LuluDB was created basing on NGS sequencing analysis of following libraries: 32 sRNA, 18 transcriptome and 2 degradome obtained from flowers and pods of yellow lupine cv. Taper. It contains sequences of miRNAs and phased siRNAs identified in L. luteus, information about their expression in individual samples and their target sequences. LuluDB also contains identified lncRNAs and protein-coding RNA sequences with their organ expression and annotations to widely used databases like GO, KEGG, NCBI, Rfam, Pfam etc.

The database contains sequences of 456 known and 32 novel miRNAs, as well as 318 phased siRNAs (ta-siRNAs) identified in yellow lupine along with information about their expression and target transcripts. Each sRNA received an unique ID number. In case of miRNAs, known miRNAs (i.e. having identical hits in miRBase [6]) were assigned IDs from 1 to 456, and the numbering of novel miRNAs (identified with ShortStack [7]) started from 457 up.

LuluDB contains 267,349 protein-coding RNA sequences. Because the reference yellow lupine genome had not been released yet, the transcripts were assembled de novo. This assembly was carried out separately for libraries derived from flowers [8] and pods with Trinity toolkit, which assigned an ID for each transcript (e.g.TRINITY_DN10038_c0_g1_i1) within each batch separately. This created the risk that completely dissimilar transcripts in flowers and pods could have the same ID. We fixed this in three ways: (i) by providing each transcript with information about its origin (flowers or pods), (ii) by adding the “F” prefix to TRINITY ID in flower dataset (e.g. FTRINITY_DN53848_c2_g1_i5) and (iii) by assigning additional ID for the database (e.g. LI_transcript_534367). All of the assembled transcripts were clustered and, within each cluster, they were assigned "Gene name" (e.g. LI_gene_11901).

By building LuluDB we aimed to popularize the genetic research on this important crop plant and integrate our RNAseq data for yellow lupine protein-coding and non-coding RNA sequences in one place. This will also support the research on universal regulatory mechanisms of plant development. Thus, regardless of the model plant you are working with, you can search the LuluDB database for homological sequences by performing BLAST using your sequence as a query.

You are welcome to deposit your sequences in our database! We encourage you to contact us.

References:

1. Liu X, Hao L, Li D, Zhu L, Hu S. Long non-coding RNAs and their biological roles in plants. Genomics Proteomics Bioinformatics. 2015 Jun;13(3):137-47.
2. Axtell, M. J. Classification and comparison of small RNAs from plants. Annu. Rev. Plant Biol. 2013 64, 137–159.
3. Fei Q, Xia R, Meyers BC. Phased, Secondary, Small Interfering RNAs in Posttranscriptional Regulatory Networks. The Plant Cell. 2013;25(7):2400-2415.
4. Luo Y, Guo Z, Li L. Evolutionary conservation of microRNA regulatory programs in plant flower development. Dev Biol. 2013 Aug 15;380(2):133-44.
5. Zhou M, Luo H. MicroRNA-mediated gene regulation: potential applications for plant genetic engineering. Plant Mol Biol. 2013 Sep;83(1-2):59-75.
6. Axtell, M. J. (2013b). ShortStack: Comprehensive annotation and quantification of small RNA genes. RNA 19, 740–751. doi:10.1261/rna.035279.112
7. Kozomara, A., Birgaoanu, M., and Griffiths-Jones, S. (2019). miRBase: from microRNA sequences to function. Nucleic Acids Res. 47, D155–D162. doi:10.1093/nar/gky1141.
8. Glazińska, P., Kulasek, M., Glinkowski, W., Wojciechowski, W., and Kosiński, J. (2019). Integrated analysis of small rna, transcriptome and degradome sequencing provides new insights into floral development and abscission in yellow lupine (Lupinus luteus l.). Int. J. Mol. Sci. 20. doi:10.3390/ijms20205122.

The main constraint on a large-scale cultivation of yellow lupine comes from its excessive shedding of generative organs, which contributes to significant yield losses. Therefore, current research focuses on the development of varieties of yellow lupine and cultivation conditions that would prevent massive flower and pod dropping, consequently stabilizing the yield in various environmental conditions [3]. Besides its practical significance, yellow lupine is also an excellent model plant for basic research on nodulation [4] or abscission of generative organs [5-7].

Contemporary advances in molecular biology e.g development of next generation sequencing (NGS) support the traditional methods for selection of new varieties of crops. Modern techniques also extend the range of possibilities of analysing the impact of various endogenous and environmental factors on the development of yellow lupine [5-8]. However, the knowledge about the mechanisms of regulation of its generative development is still fragmentary, especially concerning the involvement of short and long non-coding RNA in this process.

References

1. Ogura T, Ogihara J, Sunairi M, Takeishi H, Aizawa T, Olivos-Trujillo MR, Maureira-Butler IJ, Salvo-Garrido HE. Proteomic characterization of seeds from yellow lupin (Lupinus luteus L.). Proteomics. 2014 Jun;14(12):1543-6.
2. Musco N, Cutrignelli MI, Calabrò S, Tudisco R, Infascelli F, Grazioli R, LoPresti V, Gresta F, Chiofalo B. Comparison of nutritional and antinutritional traits among different species (Lupinus albus L., Lupinus luteus L., Lupinus angustifolius L.) and varieties of lupin seeds. J Anim Physiol Anim Nutr (Berl). 2017 Dec;101(6):1227-1241.
3. Lucas MM, Stoddard FL, Annicchiarico P, Frías J, Martínez-Villaluenga C, Sussmann D, Duranti M, Seger A, Zander PM, Pueyo JJ. The future of lupin as a protein crop in Europe. Front Plant Sci. 2015 Sep 8;6:705.
4. Legocki A.B., Karlowski W.M., Podkowiński J., Sikorski M., Stępkowski T. (1997) Advances in molecular characterization of the yellow lupin - Bradyrhizobium sp. (Lupinus) symbiotic model. In: Legocki A., Bothe H., Pühler A. (eds) Biological Fixation of Nitrogen for Ecology and Sustainable Agriculture. NATO ASI Series (Series G: Ecological Sciences), vol 39. Springer, Berlin, Heidelberg
5. Glazinska P, Wojciechowski W, Kulasek M, Glinkowski W, Marciniak K, Klajn N, Kesy J, Kopcewicz J. De novo transcriptome profiling of flowers, flower pedicels and pods of Lupinus luteus (yellow lupine) reveals complex expression changes during organ abscission. Front Plant Sci. 2017 May 2;8:641.
6. Glazińska P, Kulasek M, Glinkowski W, Wojciechowski W, and Kosiński J. Integrated analysis of small RNA, transcriptome and degradome sequencing provides new insights into floral development and abscission in yellow lupine (Lupinus luteus L.). Int. J. Mol. Sci. 2019 Oct 16;20.
7. Wilmowicz E, Kućko A, Burchardt S, Przywieczerski T. Molecular and hormonal aspects of drought-triggered flower shedding in yellow lupine. Int J Mol Sci. 2019;20(15):3731.
8. Parra-González LB, Aravena-Abarzúa GA, Navarro-Navarro CS, Udall J, Maughan J,Peterson LM, Salvo- Garrido HE, Maureira-Butler IJ. Yellow lupin (Lupinus luteus L.) transcriptome sequencing: molecular marker development and comparative studies. BMC Genomics. 2012 Aug 24;13:425.