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      Novel genetic sex markers reveal unexpected lack of, and similar susceptibility to, sex reversal in free‐living common toads in both natural and anthropogenic habitats

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          Abstract

          Anthropogenic environmental changes are affecting biodiversity and microevolution worldwide. Ectothermic vertebrates are especially vulnerable because environmental changes can disrupt their sexual development and cause sex reversal, a mismatch between genetic and phenotypic sex. This can potentially lead to sex‐ratio distortion and population decline. Despite these implications, there is scarce empirical knowledge on the incidence of sex reversal in nature. Populations in anthropogenic environments may be exposed to sex‐reversing stimuli more frequently, which may lead to higher sex‐reversal rate or, alternatively, these populations may adapt to resist sex reversal. We developed PCR‐based genetic sex markers for the common toad ( Bufo bufo) to assess the prevalence of sex reversal in wild populations living in natural, agricultural and urban habitats, and the susceptibility of the same populations to two ubiquitous oestrogenic pollutants in a common garden experiment. We found negligible sex‐reversal frequency in free‐living adults despite the presence of various endocrine‐disrupting pollutants in their breeding ponds. Individuals from different habitat types showed similar susceptibility to sex reversal in the laboratory: all genetic males developed female phenotype when exposed to 1 µg L −1 17α‐ethinylestradiol (EE2) during larval development, whereas no sex reversal occurred in response to 1 ng L −1 EE2 and a glyphosate‐based herbicide with 3 µg L −1 or 3 mg L −1 glyphosate. The latter results do not support that populations in anthropogenic habitats would have either increased propensity for or higher tolerance to chemically induced sex reversal. Thus, the extremely low sex‐reversal frequency in wild toads compared to other ectothermic vertebrates studied before might indicate idiosyncratic, potentially species‐specific resistance to sex reversal.

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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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            CD-HIT: accelerated for clustering the next-generation sequencing data

            Summary: CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. In response to the rapid increase in the amount of sequencing data produced by the next-generation sequencing technologies, we have developed a new CD-HIT program accelerated with a novel parallelization strategy and some other techniques to allow efficient clustering of such datasets. Our tests demonstrated very good speedup derived from the parallelization for up to ∼24 cores and a quasi-linear speedup for up to ∼8 cores. The enhanced CD-HIT is capable of handling very large datasets in much shorter time than previous versions. Availability: http://cd-hit.org. Contact: liwz@sdsc.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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              PEAR: a fast and accurate Illumina Paired-End reAd mergeR

              Motivation: The Illumina paired-end sequencing technology can generate reads from both ends of target DNA fragments, which can subsequently be merged to increase the overall read length. There already exist tools for merging these paired-end reads when the target fragments are equally long. However, when fragment lengths vary and, in particular, when either the fragment size is shorter than a single-end read, or longer than twice the size of a single-end read, most state-of-the-art mergers fail to generate reliable results. Therefore, a robust tool is needed to merge paired-end reads that exhibit varying overlap lengths because of varying target fragment lengths. Results: We present the PEAR software for merging raw Illumina paired-end reads from target fragments of varying length. The program evaluates all possible paired-end read overlaps and does not require the target fragment size as input. It also implements a statistical test for minimizing false-positive results. Tests on simulated and empirical data show that PEAR consistently generates highly accurate merged paired-end reads. A highly optimized implementation allows for merging millions of paired-end reads within a few minutes on a standard desktop computer. On multi-core architectures, the parallel version of PEAR shows linear speedups compared with the sequential version of PEAR. Availability and implementation: PEAR is implemented in C and uses POSIX threads. It is freely available at http://www.exelixis-lab.org/web/software/pear. Contact: Tomas.Flouri@h-its.org
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                Author and article information

                Contributors
                nemeshazi.edina@protonmail.com
                Journal
                Mol Ecol
                Mol Ecol
                10.1111/(ISSN)1365-294X
                MEC
                Molecular Ecology
                John Wiley and Sons Inc. (Hoboken )
                0962-1083
                1365-294X
                24 February 2022
                April 2022
                : 31
                : 7 ( doiID: 10.1111/mec.v31.7 )
                : 2032-2043
                Affiliations
                [ 1 ] ringgold 374774; Conservation Genetics Research Group Department of Ecology University of Veterinary Medicine Budapest Budapest Hungary
                [ 2 ] Lendület Evolutionary Ecology Research Group Plant Protection Institute Centre for Agricultural Research Eötvös Loránd Research Network Budapest Hungary
                [ 3 ] MTA‐DE Lendület Evolutionary Phylogenomics Research Group Debrecen Hungary
                [ 4 ] Molecular Ecology and Evolution at Bangor School of Natural Sciences Bangor University Bangor Wales UK
                Author notes
                [*] [* ] Correspondence

                Edina Nemesházi, Conservation Genetics Research Group, Department of Ecology, University of Veterinary Medicine Budapest, István u. 2, 1078 Budapest, Hungary.

                Email: nemeshazi.edina@ 123456protonmail.com

                Author information
                https://orcid.org/0000-0002-0179-1153
                https://orcid.org/0000-0001-8588-6362
                http://orcid.org/0000-0002-2136-5346
                Article
                MEC16388
                10.1111/mec.16388
                9544883
                35146823
                7b94cac3-73c8-40ce-80a7-cd0f6a95c180
                © 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.

                History
                : 27 January 2022
                : 21 October 2021
                : 04 February 2022
                Page count
                Figures: 3, Tables: 1, Pages: 12, Words: 9851
                Funding
                Funded by: Magyar Tudományos Akadémia
                Funded by: Innovációs és Technológiai Minisztérium
                Award ID: ÚNKP‐20‐5
                Award ID: ÚNKP‐21‐2
                Award ID: ÚNKP‐21‐5
                Funded by: National Research, Development and Innovation Office of Hungary
                Award ID: NKFIH 115402
                Award ID: NKFIH 135016
                Funded by: Emberi Eroforrások Minisztériuma
                Award ID: NTP‐NFTÖ 17‐B‐0317
                Categories
                Original Article
                ORIGINAL ARTICLES
                Population and Conservation Genetics
                Custom metadata
                2.0
                April 2022
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.2.0 mode:remove_FC converted:07.10.2022

                Ecology
                amphibians,feminization,human‐induced environmental change,molecular sex markers,sex change,sex‐chromosome identification

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