Genetic Diversity and Variance of <i><scp>S</scp>tentor coeruleus</i> (<scp>C</scp>iliophora: <scp>H</scp>eterotrichea) Inferred from Inter‐Simple Sequence Repeat (ISSR) Fingerprinting

Zhang, Wenjing; Lin, Yan; Cao, Wenqing; Yang, Jun

doi:10.1111/j.1550-7408.2011.00603.x

Cited by 4 publications

(3 citation statements)

References 23 publications

(41 reference statements)

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“…Most studies suggest a correlation between the geographical distribution of germplasm and molecular markers (Zhang et al, 2012;Zhou et al, 2012). The results presented here confirmed the existence of a correlation between the genetic relationship of D. asperoides germplasm resources and geographic distribution.…”

Section: Relationships Between Wild D Asperoides Populationssupporting

confidence: 76%

Genetic diversity and population structure of wild Dipsacus asperoides in China as indicated by ISSR markers

Chen¹,

Li²,

Zhang³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. In order to evaluate the genetic diversity and genetic structure of wild Dipsacus asperoides, we surveyed genetic polymorphisms in 288 individuals from 12 populations using ISSR. A total of 240 bands were amplified, among which 190 were polymorphic loci. At the species level, genetic diversity was found to be abundant: PPB = 79.17%, N E = 1.2152, H = 0.1361, and H sp = 0.2213. At the population level, genetic diversity was lower: PPB = 30.76 %, N E = 1.0786, H = 0.0897, and H pop = 0.1375. The calculated Nei genetic differentiation coefficient was 0.3406, which is consistent with the calculated Shannon population genetic differentiation coefficient of 0.3787. This is commonly taken to indicate that most of the genetic variation existed within the populations. Gene flow was calculated as N m = 0.9679, suggesting that gene exchange only occurred at a low level. Based on the Nei genetic distance, the 12 populations were divided into 4 categories. Our results suggest that D. asperoides has 6341 Genetic diversity in wild Dipsacus asperoides ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 13 (3): 6340-6349 (2014) abundant genetic diversity and provides a foundation for the protection and improvement of germplasm resources.

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Section: Relationships Between Wild D Asperoides Populationssupporting

confidence: 76%

Genetic diversity and population structure of wild Dipsacus asperoides in China as indicated by ISSR markers

Chen¹,

Li²,

Zhang³

et al. 2014

Genet. Mol. Res.

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“…In our analyses, we detected only two ASVs for Gastrostyla steinii while we detected considerably more ASVs of ciliates (e.g. 11 ASVs for Stentor coeruleus ) for which no high variation rates of intraspecific polymorphism have been reported (Kusch, ; Zhang et al ., ). Thus, it is possible that some of the more divergent true organismal variants of G. steinii may have been error‐corrected by DADA2.…”

Section: Discussionmentioning

confidence: 97%

Improving eDNA‐based protist diversity assessments using networks of amplicon sequence variants

Forster

Lentendu

Filker

et al. 2019

Environmental Microbiology

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Summary Effective and precise grouping of highly similar sequences remains a major bottleneck in the evaluation of high‐throughput sequencing datasets. Amplicon sequence variants (ASVs) offer a promising alternative that may supersede the widely used operational taxonomic units (OTUs) in environmental sequencing studies. We compared the performance of a recently developed pipeline based on the algorithm DADA2 for obtaining ASVs against a pipeline based on the algorithm SWARM for obtaining OTUs. Illumina‐sequencing of 29 individual ciliate species resulted in up to 11 ASVs per species, while SWARM produced up to 19 OTUs per species. To improve the congruency between species diversity and molecular diversity, we applied sequence similarity networks (SSNs) for second‐level sequence grouping into network sequence clusters (NSCs). At 100% sequence similarity in SWARM‐SSNs, NSC numbers decreased from 7.9‐fold overestimation without abundance filter, to 4.5‐fold overestimation when an abundance filter was applied. For the DADA2‐SSN approach, NSC numbers decreased from 3.5‐fold to 3‐fold overestimation. Rand index cluster analyses predicted best binning results between 97% and 94% sequence similarity for both DADA2‐SSNs and SWARM‐SSNs. Depending on the ecological questions addressed in an environmental sequencing study with protists we recommend ASVs as replacement for OTUs, best in combination with SSNs.

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“…Due to their compatibility with the modern staining methods for MS and other "omics" methods, kinetomics and argyromics are expected to be useful not only in the morphological protistology, but also in the physiological and biochemical studies, such as classification and monitoring of the populations and communities of Protozoa, together with the other "omics" method -fingerprinting and the advanced analysis of the genetic polymorphism, introduced from genomics (Skotarczak, 2004;Przyboś, 2005;Zhang, 2006;Zhang, 2012 …”

Section: Prospects Of the Development Of The New "-Omics"mentioning

confidence: 99%

Is it possible to consider «kinetomics» and «argyromics» as novel trends of functional morphology and systems biology of parasitic and nonparasitic protozoa? a brief analytical review

Градов¹

2016

Journal of Biomedical Technologies

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Abstract. This paper considers argyrophilic (i.e. stained by the silver nitrate) fibrils visualized by the well-known Klein method and later called neuroformative system of Protozoa, or neuroformium. Klein described the excitation wave propagation and coordination of the cilia moving by this network, as well as the main role in localization of the peristomes and the ciliar apparatus on the topographic microanatomy map of Protozoa before and after the cell division. However, in early 1930-th the advanced staining techniques revealed two components in the above mentioned fibrill network with the similar morphobiochemical parameters (within the limits of the silver nitrate staining selectivity), one of which provides the mechanical stabilization of the Protozoa body (a number of Paramecium species were found to possess even a third selectivelystained fiber system). This resulted in the introduction of the term "argyrome" by Chatton in 1936 for the complex of the argentophilic fibrils and a term "cinetome" for the subpellicular infraciliature. It is therefore more appropriate to speak about "kinetomics" and "argyromics" rather than of a single "omics" for all the intracellular networks of Protozoa. We consider the principles of introduction of the novel "-omics" in modern science and from the above standpoint discuss whether it is possible to consider "kinetomics" and "argyromics" as the novel trends of functional morphology and systems biology of Protozoa.

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Genetic Diversity and Variance of Stentor coeruleus (Ciliophora: Heterotrichea) Inferred from Inter‐Simple Sequence Repeat (ISSR) Fingerprinting

Cited by 4 publications

References 23 publications

Genetic diversity and population structure of wild Dipsacus asperoides in China as indicated by ISSR markers

Genetic diversity and population structure of wild Dipsacus asperoides in China as indicated by ISSR markers

Improving eDNA‐based protist diversity assessments using networks of amplicon sequence variants

Is it possible to consider «kinetomics» and «argyromics» as novel trends of functional morphology and systems biology of parasitic and nonparasitic protozoa? a brief analytical review

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