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  1. Summary

    The flowering plantArabidopsis thalianais a dicot model organism for research in many aspects of plant biology. A comprehensive annotation of its genome paves the way for understanding the functions and activities of all types of transcripts, includingmRNA, the various classes of non‐codingRNA, and smallRNA. TheTAIR10 annotation update had a profound impact on Arabidopsis research but was released more than 5 years ago. Maintaining the accuracy of the annotation continues to be a prerequisite for future progress. Using an integrative annotation pipeline, we assembled tissue‐specificRNA‐Seq libraries from 113 datasets and constructed 48 359 transcript models of protein‐coding genes in eleven tissues. In addition, we annotated various classes of non‐codingRNAincluding microRNA, long intergenicRNA, small nucleolarRNA, natural antisense transcript, small nuclearRNA, and smallRNAusing published datasets and in‐house analytic results. Altogether, we identified 635 novel protein‐coding genes, 508 novel transcribed regions, 5178 non‐codingRNAs, and 35 846 smallRNAloci that were formerly unannotated. Analysis of the splicing events andRNA‐Seq based expression profiles revealed the landscapes of gene structures, untranslated regions, and splicing activities to be more intricate than previously appreciated. Furthermore, we present 692 uniformly expressed housekeeping genes, 43% of whose human orthologs are also housekeeping genes. This updated Arabidopsis genome annotation with a substantially increased resolution of gene models will not only further our understanding of the biological processes of this plant model but also of other species.

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  2. Abstract

    Legumes, comprising one of the largest, most diverse, and most economically important plant families, are the subject of vibrant research and development worldwide. Continued improvement of legume crops will benefit from the recent proliferation of genetic (including genomic) resources; but the diversity, scale, and complexity of these resources presents challenges to those managing and using them. A workshop held in March of 2019 addressed questions of data resources and priorities for the legumes. The workshop identified various needs and recommendations: (a) Develop strategies to effectively store, integrate, and relate genetic resources collected in different projects. (b) Leverage information collected across many legume species by standardizing data formats and ontologies, improving the state of metadata about datasets, and increasing use of the FAIR data principles. (c) Advocate for the critical role that curators exercise in integrating complex datasets into databases and adding high value metadata that enable downstream analytics and facilitate practical applications. (d) Implement standardized software and database development practices to best leverage limited developer time and expertise gained from the various legume (and other) species. (e) Develop tools and databases that can manage genetic information for the world's plant genetic resources, enabling efficient incorporation of important traits into breeding programs. (f) Centralize information on databases, tools, and training materials and establish funding streams to support training and outreach.

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