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      Influence on the fermentation quality, microbial diversity, and metabolomics in the ensiling of sunflower stalks and alfalfa

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          Abstract

          With the rapid development of the livestock industry, finding new sources of feed has become a critical issue that needs to be addressed urgently. China is one of the top five sunflower producers in the world and generates a massive amount of sunflower stalks annually, yet this resource has not been effectively utilized. Therefore, in order to tap into the potential of sunflower stalks for animal feed, it is essential to explore and develop efficient methods for their utilization.In this study, various proportions of alfalfa and sunflower straw were co-ensiled with the following mixing ratios: 0:10, 2:8, 4:6, 5:5, 6:4, and 8:2, denoted as A0S10, A2S8, A4S6, A5S5, A6S4, and A8S2, respectively. The nutrient composition, fermentation quality, microbial quantity, microbial diversity, and broad-spectrum metabolomics on the 60th day were assessed. The results showed that the treatment groups with more sunflower straw added (A2S8, A4S6) could start fermentation earlier. On the first day of fermentation, Weissella spp.dominated overwhelmingly in these two groups. At the same time, in the early stage of fermentation, the pH in these two groups dropped rapidly, which could effectively reduce the loss of nutrients in the early stage of fermentation.In the later fermentation period, a declining trend in acetic acid levels was observed in A0S10, A2S8, and A4S6, while no butyric acid production was detected in A0S10 and A2S8 throughout the process. In A4S6, butyric acid production was observed only after 30 days of fermentation. From the perspective of metabolites, compared with sunflower ensiling alone, many bioactive substances such as flavonoids, alkaloids, and terpenes are upregulated in mixed ensiling.

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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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              UPARSE: highly accurate OTU sequences from microbial amplicon reads.

              Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.
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                Author and article information

                Contributors
                URI : https://loop.frontiersin.org/people/2567366Role: Role: Role: Role: Role:
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                URI : https://loop.frontiersin.org/people/1819491Role: Role: Role:
                URI : https://loop.frontiersin.org/people/1562789Role: Role:
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                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                26 January 2024
                2024
                : 15
                : 1333207
                Affiliations
                [1] 1 Institute of Grassland Research Chinese, Academy of Agricultural Science , Hohhot, China
                [2] 2 College of Grassland Science, Qingdao Agricultural University , Qingdao, China
                [3] 3 Animal Husbandry Institute of Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences , Hohhot, China
                Author notes

                Edited by: Luigi Lucini, Catholic University of the Sacred Heart, Italy

                Reviewed by: Shuai Du, Inner Mongolia Agricultural University, China

                Maghsoud Besharati, University of Tabriz, Iran

                Lin Sun, Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, China

                *Correspondence: Bin Liu, liubin0613@ 123456126.com ; Feng-Qin Gao, gaofq1211@ 123456126.com

                †These authors have contributed equally to this work

                Article
                10.3389/fpls.2024.1333207
                10853385
                38344186
                64eef928-6a2c-44a8-91c6-51ca22576cb5
                Copyright © 2024 Jiang, Wang, Wang, Jing, Qu, Sun, Wang, Liu and Gao

                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
                : 04 November 2023
                : 02 January 2024
                Page count
                Figures: 6, Tables: 2, Equations: 0, References: 61, Pages: 13, Words: 7801
                Funding
                The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This project was supported by Research and Demonstration of the Inner Mongolia Autonomous Region Science and Technology Program Projects “Research and Application of Key Technologies for Efficient Utilization of Alfalfa and Straw Resources” (2021GG0391).
                Categories
                Plant Science
                Original Research
                Custom metadata
                Crop and Product Physiology

                Plant science & Botany
                sunflower straw,alfalfa,silage,fermentation,bacterial community,metabolites
                Plant science & Botany
                sunflower straw, alfalfa, silage, fermentation, bacterial community, metabolites

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