Overview

Welcome to LGRPv2

We've launched the Legume Genomics Research Platform version 2 (LGRPv2), now with 409 genomes including 144 legumes and Tamarindus indica. It offers browsing tools, annotations for 18,050,760 protein-coding genes, synteny analyses, and identification of paralogs, orthologs, and trait genes. New tools like DotView, SynView, DecoBrowse, and AncVisual enhance exploration. Integrated resources include a species encyclopedia, omics data, and a comparative genomics toolbox with 58 tools (31 new). Our aim with LGRPv2 is to be a comprehensive resource for legume genomics. Additionally, it offers intuitive query, analysis, and visualization tools, along with statistical charts, user manuals, communities, and submission portals, ensuring usability for all users, making it a vital asset for legume genomics research.

Portals of data



8,944,924

Syn-Blocks

13,068

Syn-Dotplots

595,077

WGDs-Genes

409

Genome

11,034

Metabolomics

15,723

Transcriptome

3,027

Pan-genome

184,511

Syn-Base OGs

1,086,836

Gene-families

2499,059

Pathway

81,343,237

TEs

98,107

PKs

2,414,215

Duplication type

Currently available reference genomes and annotations
Species Abbr Chromosome number Genes number Data link References
Abrus precatorius Apr 20 24,155 Hovde BT et al.(2019)
Aeschynomene evenia Aev 20 30,827 Johan Ql et al.(2021)
Amphicarpaea edgeworthii Aed 22 27,699 Liu Y et al.(2020)
Arachis duranensis Adu 20 33,238 Bertioli DJ et al.(2016)
Arachis hypogaea Ahy 40 65,593 Bertioli DJ et al.(2019)
Arachis ipaensis Aip 20 38,608 Bertioli DJ et al.(2016)
Arachis monticola Amo 40 69,883 Yin D et al.(2018)
Cajanus cajan Cca 22 28,222 Parween S et al.(2015)
Cicer arietinum Car 16 24,711 Varshney et al.(2011)
Dalbergia odorifera Dod 20 29,344 Hong Z et al.(2020)
Glycine max Gma 40 51,824 Shen Y et al.(2018)
Glycine soja Gso 40 46,722 Xie M et al.(2019)
Lotus japonicus Lja 12 26,152 Li H et al.(2020)
Lupinus albus Lal 50 41,277 Hufnagel B et al.(2020)
Lupinus angustifolius Lan 40 29,986 Hane JK et al.(2016)
Medicago truncatula Mtr 16 31,727 Tang H et al.(2014)
Melilotus albus Mal 16 41,853 Wu F et al.(2021)
Phaseolus vulgaris Pvu 22 27,996 Vlasova A et al.(2016)
Pisum sativum Psa 14 38,312 Kreplak J et al.(2019)
Spatholobus suberectus Ssu 18 29,597 Qin S et al.(2019)
Trifolium pratense Tpr 14 33,414 De Vega JJ et al.(2015)
Trifolium subterraneum Tsu 16 36,691 Hirakawa H et al.(2016)
Vigna radiata Vra 22 22,158 Kang et al.(2014)
Senna tora Sto 26 44,405 Kang SH et al.(2020)
Bauhinia variegata Bva 28 37,886 Zhong Y et al.(2022)
... ... ... ... ... ...

Update log

  • Sept. 20, 2024   The website was deployed on the server.

  • July. 2, 2024   The communication portal is built.

  • June. 27, 2024   Updated the statistical form.

  • June. 20, 2024   Built the JBrowse module to visualize transcriptome data.

  • May. 8, 2024   Implemented the ability to obtain genes based on defined regions

  • Nov. 10, 2023   The "Karyotype animation", which can show the evolutionary trajectory of Oleaceae karyotypes, is now available

  • Dec. 27, 2022   The "Blast visualization", which can search function annotation and position, is now available

  • Nov. 6, 2022   The "Circle" has been updated

  • Nov. 5, 2022   The "Gene families", which can search gene of Triticeae by well-stueied gene of rice, maize, and Arabidopsis, is now available

  • Nov. 3, 2022   The "P-index", which can show collinearity in macro-region, is now available

  • Oct. 24, 2022   The "specie_tree", which can show collinearity in micro-region, is now available

  • Oct.16, 2022   The "Dotplot", which can search function annotation and position, is now available

  • Oct. 2, 2019   Online tool of Phylogenetics is added.

