A High-Quality Genome Sequence of Model Legume Lotus japonicus (MG-20) Provides Insights into the Evolution of Root Nodule Symbiosis

Li, Haoxing; Fan, Jun; Wu, Ping; Wang, Ke; Cao, Yangrong

doi:10.3390/genes11050483

Cited by 43 publications

(25 citation statements)

References 59 publications

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“…For both legumes, the protein lengths are given in amino acids (aa) and the alternative spliced forms (AS) are indicated where applicable. Because a new version of the L. japonicus ecotype MG‐20 genome (LjPB_v.1.0) has just been published (Li et al , 2020), although the website is not publicly available yet, we provide the new gene IDs for further reference: Lb1 and Lb2 (Lj5g0024797; still not given separate gene IDs); Lb3 (Lj5g000269); Glb1‐1 (Lj3g0017143); Glb1‐2 (Lj3g0010114); Glb2‐1 (Lj5g0004398); Glb2‐2 (Lj5g0019740); Glb3‐1 (Lj1g0018927); and Glb3‐2 (Lj1g0018426). (b) Phylogenetic tree of Lbs and Glbs of M. truncatula (names in blue) and L. japonicus (names in red).…”

Section: Hemoglobins In Indeterminate Nodules: Medicago Truncatulamentioning

confidence: 99%

Hemoglobins in the legume–Rhizobium symbiosis

et al. 2020

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Legume nodules have two types of hemoglobins: symbiotic or leghemoglobins (Lbs) and nonsymbiotic or phytoglobins (Glbs). The latter are categorized into three phylogenetic classes differing in heme coordination and O 2 affinity. This review is focused on the roles of Lbs and Glbs in the symbiosis of rhizobia with crop legumes and the model legumes for indeterminate (Medicago truncatula) and determinate (Lotus japonicus) nodulation. Only two hemoglobin functions are well established in nodules: Lbs deliver O 2 to the bacteroids and act as O 2 buffers, preventing nitrogenase inactivation; and Glb1-1 modulates nitric oxide concentration during symbiosis, from the early stage, avoiding the plant's defense response, to nodule senescence. Here, we critically examine early and recent results, update and correct the information on Lbs and Glbs with the latest genome versions, provide novel expression data and identify targets for future research. Crucial unresolved questions include the expression of multiple Lbs in nodules, their presence in the nuclei and in uninfected nodule cells, and, intriguingly, their expression in nonsymbiotic tissues. RNA-sequencing data analysis shows that Lbs are expressed as early as a few hours after inoculation and that their mRNAs are also detectable in roots and pods, which clearly suggests that these heme proteins play additional roles unrelated to nitrogen fixation. Likewise, issues awaiting investigation are the functions of other Glbs in nodules, the spatiotemporal expression profiles of Lbs and Glbs at the mRNA and protein levels, and the molecular mechanisms underlying their regulation during nodule development and in response to stress and hormones. Dedication: In memory of Professor Tom as Ruiz-Arg€ ueso, an excellent scientist, family man and friend.

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Section: Hemoglobins In Indeterminate Nodules: Medicago Truncatulamentioning

confidence: 99%

Hemoglobins in the legume–Rhizobium symbiosis

et al. 2020

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“…Numerous plants have been used in molecular and genetic studies of the flavonoid pathway. Several L. japonicus resources are now available for molecular genetics and genomics analyses (Asamizu et al 2000a , b ; Fukai et al 2012 ; Hashiguchi et al 2018 ; Hayashi et al 2001 ; Kamal et al 2020 ; Li et al 2020 ; Nakamura et al 2002 ; Pedrosa et al 2002 ; Sandal et al 2002 ; Sato et al 2001 , 2008 ). Fine mapping for cloning the VIC genes is currently under progress.…”

