A draft genome at chromosome level and metabolomes of leave, root and flowers provide insights into the molecular basis of medicinal ingredients of loquat (Eriobotrya japonica (Thunb.) Lindl)

Abstract

Eriobotrya japonica, commonly called loquat, is a type of fruit and a famous traditional Chinese medicinal material. Here, a high-quality draft genome of the E. japonica cultivar, Big Five-pointed Star, containing 733.32 million bases (Mb) covering approximately 98% of estimated whole genome size (749.25 Mb) is reported. A total of 45,492 protein-coding genes were predicted. Meanwhile, metabolomes of flower, leave and root of this loquat variety were also determined by UPLC-ESI-MS/M system. 577 metabolites were determined in total, including 98 phenolic acids, 95 flavonoids, 33 alkaloids, 28 terpenoids, one steroids. The accumulation difference of these metabolites among leaf, flower and root of loquat were also clarified. Based on KEGG annotation, genes related to the biosynthesis of medicinal ingredients including some flavonoids and terpenoids were identified. Overall, this study provides global fundamental molecular insights into the medical biology of Eriobotrya japonica.

Loquat (Eriobotrya japonica (Thunb.) Lindl) population genomics suggests a two‐staged domestication and identifies genes showing convergence/parallel selective sweeps with apple or peach

“…The remaining clean short reads were mapped to assemble a reference genome of the "Big Five-pointed Star" by using software BWA (Li and Durbin, 2009). Its whole genome sequence and the protein-coding genes sequences have been deposited in China National Center for Bioinformation (https:// bigd.big.ac.cn/gwh: WGS010381) (Wang, 2021). After mapping of clean reads to the assembled reference genome, the program Picard (http://sourceforge.net/projects/picard/) was executed to filter redundant reads (MarkDuplicates).…”

“…Here, we re‐sequenced and analyzed the genomes of 52 cultivars collected worldwide and 51 wild E. japonica accessions representing the species natural distribution. Together with a sequenced and assembled draft genome of a major loquat cultivar, “Big Five‐pointed Star,” at the chromosome level (Wang, 2021), we undertook population genetics analyses. The major aims are to clarify: (i) transition of population structure from wild to cultivated populations resulting from domestication; (ii) pathways and key nodes of origin, domestication and migration; and (ii) genomic sequences and genes affected by artificial selection.…”