02574nas a2200289   4500008004100000245010700041210006900148260009100217300001200308490000700320520153900327653002501866653001801891653001401909653002301923653001401946100002101960700002401981700002302005700002002028700001802048700001702066700002602083700001702109700002102126856013702147       2009                        eng d00aA phylogenetic tree of nematodes based on about 1200 full-length small subunit ribosomal DNA sequences0 aphylogenetic tree of nematodes based on about 1200 fulllength sm  aPLANTIJNSTRAAT 2, P O BOX 9000, 2300 PA LEIDEN, NETHERLANDSbBRILL ACADEMIC PUBLISHERS  a927-S270 v113 aAs a result of the scarcity of informative morphological and anatomical characters, nematode systematics have always been volatile. Differences in the appreciation of these characters have resulted in numerous classifications and this greatly confuses scientific communication. An advantage of the use of molecular data is that it allows for an enormous expansion of the number of characters. Here we present a phylogenetic tree based on 1215 small subunit ribosomal DNA sequences (ca 1700 bp each) covering a wide range of nematode taxa. Of the 19 nematode orders mentioned by De Ley et al. (2006) 15 are represented here. Compared with Holterman et al. (2006) the number of taxa analysed has been tripled. This did not result in major changes in the clade subdivision of the phylum, although a decrease in the number of well supported nodes was observed. Especially at the family level and below we observed a considerable congruence between morphology and ribosomal DNA-based nematode systematics and, in case of discrepancies, morphological or anatomical support could be found for the alternative grouping in most instances. The extensiveness of convergent evolution is one of the most striking phenomena observed in the phylogenetic tree presented here - it is hard to find a morphological, ecological or biological characteristic that has not arisen at least twice during nematode evolution. Convergent evolution appears to be an important additional explanation for the seemingly persistent volatility of nematode systematics.10aconvergent evolution10aDNA barcoding10amolecular10anematode evolution10aphylogeny1 avan Megen, Hanny1 avan den Elsen, Sven1 aHolterman, Martijn1 aKarssen, Gerrit1 aMooyman, Paul1 aBongers, Tom1 aHolovachov, Oleksandr1 aBakker, Jaap1 aHelder, Johannes  uhttps://nematoda.myspecies.info/content/phylogenetic-tree-nematodes-based-about-1200-full-length-small-subunit-ribosomal-dna-sequenc02970nas a2200193   4500008004100000245011600041210006900157260006900226300001200295490000800307520218500315653002102500653001802521653003102539653002102570100002402591700002402615856013702639       2010                        eng d00aBarcoding marine nematodes: an improved set of nematode 18S rRNA primers to overcome eukaryotic co-interference0 aBarcoding marine nematodes an improved set of nematode 18S rRNA   aVAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDSbSPRINGER  a245-2510 v6413 aNematodes form an important component of many benthic marine ecosystems and DNA barcoding approaches could provide an insight into nematode community composition from different environments globally. We have amplified nematode 18S rRNA sequences using standard nematode18S rRNA primers from environmental DNA extracted from intertidal sediment collected from New Jersey coast, USA to test whether the published marine nematode 18S rRNA sequences from GenBank and EMBL databases can effectively assign unknown nematode sequences into genus or species level. Most of the sequenced clones showed some degree of identities with published marine nematode 18S rRNA sequences. However, relatively very few of the sequences could be assigned even to genus level based on sequence assignment rule. In addition, other eukaryotic 18S rRNA sequences were found to be co-amplified with commonly used nematode 18S rRNA primers. We found that the majority of the current nematode 18S rRNA primers will co-amplify other eukaryotes if environmental DNA is the target template. We therefore designed a new set of nematode 18S rRNA primers and evaluated them using environmental DNA in intertidal sediment from the New Jersey coast. In total, 40 clones were screened and subsequently sequenced and all the sequences showed varying degree of identities with published nematode 18S rRNA sequences from GenBank and EMBL databases, and no obvious eukaryotic co-amplicons were detected with new primers. Only 13 out of 40 clones amplified with the new primer set showed 100% identity to published Daptonema and Metachromadora 18S rRNA sequences. The current molecular databases for nematodes are dominated by sequences from NW Europe and need to be more extensively populated with new full length 18S rRNA nematode sequences collected from different biogeographic locations. The new primers developed in this study, in combination with an updated nematode 18S rRNA sequence database, would help us to better investigate and understand the diversity and community composition of free-living marine nematodes based on DNA barcoding approaches during biodiversity or biomonitoring surveys on a global-scale.10a18S rRNA primers10aDNA barcoding10aEukaryotic co-interference10aMarine nematodes1 aBhadury, Punyasloke1 aAusten, Melanie, C.  