نتایج جستجو برای: taxonomic units

تعداد نتایج: 197687  

2009
Tiehang Wu Edward Ayres Grace Li Richard D. Bardgett Diana H. Wall James R. Garey

A major problem facing ecologists is obtaining a complete picture of the highly complex soil community. While DNA-based methods are routinely used to assess prokaryote community structure and diversity in soil, approaches for measuring the total faunal community are not yet available. This is due to difficulties such as designing primers specific to a range of soil animals while excluding other...

2016
De Chen Qiong Liu Jiang Chang Aiwu Jiang Fang Zhou Yanyun Zhang Zhengwang Zhang

The taxonomic status of subspecies has long been debated, especially in conservation biology. Some proposed subspecies must be evolutionarily distinct to be considered conservation units. White-necklaced Partridge (Arborophila gingica) comprises two subspecies, Arborophila gingica gingica and Arborophila gingica guangxiensis. Arborophila gingica guangxiensis, restricted to three isolated small ...

Journal: :Environmental microbiology reports 2011
Markus Nebel Cornelia Pfabel Alexandra Stock Micah Dunthorn Thorsten Stoeck

Delineating operational taxonomic units (OTUs) is a central element in any culture-independent analysis of environmental microbial eukaryotic diversity. Previous studies either have not justified their choice in sequence distance used to bin small-subunit ribosomal RNA (SSU rRNA) gene sequences amplified from environmental samples into OTUs, or have used a value based on the average across a br...

2013
Alexander F. Koeppel Martin Wu

The lack of a consensus bacterial species concept greatly hampers our ability to understand and organize bacterial diversity. Operational taxonomic units (OTUs), which are clustered on the basis of DNA sequence identity alone, are the most commonly used microbial diversity unit. Although it is understood that OTUs can be phylogenetically incoherent, the degree and the extent of the phylogenetic...

2014
Thomas S. B. Schmidt João F. Matias Rodrigues Christian von Mering

Operational Taxonomic Units (OTUs), usually defined as clusters of similar 16S/18S rRNA sequences, are the most widely used basic diversity units in large-scale characterizations of microbial communities. However, it remains unclear how well the various proposed OTU clustering algorithms approximate 'true' microbial taxa. Here, we explore the ecological consistency of OTUs--based on the assumpt...

Journal: :Proceedings of the National Academy of Sciences of the United States of America 2016
Gregory K Farrant Hugo Doré Francisco M Cornejo-Castillo Frédéric Partensky Morgane Ratin Martin Ostrowski Frances D Pitt Patrick Wincker David J Scanlan Daniele Iudicone Silvia G Acinas Laurence Garczarek

Prochlorococcus and Synechococcus are the two most abundant and widespread phytoplankton in the global ocean. To better understand the factors controlling their biogeography, a reference database of the high-resolution taxonomic marker petB, encoding cytochrome b6, was used to recruit reads out of 109 metagenomes from the Tara Oceans expedition. An unsuspected novel genetic diversity was unveil...

2017
Sarah L Westcott Patrick D Schloss

Assignment of 16S rRNA gene sequences to operational taxonomic units (OTUs) is a computational bottleneck in the process of analyzing microbial communities. Although this has been an active area of research, it has been difficult to overcome the time and memory demands while improving the quality of the OTU assignments. Here, we developed a new OTU assignment algorithm that iteratively reassign...

2017
Mohamed Mysara Mercy Njima Natalie Leys Jeroen Raes Pieter Monsieurs

The development of high-throughput sequencing technologies has provided microbial ecologists with an efficient approach to assess bacterial diversity at an unseen depth, particularly with the recent advances in the Illumina MiSeq sequencing platform. However, analyzing such high-throughput data is posing important computational challenges, requiring specialized bioinformatics solutions at diffe...

2011
Martin Jones Anisah Ghoorah Mark Blaxter

BACKGROUND DNA barcoding and other DNA sequence-based techniques for investigating and estimating biodiversity require explicit methods for associating individual sequences with taxa, as it is at the taxon level that biodiversity is assessed. For many projects, the bioinformatic analyses required pose problems for laboratories whose prime expertise is not in bioinformatics. User-friendly tools ...

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