Barley remains dated to the dawn of agriculture have been found at several archaeological sites 1,2 . In addition to indications that barley was an important food crop, recent excavations have fuelled speculation that beverages from fermented grains may have motivated early Neolithic hunter-gatherers to erect some of humankind's oldest monuments 3,4 . Moreover, brewing beer may also have played a role in the eastward spread of the crop after its initial domestication in the Fertile Crescent 5,6 . Since 2012, both genetic research and crop improvement in barley have benefited from a partly ordered draft sequence assembly 7 . This community resource has underpinned gene isolation 8,9 and population genomic studies 10 . However, these and other efforts have also revealed limitations of the current draft assembly. The limitations are often direct consequences of two characteristic genomic features: the extreme abundance of repetitive elements, and the severely reduced frequency of meiotic recombination in pericentromeric regions 11 .These factors have limited the contiguity of whole-genome assemblies to kilobase-sized sequences originating from low-copy regions of the genome. Thus, a detailed investigation of the composition of the repetitive fraction of the genome-including expanded gene families-and of the distribution of targets of selection and crop improvement in (genetically defined) pericentromeric regions has been beyond reach.Here we present a map-based reference sequence of the barley genome including the first comprehensively ordered assembly of the pericentromeric regions of a Triticeae genome. The resource highlights a conspicuous distinction between distal and proximal regions of chromosomes that is reflected by the intranuclear chromatin organization. Moreover, chromosomal compartments are differentiated by an exponential gradient of gene density and recombination rate, striking contrasts in the distribution of retrotransposon families, and distinct patterns of genetic diversity.Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlightin...

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. ‘Morex’ was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).

Our previous studies showed that high salt tolerance in Tibetan wild barley accessions was associated with HvHKT1;1, a member of the high-affinity potassium transporter family. However, molecular mechanisms of HvHKT1;1 for salt tolerance and its roles in K+/Na+ homeostasis remain to be elucidated. Functional characterization of HvHKT1;1 was conducted in the present study. NaCl-induced transcripts of HvHKT1;1 were significantly higher in the roots of Tibetan wild barley XZ16 relative to other genotypes, being closely associated with its higher biomass and lower tissue Na+ content under salt stress. Heterologous expression of HvHKT1;1 in Saccharomyces cerevisiae (yeast) and Xenopus laevis oocytes showed that HvHKT1;1 had higher selectivity for Na+ over K+ and other monovalent cations. HvHKT1;1 was found to be localized at the cell plasma membrane of root stele and epidermis. Knock-down of HvHKT1;1 in barley led to higher Na+ accumulation in both roots and leaves, while overexpression of HvHKT1;1 in salt-sensitive Arabidopsis hkt1-4 and sos1-12 loss-of-function lines resulted in significantly less shoot and root Na+ accumulation. Additionally, microelectrode ion flux measurements and root elongation assay revealed that the transgenic Arabidopsis plants exhibited a remarkable capacity for regulation of Na+, K+, Ca2+ and H+ homeostasis under salt stress. These results indicate that HvHKT1;1 is critical in radial root Na+ transport, which eventually reduces shoot Na+ accumulation. Additionally, HvHKT1;1 may be indirectly involved in retention of K+ and Ca2+ in root cells, which also improves plant salt tolerance.

BackgroundStudies which focused on the character of miR-144-3p in hepatocellular carcinoma (HCC) are limited. This study aimed to explore the expression, clinical significance and the potential targets of miR-144-3p in HCC.MethodsThe Cancer Genome Atlas (TCGA) and a cohort of 95 cases of HCC were applied to investigate aberrant miR-144-3p expression in HCC. A meta-analysis was performed to accumulate data on miR-144-3p expression in HCC based on TCGA, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and Gene Expression Omnibus (GEO). Additionally, the potential regulatory mechanisms of miR-144-3p in HCC were explored by bioinformatics.ResultsMiR-144-3p expression was downregulated distinctly in HCC compared to para-HCC tissue both in TCGA data (8.9139±1.5986 vs 10.7721±0.9156, P<0.001) and in our qRT-PCR validation (1.3208±0.7594 vs 2.6200±0.9263, P<0.001). The meta-analysis based on TCGA, qRT-PCR and GEO data confirmed a consistent result (standard mean difference =−0.854, 95% CI: −1.224 to −0.484, P<0.001). The receiver operating characteristic curve of miR-144-3p gained a significant diagnostic value both in TCGA data (area under the curve [AUC] =0.852, 95% CI: 0.810 to 0.894, P<0.001) and in qRT-PCR validation (AUC =0.867, 95% CI: 0.817 to 0.916, P<0.001), especially in alpha-fetoprotein–negative HCC patients (AUC =0.900, 95% CI: 0.839 to 0.960, P<0.001). Furthermore, we identified 119 potential targets of miR-144-3p in HCC by bioinformatics. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that several significant biologic functions and pathways correlated with the pathogenesis of HCC, including the p53 signaling pathway.ConclusionMiR-144-3p may function as a cancer suppressor microRNA, which is essential for HCC progression through the regulation of various signaling pathways. Thus, interactions with miR-144-3p may provide a novel treatment strategy for HCC in the future.

BackgroundMiR-182-5p, as a member of miRNA family, can be detected in lung cancer and plays an important role in lung cancer. To explore the clinical value of miR-182-5p in lung squamous cell carcinoma (LUSC) and to unveil the molecular mechanism of LUSC.MethodsThe clinical value of miR-182-5p in LUSC was investigated by collecting and calculating data from The Cancer Genome Atlas (TCGA) database, the Gene Expression Omnibus (GEO) database, and real-time quantitative polymerase chain reaction (RT-qPCR). Twelve prediction platforms were used to predict the target genes of miR-182-5p. Protein-protein interaction (PPI) networks and gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used to explore the molecular mechanism of LUSC.ResultsThe expression of miR-182-5p was significantly over-expressed in LUSC than in non-cancerous tissues, as evidenced by various approaches, including the TCGA database, GEO microarrays, RT-qPCR, and a comprehensive meta-analysis of 501 LUSC cases and 148 non-cancerous cases. Furthermore, a total of 81 potential target genes were chosen from the union of predicted genes and the TCGA database. GO and KEGG analyses demonstrated that the target genes are involved in pathways related to biological processes. PPIs revealed the relationships between these genes, with EPAS1, PRKCE, NR3C1, and RHOB being located in the center of the PPI network.ConclusionsMiR-182-5p upregulation greatly contributes to LUSC and may serve as a biomarker in LUSC.