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

Legumes are of great interest for sustainable agricultural production as they fix atmospheric nitrogen to improve the soil. is a well-established model legume, and extensive studies in fundamental molecular, physiological, and developmental biology have been undertaken to translate into trait improv...

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Published inInternational journal of molecular sciences Vol. 22; no. 9; p. 4326
Main Authors Kaur, Parwinder, Lui, Christopher, Dudchenko, Olga, Nandety, Raja Sekhar, Hurgobin, Bhavna, Pham, Melanie, Lieberman Aiden, Erez, Wen, Jiangqi, Mysore, Kirankumar
Format Journal Article
LanguageEnglish
Published Switzerland MDPI AG 21.04.2021
MDPI
Subjects
Agricultural production
Chromosome 4
Chromosome Mapping
chromosome-length genome assembly
Chromosomes
Developmental biology
Gene mapping
Genes
Genome, Plant
Genomes
Genomics
HiC
Insertion
Legumes
Leguminosae
Medicago truncatula
Medicago truncatula - genetics
Medicago truncatula cv. R108
Population
Proteins
Retroelements
Scaffolds
Sequence Analysis, DNA
Soil improvement
Sustainable agriculture
Synteny
Tnt1 insertion landscape
Medicago truncatula cv. R108
Tnt1 insertion landscape
HiC
Leguminosae
chromosome-length genome assembly
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Abstract Legumes are of great interest for sustainable agricultural production as they fix atmospheric nitrogen to improve the soil. 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, reference genome was generated in the accession Jemalong A17, which is highly recalcitrant to transformation. R108 is more attractive for genetic studies due to its high transformation efficiency and -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 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 insertion landscape on this reference assembly presents an important resource for functional genomics by supporting efficient mutant gene identification in 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.
AbstractList Legumes are of great interest for sustainable agricultural production as they fix atmospheric nitrogen to improve the soil. 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, reference genome was generated in the accession Jemalong A17, which is highly recalcitrant to transformation. R108 is more attractive for genetic studies due to its high transformation efficiency and -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 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 insertion landscape on this reference assembly presents an important resource for functional genomics by supporting efficient mutant gene identification in 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.
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.
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.
Author Nandety, Raja Sekhar
Mysore, Kirankumar
Lui, Christopher
Hurgobin, Bhavna
Lieberman Aiden, Erez
Wen, Jiangqi
Kaur, Parwinder
Pham, Melanie
Dudchenko, Olga
AuthorAffiliation 5 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; bhavna.hurgobin@hotmail.com
1 UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA 6009, Australia; erez.Lieberman@bcm.edu
2 The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; christopher.g.lui@gmail.com (C.L.); olga.Dudchenko@bcm.edu (O.D.); melanie_pham@ymail.com (M.P.)
6 Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
4 Noble Research Institute, LLC., Ardmore, OK 73401, USA; rsnandety@noble.org (R.S.N.); jwen@noble.org (J.W.)
7 Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
8 Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China
3 Center for Theoret
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Keywords Medicago truncatula cv. R108
Tnt1 insertion landscape
HiC
Leguminosae
chromosome-length genome assembly
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SSID ssj0023259
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Snippet Legumes are of great interest for sustainable agricultural production as they fix atmospheric nitrogen to improve the soil. is a well-established model legume,...
Legumes are of great interest for sustainable agricultural production as they fix atmospheric nitrogen to improve the soil. Medicago truncatula is a...
Legumes are of great interest for sustainable agricultural production as they fix atmospheric nitrogen to improve the soil. Medicago truncatula is a...
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proquest
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pubmed
SourceType Open Website
Open Access Repository
Aggregation Database
Index Database
StartPage 4326
SubjectTerms Agricultural production
Chromosome 4
Chromosome Mapping
chromosome-length genome assembly
Chromosomes
Developmental biology
Gene mapping
Genes
Genome, Plant
Genomes
Genomics
HiC
Insertion
Legumes
Leguminosae
Medicago truncatula
Medicago truncatula - genetics
Medicago truncatula cv. R108
Population
Proteins
Retroelements
Scaffolds
Sequence Analysis, DNA
Soil improvement
Sustainable agriculture
Synteny
Tnt1 insertion landscape
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Title Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly
URI https://www.ncbi.nlm.nih.gov/pubmed/33919286
https://www.proquest.com/docview/2528272606
https://search.proquest.com/docview/2520875326
https://pubmed.ncbi.nlm.nih.gov/PMC8122578
https://doaj.org/article/c443e3f36e7744d2802bcbcbca0eae3b
Volume 22
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