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

doi:10.3390/ijms22094326

KMS > 免疫化学研究所 > 特聘教授组 > Roger D. Kornberg组

	Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly
	Kaur, Parwinder 1; Lui, Christopher 2; Dudchenko, Olga 2,3,4; Nandety, Raja Sekhar 5; Hurgobin, Bhavna 6,7; Pham, Melanie 2,3,4; Lieberman Aiden, Erez1,2,3,4,8,9 ; Wen, Jiangqi 5; Mysore, Kirankumar S.5
	2021
发表期刊	INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
EISSN	1422-0067
卷号	22 期号:9
DOI	10.3390/ijms22094326
摘要	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 (48x) 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.
关键词	Leguminosae Medicago truncatula cv R108 HiC chromosome-length genome assembly Tnt1 insertion landscape
URL	查看原文
收录类别	SCIE
语种	英语
WOS研究方向	Biochemistry & Molecular Biology ; Chemistry
WOS类目	Biochemistry & Molecular Biology ; Chemistry, Multidisciplinary
WOS记录号	WOS:000650361400001
出版者	MDPI
原始文献类型	Article
引用统计
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/126665
专题	免疫化学研究所_特聘教授组_结构生物化学实验室
通讯作者	Kaur, Parwinder; Mysore, Kirankumar S.
作者单位	1.Univ Western Australia, UWA Sch Agr & Environm, Crawley, WA 6009, Australia; 2.Baylor Coll Med, Dept Mol & Human Genet, Ctr Genome Architecture, Houston, TX 77030 USA; 3.Rice Univ, Ctr Theoret & Biol Phys, Dept Comp Sci, Houston, TX 77030 USA; 4.Rice Univ, Ctr Theoret & Biol Phys, Dept Computat & Appl Math, Houston, TX 77030 USA; 5.Noble Res Inst LLC, Ardmore, OK 73401 USA; 6.La Trobe Univ, Dept Anim Plant & Soil Sci, La Trobe Inst Agr & Food, Sch Life Sci, AgriBio Bldg, Bundoora, Vic 3086, Australia; 7.La Trobe Univ, Australian Res Council Res Hub Med Agr, AgriBio Bldg, Bundoora, Vic 3086, Australia; 8.Broad Inst MIT & Harvard, Cambridge, MA 02139 USA; 9.ShanghaiTech, Shanghai Inst Adv Immunochem Studies, Pudong 201210, Peoples R China
推荐引用方式 GB/T 7714	Kaur, Parwinder,Lui, Christopher,Dudchenko, Olga,et al. Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly[J]. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,2021,22(9).
APA	Kaur, Parwinder.,Lui, Christopher.,Dudchenko, Olga.,Nandety, Raja Sekhar.,Hurgobin, Bhavna.,...&Mysore, Kirankumar S..(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(9).
MLA	Kaur, Parwinder,et al."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 22.9(2021).