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

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.

Keywords: comparative genomics; expression atlas; legume; rhizobium; symbiosis.

Figure 1

(A) Circos diagram displaying heatmaps of the numbers of genes and ncRNAs (100 Mb bins) and bases covered by repetitive elements (10 Mb bins) in the Lotus Gifu genome. (B) BUSCO version 4 scores of the Lotus Gifu assembly (98.2%), the HC gene set (94%), the high- and LC gene set (96.1%) and of only the longest transcript of each gene (91.8%) from the joint HC and LC gene set. Lineage used: embryophyta_odb10. (C) Distribution of repetitive elements in the Lotus Gifu genome.

Figure 2

Expression profiles of known symbiosis genes. Expression values from the Lotus Gifu RNA-seq expression atlas are shown for the indicated genes. A full description of the conditions included is shown in Supplementary Table S1. The heatmap was generated from https://lotus.au.dk/expat/ using the normalize by row function.

Figure 3

Symbiotic island gene expression. (A) Log(nodule/root) expression ratios for genes in Medicago A17 symbiotic islands and their best Lotus Gifu BLAST matches. n: gene count. r: Pearson correlation coefficient for the Lotus Gifu and Medicago A17 log(nodule/root) ratios. (B–C) Histograms of Pearson correlation coefficients for symbiotic islands. The Pearson correlation coefficient for each island is an average of the coefficients resulting from pairwise comparisons of the gene expression profiles of all genes residing within that island. n: symbiotic island count. (B) All genes in Medicago A17 symbiotic islands with a putative Lotus Gifu homolog with expression data. Multiple copies of the same Lotus Gifu gene are allowed. (C) Only one Lotus Gifu copy and one corresponding Medicago A17 gene is included in the analysis and it is further required that each Lotus Gifu island contains at least three members. Lotus: expression data from Lotus Gifu. Medicago: expression data from Medicago A17.