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. 2023 Mar 9:14:1106104.
doi: 10.3389/fpls.2023.1106104. eCollection 2023.

LMTdb: A comprehensive transcriptome database for climate-resilient, nutritionally rich little millet (Panicum sumatrense)

Shweta Shekhar  1 , Archana S Prasad  1 , Kalpana Banjare  2 , Abhijeet Kaushik  2 , Ajit K Mannade  1 , Mahima Dubey  3 , Arun Patil  3 , Vinay Premi  1 , Ashish K Vishwakarma  4 , Abhinav Sao  5 , Ravi R Saxena  2 , Amit Dubey  6 , Girish Chandel  1
Affiliations

LMTdb: A comprehensive transcriptome database for climate-resilient, nutritionally rich little millet (Panicum sumatrense)

Shweta Shekhar et al. Front Plant Sci. .

Abstract

Little millet (Panicum sumatrense) a native of Chhattisgarh, belongs to the minor millet group and is primarily known as a climate-resilient and nutritionally rich crop. However, due to the lack of enough Omic studies on the crop, the scientific community has largely remained unaware of the potential of this crop, resulting in less scope for its utilization in crop improvement programs. Looking at global warming, erratic climate change, nutritional security, and limited genetic information available, the Little Millet Transcriptome Database (LMTdb) (https://igkv.ac.in/xenom/index.aspx) was conceptualized upon completion of the transcriptome sequencing of little millet with the aim of deciphering the genetic signatures of this largely unknown crop. The database was developed with the view of providing information about the most comprehensive part of the genome, the 'Transcriptome'. The database includes transcriptome sequence information, functional annotation, microsatellite markers, DEGs, and pathway information. The database is a freely available resource that provides breeders and scientists a portal to search, browse, and query data to facilitate functional and applied Omic studies in millet crops.

Keywords: DEGs; LMTdb; Little Millet; SSRs; database; functional annotation; metabolic pathway; transcriptome.

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Conflict of interest statement

Authors MD and ArP are employed by VNR Seeds Private Limited at present and were Ph.D. students at the Department of Plant Molecular Biology and Biotechnology, IGKVV during the course of study. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Schematics of Little Millet transcriptome database (LMTdb v.1.0.0) structure and web interface features along with transcriptome sequencing, assembly, and annotation pipeline.
Figure 2
Figure 2
Schematic representation and screenshots of Little Millet transcriptome database (LMTdb v.1.0.0). (A) Representation of key elements (DEGs, SSRs, Functional Search, Pathway, and Portfolio) of the database as displayed on the database homepage. (B) Functional Search page displaying information related to CYP71A1 like gene (TRINITY_DN6320_c0_g1_i4). (C) BLAST details for CYP71A1 like gene (TRINITY_DN6320_c0_g1_i4) (D) Comparative search for CYP71A1 like gene under DEG module. (E) Downregulation of CYP71A1 like gene in secondary under drought stress. (F) Representation of SSRs information for CYP71A1 like gene. (G) Primer details corresponding to CYP71A1 like gene. (H) Metabolic pathway information with enzymes and pathway IDs corresponding to different transcripts.
Figure 3
Figure 3
Schematics regarding access, browse and search gene functions in Little Millet transcriptome database (LMTdb v.1.0.0).
Figure 4
Figure 4
Comparative representation of Little Millet transcriptome database (LMTdb v.1.0.0) and MOROKOSHI database. (A) A view of home page in Little Millet Transcriptome Database (LMTdb v.1.0.0) vs MOROKOSHI Database. (B) Comparative search options available at Little Millet Transcriptome Database (LMTdb v.1.0.0) vs MOROKOSHI Database. (C) Information about gene annotation in Little Millet Transcriptome Database (LMTdb v.1.0.0) vs MOROKOSHI Database.
See this image and copyright information in PMC

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