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      Achiasmatic meiosis in the unisexual Amazon molly, Poecilia formosa

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          Abstract

          Unisexual reproduction, which generates clonal offspring, is an alternative strategy to sexual breeding and occurs even in vertebrates. A wide range of non-sexual reproductive modes have been described, and one of the least understood questions is how such pathways emerged and how they mechanistically proceed. The Amazon molly, Poecilia formosa, needs sperm from males of related species to trigger the parthenogenetic development of diploid eggs. However, the mechanism, of how the unreduced female gametes are produced, remains unclear. Cytological analyses revealed that the chromosomes of primary oocytes initiate pachytene but do not proceed to bivalent formation and meiotic crossovers. Comparing ovary transcriptomes of P. formosa and its sexual parental species revealed expression levels of meiosis-specific genes deviating from P. mexicana but not from P. latipinna. Furthermore, several meiosis genes show biased expression towards one of the two alleles from the parental genomes. We infer from our data that in the Amazon molly diploid oocytes are generated by apomixis due to a failure in the synapsis of homologous chromosomes. The fact that this failure is not reflected in the differential expression of known meiosis genes suggests the underlying molecular mechanism may be dysregulation on the protein level or misexpression of a so far unknown meiosis gene, and/or hybrid dysgenesis because of compromised interaction of proteins from diverged genomes.

          Supplementary Information

          The online version contains supplementary material available at 10.1007/s10577-022-09708-2.

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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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            The Sequence Alignment/Map format and SAMtools

            Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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              STAR: ultrafast universal RNA-seq aligner.

              Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
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                Author and article information

                Contributors
                phch1@biozentrum.uni-wuerzburg.de
                Journal
                Chromosome Res
                Chromosome Res
                Chromosome Research
                Springer Netherlands (Dordrecht )
                0967-3849
                1573-6849
                2 December 2022
                2 December 2022
                2022
                : 30
                : 4
                : 443-457
                Affiliations
                [1 ]GRID grid.418095.1, ISNI 0000 0001 1015 3316, Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics, , Czech Academy of Sciences, ; Rumburská 89, Liběchov, 277 21 Czech Republic
                [2 ]GRID grid.8379.5, ISNI 0000 0001 1958 8658, Developmental Biochemistry, Biocenter, , University of Wuerzburg, ; Am Hubland, 97074 Wuerzburg, Germany
                [3 ]GRID grid.8379.5, ISNI 0000 0001 1958 8658, Biochemistry and Cell Biology, Biocenter, , University of Wuerzburg, ; Am Hubland, 97074 Wuerzburg, Germany
                [4 ]Institute of Zoology, Academiei 1, 2001, MD-2028 Chisinau, Moldova
                [5 ]GRID grid.14509.39, ISNI 0000 0001 2166 4904, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, , University of South Bohemia in České Budějovice, ; Zátiší 728/II, 389 25 Vodňany, Czech Republic
                [6 ]GRID grid.264772.2, ISNI 0000 0001 0682 245X, Xiphophorus Genetic Stock Center, , Texas State University, ; San Marcos, TX 78666 USA
                [7 ]GRID grid.8379.5, ISNI 0000 0001 1958 8658, Cell and Developmental Biology, , University of Wuerzburg, ; Am Hubland, 97074 BiocenterWuerzburg, Germany
                [8 ]GRID grid.412684.d, ISNI 0000 0001 2155 4545, Department of Biology and Ecology, Faculty of Science, , University of Ostrava, ; Chittussiho 10, 710 00 Ostrava, Czech Republic
                Article
                9708
                10.1007/s10577-022-09708-2
                9771850
                36459298
                ecd13281-084c-439e-8da1-ac46131ecdc5
                © This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2022

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 5 July 2022
                : 30 September 2022
                : 27 October 2022
                Funding
                Funded by: Czech Science Foundation
                Award ID: PPLZ L200452002
                Award Recipient :
                Funded by: Ministry of Education, Youth and Sports of the Czech Republic
                Award ID: 539 EXCELLENCE CZ.02.1.01/0.0/0.0/15_003/0000460 OP RDE
                Award Recipient :
                Funded by: Julius-Maximilians-Universität Würzburg (3088)
                Categories
                Research
                Custom metadata
                © Springer Nature B.V. 2022

                Genetics
                meiosis,parthenogenesis,synaptonemal complex,recombination,crossing-over,achiasmatic,transcriptome,oogenesis

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