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The complete chloroplast genome sequence of Coix lacryma-jobi L. (Poaceae), a cereal and medicinal crop.

ABSTRACT: Coix lacryma-jobi is a cereal and medicinal crop belonging to the Poaceae family. This study characterized complete chloroplast genome sequence of a Korean cultivar Johyun of C. lacryma-jobi var. ma-yuen through the de novo hybrid assembly with Illumina and PacBio genomic reads. The chloroplast genome is 140,863 bp long and composed of large single copy (82,827 bp), small single copy (12,522 bp), and a pair of inverted repeats (each 22,757 bp). A total of 123 genes including 87 protein-coding genes, 32 tRNA genes, and four rRNA genes were predicted in the genome. Phylogenetic analysis confirmed a close relationship of C. lacryma-jobi with species in the Panicoideae subfamily of the Poaceae family.

SUBMITTER: Kang SH

PROVIDER: S-EPMC7800251 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description: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.

Project description:BACKGROUND: Coix, Sorghum and Zea are closely related plant genera in the subtribe Maydeae. Coix comprises 9-11 species with different ploidy levels (2n = 10, 20, 30, and 40). The exclusively cultivated C. lacryma-jobi L. (2n = 20) is widely used in East and Southeast Asia for food and medicinal applications. Three fertile cytotypes (2n = 10, 20, and 40) have been reported for C. aquatica Roxb. One sterile cytotype (2n = 30) closely related to C. aquatica has been recently found in Guangxi of China. This putative hybrid has been named C. aquatica HG (Hybrid Guangxi). The genome composition and the evolutionary history of C. lacryma-jobi and C. aquatica HG are largely unclear. RESULTS: About 76% of the genome of C. lacryma-jobi and 73% of the genome of C. aquatica HG are repetitive DNA sequences as shown by low coverage genome sequencing followed by similarity-based cluster analysis. In addition, long terminal repeat (LTR) retrotransposable elements are dominant repetitive sequences in these two genomes, and the proportions of many repetitive sequences in whole genome varied greatly between the two species, indicating evolutionary divergence of them. We also found that a novel 102 bp variant of centromeric satellite repeat CentX and two other satellites only appeared in C. aquatica HG. The results from FISH analysis with repeat probe cocktails and the data from chromosomes pairing in meiosis metaphase showed that C. lacryma-jobi is likely a diploidized paleotetraploid species and C. aquatica HG is possibly a recently formed hybrid. Furthermore, C. lacryma-jobi and C. aquatica HG shared more co-existing repeat families and higher sequence similarity with Sorghum than with Zea. CONCLUSIONS: The composition and abundance of repetitive sequences are divergent between the genomes of C. lacryma-jobi and C. aquatica HG. The results from fine karyotyping analysis and chromosome pairing suggested diploidization of C. lacryma-jobi during evolution and C. aquatica HG is a recently formed hybrid. The genome-wide comparison of repetitive sequences indicated that the repeats in Coix were more similar to those in Sorghum than to those in Zea, which is consistent with the phylogenetic relationship reported by previous work.

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The complete chloroplast genome sequence of Coix lacryma-jobi L. (Poaceae), a cereal and medicinal crop.

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