BpGDB: A genomic resource database of Bunium persicum for genetics and breeding

Abstract

Bunium persicum or black cumin, holds significant medicinal and culinary importance within the Apiaceae family. Its seeds are prized in Persian and Indian cuisines for flavour-enhancing and preservative properties. Traditional medicine employs it for treating digestive disorders, urinary ailments, diabetes, obesity, and lactation enhancement. Despite its economic value, genomic resources for this plant species are scarce. To address this gap and foster genetic research, we introduce “BpGDB,” the first comprehensive genomic resources database for B. persicum. BpGDB features 5939 EST-SSR markers derived from 88,309 non-redundant transcripts assembled de novo. Additionally, it incorporates 37,232 genomic SSR markers obtained from recent de novo genome sequencing efforts of our laboratory. It also includes B. persicum transcripts annotated using NCBI-NR and gene ontology (GO) databases, encompassing key gene families such as cytochrome P450, protein kinases, heat shock proteins (HSPs) etc. and biosynthetic enzymes for bioactive compounds of medicinal value. Moreover, BpGDB catalogues 4617 transcription factors (TFs) categorized into 57 families, along with their coding sequence (CDS), translated protein information. This database is user friendly and interactive with advanced search functionalities and multiple search options including SSR search, TF search, GO search etc. Users can directly access the desired information/data by either clicking on the interactive pie charts or through the menu given at the left side bar available on the homepage of database. It is aimed to facilitate researchers globally in understanding genetic traits related to therapeutic and culinary properties, while enhancing breeding strategies to improve crop productivity that may include marker-assisted selection, linkage mapping, genetic diversity studies, and population analyses in the species. Furthermore, it will open avenues for comparative genomics study within the Apiaceae family, facilitating the exploration and harnessing of the therapeutic potential of B. persicum.