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, 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 variety (soft-shelled adlay) Korean cultivar, Johyun, by 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 and -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 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.

Coix lacryma-jobi L. is one of the most economically and medicinally important corns. This study constructed a high-density genetic linkage map of C. lacryma-jobi based on a cross between the parents 'Qianyi No. 2' × 'Wenyi No. 2' and their F 2 progeny through high-throughput sequencing and the construction of a specific-locus amplified fragment (SLAF) library. After pre-processing, 325.49 GB of raw data containing 1628 M reads were obtained. A total of 22,944 high-quality SLAFs were identified, among which 3952 SLAFs and 3646 polymorphic markers met the requirements for the construction of a genetic linkage map. The integrated map contained 3605 high-quality SLAFs, which were grouped into ten genetic linkage groups. The total length of the map was 1620.39 cM, with an average distance of 0.45 cM and an average of 360.5 markers per linkage group. This report presents the first high-density genetic map of C. lacryma-jobi . This map was constructed using an F 2 population and SLAF-seq approach, which allows the development of a large number of polymorphic markers in a short period. These results provide a platform for precise gene/quantitative trait locus (QTL) mapping, map-based gene separation, and molecular breeding in C. lacryma-jobi . They also help identify a target gene for tracking, splitting quantitative traits, and estimating the phenotypic effects of each QTL for QTL mapping. They are of great significance for improving the efficiency of discovering and utilizing excellent gene resources of C. lacryma-jobi .

In order to provide a method for quality control of glyceryl trioleate in Coix lacryma-jobi L., this paper focused on differentiating the glyceryl trioleate compound in 14 cultivars and effect of nitrogen on glyceryl trioleate in Coix seed by clustering of High Performance Liquid Chromatography (HPLC). This research was carried out to find a variety that has active glyceryl trioleate with the highest content and to investigate the effect of nitrogen to the active ingredients of glyceryl trioleate in Coix lacryma-jobi L. and its effect in Coix lacryma-jobi L. treatment. The standard regressive curve equation of glyceryl trioleate obtained by using HPLC was: Y = (7.106) X- 495293, R² = 0.9997. The average reproducible experiment result of glyceryl trioleate is 0.097, RSD (relative standard deviation) is 1.95%; recovery rate is 97.69% and RSD is 0.89%. The experiment measured the glyceryl trioleate content of 14 varieties of Coix lacryma-jobi L using Qianyin #1 (C14). The result showed that fertilizer combination N10F2 (4:1:2:3) produced the highest glyceryl trioleate content in Coix lacryma-jobi L. Thus, nitrogen that applied in the fertilizer for 150kg ha-1 and the ratio of pre plant application including seedbed application, tillering application and earing application were optimized at 4:1:2:3 ratio.

True ileal digestibility (TID) values of amino acid (AA) obtained using growing rats are often used for the characterisation of protein quality in different foods and acquisition of digestible indispensable amino acid scores (DIAAS) in adult humans. Here, we conducted an experiment to determine the TID values of AA obtained from nine cooked cereal grains (brown rice, polished rice, buckwheat, oats, proso millet, foxtail millet, tartary buckwheat, adlay and whole wheat) fed to growing Sprague–Dawley male rats. All rats were fed a standard basal diet for 7 d and then received each diet for 7 d. Ileal contents were collected from the terminal 20 cm of ileum. Among the TID values obtained, whole wheat had the highest values ( P <0·05), and polished rice, proso millet and tartary buckwheat had relatively low values. The TID indispensable AA concentrations in whole wheat were greater than those of brown rice or polished rice ( P <0·05), and polished rice was the lowest total TID concentrations among the other cereal grains. The DIAAS was 68 for buckwheat, 47 for tartary buckwheat, 43 for oats, 42 for brown rice, 37 for polished rice, 20 for whole wheat, 13 for adlay, 10 for foxtail millet and 7 for proso millet. In this study, the TID values of the nine cooked cereal grains commonly consumed in China were used for the creation of a DIAAS database and thus gained public health outcomes.

Stomatal regulation plays a vital role in enhancing drought resistance in plants, yet the underlying molecular mechanisms in C 4 crops remain largely unexplored. Focusing on the nutritionally important C 4 species Coix lacryma-jobi , we identified key anion transporters— ClSLAC1 , ClSLAH3 , and ClALMT12 —with elevated leaf expression, notably higher for ClSLAC1 and ClSLAH3 than ClALMT12 . Utilizing computational modeling with OnGuard, we predicted that increased expression of ClSLAC s promote stomatal opening and closing. Experimental validation further revealed that Coix has both faster stomatal kinetics and reduced stomatal aperture relative to Arabidopsis . Our findings indicate that enhanced ClSLAC1/ClSLAH3 expression significantly improves water retention of Coix , providing a molecular foundation for the water use. These insights could pave the way for developing stress-resilient crops through targeted engineering strategies.

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.

