Amaranth Genomic Resource Database: an integrated database resource of Amaranth genes and genomics

Akshay Singh; Ajay Kumar Mahato; Avantika Maurya; S Rajkumar; A K Singh; Rakesh Bhardwaj; S K Kaushik; Sandeep Kumar; Veena Gupta; Kuldeep Singh; Rakesh Singh

doi:10.3389/fpls.2023.1203855

Amaranth Genomic Resource Database: an integrated database resource of Amaranth genes and genomics

Front Plant Sci. 2023 Jun 28:14:1203855. doi: 10.3389/fpls.2023.1203855. eCollection 2023.

Authors

Affiliations

¹ Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India.
² The Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.
³ Division of Germplasm Evaluation, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India.
⁴ Division of Germplasm Conservation, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India.
⁵ International Crop Research Institute for the Semi-Arid Tropics, Hyderabad, India.

Abstract

Amaranth (Amaranthus L.) is native to Mexico and North America, where it was cultivated thousands of years ago, but now amaranth is grown worldwide. Amaranth is one of the most promising food crops with high nutritional value and belongs to the family Amaranthaceae. The high-quality genome assembly of cultivated amaranth species (A. hypochondriacus, A. cruentus) and wild/weedy species (A. tuberculatus, A. hybridus, and A. palmeri) has already been reported; therefore, we developed an Amaranth Genomic Resource Database (AGRDB) to provide access to all the genomic information such as genes, SSRs, SNPs, TFs, miRNAs, and transporters in one place. The AGRDB database contains functionally annotated gene information with their sequence details, genic as well as genomic SSRs with their three sets of primers, transcription factors classified into different families with their sequence information and annotation details, putative miRNAs with their family, sequences, and targeted gene details, transporter genes with their superfamily, trans-membrane domain details, and details of genic as well as nongenic SNPs with 3' and 5' flanking sequence information of five amaranth species. A database search can be performed using the gene ID, sequence ID, sequence motif, motif repeat, family name, annotation keyword, scaffold or chromosome numbers, etc. This resource also includes some useful tools, including JBrowse for the visualization of genes, SSRs, SNPs, and TFs on the respective amaranth genomes and BLAST search to perform a BLAST search of the user's query sequence against the amaranth genome as well as protein sequences. The AGRDB database will serve as a potential platform for genetic improvement and characterization of this futuristic crop. The AGRDB database will be accessible via the link: http://www.nbpgr.ernet.in:8080/AmaranthGRD/.

Keywords: Amaranth Genomic Resource Database; SNPs; SSRs; TFs; Transporters; miRNAs.

Grants and funding

This research was funded by the Department of Biotechnology Government of India, under grant number “BT/PR23811/AGIII/103/1029/2018.” The funder has no role in the design of the study, the collection, analysis, and interpretation of data, or the writing of the manuscript.