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      Variation and diversification of the microbiome of Schlechtendalia chinensis on two alternate host plants

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          Abstract

          Schlechtendalia chinensis, a gall-inducing aphid, has two host plants in its life cycle. Its wintering host is a moss (typically Plagiomnium maximoviczii) and its main host is Rhus chinensis (Sumac), on which it forms galls during the summer. This study investigated bacteria associated with S. chinensis living on the two different host plants by sequencing 16S rRNAs. A total of 183 Operational Taxonomic Units (OTUs) from 50 genera were identified from aphids living on moss, whereas 182 OTUs from 49 genera were found from aphids living in Sumac galls. The most abundant bacterial genus among identified OTUs from aphids feeding on both hosts was Buchnera. Despite similar numbers of OTUs, the composition of bacterial taxa showed significant differences between aphids living on moss and those living on R. chinensis. Specifically, there were 12 OTUs from 5 genera (family) unique to aphids living on moss, and 11 OTUs from 4 genera (family) unique to aphids feeding in galls on R. chinensis. Principal Coordinate Analysis (PCoA) also revealed that bacteria from moss-residing aphids clustered differently from aphids collected from galls. Our results provide a foundation for future analyses on the roles of symbiotic bacteria in plant-aphid interactions in general, and how gall-specific symbionts differ in this respect.

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          Most cited references31

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          FLASH: fast length adjustment of short reads to improve genome assemblies.

          Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.
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            The gut bacteria of insects: nonpathogenic interactions.

            The diversity of the Insecta is reflected in the large and varied microbial communities inhabiting the gut. Studies, particularly with termites and cockroaches, have focused on the nutritional contributions of gut bacteria in insects living on suboptimal diets. The indigenous gut bacteria, however, also play a role in withstanding the colonization of the gut by non-indigenous species including pathogens. Gut bacterial consortia adapt by the transfer of plasmids and transconjugation between bacterial strains, and some insect species provide ideal conditions for bacterial conjugation, which suggests that the gut is a "hot spot" for gene transfer. Genomic analysis provides new avenues for the study of the gut microbial community and will reveal the molecular foundations of the relationships between the insect and its microbiome. In this review the intestinal bacteria is discussed in the context of developing our understanding of symbiotic relationships, of multitrophic interactions between insects and plant or animal host, and in developing new strategies for controlling insect pests.
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              Applications of next generation sequencing in molecular ecology of non-model organisms.

              As most biologists are probably aware, technological advances in molecular biology during the last few years have opened up possibilities to rapidly generate large-scale sequencing data from non-model organisms at a reasonable cost. In an era when virtually any study organism can 'go genomic', it is worthwhile to review how this may impact molecular ecology. The first studies to put the next generation sequencing (NGS) to the test in ecologically well-characterized species without previous genome information were published in 2007 and the beginning of 2008. Since then several studies have followed in their footsteps, and a large number are undoubtedly under way. This review focuses on how NGS has been, and can be, applied to ecological, population genetic and conservation genetic studies of non-model species, in which there is no (or very limited) genomic resources. Our aim is to draw attention to the various possibilities that are opening up using the new technologies, but we also highlight some of the pitfalls and drawbacks with these methods. We will try to provide a snapshot of the current state of the art for this rapidly advancing and expanding field of research and give some likely directions for future developments.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Project administrationRole: Writing – original draft
                Role: ConceptualizationRole: Formal analysisRole: Funding acquisition
                Role: ConceptualizationRole: Funding acquisitionRole: Project administration
                Role: Data curationRole: Methodology
                Role: ConceptualizationRole: Data curationRole: Investigation
                Role: MethodologyRole: Software
                Role: Investigation
                Role: Investigation
                Role: Investigation
                Role: Project administrationRole: Writing – review & editing
                Role: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                8 November 2018
                2018
                : 13
                : 11
                : e0200049
                Affiliations
                [1 ] Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming, China
                [2 ] The Key Laboratory of Cultivating and Utilization of Resources Insects, State Forestry Administration, Kunming, China
                [3 ] Southwest Forestry University, Bailongsi, Kunming City, Yunnan, PR. China
                [4 ] Department of Biological Sciences, University of Alberta, Biological Sciences Bldg., Edmonton, Alberta, Canada
                [5 ] Department of Entomology, Kansas State University, Manhattan, KS, United States of America
                Oklahoma State University, UNITED STATES
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0002-7169-6717
                http://orcid.org/0000-0002-9089-8015
                Article
                PONE-D-18-17693
                10.1371/journal.pone.0200049
                6224032
                30408037
                1f2c0149-270c-46cb-be4e-b83b38c2fcc9
                © 2018 Wu et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 13 June 2018
                : 23 October 2018
                Page count
                Figures: 3, Tables: 3, Pages: 11
                Funding
                Funded by: CAFYBB2014QB019
                Award ID: CAFYBB2014QB019
                Award Recipient :
                Funded by: CAFYBB2014ZD005
                Award ID: CAFYBB2014ZD005
                Award Recipient :
                Funded by: U1402263
                Award ID: U1402263
                Award Recipient :
                This study is funded by the Grant for Essential Scientific Research of National Non-profit Institute (No. CAFYBB2014ZD005; CAFYBB2014QB019); and the National Natural Science Foundation of China (Grant No. U1402263; 31772542; 31300019). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Invertebrates
                Arthropoda
                Insects
                Aphids
                Biology and Life Sciences
                Organisms
                Eukaryota
                Plants
                Nonvascular Plants
                Mosses
                Biology and Life Sciences
                Organisms
                Eukaryota
                Plants
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Invertebrates
                Arthropoda
                Insects
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
                Research and Analysis Methods
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
                Biology and Life Sciences
                Organisms
                Bacteria
                Biology and Life Sciences
                Organisms
                Bacteria
                Bacillus
                Biology and Life Sciences
                Microbiology
                Medical Microbiology
                Microbial Pathogens
                Bacterial Pathogens
                Bacillus
                Medicine and Health Sciences
                Pathology and Laboratory Medicine
                Pathogens
                Microbial Pathogens
                Bacterial Pathogens
                Bacillus
                Biology and Life Sciences
                Organisms
                Bacteria
                Pseudomonas
                Custom metadata
                All relevant data are within the paper and its Supporting Information files.

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