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

TY - JOUR

T1 - Insights into the evolution of symbiosis gene copy number and distribution from a chromosome-scale Lotus japonicus Gifu genome sequence

AU - Kamal, Nadia

AU - Mun, Terry

AU - Reid, Dugald

AU - Lin, Jie-Shun

AU - Akyol, Turgut Yigit

AU - Sandal, Niels

AU - Asp, Torben

AU - Hirakawa, Hideki

AU - Stougaard, Jens

AU - Mayer, Klaus F X

AU - Sato, Shusei

AU - Andersen, Stig Uggerhøj

N1 - © The Author(s) 2020. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

PY - 2020/6/1

Y1 - 2020/6/1

N2 - 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.

AB - 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.

KW - comparative genomics

KW - expression atlas

KW - legume

KW - rhizobium

KW - symbiosis

UR - http://www.scopus.com/inward/record.url?scp=85091563636&partnerID=8YFLogxK

U2 - 10.1093/dnares/dsaa015

DO - 10.1093/dnares/dsaa015

M3 - Journal article

C2 - 32658273

SN - 1340-2838

VL - 27

JO - D N A Research

JF - D N A Research

IS - 3

M1 - dsaa015

ER -