Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family

Abstract

Legume Information System (LIS), at http://legumeinfo.org, is a genomic data portal (GDP) for the legume family. LIS provides access to genetic and genomic information for major crop and model legumes. With more than two-dozen domesticated legume species, there are numerous specialists working on particular species, and also numerous GDPs for these species. LIS has been redesigned in the last three years both to better integrate data sets across the crop and model legumes, and to better accommodate specialized GDPs that serve particular legume species. To integrate data sets, LIS provides genome and map viewers, holds synteny mappings among all sequenced legume species and provides a set of gene families to allow traversal among orthologous and paralogous sequences across the legumes. To better accommodate other specialized GDPs, LIS uses open-source GMOD components where possible, and advocates use of common data templates, formats, schemas and interfaces so that data collected by one legume research community are accessible across all legume GDPs, through similar interfaces and using common APIs. This federated model for the legumes is managed as part of the ‘Legume Federation’ project (accessible via http://legumefederation.org), which can be thought of as an umbrella project encompassing LIS and other legume GDPs.

Lotus Base: An integrated information portal for the model legume Lotus japonicus

“…Lotus Base distinguishes itself from other cross-species integration platform such as Legume Information System (LIS)7576, PlantGDB77, and Phytozome78, by offering comprehensive species-specific data. In addition, Lotus genomic data is available on LIS7576, PlantGDB77, Phytozome78, and through the Kazusa DNA Research Institute website9; and Lotus expression data on LjGEA10.…”

“…In addition, Lotus genomic data is available on LIS7576, PlantGDB77, Phytozome78, and through the Kazusa DNA Research Institute website9; and Lotus expression data on LjGEA10. However, there are hitherto neither LORE1 mutant population nor Lotus expression data integrated with the sequenced and annotated genome of Lotus .…”

QTLomics in Soybean: A Way Forward for Translational Genomics and Breeding

“…This process is now very much possible due to the availability of several legume specific databases like Legume Information System (LIS) (Gonzales et al, 2005; Dash et al, 2016), LegumeIP 2.0 (Li J. et al, 2016), SoyBase (Grant et al, 2010) and Soybean knowledge base (SoyKB) (Joshi et al, 2014). The first two databases namely LIS and LegumeIP 2.0 are facilitating translational genomics and breeding in major legumes by integrating genetic, genomic, transcriptomic data, and comparative genomics across important legume crops while the SoyBase and SoyKB are facilitating translational genomics and breeding mainly in soybean.…”

Achievement, Challenge and Future Perspective of BAC Library Technology with a Focus on its Application to Soybean Genomics Researches

“…Since the emergence of the next generations of sequencing technology, BAC library technology has faced strong challenge since construction, screening and application of BAC libraries are time and labor intensive [42][43][44][45][46][47][48][49]. Recent third-generation sequencing technology, which can yield longer multi kilo base reads and is getting popular in various genomic researches, further despoils the the applications of BAC library technology.…”