Bambusoideae is the only subfamily that contains woody members in the grass family, Poaceae. In phylogenetic analyses, Bambusoideae, Pooideae and Ehrhartoideae formed the BEP clade, yet the internal relationships of this clade are controversial. The distinctive life history (infrequent flowering and predominance of asexual reproduction) of woody bamboos makes them an interesting but taxonomically difficult group. Phylogenetic analyses based on large DNA fragments could only provide a moderate resolution of woody bamboo relationships, although a robust phylogenetic tree is needed to elucidate their evolutionary history. Phylogenomics is an alternative choice for resolving difficult phylogenies. Here we present the complete nucleotide sequences of six woody bamboo chloroplast (cp) genomes using Illumina sequencing. These genomes are similar to those of other grasses and rather conservative in evolution. We constructed a phylogeny of Poaceae from 24 complete cp genomes including 21 grass species. Within the BEP clade, we found strong support for a sister relationship between Bambusoideae and Pooideae. In a substantial improvement over prior studies, all six nodes within Bambusoideae were supported with ≥0.95 posterior probability from Bayesian inference and 5/6 nodes resolved with 100% bootstrap support in maximum parsimony and maximum likelihood analyses. We found that repeats in the cp genome could provide phylogenetic information, while caution is needed when using indels in phylogenetic analyses based on few selected genes. We also identified relatively rapidly evolving cp genome regions that have the potential to be used for further phylogenetic study in Bambusoideae. The cp genome of Bambusoideae evolved slowly, and phylogenomics based on whole cp genome could be used to resolve major relationships within the subfamily. The difficulty in resolving the diversification among three clades of temperate woody bamboos, even with complete cp genome sequences, suggests that these lineages may have diverged very rapidly.

Background Valine-glutamine (VQ) proteins are non-specific plant proteins that have a highly conserved motif: FxxhVQxhTG. These proteins are involved in the development of various plant organs such as seeds, hypocotyls, flowers, leaves and also play a role in response to salt, drought and cold stresses. Despite their importance, there is limited information available on the evolutionary and structural characteristics of VQ family genes in Coix lacryma-jobi . Results In this study, a total of 31 VQ genes were identified from the coix genome and classified into seven subgroups (I–VII) based on phylogenetic analysis. These genes were found to be unevenly distributed on 10 chromosomes. Gene structure analysis revealed that these genes had a similar type of structure within each subfamily. Moreover, 27 of ClVQ genes were found to have no introns. Conserved domain and multiple sequence alignment analysis revealed the presence of a highly conserved sequences in the ClVQ protein. This research utilized quantitative real-time PCR (qRT-PCR) and promoter analysis to investigate the expression of ClVQ genes under different stress conditions. Results showed that most ClVQ genes responded to polyethylene glycol, heat treatment, salt, abscisic acid and methyl jasmonate treatment with varying degrees of expression. Furthermore, some ClVQ genes exhibited significant correlation in expression changes under abiotic stress, indicating that these genes may act synergistically in response to adversarial stress. Additionally, yeast dihybrid verification revealed an interaction between ClVQ4, ClVQ12, and ClVQ26. Conclusions This study conducted a genome-wide analysis of the VQ gene family in coix, including an examination of phylogenetic relationships, conserved domains, cis-elements and expression patterns. The goal of the study was to identify potential drought resistance candidate genes, providing a theoretical foundation for molecular resistance breeding.

Coix lacryma-jobi L. is a very important economic crop widely cultivated in Southeast Asia. Drought affects more than four million square kilometers every year, and is a significant factor limiting agricultural productivity. However, relatively little is known about how Coix lacryma-jobi L. responds to drought treatments. To obtain a detailed and comprehensive understanding of the mechanisms regulating the transcriptional responses of Coix lacryma-jobi L. to drought treatment, we employed high throughput short-read sequencing of cDNA prepared from polyadenylated RNA to explore global gene expression after a seven-day drought treatment. We generated a de novo assembled transcriptome comprising 65,480 unique sequences. Differential expression analysis based on RSEM-estimated transcript abundances identified 5,315 differentially expressed genes (DEGs) when comparing samples from plants following drought-treatment and from the appropriate controls. Among these, the transcripts for 3,460 genes were increased in abundance, whereas 1,855 were decreased. Real-time quantitative PCR for 5 transcripts confirmed the changes identified by RNA-Seq. The results provide a transcriptional overview of the changes in Coix lacryma-jobi L. in response to drought, and will be very useful for studying the function of associated genes and selection of molecular marker of Coix lacryma-jobi L in the future.

Background Coix lacryma jobi L., a member of the Poaceae family, is a traditional Chinese medicine ingredient with a long history. In recent years, research and clinical treatment have shown that Coix lacryma jobi L. seed oil exhibits significant anti-cancer effects and enhances the efficacy of chemotherapy. As Diacylglycerol Acyltransferase is a key rate-limiting enzyme in lipid synthesis, a thorough understanding of the Diacylglycerol Acyltransferase gene family in Coix lacryma jobi L. could pave the way for increasing its lipid content. Results This study used the website NCBI to search for the CDS sequences of the Diacylglycerol Acyltransferase family genes in different plants and find the homologous genes in Coix lacryma jobi L. genome by blast screening. A total of ten Diacylglycerol Acyltransferase family genes were identified in Coix lacryma jobi L., which were named ClDGAT1_1, ClDGAT1_2 , ClDGAT1_3 , ClDGAT2_1 , ClDGAT2-2 , ClDGAT3 , ClWS/DGAT_1 , ClWS/DGAT_2 , ClWS/DGAT_3 , and ClWS/DGAT_4 . We analyzed the protein physicochemical properties, gene structure, gene homology and evolutionary analysis of them to elaborate the information of ClDGAT family genes. Meanwhile, functional assays revealed significant differences in oil and fatty acid synthesis among the ClDGAT s. By expressing ten ClDGAT genes in H1246 yeast and comparing the differences in oil and fatty acid content in these yeasts, we found that ClDGAT3 and ClDGAT1_2 had the best oil and triglyceride synthesis ability. This study advanced research on the Diacylglycerol Acyltransferase gene family and expanded the understanding of lipid synthesis-related genes in Coix lacryma jobi L.. Conclusions In this study, we systematically identified and characterized ten DGAT family genes in the Coix lacryma jobi L. genome. Functional validation in the H1246 yeast demonstrated significant divergence in lipid synthesis capacity of ClDGAT isoforms. And ClDGAT3 and ClDGAT1_2 had the best oil and triglyceride synthesis ability.