La Trobe
1165048_Kaur,P_2021.pdf (2.05 MB)

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

Download (2.05 MB)
journal contribution
posted on 07.07.2021, 23:27 by P Kaur, C Lui, O Dudchenko, RS Nandety, Bhavna Hurgobin, M Pham, EL Aiden, J Wen, K Mysore
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.


This work was supported by NSF Physics Frontiers Center Award (PHY-1427654, Center for Theoretical Biological Physics), the Welch Foundation (Q-1866), Noble Research Institute, LLC., McNair Medical Institute Scholar Award, NIH 4D Nucleome Grant (U01HL130010) and NIH Encyclopedia of DNA Elements (ENCODE) Mapping Center Award (UM1HG009375) to E.L.A., and NSF Plant Genome Grant (IOS-1733470) to K.SM.


Publication Date



International Journal of Molecular Sciences





Article Number








Rights Statement

The Author reserves all moral rights over the deposited text and must be credited if any re-use occurs. Documents deposited in OPAL are the Open Access versions of outputs published elsewhere. Changes resulting from the publishing process may therefore not be reflected in this document. The final published version may be obtained via the publisher’s DOI. Please note that additional copyright and access restrictions may apply to the published version.