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

2021 ◽  
Vol 22 (9) ◽  
pp. 4326
Author(s):  
Parwinder Kaur ◽  
Christopher Lui ◽  
Olga Dudchenko ◽  
Raja Sekhar Nandety ◽  
Bhavna Hurgobin ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Medicago Truncatula ◽  
Genome Assembly ◽  
Mutant Gene ◽  
Chromosome Length ◽  
Model Legume ◽  
Physical Information ◽  
High Transformation ◽  
Genome Scale

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.

scholarly journals A functional genomics approach to (iso)flavonoid glycosylation in the model legume Medicago truncatula

2007 ◽  
Vol 64 (5) ◽  
pp. 499-518 ◽  
Author(s):  
Luzia V. Modolo ◽  
Jack W. Blount ◽  
Lahoucine Achnine ◽  
Marina A. Naoumkina ◽  
Xiaoqiang Wang ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Medicago Truncatula ◽  
Model Legume

scholarly journals Hi-C yields chromosome-length scaffolds for a legume genome, Trifolium subterraneum

2018 ◽  
Author(s):  
Olga Dudchenko ◽  
Melanie Pham ◽  
Christopher Lui ◽  
Sanjit S. Batra ◽  
Marie Hoeger ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Subterranean Clover ◽  
Trifolium Subterraneum ◽  
Chromosome Length ◽  
Pasture Legume

AbstractWe present a chromosome-length assembly of the genome of subterranean clover, Trifolium subterraneum, a key Australian pasture legume. Specifically, in situ Hi-C data (48X) was used to correct misjoins and anchor, order, and orient scaffolds in a previously published genome assembly (TSUd_r1.1; scaffold N50: 287kb). This resulted in an improved genome assembly (TrSub3; scaffold N50: 56Mb) containing eight chromosome-length scaffolds that span 95% of the sequenced bases in the input assembly.

scholarly journals An improved genome release (version Mt4.0) for the model legume Medicago truncatula

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 312 ◽  
Author(s):  
Haibao Tang ◽  
Vivek Krishnakumar ◽  
Shelby Bidwell ◽  
Benjamin Rosen ◽  
Agnes Chan ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Model Legume

scholarly journals Guidelines for Genetic Nomenclature and Community Governance for the Model Legume Medicago truncatula

2001 ◽  
Vol 14 (12) ◽  
pp. 1364-1367 ◽  
Author(s):  
Kathryn A. VandenBosch ◽  
Julia Frugoli
Keyword(s):  
Medicago Truncatula ◽  
Rapid Growth ◽  
Model System ◽  
Gene Nomenclature ◽  
Community Governance ◽  
Model Legume ◽  
The Past ◽  
Genetic Nomenclature ◽  
International Collaborations

At the 2nd Medicago meeting (a satellite of the 1999 IS-MPMI meeting in Amsterdam), investigators perceived a need for standardization of genetic nomenclature in Medicago truncatula, due to the rapid growth of research on this species in the past few years. Establishment of such standards grew out of discussions begun at this meeting and continued electronically throughout the M. truncatula community. The proposed standards presented here are the consensus results of those discussions. In addition to standards for gene nomenclature, a method for community governance and a website for cataloging gene names and submitting new ones are presented. The purpose of implementing these guidelines is to help maintain consistency in the literature, to avoid redundancy, to contribute to the accuracy of databases, and, in general, to aid the international collaborations that have made M. truncatula a model system for legume biology.

scholarly journals Structure and antimicrobial activity of NCR169, a nodule-specific cysteine-rich peptide of Medicago truncatula

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Noriyoshi Isozumi ◽  
Yuya Masubuchi ◽  
Tomohiro Imamura ◽  
Masashi Mori ◽  
Hironori Koga ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Medicago Truncatula ◽  
Mechanism Of Action ◽  
Disulfide Bonds ◽  
Sinorhizobium Meliloti ◽  
Bound State ◽  
Disulfide Linkage ◽  
Model Legume ◽  
Nmr Structures ◽  
And Function

