LuluDB-The Database Created Based on Small RNA, Transcriptome, and Degradome Sequencing Shows the Wide Landscape of Non-coding and Coding RNA in Yellow Lupine (Lupinus luteus L.) Flowers and Pods.

Paulina Glazinska,Jan Grzegorz Kosiński,Wojciech Glinkowski,Milena Kulasek,Marta Wysocka

doi:10.3389/fgene.2020.00455

Paulina Glazinska, Jan Grzegorz Kosiński + Show 3 more

Open Access

https://doi.org/10.3389/fgene.2020.00455

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Abstract

Yellow lupine (Lupinus luteus L.) belongs to a legume family that benefits from symbiosis with nitrogen-fixing bacteria. Its seeds are rich in protein, which makes it a valuable food source for animals and humans. Yellow lupine is also the model plant for basic research on nodulation or abscission of organs. Nevertheless, the knowledge about the molecular regulatory mechanisms of its generative development is still incomplete. The RNA-Seq technique is becoming more prominent in high-throughput identification and expression profiling of both coding and non-coding RNA sequences. However, the huge amount of data generated with this method may discourage other scientific groups from making full use of them. To overcome this inconvenience, we have created a database containing analysis-ready information about non-coding and coding L. luteus RNA sequences (LuluDB). LuluDB was created on the basis of RNA-Seq analysis of small RNA, transcriptome, and degradome libraries obtained from yellow lupine cv. Taper flowers, pod walls, and seeds in various stages of development, flower pedicels, and pods undergoing abscission or maintained on the plant. 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 also provides sequence homology search by BLAST using, e.g., an unknown sequence as a query. To present the full capabilities offered by our database, we performed a case study concerning transcripts annotated as DCL 1–4 (DICER LIKE 1–4) homologs involved in small non-coding RNA biogenesis and identified miRNAs that most likely regulate DCL1 and DCL2 expression in yellow lupine. LuluDB is available at http://luluseqdb.umk.pl/basic/web/index.php.

Highlights

Yellow lupine (Lupinus luteus L.) belongs to a legume family that benefits from symbiosis with nitrogen-fixing bacteria
To prove the usefulness of the database, we present a case study of transcripts identified as DCL1–4 (DICER LIKE 1–4) homologs involved in the small non-coding RNAs (ncRNA) biogenesis process (Fukudome and Fukuhara, 2017) and identified miRNAs that most likely regulate DCL1 and DCL2 expression in yellow lupine
We have identified Long ncRNAs (lncRNAs) by performing BLASTn search within CantataDB (Szczesniak et al, 2019) in which G. max lncRNAs were queried by transcripts obtained in our experiment

Summary

Introduction

Yellow lupine (Lupinus luteus L.) belongs to a legume family that benefits from symbiosis with nitrogen-fixing bacteria. Seeds of this species are rich in proteins that constitute up to 40% of their dry mass (Ogura et al, 2014). Years of research and selective breeding have led to the development of alkaloid-free “sweet” cultivars. All these traits make lupine seeds a valuable food source for animals and humans primarily in climatic conditions unfavorable for soybean cultivation (Musco et al, 2017). 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. Yellow lupine is an excellent model plant for basic research on nodulation (Frankowski et al, 2015) or abscission of generative organs (Glazinska et al, 2017, 2019)

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