The First Internal Transcribed Spacer (ITS-1) of Ribosomal DNA as a Molecular Marker for Phylogenetic and Population Analyses in Crustacea

Chu, Ka Hou; Li, C.P.; Ho, Hsuan-Ching

doi:10.1007/s10126001-0014-5

Cited by 86 publications

(59 citation statements)

References 20 publications

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“…Thus, there appears to be genetic structuring on at least a macrogeographic scale. The level of sequence divergence in the ITS1 region of M. subnitida is considerably greater than the values of most published studies on intraspecific ITS variation for a variety of organisms (Chu et al, 2001;Luo et al, 2002;Otranto and Traversa, 2004). Intraspecific nucleotide divergence in ITS1 from M. subnitida is also greater than those found for ITS2 in different organisms.…”

Section: Discussionmentioning

confidence: 56%

Intraspecific variation in the first internal transcribed spacer (ITS1) of the nuclear ribosomal DNA inMelipona subnitida(Hymenoptera, Apidae), an endemic stingless bee from northeastern Brazil

et al. 2006

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-Melipona subnitida is endemic to northeastern Brazil where it has been exploited for the production of honey. In this work, partial sequences (about 600 bp) of the first internal transcribed spacer (ITS1) of the ribosomal DNA were obtained from M. subnitida specimens collected in thirteen localities in northeastern Brazil. All the sequences were deposited in GenBank (accession numbers DQ078726-DQ078738). The mean nucleotide divergence (excluding sites with insertions/deletions) in the ITS1 sequences was about 5%, ranging from 0 to 13%. However, when the sites with insertions/deletions were taken into account each sequence was unique, with nucleotide divergences varying from 1.1 to 18%. The intraspecific variation in the M. subnitida ITS1 is therefore greater than most of those previously published studies comprising a wide range of organisms. This high variation is taken as an evidence of isolated populations evolving individually for a long period of time. This information is also of importance for the development of appropriate conservation strategies for this species.Melipona subnitida / stingless bee / nuclear ribosomal DNA / ITS/5.8S region / genetic variability

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Section: Discussionmentioning

confidence: 56%

Intraspecific variation in the first internal transcribed spacer (ITS1) of the nuclear ribosomal DNA inMelipona subnitida(Hymenoptera, Apidae), an endemic stingless bee from northeastern Brazil

et al. 2006

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“…A 1800 bp fragment of the nuclear 18S rRNA (18S) gene was amplified using the primers 18e [25] and 18p [26]. An approximately 800 bp fragment of the nuclear ribosomal complex including the internal transcribed spacer 1 (ITS-1) was amplified using the primers Sp1-5: 5′-CACACCGCCCGTCGCTACTA-3′ and Sp1-3: 5′-ATTTAGCTGCGGTCTTCATC-3′ [27].…”

Section: Methodsmentioning

confidence: 99%

Evolutionary Divergence of Geographic Subspecies within the Scalloped Spiny Lobster Panulirus homarus (Linnaeus 1758)

et al. 2014

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Panulirus homarus is an economically important spiny lobster that is widespread through the Indo-West Pacific Region, but has an uncertain taxonomic status, with three or four geographic subspecies having been described. This study used mitochondrial (16S, COI and control region) and nuclear (18S, ITS-1) DNA sequences to examine specimens of all putative subspecies and forms from throughout their range, in order to determine their genetic validity, and understand the evolutionary history of this species. Despite the range of diversity present in the loci examined, the results were consistent across genes. P. h. rubellus from the SW Indian Ocean comprised the most divergent lineage that was reciprocally monophyletic with respect to all other P. homarus (approx. 9% divergence in COI), and has likely evolved reproductive barriers. The putative P. h. “Brown” subspecies from the Marquesas Is in the central Pacific also comprised a somewhat divergent monophyletic lineage (approx. 3% in COI), but may simply be an allopatric population. The widespread P. h. homarus was not diverged at all from the described P. h. megasculpta from the NW Indian Ocean. The degree of evolutionary divergence of populations at the extremes distribution of the species is somewhat surprising, given the long pelagic larval stage, but suggests that allopatric speciation has been an important driver in the evolution of the genus.

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“…small subunit (ssu) and large subunit (lsu) rDNA -belong to multigene families, and although these are thought to exhibit concerted evolution there are many cases where intragenomic variation has been detected, especially in the internal transcribed spacer regions (e.g. ITS 1 and ITS 2; Harris & Crandall 2000, Chu et al 2001.…”

Section: Introductionmentioning

confidence: 99%

Denaturing gradient gel electrophoresis (DGGE) as a tool for identification of marine nematodes

Cook¹,

Bhadury²,

Debenham³

et al. 2005

Mar. Ecol. Prog. Ser.

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Many phyla of marine invertebrates are difficult to identify using conventional morphological taxonomy. Larvae of a wider set of phyla are also difficult to identify as a result of conservation of morphology between species or because morphological characters are destroyed during sampling and preservation. DNA sequence analysis has the potential for identification of marine organisms to the species level. However, sequence analysis of specimens is time-consuming and impractical when species diversity is very high and densities of individuals huge, as they are in many marine habitats. The effectiveness of the 18S rRNA gene sequences for identification of one speciesrich marine group, the Nematoda, is analysed. Following identification of variable regions of the 18S rRNA gene, primers were designed to amplify a small segment of sequences suitable for denaturing gradient gel electrophoresis (DGGE). The effectiveness of DGGE for identifying individual species is analysed. DGGE analysis of natural communities of nematodes detected less than 2 ⁄ 3 of the species present. This fraction of the community probably represents the abundant species in the original samples. It is concluded that DGGE is not a useful tool for analysis of species richness in marine communities as it fails to detect rare species of which there are usually many in the marine benthic environment. However, DGGE may be a useful method for detecting changes in communities that influence the abundance of the most common taxa. KEY WORDS: Marine nematodes · 18S ribosomal DNA · Denaturing gradient gel electrophoresisResale or republication not permitted without written consent of the publisher

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The First Internal Transcribed Spacer (ITS-1) of Ribosomal DNA as a Molecular Marker for Phylogenetic and Population Analyses in Crustacea

Cited by 86 publications

References 20 publications

Intraspecific variation in the first internal transcribed spacer (ITS1) of the nuclear ribosomal DNA inMelipona subnitida(Hymenoptera, Apidae), an endemic stingless bee from northeastern Brazil

Intraspecific variation in the first internal transcribed spacer (ITS1) of the nuclear ribosomal DNA inMelipona subnitida(Hymenoptera, Apidae), an endemic stingless bee from northeastern Brazil

Evolutionary Divergence of Geographic Subspecies within the Scalloped Spiny Lobster Panulirus homarus (Linnaeus 1758)

Denaturing gradient gel electrophoresis (DGGE) as a tool for identification of marine nematodes

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