate by-catch studies from commercial fisheries. In this study we describe two new species of deep-sea bamboo corals from New Zealand waters, including the Ross Sea (Antarctica) using morphological and molecular approaches. For the morphological description we used macro-structural characters such as branching pattern, color and polyp arrangement, along with axis architecture and sclerite shape and arrangement. The new species fit in the subfamily Keratoisidinae and the genus Keratoisis. Keratoisis magnifica n.sp. is characterized by having big, highly armed conical polyps and K. peara n.sp. has long, smooth internodes with an unusual nacreous lustre. Additionally, we amplified three mitochondrial genes (16S, igr4 and mtMutS), and obtained optimal topologies through maximum likelihood and Bayesian approaches. The resulting molecular phylogenies corroborated the status of the new taxa and elucidated their relationships to closely related species. Additionally, we show further genetic evidence that branching pattern, as previously thought, could be an unreliable character not only for Lepidisis/Keratoisis, but also for other genera within the Keratoisidinae.
    Molecular Phylogenetics and Evolution 02/2014; 74:15-28. DOI:10.1016/j.ympev.2014.01.031 · 4.02 Impact Factor
  • Source
    • "For example, the sequence variations in large subunit ribosomal RNA among families of Octocorallia (2.7–6.3%) are significantly lower than those of Hexacorallia (16.1–26.3%) (France et al., 1996). The nucleotide sequences of the msh1 gene are often used for the construction of phylogeny of octocorallian species because this gene shows a relatively faster evolutionary rate among the mitochondrial genes of Octocorallia (France, 2007; Herrera et al., 2010). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Precious corals are soft corals belonging to the family Coralliidae (Anthozoa: Octocorallia: Alcyonacea) and class Anthozoa, whose skeletal axes are used for jewelry. The family Coralliidae includes ca. 40 species and was originally thought to comprise of the single genus Corallium. In 2003, Corallium was split into two genera, Corallium and Paracorallium, and seven species were moved to this newly identified genus on the bases of morphological features. Previously, we determined the complete mitochondrial genome sequence of two precious corals Paracorallium japonicum and Corallium konojoi, in order to clarify their systematic positions. The two genomes showed high nucleotide sequence identity, but their gene order arrangements were not identical. Here, we determined three complete mitochondrial genome sequences from the one specimen of Mediterranean Corallium rubrum and two specimens of Corallium elatius coming from Kagoshima (South Japan). The circular mitochondrial genomes of C. rubrum and C. elatius are 18,915bp and 18,969-18,970bp in length, respectively, and encode 14 typical octocorallian protein-coding genes (nad1-6, nad4L, cox1-3, cob, atp6, atp8, and mtMutS, which is an octocoral-specific mismatch repair gene homologue), two ribosomal RNA genes (rns and rnl), and one transfer RNA (trnM). The overall nucleotide differences between C. konojoi and each C. elatius haplotype (T2007 and I2011) are only 10 and 11 nucleotides, respectively; this degree of similarity indicates that C. elatius and C. konojoi are very closely related species. Notably, the C. rubrum mitochondrial genome shows more nucleotide sequence identity to P. japonicum (99.5%) than to its congeneric species C. konojoi (95.3%) and C. elatius (95.3%). Moreover, the gene order arrangement of C. rubrum was the same as that of P. japonicum, while that of C. elatius was the same as C. konojoi. Phylogenetic analysis based on three mitochondrial genes from 24 scleraxonian species shows that the family Coralliidae is separated into two distinct groups, recovering Corallium as a paraphyletic genus. Our results indicate that the currently accepted generic classification of Coralliidae should be reconsidered.
    Comparative Biochemistry and Physiology Part D Genomics and Proteomics 06/2013; 8(3):209-219. DOI:10.1016/j.cbd.2013.05.003 · 2.82 Impact Factor
Show more