Insights into the evolution of symbiosis gene copy number and distribution from a chromosome-scale Lotus japonicus Gifu genome sequence

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DOI

  • Nadia Kamal, German Research Center for Environmental Health
  • ,
  • Terry Mun
  • ,
  • Dugald Reid
  • Jie-Shun Lin, Institut for Molekylærbiologi og Genetik - Molekylær celle-og udviklingsbiologi, Aarhus Universitet
  • ,
  • Turgut Yigit Akyol
  • Niels Sandal
  • Torben Asp
  • Hideki Hirakawa, Kazusa DNA Research Institute
  • ,
  • Jens Stougaard
  • Klaus F X Mayer, German Research Center for Environmental Health
  • ,
  • Shusei Sato, Tohoku Univ, Tohoku University, RCNS
  • ,
  • Stig Uggerhøj Andersen

AIM: Lotus japonicus is a herbaceous perennial legume that has been used extensively as a genetically tractable model system for deciphering the molecular genetics of symbiotic nitrogen fixation. 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 contained a large fraction of unanchored contigs.

METHODS AND RESULTS: 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 telomeric repeats at their extremes and large centromeric regions with low gene density.

CONCLUSION AND PERSPECTIVES: 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 conserved in L. japonicus.

Original languageEnglish
Article numberdsaa015
JournalD N A Research
Volume27
Issue3
ISSN1340-2838
DOIs
Publication statusPublished - Jul 2020

Bibliographical note

© The Author(s) 2020. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

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