Section: Discussionmentioning

confidence: 99%

Mutants of Lotus japonicus deficient in flavonoid biosynthesis

et al. 2021

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Spatiotemporal features of anthocyanin accumulation in a model legume Lotus japonicus (Regel) K.Larsen were elucidated to develop criteria for the genetic analysis of flavonoid biosynthesis. Artificial mutants and wild accessions, with lower anthocyanin accumulation in the stem than the standard wild type (B-129 ‘Gifu’), were obtained by ethyl methanesulfonate (EMS) mutagenesis and from a collection of wild-grown variants, respectively. The loci responsible for the green stem of the mutants were named as VIRIDICAULIS (VIC). Genetic and chemical analysis identified two loci, namely, VIC1 and VIC2, required for the production of both anthocyanins and proanthocyanidins (condensed tannins), and two loci, namely, VIC3 and VIC4, required for the steps specific to anthocyanin biosynthesis. A mutation in VIC5 significantly reduced the anthocyanin accumulation. These mutants will serve as a useful system for examining the effects of anthocyanins and proanthocyanidins on the interactions with herbivorous pests, pathogenic microorganisms and nitrogen-fixing symbiotic bacteria, Mesorhizobium loti.

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“…Moreover, we extended this query flexibility to gene acronyms, based on a list manually extracted from publications, available on the Mt5.0 genome browser https://medicago.toulouse.inrae.fr/MtrunA17r5.0-ANR/. Furthermore, gene IDs from Arabidopsis thaliana ( A.thaliana Col-0 [Araport11]) (Cheng et al 2017) and four major legumes, namely soybean ( Glycine max Williams 82 [Phytozome.12]) (Schmutz et al 2010)), Lotus japonicus ( L. japonicus Miyakojima MG-20 [3.0] (Li et al 2020)), common bean ( Phaseolus vulgaris BAT93 [EnsemblPlants.38] (Schmutz et al 2014)) and pea ( Pisum sativum cv. ‘Caméor’ v1a (Kreplak et al 2019), can be used to get the expression pattern of putative orthologues in M. truncatula (Carrère et al 2019).…”

Section: Resultsmentioning

confidence: 99%

MtExpress, a Comprehensive and Curated RNAseq-based Gene Expression Atlas for the Model Legume Medicago truncatula

Carrère

Verdier

Gamas

2021

Preprint

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Although RNA sequencing has been becoming the main transcriptomic approach in the model legume Medicago truncatula, there is currently no genome-wide gene expression atlas covering the whole set of RNAseq data published for this species. Nowadays, such tool is highly valuable to provide a global view of gene expression in a wide range of conditions and tissues/organs. Here, we present MtExpress, a gene expression atlas that compiles an exhaustive set of published M. truncatula RNAseq data (https://medicago.toulouse.inrae.fr/MtExpress). MtExpress makes use of recent releases of M. truncatula genome sequence and annotation, as well as up-to-date tools to perform mapping, quality control, statistical analysis and normalization of RNAseq data. MtExpress combines semi-automated pipelines with manual re-labelling and organization of samples, to produce an attractive and user-friendly interface, fully integrated with other available Medicago genomic resources. Importantly, MtExpress is highly flexible, in terms of both queries, e.g. allowing searches with gene names and orthologous gene IDs from Arabidopsis and other legume species, and outputs, to customize visualization and redirect gene study to relevant Medicago webservers. Thanks to its semi-automated pipeline, MtExpress will be frequently updated to follow the rapid pace of M. truncatula RNAseq data publications, as well as the constant improvement of genome annotation.

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A High-Quality Genome Sequence of Model Legume Lotus japonicus (MG-20) Provides Insights into the Evolution of Root Nodule Symbiosis

Cited by 43 publications

References 59 publications

Hemoglobins in the legume–Rhizobium symbiosis

Hemoglobins in the legume–Rhizobium symbiosis

Mutants of Lotus japonicus deficient in flavonoid biosynthesis

MtExpress, a Comprehensive and Curated RNAseq-based Gene Expression Atlas for the Model Legume Medicago truncatula

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