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

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...

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Autores principales: Singh, Akshay, Mahato, Ajay Kumar, Maurya, Avantika, Rajkumar, S., Singh, A. K., Bhardwaj, Rakesh, Kaushik, S. K., Kumar, Sandeep, Gupta, Veena, Singh, Kuldeep, Singh, Rakesh
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10337998/
https://www.ncbi.nlm.nih.gov/pubmed/37448872
http://dx.doi.org/10.3389/fpls.2023.1203855
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author Singh, Akshay
Mahato, Ajay Kumar
Maurya, Avantika
Rajkumar, S.
Singh, A. K.
Bhardwaj, Rakesh
Kaushik, S. K.
Kumar, Sandeep
Gupta, Veena
Singh, Kuldeep
Singh, Rakesh
author_facet Singh, Akshay
Mahato, Ajay Kumar
Maurya, Avantika
Rajkumar, S.
Singh, A. K.
Bhardwaj, Rakesh
Kaushik, S. K.
Kumar, Sandeep
Gupta, Veena
Singh, Kuldeep
Singh, Rakesh
author_sort Singh, Akshay
collection PubMed
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/.
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spelling pubmed-103379982023-07-13 Amaranth Genomic Resource Database: an integrated database resource of Amaranth genes and genomics Singh, Akshay Mahato, Ajay Kumar Maurya, Avantika Rajkumar, S. Singh, A. K. Bhardwaj, Rakesh Kaushik, S. K. Kumar, Sandeep Gupta, Veena Singh, Kuldeep Singh, Rakesh Front Plant Sci Plant Science 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/. Frontiers Media S.A. 2023-06-28 /pmc/articles/PMC10337998/ /pubmed/37448872 http://dx.doi.org/10.3389/fpls.2023.1203855 Text en Copyright © 2023 Singh, Mahato, Maurya, Rajkumar, Singh, Bhardwaj, Kaushik, Kumar, Gupta, Singh and Singh https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Singh, Akshay
Mahato, Ajay Kumar
Maurya, Avantika
Rajkumar, S.
Singh, A. K.
Bhardwaj, Rakesh
Kaushik, S. K.
Kumar, Sandeep
Gupta, Veena
Singh, Kuldeep
Singh, Rakesh
Amaranth Genomic Resource Database: an integrated database resource of Amaranth genes and genomics
title Amaranth Genomic Resource Database: an integrated database resource of Amaranth genes and genomics
title_full Amaranth Genomic Resource Database: an integrated database resource of Amaranth genes and genomics
title_fullStr Amaranth Genomic Resource Database: an integrated database resource of Amaranth genes and genomics
title_full_unstemmed Amaranth Genomic Resource Database: an integrated database resource of Amaranth genes and genomics
title_short Amaranth Genomic Resource Database: an integrated database resource of Amaranth genes and genomics
title_sort amaranth genomic resource database: an integrated database resource of amaranth genes and genomics
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10337998/
https://www.ncbi.nlm.nih.gov/pubmed/37448872
http://dx.doi.org/10.3389/fpls.2023.1203855
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