Legume Information System
The Legume Information System (LIS) is legume sciences portal specifically for legume breeders and researchers, established and supported by the Agricultural Research Service of the United States Department of Agriculture. The mission of the Legume Information System is "to facilitate discoveries and crop improvement in the legumes," in particular to improve crop yields, their nutritional value, and our understanding of basic legume science.
Development of the Legume Information System is a joint venture between the National Center for Genome Resources (NCGR) and the USDA-ARS at Iowa State University. In 2014, development effort on LIS shifted from the comparative-legumes.org domain to [http://legumeinfo.org/ legumeinfo.org]. The comparative-legumes site was developed using the Ruby on Rails framework, and the LegumeInfo site is developed using the [http://tripal.info/ Tripal] content management system.
The reference species as a backbone for orphan species research
A fundamental approach taken in LIS is facilitate research in the orphan species by taking advantage of more extensive knowledge developed for the reference species. Use of synteny and local similarity, for instance, provides a basis for trait inference.
=Reference species=
Note that LIS makes use of the UniProt [https://www.uniprot.org/docs/speclist organism mnemonics] for identifying species whenever possible.
The current legume reference species (also referred to as model organisms) are the following:
- Glycine max (soybean), [http://legumeinfo.org/organism/Glycine/max GLYMA]
- Lotus japonicus (lotus), [http://legumeinfo.org/organism/Lotus/japonicus LOTJA ]
- Medicago truncatula (barrel medic), [http://legumeinfo.org/organism/Medicago/truncatula MEDTR ]
- Phaseolus vulgaris (common bean), [http://legumeinfo.org/organism/Phaseolus/vulgaris PHAVU ]
=Orphan species=
Orphan species represented at LIS are:
- Arachis duranensis (wild peanut), [http://peanutbase.org/Arachis/duranensis ARADU]
- Arachis ipaensis (wild peanut), [http://peanutbase.org/Arachis/ipaensis ARAIP]
- Arachis hypogaea (peanut), [http://legumeinfo.org/organism/Arachis/hypogaea ARAHY]
- Cajanus cajan (pigeon pea), [http://legumeinfo.org/organism/Cajanus/cajan CAJCA]
- Chamaecrista fasciculata (partidge pea), [http://legumeinfo.org/organism/Chamaecrista/fasciculata CHAFS]
- Cicer arietinum (chickpea), [http://legumeinfo.org/organism/Cicer/arietinum CICAR]
- Lens culinaris (lentil), [http://legumeinfo.org/organism/Lens/culinaris LENCU]
- Lupinus albus (white lupin), [http://legumeinfo.org/organism/Lupinus/albus LUPAL]
- Lupinus angustifolius (narrow-leafed lupin), [http://legumeinfo.org/organism/Lupinus/angustifolius LUPAN]
- Medicago sativa (alfalfa), [http://legumeinfo.org/organism/Medicago/sativa MEDSA]
- Pisum sativum (garden pea), [http://legumeinfo.org/organism/Pisum/sativum PISSA]
- Trifolium pratense (red clover), [http://legumeinfo.org/organism/Trifolium/pratense TRIPR]
- Trifolium repens (white clover), [http://legumeinfo.org/organism/Trifolium/repens TRIRE]
- Vicia faba (faba bean), [http://legumeinfo.org/organism/Vicia/faba VICFA]
- Vigna angularis (adzuki bean), [http://legumeinfo.org/organism/Vigna/angularis VIGAN]
- Vigna unguiculata (cowpea), [http://legumeinfo.org/organism/Vigna/unguiculata VIGUN]
See also
External links
- [http://legumeinfo.org/ Home page] for the Legume Information System.
- {{cite book |pmid=18287696 |year=2007 |last1=Gonzales |first1=MD |last2=Gajendran |first2=K |last3=Farmer |first3=AD |last4=Archuleta |first4=E |last5=Beavis |first5=WD |title=Plant Bioinformatics |chapter=Leveraging model legume information to find candidate genes for soybean sudden death syndrome using the legume information system |volume=406 |pages=245–59 |series=Methods in Molecular Biology|doi=10.1007/978-1-59745-535-0_11 |isbn=978-1-58829-653-5 }}
- {{cite journal |pages=D660–5 |doi=10.1093/nar/gki128 |title=The Legume Information System (LIS): An integrated information resource for comparative legume biology |year=2004 |last1=Gonzales |first1=M. D. |journal=Nucleic Acids Research |volume=33 |pmid=15608283 |last2=Archuleta |first2=E |last3=Farmer |first3=A |last4=Gajendran |first4=K |last5=Grant |first5=D |last6=Shoemaker |first6=R |last7=Beavis |first7=WD |last8=Waugh |first8=ME |issue=Database issue |pmc=540082}}
- Dash, S.; Campbell, J.D.; Cannon, E.K.S.; Cleary, A.M.; Huang, W.; Kalberer, S.R.; Karingula, V.; Rice, A.G.; Singh, J.; Umale, P.E.; Weeks, N.T.; Wilkey, A.P.; Farmer, A.D.; Cannon, S.B. (2016). [https://web.archive.org/web/20160516055205/http://nar.oxfordjournals.org/content/44/D1/D1181 Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family] Nucleic Acids Research 44 (Database issue): D1181-D1188. [https://web.archive.org/web/20160516055205/http://nar.oxfordjournals.org/content/44/D1/D1181 doi:10.1093/nar/gkv1159] [https://web.archive.org/web/20160516055205/http://nar.oxfordjournals.org/content/44/D1/D1181 PMC4702835]