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      Gut Bacteria Associated With Monochamus saltuarius (Coleoptera: Cerambycidae) and Their Possible Roles in Host Plant Adaptations

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          Abstract

          Monochamus saltuarius (Coleoptera: Cerambycidae) is an important native pest in the pine forests of northeast China and a dispersing vector of an invasive species Bursaphelenchus xylophilus. To investigate the bacterial gut diversity of M. saltuarius larvae in different host species, and infer the role of symbiotic bacteria in host adaptation, we used 16S rRNA gene Illumina sequencing and liquid chromatography-mass spectrometry metabolomics processing to obtain and compare the composition of the bacterial community and metabolites in the midguts of larvae feeding on three host tree species: Pinus koraiensis, Pinus sylvestris var. mongolica, and Pinus tabuliformis. Metabolomics in xylem samples from the three aforementioned hosts were also performed. Proteobacteria and Firmicutes were the predominant bacterial phyla in the larval gut. At the genus level, Klebsiella, unclassified_f__ Enterobacteriaceae, Lactococcus, and BurkholderiaCaballeroniaParaburkholderia were most dominant in P. koraiensis and P. sylvestris var. mongolica feeders, while BurkholderiaCaballeroniaParaburkholderia, Dyella, Pseudoxanthomonas, and Mycobacterium were most dominant in P. tabuliformis feeders. Bacterial communities were similar in diversity in P. koraiensis and P. sylvestris var. mongolica feeders, while communities were highly diverse in P. tabuliformis feeders. Compared with the other two tree species, P. tabuliformis xylems had more diverse and abundant secondary metabolites, while larvae feeding on these trees had a stronger metabolic capacity for secondary metabolites than the other two host feeders. Correlation analysis of the association of microorganisms with metabolic features showed that dominant bacterial genera in P. tabuliformis feeders were more negatively correlated with plant secondary metabolites than those of other host tree feeders.

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          QIIME allows analysis of high-throughput community sequencing data.

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            fastp: an ultra-fast all-in-one FASTQ preprocessor

            Abstract Motivation Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient. Results We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2–5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools. Availability and implementation The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.
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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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                Author and article information

                Contributors
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                21 June 2021
                2021
                : 12
                : 687211
                Affiliations
                [1] 1Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University , Beijing, China
                [2] 2Sino-French Joint Laboratory for Invasive Forest Pests in Eurasia, French National Research Institute for Agriculture, Food and Environment (INRAE), Beijing Forestry University , Beijing, China
                Author notes

                Edited by: Yoshitomo Kikuchi, National Institute of Advanced Industrial Science and Technology (AIST), Japan

                Reviewed by: Zhanghong Shi, Fujian Agriculture and Forestry University, China; Kazutaka Takeshita, Akita Prefectural University, Japan

                *Correspondence: Shi-Xiang Zong, zongshixiang@ 123456bjfu.edu.cn

                This article was submitted to Microbial Symbioses, a section of the journal Frontiers in Microbiology

                Article
                10.3389/fmicb.2021.687211
                8256174
                34234761
                3adb558b-e495-460d-b204-b800ec16ade5
                Copyright © 2021 Ge, Shi, Pei, Hou, Zong and Ren.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 30 March 2021
                : 31 May 2021
                Page count
                Figures: 8, Tables: 0, Equations: 0, References: 63, Pages: 17, Words: 0
                Categories
                Microbiology
                Original Research

                Microbiology & Virology
                microbiota,metabolomics,host adaptation,host-microbe interaction,intestinal bacterial composition,borer

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