Extreme genetic signatures of local adaptation during Lotus japonicus colonization of Japan

Abstract

Colonization of new habitats is expected to require genetic adaptations to overcome environmental challenges. Here, we use full genome re-sequencing and extensive common garden experiments to investigate demographic and selective processes associated with colonization of Japan by Lotus japonicus over the past~20,000 years. Based on patterns of genomic variation, we infer the details of the colonization process where L. japonicus gradually spread from subtropical conditions to much colder climates in northern Japan. We identify genomic regions with extreme genetic differentiation between northern and southern subpopulations and perform population structure-corrected association mapping of phenotypic traits measured in a common garden. Comparing the results of these analyses, we find that signatures of extreme subpopulation differentiation overlap strongly with phenotype association signals for overwintering and flowering time traits. Our results provide evidence that these traits were direct targets of selection during colonization and point to associated candidate genes.

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

“…Using the new Gifu sequence, the LORE1 insertions can now be more accurately characterised. Likewise, Gifu is more closely related to the majority of the collection of wild Lotus accessions that was recently characterized 13 , and the new reference assembly should allow an improved characterization of the genetic diversity. Here, we have mapped existing and new RNAseq data to the Gifu assembly to provide a consistently normalized and updated Lotus gene expression atlas readily available through Lotus Base 31 .…”

Insights into the evolution of symbiosis gene copy number and distribution from a chromosome-scaleLotus japonicusGifu genome sequence

“… 14 Using the new Lotus Gifu sequence, the LORE1 insertions can now be more accurately characterized. Likewise, Gifu is more closely related to the majority of the collection of natural Lotus accessions that was recently characterized, 10 and the new reference assembly should allow an improved characterization of the genetic diversity. Here, we have mapped existing and new RNA-seq data to the Gifu assembly to provide a consistently normalized and updated Lotus gene expression atlas readily available through Lotus Base.…”

“…The genetic resources already available for Lotus include sequenced natural accessions 10 and recombinant inbred lines (RILs), 11 , 12 as well as extensive populations of TILLING lines 13 and LORE1 insertion mutants. 14 In addition, large volumes of Lotus expression and LORE1 data have been integrated in the online portal Lotus Base 15 ( https://lotus.au.dk ).…”

“…This MG-20 assembly has proved very useful for genetic mapping and for genome-wide transcriptome, methylation, and insertion mutant analyses, 7 , 14 , 18 , 19 but it remains incomplete. Gifu originates from central Japan and is closely related to most of the sequenced accessions, 10 whereas MG-20 is an atypical Lotus accession that originates from Miyakojima Island in the far south of Japan close to Taiwan. Considering also that the LORE1 insertion mutant collection 14 was generated in the Gifu background, a high-quality Lotus Gifu reference genome would not only facilitate comparative genomics studies, but also serve to underpin improvement of functional genomics and intraspecific diversity resources in Lotus.…”

A High-Quality Genome Sequence of Model Legume Lotus japonicus (MG-20) Provides Insights into the Evolution of Root Nodule Symbiosis

“…Several essential components involved in the nodulation signaling pathway have been cloned and functionally characterized via forward genetics in L. japonicus, including Nod Factor Receptors 1 and 5 (NFR1 and NFR5), Symbiosis Receptor Kinase (SYMRK), NSP1, etc. Genome-wide research not only helps to reveal the relationship between genetics and evolution, but also to discover some new genes with unknown functions: for example, new genes related to phosphate accumulation [3], as well as genes related to the phenotypic changes in overwintering and flowering time due to regional differences [4].…”