Assessing species boundaries and host ranges of bark beetle-associated tortoise mites, using morphometric and molecular markers

2016 ◽  
Author(s):  
Wayne Knee
Keyword(s):  
Molecular Markers ◽  
Bark Beetle ◽  
Species Boundaries

scholarly journals Species Boundaries and Molecular Markers for the Classification of 16SrI Phytoplasmas Inferred by Genome Analysis

2020 ◽  
Vol 11 ◽  
Author(s):  
Shu-Ting Cho ◽  
Hung-Jui Kung ◽  
Weijie Huang ◽  
Saskia A. Hogenhout ◽  
Chih-Horng Kuo
Keyword(s):  
Molecular Markers ◽  
Genome Analysis ◽  
Species Boundaries

An Application of Molecular Tools in Plant Genetic Diversity Conservation

2014 ◽  
Vol 955-959 ◽  
pp. 830-833
Author(s):  
Zhou Xuan ◽  
Zheng Hong Li ◽  
Cheng Zhang ◽  
Hong Dao Zhang ◽  
Ji Lin Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sustainable Development ◽  
Genetic Variation ◽  
Molecular Markers ◽  
Poverty Alleviation ◽  
Molecular Basis ◽  
Species Boundaries ◽  
Molecular Tools ◽  
New Techniques ◽  
Forestry Production

The conservation and use of plant genetic diversity are essential to the continued maintenance and improvement of agricultural and forestry production and thus, to sustainable development and poverty alleviation. The dramatic advances in molecular genetics over the last decade years have provided workers involved in the conservation of plant genetic diversity with a range of new techniques. Molecular tools, such as molecular markers and other genomic applications, have been highly successful in characterizing existing genetic variation within species, which generates new genetic diversity that often extends beyond species boundaries. The objectives of this article are to review the molecular basis on plant genetic diversity conservation and summarize the continuously rising and application of molecular tool. Then, we look forward and consider the significant of application of molecular tools in plant genetic diversity conservation.

scholarly journals DNA barcodes reveal inconsistent species boundaries in Diplolepis rose gall wasps and their Periclistus inquilines (Hymenoptera: Cynipidae)

2019 ◽  
Vol 151 (6) ◽  
pp. 717-727 ◽  
Author(s):  
Y. Miles Zhang ◽  
Zoltán László ◽  
Chris Looney ◽  
Avar-Lehel Dénes ◽  
Robert H. Hanner ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Mitochondrial Gene ◽  
Taxonomic Revision ◽  
Molecular Data ◽  
Species Boundaries ◽  
Dna Barcodes ◽  
Gall Wasps ◽  
Taxonomic Changes ◽  
Species Groups ◽  
Morphological And Molecular Data

AbstractRose gall wasps, Diplolepis Geoffroy (Hymenoptera: Cynipidae), induce structurally distinct galls on wild roses (Rosa Linnaeus; Rosaceae), which provide gallers with food and shelter. These galls are attacked by a wide variety of micro-hymenopterans, including Periclistus Förster (Hymenoptera: Cynipidae), which act as inquilines. Both Diplolepis and Periclistus are difficult to distinguish based on adult morphology, instead the structural appearance of galls is often used to distinguish species. Using the mitochondrial gene cytochrome c oxidase subunit I, we tested the species boundaries and built phylogenies of both Diplolepis and Periclistus. The molecular results have largely supported the validity of species described in the literature, with notable exceptions in four species groups. Periclistus exhibits a divide between the Palaearctic and Nearctic clades, and ranges from specialists to generalists in terms of host specificity. While it is premature to enact any taxonomic changes without additional molecular markers, this incongruence between morphological and molecular data indicates these groups need taxonomic revision and gall morphology alone may be inadequate to delimit species.

scholarly journals Species Boundaries and Host Range of Tortoise Mites (Uropodoidea) Phoretic on Bark Beetles (Scolytinae), Using Morphometric and Molecular Markers

PLoS ONE ◽  
2012 ◽  
Vol 7 (10) ◽  
pp. e47243 ◽  
Author(s):  
Wayne Knee ◽  
Frédéric Beaulieu ◽  
Jeffrey H. Skevington ◽  
Scott Kelso ◽  
Anthony I. Cognato ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Host Range ◽  
Bark Beetles ◽  
Species Boundaries

scholarly journals Species boundaries and molecular markers for the classification of 16SrI phytoplasmas inferred by genome analysis

