Overview

Welcome to LGRPv2

We've launched the Legume Genomics Research Platform version 2 (LGRPv2), now with 112 genomes including 62 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 57 tools (29 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

12,288

Paired dotplots

16,384

Collinear and KaKs

595,077

Event-related genes

56,160

Hierarchical alignments

136

Genome

8,470,419

Gene annotation

15,723

Transcriptome

2,027

Pan-genome

50,056

Transcription factors

38,690

synteny-based orthogroups

50,178

Functional genes

940,454

Pathway

32,815,908

TE number

115,229

ncRNA

1,362,684

Duplication type

8,206

Reactome pathway

286,467

Publication

39

Karyotype animation

26

JBrowse

13

Database link

45

Tools

89257

Species introduce

Tools quick links

Polyploidy

Dating

Fractionation

Karyotype

Gene Family

Other
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)
... ... ... ... ... ...

Citation

If you use LGRPv2 in your scientific research, please cite us:

・Fabaceae genomes bioinformatics platform: A comprehensive database of Fabaceae genomes

・Multi-dimensional reshuffling of ancestral genome during post-polyploid diploidization shaped family Fabaceae

Update log

  • 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
    
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