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      Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage

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          Abstract

          Sex chromosomes differentiated from different ancestral autosomes in various vertebrate lineages. Here, we trace the functional evolution of the XY Chromosomes of the green anole lizard ( Anolis carolinensis), on the basis of extensive high-throughput genome, transcriptome and histone modification sequencing data and revisit dosage compensation evolution in representative mammals and birds with substantial new expression data. Our analyses show that Anolis sex chromosomes represent an ancient XY system that originated at least ≈160 million years ago in the ancestor of Iguania lizards, shortly after the separation from the snake lineage. The age of this system approximately coincides with the ages of the avian and two mammalian sex chromosomes systems. To compensate for the almost complete Y Chromosome degeneration, X-linked genes have become twofold up-regulated, restoring ancestral expression levels. The highly efficient dosage compensation mechanism of Anolis represents the only vertebrate case identified so far to fully support Ohno's original dosage compensation hypothesis. Further analyses reveal that X up-regulation occurs only in males and is mediated by a male-specific chromatin machinery that leads to global hyperacetylation of histone H4 at lysine 16 specifically on the X Chromosome. The green anole dosage compensation mechanism is highly reminiscent of that of the fruit fly, Drosophila melanogaster. Altogether, our work unveils the convergent emergence of a Drosophila-like dosage compensation mechanism in an ancient reptilian sex chromosome system and highlights that the evolutionary pressures imposed by sex chromosome dosage reductions in different amniotes were resolved in fundamentally different ways.

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          Fast gapped-read alignment with Bowtie 2.

          As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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            Fast and accurate short read alignment with Burrows–Wheeler transform

            Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk
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              Basic local alignment search tool.

              A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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                Author and article information

                Journal
                Genome Res
                Genome Res
                genome
                genome
                GENOME
                Genome Research
                Cold Spring Harbor Laboratory Press
                1088-9051
                1549-5469
                December 2017
                December 2017
                : 27
                : 12
                : 1974-1987
                Affiliations
                [1 ]Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland;
                [2 ]Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland;
                [3 ]Center for Genomic Sciences, UNAM, CP62210 Cuernavaca, Mexico;
                [4 ]Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany;
                [5 ]School of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom;
                [6 ]EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, 08003 Barcelona, Spain;
                [7 ]Department of Theoretical Bioinformatics, German Cancer Research Center/BioQuant, D-69120 Heidelberg, Germany;
                [8 ]Neuroscience Program, Michigan State University, East Lansing, Michigan 48824, USA;
                [9 ]Department of Psychology, Michigan State University, East Lansing, Michigan 48824, USA;
                [10 ]Institute of Zoology, University of Basel, 4051 Basel, Switzerland
                Author notes
                [11]

                These authors contributed equally to this work.

                Article
                9509184
                10.1101/gr.223727.117
                5741051
                29133310
                52764d34-93b8-496d-8986-d9d5274a3823
                © 2017 Marin et al.; Published by Cold Spring Harbor Laboratory Press

                This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

                History
                : 7 April 2017
                : 23 October 2017
                Page count
                Pages: 14
                Funding
                Funded by: Baden-Württemberg
                Funded by: German Research Foundation (DFG)
                Award ID: INST 35/1134-1 FUGG
                Funded by: M. Baumann and S. Richling from the Heidelberg University Computational Center (Universitätsrechenzentrum, URZ)
                Funded by: European Research Council , open-funder-registry 10.13039/501100000781;
                Award ID: 615253
                Funded by: Swiss National Science Foundation , open-funder-registry 10.13039/100000001;
                Award ID: 146474
                Funded by: CONACyT-SEP Basic Science
                Award ID: 254240
                Categories
                Research

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