2020 ◽  
Author(s):  
Shu-Ting Cho ◽  
Hung-Jui Kung ◽  
Weijie Huang ◽  
Saskia A. Hogenhout ◽  
Chih-Horng Kuo
Keyword(s):  
Molecular Markers ◽  
16S Rrna ◽  
Classification System ◽  
Pathogenic Bacteria ◽  
Rflp Analysis ◽  
Cost Effective ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Species Boundaries ◽  
Critical Examination

AbstractPhytoplasmas are plant-pathogenic bacteria that impact agriculture worldwide. The commonly adopted classification system for phytoplasmas is based on the restriction fragment length polymorphism (RFLP) analysis of their 16S rRNA genes. With the increased availability of phytoplasma genome sequences, the classification system can now be refined. This work examined 11 strains in the 16SrI group within the genus ‘Candidatus Phytoplasma’ and investigated the possible species boundaries. We confirmed that the RFLP classification method is problematic due to intragenomic variation of the 16S rRNA genes and uneven weighing of different nucleotide positions. Importantly, our results based on the molecular phylogeny, differentiations in chromosomal segments and gene content, and divergence in homologous sequences, all supported that these strains may be classified into multiple operational taxonomic units (OTUs) equivalent to species. Strains assigned to the same OTU share >97% genome-wide average nucleotide identity (ANI) and >78% of their protein-coding genes. In comparison, strains assigned to different OTUs share <94% ANI and <75% of their genes. Reduction in homologous recombination between OTUs is one possible explanation for the discontinuity in genome similarities, and these findings supported the proposal that 95% ANI could serve as a cutoff for distinguishing species in bacteria. Additionally, critical examination of these results and the raw sequencing reads led to the identification of one genome that was presumably mis-assembled by combining two sequencing libraries built from phytoplasmas belonging to different OTUs. This finding provided a cautionary tale for working on uncultivated bacteria. Based on the new understanding of phytoplasma divergence and the current genome availability, we developed five molecular markers that could be used for multilocus sequence analysis (MLSA). By selecting markers that are short yet highly informative, and are distributed evenly across the chromosome, these markers provided a cost-effective system that is robust against recombination. Finally, examination of the effector gene distribution further confirmed the rapid gains and losses of these genes, as well as the involvement of potential mobile units (PMUs) in their molecular evolution. Future improvements on the taxon sampling of phytoplasma genomes will allow further expansions of similar analysis, and thus contribute to phytoplasma taxonomy and diagnostics.

scholarly journals New Insights into Interspecific Hybridization in Lemna L. Sect. Lemna (Lemnaceae Martinov)

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2767
Author(s):  
Luca Braglia ◽  
Diego Breviario ◽  
Silvia Gianì ◽  
Floriana Gavazzi ◽  
Jacopo de Gregori ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Species Delimitation ◽  
Interspecific Hybrids ◽  
Lemna Minor ◽  
Lemna Gibba ◽  
Species Boundaries ◽  
Solid Base ◽  
Correct Identification ◽  
Potential Applications ◽  
New Crop

Duckweeds have been increasingly studied in recent years, both as model plants and in view of their potential applications as a new crop in a circular bioeconomy perspective. In order to select species and clones with the desired attributes, the correct identification of the species is fundamental. Molecular methods have recently provided a more solid base for taxonomy and yielded a consensus phylogenetic tree, although some points remain to be elucidated. The duckweed genus Lemna L. comprises twelve species, grouped in four sections, which include very similar sister species. The least taxonomically resolved is sect. Lemna, presenting difficulties in species delimitation using morphological and even barcoding molecular markers. Ambiguous species boundaries between Lemna minor L. and Lemna japonica Landolt have been clarified by Tubulin Based Polymorphism (TBP), with the discovery of interspecific hybrids. In the present work, we extended TBP profiling to a larger number of clones in sect. Lemna, previously classified using only morphological features, in order to test that classification, and to investigate the possible existence of other hybrids in this section. The analysis revealed several misidentifications of clones, in particular among the species L. minor, L. japonica and Lemna gibba L., and identified six putative ‘L. gibba’ clones as interspecific hybrids between L. minor and L. gibba.

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