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Article

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

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UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA 6009, Australia
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The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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Center for Theoretical and Biological Physics, Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA
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Noble Research Institute, LLC., Ardmore, OK 73401, USA
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La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Life Sciences, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
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Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
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Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
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Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China
*
Authors to whom correspondence should be addressed.
Academic Editors: Fatemeh Maghuly, Eva M. Sehr, Rachit Saxena and David J. Konkin
Int. J. Mol. Sci. 2021, 22(9), 4326; https://doi.org/10.3390/ijms22094326
Received: 17 March 2021 / Revised: 13 April 2021 / Accepted: 15 April 2021 / Published: 21 April 2021
(This article belongs to the Special Issue Functional Genomics for Plant Breeding 2.0)
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. View Full-Text
Keywords: Leguminosae; Medicago truncatula cv. R108; HiC; chromosome-length genome assembly; Tnt1 insertion landscape Leguminosae; Medicago truncatula cv. R108; HiC; chromosome-length genome assembly; Tnt1 insertion landscape
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MDPI and ACS Style

Kaur, P.; Lui, C.; Dudchenko, O.; Nandety, R.S.; Hurgobin, B.; Pham, M.; Lieberman Aiden, E.; Wen, J.; Mysore, K.S. Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly. Int. J. Mol. Sci. 2021, 22, 4326. https://doi.org/10.3390/ijms22094326

AMA Style

Kaur P, Lui C, Dudchenko O, Nandety RS, Hurgobin B, Pham M, Lieberman Aiden E, Wen J, Mysore KS. Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly. International Journal of Molecular Sciences. 2021; 22(9):4326. https://doi.org/10.3390/ijms22094326

Chicago/Turabian Style

Kaur, Parwinder, Christopher Lui, Olga Dudchenko, Raja S. Nandety, Bhavna Hurgobin, Melanie Pham, Erez Lieberman Aiden, Jiangqi Wen, and Kirankumar S. Mysore 2021. "Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly" International Journal of Molecular Sciences 22, no. 9: 4326. https://doi.org/10.3390/ijms22094326

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