  • Sep. 5, 2019   Realization of collinearity visualization function for 25 Fabaceae.


Articles that have referenced this platform are

  • Nov. 6, 2022  Allopolyploidizations and highly dynamic reshuffling of paleogenome contributed to the successful establishment of Orchidaceae

  • Nov. 15, 2022  Two-step model of paleohexaploidy, reshuffling of ancient genome and plasticity of heat shock response in Asteraceae

  • Nov. 23, 2022  ・Multi-dimensional reshuffling of ancestral genome during post-polyploid diploidization shaped family Fabaceae

  • 2024 Aug 31  ・Transcriptome-wide identification of the Hsp70 gene family in Pugionium cornutum and functional analysis of PcHsp70-5 under drought stress

  • 2024 Jul 8  ・A reference-grade genome of the xerophyte Ammopiptanthus mongolicus sheds light on its evolution history in legumes and drought-tolerance mechanisms

  • 2024 Jan 23  ・Translocations and inversions: major chromosomal rearrangements during Vigna (Leguminosae) evolution

  • 2023 Nov 21  ・Genome-Wide Analysis of Cation/Proton Antiporter Family in Soybean (Glycine max) and Functional Analysis of GmCHX20a on Salt Response

  • 2023 Dec 1  ・Unraveling the Unusual Subgenomic Organization in the Neopolyploid Free-Living Flatworm Macrostomum lignano

  • 2023 Sep 3  ・Genes of Green Plants: Multiple Parallel Length Expansions, Intron Gains and Losses, Partial Gene Duplications, and Alternative Splicing

  • 2023 Jul 31  ・Chromosome-level genome assembly and population genomics of Robinia pseudoacacia reveal the genetic basis for its wide cultivation

  • 2023 Jun 20  ・Genome-wide identification and expression analysis of VQ gene family under abiotic stress in Coix lacryma-jobi L

  • 2023 Apr 19  ・Two-step model of paleohexaploidy, ancestral genome reshuffling and plasticity of heat shock response in Asteraceae

  • 2023 Jun 1  ・Genomic Insights into daptation to Karst Limestone and Incipient Speciation in East Asian Platycarya spp

  • 2022 Dec  ・Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement

  • 2022 Sep 29  ・Genomic analyses of rice bean landraces reveal adaptation and yield related loci to accelerate breeding

  • 2022 Nov 28  ・A common whole-genome paleotetraploidization in Cucurbitales. Plant Physiol

  • 2022 Nov 14  ・Integrated network analyses identify MYB4R1 neofunctionalization in the UV-B adaptation of Tartary buckwheat

  • 2022 May 31  ・Paleopolyploidies and Genomic Fractionation in Major Eudicot Clades

  • 2022 Jun 17  ・Conversion between duplicated genes generated by polyploidization contributes to the divergence of poplar and willow

  • 2022 Apr 20  ・PolyReco: A Method to Automatically Label Collinear Regions and Recognize Polyploidy Events Based on the Ks Dotplot

  • 2022 May 27  ・Chromosome-level genome assembly and characterization of Sophora Japonica

  • 2022 Apr 7  ・Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax

  • 2022 Jul  ・Genome sequence and population genomics provide insights into chromosomal evolution and phytochemical innovation of Hippophae rhamnoides

  • 2021 Dec 1  ・Illegitimate Recombination between Duplicated Genes Generated from Recursive Polyploidizations Accelerated the Divergence of the Genus Arachis

  • 2021 Dec 6  ・Genome-wide and expression analysis of B-box gene family in pepper

  • 2021 Oct 26  ・Integrated Transcriptomic and Bioinformatics Analyses Reveal the Molecular Mechanisms for the Differences in Seed Oil and Starch Content Between Glycine max and Cicer arietinum

  • 2021 Oct 26  ・Integrated Transcriptomic and Bioinformatics Analyses Reveal the Molecular Mechanisms for the Differences in Seed Oil and Starch Content Between Glycine max and Cicer arietinum

  • 2021 Sep 7  ・A tetraploidization event shaped theAquilaria sinensis genome and contributed to the ability of sesquiterpenessynthesis

  • 2022 Jan  ・The genome sequenceprovides insights into salt tolerance of Achnatherum splendens (Gramineae), aconstructive species of alkaline grassland

  • 2021 Jun 19  ・Conversionbetween 100-million-year-old duplicated genes contributes to rice subspeciesdivergence

  • 2020 Oct 29  ・A multilayered cross-speciesanalysis of GRAS transcription factors uncovered their functional networks inplant adaptation to the environment