uhttps://nematoda.myspecies.info/content/barcoding-marine-nematodes-improved-set-nematode-18s-rrna-primers-overcome-eukaryotic-co-int02854nas a2200313   4500008004100000245010100041210006900142260008700211300001400298490000600312520175000318653002902068653001702097653001802114653003102132653001602163653001302179100002702192700002802219700001702247700002202264700002102286700002402307700002302331700002402354700001402378700001902392856012902411       2009                        eng d00aEvaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity0 aEvaluating highthroughput sequencing as a method for metagenomic  aCOMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USAbWILEY-BLACKWELL PUBLISHING, INC  a1439-14500 v93 aNematodes play an important role in ecosystem processes, yet the relevance of nematode species diversity to ecology is unknown. Because nematode identification of all individuals at the species level using standard techniques is difficult and time-consuming, nematode communities are not resolved down to the species level, leaving ecological analysis ambiguous. We assessed the suitability of massively parallel sequencing for analysis of nematode diversity from metagenomic samples. We set up four artificial metagenomic samples involving 41 diverse reference nematodes in known abundances. Two samples came from pooling polymerase chain reaction products amplified from single nematode species. Two additional metagenomic samples consisted of amplified products of DNA extracted from pooled nematode species. Amplified products involved two rapidly evolving similar to 400-bp sections coding for the small and large subunit of rRNA. The total number of reads ranged from 4159 to 14771 per metagenomic sample. Of these, 82% were > 199 bp in length. Among the reads > 199 bp, 86% matched the referenced species with less than three nucleotide differences from a reference sequence. Although neither rDNA section recovered all nematode species, the use of both loci improved the detection level of nematode species from 90 to 97%. Overall, results support the suitability of massively parallel sequencing for identification of nematodes. In contrast, the frequency of reads representing individual species did not correlate with the number of individuals in the metagenomic samples, suggesting that further methodological work is necessary before it will be justified for inferring the relative abundances of species within a nematode community.10a454 genome sequencer FLX10aBiodiversity10aDNA barcoding10ahigh-throughput sequencing10ametagenomic10anematode1 aPorazinska, Dorota, L.1 aGiblin-Davis, Robin, M.1 aFaller, Lina1 aFarmerie, William1 aKanzaki, Natsumi1 aMorris, Krystalynne1 aPowers, Thomas, O.1 aTucker, Abraham, E.1 aSung, Way1 aThomas, Kelley  uhttps://nematoda.myspecies.info/content/evaluating-high-throughput-sequencing-method-metagenomic-analysis-nematode-diversity02603nas a2200253   4500008004100000245010100041210006900142260006600211300000800277490000800285520170100293653001301994653001802007653002202025653001902047653002102066100002402087700002402111700002202135700002402157700002102181700002202202856012502224       2006                        eng d00aDevelopment and evaluation of a DNA-barcoding approach for the rapid identification of nematodes0 aDevelopment and evaluation of a DNAbarcoding approach for the ra  aNORDBUNTE 23, D-21385 OLDENDORF LUHE, GERMANYbINTER-RESEARCH  a1-90 v3203 aFree-living nematodes are abundant in all marine habitats, are highly diverse, and can be useful for monitoring anthropogenic impacts on the environment. Despite such attributes, nematodes are effectively ignored by many marine ecologists because of their time-consuming taxonomy. Nematode diagnostics has traditionally relied on detailed comparison of morphological characters which, given their abundance, is difficult and laborious, meaning that the biodiversity of the group is typically underestimated. Molecular methods such as DNA-barcoding offer potentially efficient alternative approaches to studying the biodiversity of marine nematode communities, allowing these organisms to be more effectively exploited in ecological surveys and environmental assessments. In this study, a number of nuclear and mitochondrial genomic regions were evaluated as potential diagnostic loci for marine nematode species identification. Of these, the 18S ribosomal RNA gene amplified most reliably from a range of taxa, and was therefore evaluated as a DNA barcode. In a comparison of molecular and morphological identifications, over 97 % of specimens sequenced were correctly assigned on the basis of a short stretch of 18S rRNA sequence (approximately 345 bp), making this a potentially useful marker for the rapid molecular assignment of unknown nematode species, and evaluation of nematode species richness during ecological surveys or environmental assessments. This study showed that a single marker approach based on amplification and sequencing may prove invaluable in the rapid identification of nematodes during ecological surveys and, indeed, other taxonomically challenging invertebrate taxa.10a18S rRNA10aDNA barcoding10aecological survey10aidentification10aMarine nematodes1 aBhadury, Punyasloke1 aAusten, Melanie, C.1 aBilton, David, T.1 aLambshead, John, D.1 aRogers, Alex, D.1 aSmerdon, Gary, R.  uhttps://nematoda.myspecies.info/content/development-and-evaluation-dna-barcoding-approach-rapid-identification-nematodes