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
Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India.
The Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.
Front Plant Sci. 2023 Jun 28;14:1203855. doi: 10.3389/fpls.2023.1203855. eCollection 2023.
Amaranth ( 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 (, ) and wild/weedy species (, , and ) 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/.
苋属植物原产于墨西哥和北美洲，数千年前就在那里种植，而现在苋属植物在全球范围内都有种植。苋属植物是最具潜力的具有高营养价值的粮食作物之一，属于苋科。已报道了栽培苋属物种（ ， ）和野生/杂草物种（ ， ，和 ）的高质量基因组组装；因此，我们开发了苋属植物基因组资源数据库（AGRDB），以便在一个地方提供对所有基因组信息的访问，如基因、简单序列重复（SSRs）、单核苷酸多态性（SNPs）、转录因子（TFs）、微小RNA（miRNAs）和转运蛋白。AGRDB数据库包含功能注释的基因信息及其序列细节、基因和基因组SSRs及其三组引物、分为不同家族的转录因子及其序列信息和注释细节、推测的miRNAs及其家族、序列和靶向基因细节、转运蛋白基因及其超家族、跨膜结构域细节，以及五个苋属物种的基因和非基因SNPs的细节及其3'和5'侧翼序列信息。可以使用基因ID、序列ID、序列基序、基序重复、家族名称、注释关键词、支架或染色体编号等进行数据库搜索。该资源还包括一些有用的工具，包括用于在各自苋属植物基因组上可视化基因、SSRs、SNPs和TFs的JBrowse，以及用于对用户查询序列与苋属植物基因组以及蛋白质序列进行BLAST搜索的BLAST搜索。AGRDB数据库将作为这种未来作物遗传改良和特性分析的潜在平台。AGRDB数据库可通过以下链接访问：http://www.nbpgr.ernet.in:8080/AmaranthGRD/ 。
