Evolution and Domestication Footprints Uncovered from the Genomes of Coix.

Coix lacryma-jobi, a plant species closely related to Zea and Sorghum, is an important food and medicinal crop in Asia. However, no reference genome of this species has been reported, and its exact phylogeny within the Andropogoneae remains unresolved. Here, we generated a high-quality genome assembly of coix comprising ∼1.73 Gb with 44 485 predicted protein-coding genes. We found coix to be a typical diploid plant with an overall 1-to-1 syntenic relationship with the Sorghum genome, despite its drastic genome expansion (∼2.3-fold) due mainly to the activity of transposable elements. Phylogenetic analysis revealed that coix diverged with sorghum ∼10.41 million years ago, which was ∼1.49 million years later than the divergence between sorghum and maize. Resequencing of 27 additional coix accessions revealed that they could be unambiguously separated into wild relatives and cultivars, and suggested that coix experienced a strong genetic bottleneck, resulting in the loss of about half of the genetic diversity during domestication, even though many traits have remained undomesticated. Our data not only provide novel comparative genomic and evolutionary insights into the Andropogoneae lineage, but also an important resource that will greatly benefit molecular breeding of this important crop.

The Coix Genome Provides Insights into Panicoideae Evolution and Papery Hull Domestication.

Coix is a grass crop domesticated as early as the Neolithic era. It is still widely cultivated for both highly nutritional food and medicinal use. However, the genetic study and breeding of this crop are hindered by the lack of a sequenced genome. Here, we report de novo sequencing and assembly of the 1619-Mb genome of Coix, and annotation of 75.39% repeats and 39 629 protein-coding genes. Comparative genomics analysis showed that Coix is more closely related to sorghum than maize, but intriguingly only Coix and maize had a recent genome duplication event, which was not detected in sorghum. We further constructed a genetic map and mapped several important traits, especially the strength of hull. Selection of papery hull (thin: easy dehulling) from the stony hull (thick: difficult dehulling) in wild progenitors was a key step in Coix domestication. The papery hull makes seed easier to process and germinate. Anatomic and global transcriptome analysis revealed that the papery hull is a result of inhibition of cell division and wall biogenesis. We also successfully demonstrated that seed hull pressure resistance is controlled by two major quantitative trait loci (QTLs), which are associated with hull thickness and color, respectively. The two QTLs were further fine mapped within intervals of 250 kb and 146 kb, respectively. These resources provide a platform for evolutionary studies and will facilitate molecular breeding of this important crop.

Assessment of the Genetic Diversity of Different Job's Tears (Coix lacryma-jobi L.) Accessions and the Active Composition and Anticancer Effect of Its Seed Oil.

Job's tears (Coix lachryma-jobi L.) is an important crop used as food and herbal medicine in Asian countries. A drug made of Job's tears seed oil has been clinically applied to treat multiple cancers. In this study, the genetic diversity of Job's tears accessions and the fatty acid composition, triglyceride composition, and anti-proliferative effect of Job's tears seed oil were analyzed using morphological characteristics and ISSR markers, GC-MS, HPLC-ELSD, and the MTT method. ISSR analysis demonstrated low genetic diversity of Job's tears at the species level (h = 0.21, I = 0.33) and the accession level (h = 0.07, I = 0.10), and strong genetic differentiation (GST = 0.6702) among all accessions. It also clustered the 11 accessions into three cultivated clades corresponding with geographical locations and two evidently divergent wild clades. The grouping patterns based on morphological characteristics and chemical profiles were in accordance with those clustered by ISSR analysis. Significant differences in morphological characteristics, fatty acid composition, triglyceride composition, and inhibition rates of seed oil were detected among different accessions, which showed a highly significant positive correlation with genetic variation. These results suggest that the seed morphological characteristics, fatty acid composition, and triglyceride composition may be mainly attributed to genetic factors. The proportion of palmitic acid and linoleic acid to oleic acid displayed a highly significant positive correlation with the inhibition rates of Job's tears seed oil for T24 cells, and thus can be an important indicator for quality control for Job's tears.

Differential genome evolution and speciation of Coix lacryma-jobi L. and Coix aquatica Roxb. hybrid guangxi revealed by repetitive sequence analysis and fine karyotyping.

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.

[Rapid identification of Coix seed varieties by near infrared spectroscopy].

Unsupervised learning algorithm-principal component analysis (PCA), and supervised learning algorithm-learning vector quantization (LVQ) neural network and support vector machine (SVM) were used to carry out qualitative discriminant analysis of different varieties of coix seed from different regions. Since nutrient compositions of different varieties coix seed samples from different origins were complex and the contents were similar, characteristic variables of two kinds of coix seed were alike, the scores plot of their principal components seriously overlapped and the categories of coix seed were difficult to distinguish While satisfactory results were obtained by LVQ neural network and SVM. The accuracy of LVQ neural network prediction is 90. 91%, while the classification accuracy of SVM, whose penalty parameter and kernel function parameter were optimized, can be up to 100%. The results show that NIRS combined with chemometrics can be used as a rapid, nondestructive and reliable method to identify coix seed varieties and provide technical reference for market regulation.

Phytochemical profiles and antioxidant activity of adlay varieties.

Consumption of whole grains has been associated with reduced risk of developing major chronic diseases. These health benefits have been attributed in part to their unique phytochemicals. Little is known about the complete profiles of phytochemicals and antioxidant activities of different adlay varieties. The objectives of this study were to determine the phytochemicals profiles of the three adlay varieties, including both free and bound of total phenolics and total flavonoids, and to determine the total antioxidant activity of adlay. The free, bound, and total phenolic contents of adlay samples ranged from 31.23 to 45.19 mg of gallic acid equiv/100 g of sample, from 28.07 to 30.86 mg of gallic acid equiv/100 g of sample, and from 59.30 to 76.04 mg of gallic acid equiv/100 g of sample, respectively. On average, the bound phenolics contributed 45.3% of total phenolic content of the adlay varieties analyzed. The free, bound, and total flavonoid contents of adlay samples ranged from 6.21 to 18.24 mg of catechin equiv/100 g, from 18.68 to 35.27 mg of catechin equiv/100 g, and from 24.88 to 52.86 mg of catechin equiv/100 g, respectively. The average values of bound flavonoids contributed 71.1% of total flavonoids of the adlay varieties analyzed. The percentage contribution of flavonoid content to phenolic content of free, bound, and total ranged from 11.6 to 35.2%, from 50.5 to 66.8%, and from 24.6 to 50.5%. The free, bound, and total oxygen radical absorbance capacity (ORAC) values of adlay samples ranged from 231.9 to 316.6 mg of Trolox equiv/100 g, from 209.0 to 351.4 mg of Trolox equiv/100 g, and from 440.9 to 668.0 mg of Trolox equiv/100 g, respectively. The average ORAC values of bound phytochemicals contributed 48.1% of total antioxidant activity of the adlay varieties analyzed. The content of total polyphenol and the antioxidant capacity are obviously different among different species. Liaoning 5 adlay and Longyi 1 adlay are significantly better than Guizhou heigu adlay. The adlay extracts have obvious proliferate inhibition on human liver cancer cells, and substantially in the experimental concentration range, the adlay sample itself has no cytotoxicity. Knowing the phytochemical profiles and antioxidant activity of adlay gives insights to its potential application to promote health.