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

Nadia Kamal, Terry Mun, Dugald Reid, Jie Shun Lin, Turgut Yigit Akyol, Niels Sandal, Torben Asp, Hideki Hirakawa, Jens Stougaard, Klaus F.X. Mayer, Shusei Sato, Stig Uggerhøj Andersen

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)

Abstract

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. 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. 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
JournalDNA Research
Volume27
Issue number3
DOIs
Publication statusPublished - 2020 Jun 1

Keywords

  • comparative genomics
  • expression atlas
  • legume
  • rhizobium
  • symbiosis

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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