Abstract
Coix lacryma-jobi, also called adlay or Job’s tears, is an annual herbal plant belonging to the Poaceae family that has been cultivated as a cereal and medicinal crop in Asia. Despite its importance, however, genomic resources for better understanding this plant species at the molecular level and informing improved breeding strategies remain limited. To address this, we generated a draft genome of the C. lacryma-jobi variety ma-yuen (soft-shelled adlay) Korean cultivar, Johyun, by de novo assembly, using PacBio and Illumina sequencing data. A total of 3,362 scaffold sequences, 1.28 Gb in length, were assembled, representing 82.1% of the estimated genome size (1.56 Gb). Genome completeness was confirmed by the presence of 91.4% of the BUSCO angiosperm genes and mapping ratio of 98.3% of Illumina paired-end reads. We found that approximately 77.0% of the genome is occupied by repeat sequences, most of which are Gypsy and Copia-type retrotransposons, and evidence-based genome annotation predicts 39,574 protein-coding genes, 85.5% of which were functionally annotated. We further predict that soft-shelled adlay diverged from a common ancestor with sorghum 9.0–11.2 MYA. Transcriptome profiling revealed 3,988 genes that are differentially expressed in seeds relative to other tissues, of which 1,470 genes were strongly up-regulated in seeds and the most enriched Gene Ontology terms were assigned to carbohydrate and protein metabolism. In addition, we identified 76 storage protein genes including 18 seed-specific coixin genes and 13 candidate genes involved in biosynthesis of benzoxazinoids (BXs) including coixol, a unique BX compound found in C. lacryma-jobi species. The characterization of those genes can further our understanding of unique traits of soft-shelled adlay, such as high seed protein content and medicinal compound biosynthesis. Taken together, our genome sequence data will provide a valuable resource for molecular breeding and pharmacological study of this plant species.
Highlights
Coix lacryma-jobi is an annual herbal plant belonging to the Poaceae family that is commonly called adlay or Job’s tears
Using Illumina MP and PacBio long reads, these contig sequences were merged into 3,362 scaffold sequences (Table 1 and Supplementary Table S4), totaling 1.28 Gb in length, with an N50 of 594.3 kb; this was designated as the soft-shelled adlay draft genome ver. 1.0
The genome sequence was further validated by mapping PE data, demonstrating that 98.3% of PE reads are covered by the genome sequences (Supplementary Table S7)
Summary
Coix lacryma-jobi is an annual herbal plant belonging to the Poaceae family that is commonly called adlay or Job’s tears. Four varieties of this species are known, including C. lacryma-jobi variety (var.) lacryma-jobi, ma-yuen, puellarum, and stenocarpa. Ma-yuen (hereafter, soft-shelled adlay) is a cultivated variety with soft shells. This plant, which is called softshelled adlay, yi yi (China), and yulmu (Korea), is widely grown as a cereal and medicinal crop in Asian countries, including China, Japan, and Korea (Arora, 1977; Chen et al, 2006; Rural Development administration [RDA], 2013; Zhu, 2017). The origin of Coix species has been traced to Southeast Asia (Arora, 1977), whereas maize and sorghum originate from America and Africa, respectively (Piperno et al, 2009; Winchell et al, 2018)
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