Resource Article: Genomes Explored Insights into the evolution of symbiosis gene copy number and distribution from a chromosome-scale Lotus japonicus Gifu genome sequence Nadia Kamal 1 , Terry Mun 2 , Dugald Reid 2 , Jie-Shun Lin 2 , Turgut Yigit Akyol 3 , Niels Sandal 2 , Torben Asp 2 , Hideki Hirakawa 4 , Jens Stougaard 2 , Klaus F. X. Mayer 1,5 *, Shusei Sato 3 *, and Stig Uggerhøj Andersen 2 * 1 Helmholtz Zentrum Mu ¨ nchen, German Research Center for Environmental Health, Plant Genome and Systems Biology, 85764 Neuherberg, Germany, 2 Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark, 3 Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan, 4 Kazusa DNA Research Institute, Kisarazu, Chiba 292-0816, Japan, and 5 School of Life Sciences, Technical University Munich, Munich, Germany *To whom correspondence should be addressed. Email: k.mayer@helmholtz-muenchen.de (K.F.X.M.); shuseis@ige.tohoku.ac.jp (S.S.); sua@mbg.au.dk (S.U.A.) Received 23 April 2020; Editorial decision 13 July 2020; Accepted 7 July 2020 Abstract Lotus japonicus is a herbaceous perennial legume that has been used extensively as a geneti- cally tractable model system for deciphering the molecular genetics of symbiotic nitrogen fixa- tion. Our aim is to improve the L. japonicus reference genome sequence, which has so far been based on Sanger and Illumina sequencing reads from the L. japonicus accession MG-20 and con- tained a large fraction of unanchored contigs. Here, we use long PacBio reads from L. japonicus Gifu combined with Hi-C data and new high-density genetic maps to generate a high-quality chromosome-scale reference genome assembly for L. japonicus. The assembly comprises 554 megabases of which 549 were assigned to six pseudomolecules that appear complete with telo- meric repeats at their extremes and large centromeric regions with low gene density. The new L. japonicus Gifu reference genome and associated expression data represent valuable resources for legume functional and comparative genomics. Here, we provide a first example by showing that the symbiotic islands recently described in Medicago truncatula do not appear to be con- served in L. japonicus. Key words: legume, symbiosis, rhizobium, comparative genomics, expression atlas 1. Introduction The roots of most plants are colonized by mycorrhizal fungi. This symbiotic interaction is ancient, perhaps dating back to the origin of land plants, and many of its genetic components have been co-opted to allow symbiotic nitrogen fixation in legumes. 1 Much of the over- lapping genetic framework, as well as components specific to both V C The Author(s) 2020. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. 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. 1 DNA Research, 2020, 27(3), 1–11 doi: 10.1093/dnares/dsaa015 Advance Access Publication Date: 13 July 2020 Resource Article: Genomes Explored Downloaded from https://academic.oup.com/dnaresearch/article/27/3/dsaa015/5870829 by guest on 28 November 2022