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

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Relation http://oar.icrisat.org/12556/
https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1203855/full
https://doi.org/10.3389/fpls.2023.1203855
 
Title Amaranth Genomic Resource Database: an integrated database resource of Amaranth genes and genomics
 
Creator Singh, A
Mahato, A K
Maurya, A
Rajkumar, S
Singh, A K
Bhardwaj, R
Kaushik, S K
Kumar, S
Gupta, V
Singh, K
Singh, R
 
Subject Plant Genetic Resources
Genetics and Genomics
 
Description 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/.
 
Publisher Frontiers Media
 
Date 2023-06-28
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Rights cc_attribution
 
Identifier http://oar.icrisat.org/12556/1/Frontiers%20in%20Plant%20Science_14_01-13_2023.pdf
Singh, A and Mahato, A K and Maurya, A and Rajkumar, S and Singh, A K and Bhardwaj, R and Kaushik, S K and Kumar, S and Gupta, V and Singh, K and Singh, R (2023) Amaranth Genomic Resource Database: an integrated database resource of Amaranth genes and genomics. Frontiers in Plant Science (TSI), 14. 01-13. ISSN 1664-462X