  • 2021 Jan 6  ・Genome-wide identification and characterization of small auxin-up RNA (SAUR) genefamily in plants: evolution and expression profiles during normal growth andstress response

  • 2020 Dec1  ・A chromosome-scale genome assembly of adiploid alfalfa, the progenitor of autotetraploid alfalfa

  • 2020 Jun  ・Paleo-polyploidization in Lycophytes

  • 2021 Apr  ・The celery genome sequence reveals sequential paleo-polyploidizations,karyotype evolution and resistance gene reduction in apiales

  • 2020 Jul 21  ・Illegitimate Recombination Between Homeologous Genes in Wheat Genome

  • 2020 Jul 6  ・Pervasive duplication, biased molecular evolution and comprehensive functionalanalysis of the PP2C family in Glycine max

  • 2020 Jun 26  ・Transcriptome Analysis RevealsPotential Roles of Abscisic Acid and Polyphenols in Adaptation of Onobrychisviciifolia to Extreme Environmental Conditions in the Qinghai-TibetanPlateau

  • 2020 May 19  ・Allele-aware chromosome-level genome assemblyand efficient transgene-free genome editing for the autotetraploid cultivatedalfalfa

  • 2020 Apr 23  ・CottonDuplicated Genes Produced by Polyploidy Show Significantly Elevated andUnbalanced Evolutionary Rates, Overwhelmingly Perturbing Gene Tree Topology

  • 2020 Mar 8  ・Reconstruction of the EvolutionaryHistories of UGT Gene Superfamily in Legumes Clarifies the Functional Divergenceof Duplicates in Specialized Metabolism

  • 2020 Feb 21  ・Preferentialgene retention increases the robustness of cold regulation in Brassicaceae and other plants after polyploidization

  • 2020 Feb 4  ・Genome-wide identification andexpression analysis of the VQ gene family in Cicer arietinumand Medicago truncatula

  • 2020 Sep  ・Trait associations in the pangenome of pigeonpea (Cajanus cajan)

  • 2020 Jan 31  ・Sequential Paleotetraploidization shaped the carrot genome

  • 2020 Sep  ・Genome-wide identification and expression analysis of the 14-3-3 genefamily in soybean (Glycine max)

  • 2020 Jun  ・Deciphering thehigh-quality genome sequence of coriander that causes controversial feelings

  • 2019 Nov 14  ・The wax gourdgenomes offer insights into the genetic diversity and ancestral cucurbitkaryotype

  • 2019 Sep 10  ・Polyploidy Index and Its Implications forthe Evolution of Polyploids

  • 2019 Aug 21  ・Genome-wide identification and expression analysis of the VQ genefamily in soybean (Glycine max)

  • 2019 Aug 6  ・Alignment of Rutaceae Genomes Reveals Lower Genome Fractionation Level ThanEudicot Genomes Affected by Extra Polyploidization

  • 2019 Nov  ・Development of gene-based molecular markerstagging low alkaloid pauper locus in white lupin (Lupinus albus L.)

  • 2019 Feb 11  ・Paleogenomics:reconstruction of plant evolutionary trajectories from modern and ancient DNA

  • 2019 Jan  ・Recursive Paleohexaploidization Shaped the Durian Genome

  • 2019 Feb 1  ・Landscape of gene transposition-duplication within theBrassicaceae family

  • 2018 Oct 17  ・WRKY transcription factors in legumes

  • 2018 Sep 28  ・Two Likely Auto-Tetraploidization Events ShapedKiwifruit Genome and Contributed to Establishment of the Actinidiaceae Family

  • 2018 Sep 8  ・Physiology BasedApproaches for Breeding of Next-Generation Food Legumes

  • 2018 Jun 14  ・Investigation of BaselineIron Levels in Australian Chickpea and Evaluation of a TransgenicBiofortification Approach

  • 2017 Nov 30  ・Non-Additive Transcriptomic Responses to Inoculationwith Rhizobia in a Young Allopolyploid Compared with Its Diploid Progenitors.Genes (Basel)

  • 2017 Dec  ・Patterns and Consequences of SubgenomeDifferentiation Provide Insights into the Nature of Paleopolyploidy in Plants

  • 2018 Jan 1  ・An OverlookedPaleotetraploidization in Cucurbitaceae

  • 2017 Sep 2  ・Oil body biogenesis and biotechnology in legumeseeds

    
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