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      Comparative Transcriptome and DNA Methylation Analysis of Phenotypic Plasticity in the Pacific Abalone ( Haliotis discus hannai)

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          Abstract

          Phenotypic plasticity is an adaptive mechanism used by organisms to cope with environmental fluctuations. Pacific abalone ( Haliotis discus hannai) are large-scale farmed in the temperate area of northern China and in the warmer waters of southern China. RNA-seq and comparative transcriptomic analysis here were performed to determine if the northern and southern populations have evolved divergent plasticity and if functional differences are associated with protein synthesis and growth-related biological progress. The DNA methylation (5mC) landscape of H. discus hannai from the two populations using whole genomic bisulfite sequencing (WGBS), exhibited different epigenetic patterns. The southern population had significant genomic hypo-methylation that may have resulted from long-term acclimation to heat stress. Combining 790 differentially expressed genes (DEGs) and 7635 differentially methylated genes (DMGs), we found that methylation within the gene body might be important in predicting abalone gene expression. Genes related to growth, development, transduction, and apoptosis may be regulated by methylation and could explain the phenotypic divergence of H. discus hannai. Our findings not only emphasize the significant roles of adaptive plasticity in the acclimation of H. discus hannai to high temperatures but also provide a new understanding of the epigenetic mechanism underlying the phenotypic plasticity in adaptation to climate change for marine organisms.

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          Most cited references38

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            clusterProfiler: an R package for comparing biological themes among gene clusters.

            Increasing quantitative data generated from transcriptomics and proteomics require integrative strategies for analysis. Here, we present an R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters. The analysis module and visualization module were combined into a reusable workflow. Currently, clusterProfiler supports three species, including humans, mice, and yeast. Methods provided in this package can be easily extended to other species and ontologies. The clusterProfiler package is released under Artistic-2.0 License within Bioconductor project. The source code and vignette are freely available at http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html.
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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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                Author and article information

                Contributors
                Journal
                Front Physiol
                Front Physiol
                Front. Physiol.
                Frontiers in Physiology
                Frontiers Media S.A.
                1664-042X
                29 June 2021
                2021
                : 12
                : 683499
                Affiliations
                [1] 1State Key Laboratory of Marine Environmental Science, Xiamen University , Xiamen, China
                [2] 2College of Ocean and Earth Sciences, Xiamen University , Xiamen, China
                [3] 3Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University , Xiamen China
                [4] 4College of Fisheries, Jimei University , Xiamen, China
                Author notes

                Edited by: Xiaotong Wang, Ludong University, China

                Reviewed by: Zhiyi Bai, Shanghai Ocean University, China; Cristian Gallardo-Escárate, University of Concepcion, Chile

                *Correspondence: Weiwei You, wwyou@ 123456xmu.edu.cn

                This article was submitted to Aquatic Physiology, a section of the journal Frontiers in Physiology

                Article
                10.3389/fphys.2021.683499
                8277243
                34267674
                fde58376-9a35-4021-b179-d46a7d2d35b1
                Copyright © 2021 Huang, Xiao, Yu, Gan, Lu, Peng, Zhang, Luo, Chen, You and Ke.

                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
                : 21 March 2021
                : 07 June 2021
                Page count
                Figures: 5, Tables: 2, Equations: 0, References: 38, Pages: 11, Words: 0
                Funding
                Funded by: National Key Research and Development Program of China 10.13039/501100012166
                Award ID: 2018YFD0901401
                Categories
                Physiology
                Original Research

                Anatomy & Physiology
                transcriptome,dna methylation,phenotypic plasticity,haliotis discus hannai,climate change,high temperatures

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