Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly.

Parwinder Kaur,Raja Sekhar Nandety,Melanie Pham,Jiangqi Wen,Olga Dudchenko,Christopher Lui,Bhavna Hurgobin,Erez Lieberman Aiden,Kirankumar S Mysore

doi:10.3390/ijms22094326

Abstract

Legumes are of great interest for sustainable agricultural production as they fix atmospheric nitrogen to improve the soil. Medicago truncatula is a well-established model legume, and extensive studies in fundamental molecular, physiological, and developmental biology have been undertaken to translate into trait improvements in economically important legume crops worldwide. However, M. truncatula reference genome was generated in the accession Jemalong A17, which is highly recalcitrant to transformation. M. truncatula R108 is more attractive for genetic studies due to its high transformation efficiency and Tnt1-insertion population resource for functional genomics. The need to perform accurate synteny analysis and comprehensive genome-scale comparisons necessitates a chromosome-length genome assembly for M. truncatula cv. R108. Here, we performed in situ Hi-C (48×) to anchor, order, orient scaffolds, and correct misjoins of contigs in a previously published genome assembly (R108 v1.0), resulting in an improved genome assembly containing eight chromosome-length scaffolds that span 97.62% of the sequenced bases in the input assembly. The long-range physical information data generated using Hi-C allowed us to obtain a chromosome-length ordering of the genome assembly, better validate previous draft misjoins, and provide further insights accurately predicting synteny between A17 and R108 regions corresponding to the known chromosome 4/8 translocation. Furthermore, mapping the Tnt1 insertion landscape on this reference assembly presents an important resource for M. truncatula functional genomics by supporting efficient mutant gene identification in Tnt1 insertion lines. Our data provide a much-needed foundational resource that supports functional and molecular research into the Leguminosae for sustainable agriculture and feeding the future.

Highlights

Sustainable agricultural production involves growing food with low fertilizer input without damaging the underlying soil [1]
The M. truncatula reference genome was generated in A17, which is highly recalcitrant to transformation, whereas the Tnt1 mutant population was generated in R108, with a much higher transformation efficiency
R108 has become popular in legume research communities with its near-saturated Tnt1-insertion population, which is widely used in most areas of legume functional genomic analysis [10,12]

Summary

Introduction

Sustainable agricultural production involves growing food with low fertilizer input without damaging the underlying soil [1]. Most legumes have large/complex genomes and are outcrossing species, making genetic studies difficult. The release of the M. truncatula accession Jemalong A17 reference genome sequence and generation of the Tnt1-based insertion mutant population for accession R108 have greatly accelerated functional genomics studies in M. truncatula [10,11,12]. The M. truncatula reference genome was generated in A17, which is highly recalcitrant to transformation, whereas the Tnt mutant population was generated in R108, with a much higher transformation efficiency. Compared to R108 and other M. truncatula genotypes, A17 has a large (~30 Mb) reciprocal translocation between chromosomes 4 and 8 [4], resulting in inaccurate synteny analysis between M. truncatula and other legume genomes and aberrant recombination in genetic crosses, including crosses between A17 and R108 [14].

Methods

Results

Discussion

Conclusion