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      Mutation of the nuclear pore complex component, aladin1, disrupts asymmetric cell division in Zea mays (maize)

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          Abstract

          The nuclear pore complex (NPC) regulates the movement of macromolecules between the nucleus and cytoplasm. Dysfunction of many components of the NPC results in human genetic diseases, including triple A syndrome (AAAS) as a result of mutations in ALADIN. Here, we report a nonsense mutation in the maize ortholog, aladin1 ( ali1-1), at the orthologous amino acid residue of an AAAS allele from humans, alters plant stature, tassel architecture, and asymmetric divisions of subsidiary mother cells (SMCs). Crosses with the stronger nonsense allele ali1-2 identified complex allele interactions for plant height and aberrant SMC division. RNA-seq analysis of the ali1-1 mutant identified compensatory transcript accumulation for other NPC components as well as gene expression consequences consistent with conservation of ALADIN1 functions between humans and maize. These findings demonstrate that ALADIN1 is necessary for normal plant development, shoot architecture, and asymmetric cell division in maize.

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          Most cited references63

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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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            Trimmomatic: a flexible trimmer for Illumina sequence data

            Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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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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                Author and article information

                Journal
                G3 (Bethesda)
                Genetics
                g3journal
                G3: Genes|Genomes|Genetics
                Oxford University Press
                2160-1836
                July 2021
                16 June 2021
                16 June 2021
                : 11
                : 7
                : jkab106
                Affiliations
                [1 ] Plant Genetics Research Unit, USDA, Agriculture Research Service , Columbia, MO 65211, USA
                [2 ] Department of Horticulture & Landscape Architecture, Purdue University , West Lafayette, IN 47907, USA
                [3 ] Department of Biochemistry, Purdue University , West Lafayette, IN 47907, USA
                [4 ] Natural Sciences and Mathematics Division , Lewis-Clark State College, Lewiston, ID 83501, USA
                [5 ] Department of Botany and Plant Pathology, Purdue University , West Lafayette, IN 47907, USA
                [6 ] Department of Agronomy, Purdue University , West Lafayette, IN 47907, USA
                [7 ] Center for Plant Biology, Purdue University , West Lafayette, IN 47907, USA
                Author notes
                Corresponding author: Department of Biochemistry, Purdue University, Whistler Building Room B036B, West Lafayette, IN 47907, USA. bdilkes@ 123456purdue.edu (B.P.D.); University of Missouri, USDA-ARS, 203 Curtis Hall, Columbia, MO 65211, USA. norman.best@ 123456usda.gov (N.B.B.)
                Author information
                https://orcid.org/0000-0002-6572-5999
                https://orcid.org/0000-0003-0598-5980
                https://orcid.org/0000-0001-8101-8410
                Article
                jkab106
                10.1093/g3journal/jkab106
                8495933
                36351283
                e4de17ef-9b4d-4224-acdf-ef2878d32d7b
                © The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 17 March 2021
                : 20 January 2021
                Page count
                Pages: 11
                Funding
                Funded by: National Science Foundation, DOI 10.13039/100000001;
                Award ID: PGRP # 1444503
                Award ID: CAREER #1054918
                Award ID: PGRP #1025976
                Funded by: Department of Agriculture, DOI 10.13039/501100003526;
                Funded by: National Institute of Food and Agriculture, DOI 10.13039/100005825;
                Award ID: NIFA #2017-67011-26077
                Award ID: #2019-67012-29655
                Categories
                Investigation
                AcademicSubjects/SCI01180
                AcademicSubjects/SCI01140
                AcademicSubjects/SCI00010
                AcademicSubjects/SCI00960

                Genetics
                nuclear pore complex,asymmetric cell division,stomata,subsidiary cells,maize
                Genetics
                nuclear pore complex, asymmetric cell division, stomata, subsidiary cells, maize

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