AbstractA model legume, Medicago truncatula, has over 600 nodule-specific cysteine-rich (NCR) peptides required for symbiosis with rhizobia. Among them, NCR169, an essential factor for establishing symbiosis, has four cysteine residues that are indispensable for its function. However, knowledge of NCR169 structure and mechanism of action is still lacking. In this study, we solved two NMR structures of NCR169 caused by different disulfide linkage patterns. We show that both structures have a consensus C-terminal β-sheet attached to an extended N-terminal region with dissimilar features; one moves widely, whereas the other is relatively stapled. We further revealed that the disulfide bonds of NCR169 contribute to its structural stability and solubility. Regarding the function, one of the NCR169 oxidized forms could bind to negatively charged bacterial phospholipids. Furthermore, the positively charged lysine-rich region of NCR169 may be responsible for its antimicrobial activity against Escherichia coli and Sinorhizobium meliloti. This active region was disordered even in the phospholipid bound state, suggesting that the disordered conformation of this region is key to its function. Morphological observations suggested the mechanism of action of NCR169 on bacteria. The present study on NCR169 provides new insights into the structure and function of NCR peptides.

Functional specialization of Arf paralogs in nodules of model legume, Medicago truncatula

2016 ◽  
Vol 81 (3) ◽  
pp. 501-510 ◽  
Author(s):  
Elif Yüzbaşıoğlu ◽  
Eda Dalyan ◽  
Abdülrezzak Memon ◽  
Gül Öz ◽  
Bayram Yüksel
Keyword(s):  
Medicago Truncatula ◽  
Functional Specialization ◽  
Model Legume

scholarly journals The hormone neuroparsin seems essential in Lepidoptera but not in domesticated silkworms

2019 ◽  
Author(s):  
Jan A. Veenstra
Keyword(s):  
Bombyx Mori ◽  
Genome Assembly ◽  
Galleria Mellonella ◽  
Sequence Similarity ◽  
Neuroendocrine Cells ◽  
Primary Sequence ◽  
Genome Assemblies ◽  
Limited Sequence ◽  
Wax Moth

AbstractThe primary sequence of the Arthropod neurohormone neuroparsin is so variable that so far no orthologs from moths and butterflies have been characterized, even though classical neurosecretory stains identify cells that are homologous to those producing this hormone in other insect species. Here Lepidopteran cDNAs showing limited sequence similarity to other insect neuroparsins are described. That these cDNAs do indeed code for authentic neuroparsins was confirmed by in situ hybridization in the wax moth, Galleria mellonella, which labeled the neuroparsin neuroendocrine cells. Although in virtually all genome assemblies from Lepidoptera a neuroparsin gene could be identified, the genome assembly from the silkworm, Bombyx mori, has a neuroparsin gene containing a 16 nucleotide deletion that renders this gene nonfunctional. Although only a small number of all silkworm strains carry this deletion, it suggests that the domestication of the silkworm has rendered the function of this neurohormone dispensable.

scholarly journals Comparison of nodule endophyte composition, diversity, and gene content between Medicago truncatula genotypes

2021 ◽  
Author(s):  
Mannix Burns ◽  
Brendan Epstein ◽  
Liana Burghardt
Keyword(s):  
Functional Groups ◽  
Medicago Truncatula ◽  
Root Nodules ◽  
Bacterial Endophytes ◽  
Host Genotype ◽  
Model Legume ◽  
Symbiotic Relationships ◽  
Functional Assays ◽  
Altered Gene ◽  
Significant Direct Effect

Leguminous plants form symbiotic relationships with rhizobia. These nitrogen-fixing bacteria live in specialized root organs called nodules. While rhizobia form the most notable host relationship within root nodules, other bacterial endophytes also inhabit these root nodules and can influence host-rhizobia interactions as well as exert effects of their own, whether beneficial or detrimental. In this study, we investigate differences in nodule communities between genotypes (A17 and R108) of a single plant species, the model legume Medicago truncatula. While diversity of endophytes in nodules was similar across hosts, both nodule endophyte composition and gene functional groups differed. In contrast to the significant direct effect of host genotype, neither the presence nor identity of a host in the previous generation (either A17 or R108) had a significant effect on the nodule endophyte diversity or composition. However, whether or not a host was present altered gene functional groups. We conclude that genetic variation within a legume host species can play an important role in the establishment of nodule microbiomes. Further studies, including GWAS and functional assays, can open the door for engineering and optimizing nodule endophyte communities that promote growth or have other beneficial qualities.

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