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, highlighting regions vulnerable to genetic erosion. The International Barley Genome Sequencing Consortium reports sequencing and assembly of a reference genome for barley, Hordeum vulgare. Triticeae grasses, which include barley, wheat and rye, are widely cultivated plants with particularly complex genomes and evolutionary histories. Sequencing of the barley genome has been particularly challenging owing to its large size and particular genomic features, such as an abundance of repetitive elements. Nils Stein and colleagues of the International Barley Genome Sequencing Consortium report sequencing and assembly of a reference genome for barley (Hordeumvulgare L). They use a combined approach of hierarchical shotgun sequencing of bacterial artificial chromosomes, genome mapping on nanochannel arrays and chromosome-scale scaffolding with Hi-C sequencing. This brings the first comprehensive, completely ordered assembly of the pericentromeric regions of a Triticeae genome. The authors also sequenced and examined genetic diversity in the exomes of 96 European elite barley lines with a spring or winter growth habit, and highlight the utility of this resource for cereal genomics and breeding programs.
With 5 figures and 5 tables Abstract The phenomenon of degenerated spikelets is very common in cereal crops, and considered as a serious physiological defect to grain production. However, little is known about the genetic base of the spikelet degeneration in rice. To identify genetic factors conferring spikelet degeneration in rice, a line showing severe degenerated spikelets on the top of panicle was selected from a set of chromosomal segment substitution lines that derived from a cross of the sequenced japonica variety ‘Nipponbare’ and the indica variety ‘9311’. Using its derived progeny, two quantitative trait loci (QTL) for the degenerated spikelets were identified on chromosomes 3 and 9. The one on chromosome 3 was confirmed in an about 600‐kb physical interval, and had an epistatic interaction with the other QTL on chromosome 9. The QTL region on chromosome 3 was also found conferring primary panicle length, heading date, the number of primary branches and second branches simultaneously. These results would be helpful in understanding the genetic control of spikelet degeneration on the top of panicle in rice.
Genotyping of sequence-defined SNP markers and InDel markers from the genetic linkage map [38] on 10 commercial cultivars through genome sequencing and re-sequencing in Lupinus angustifolius. (XLSX 475 kb)
Abstract The red swamp crayfish, Procambarus clarkii (Girard, 1852), is currently an economically important aquaculture animal. Its genetic basis has been scarcely reported, however, partly due to the absence of abundant molecular markers in the genome. In this study, Simple Sequence Repeat (SSR) loci were mined, based on genome survey sequencing via the next generation sequence of the red swamp crayfish. A total of 4897 SSR loci were identified, with the most abundant type being the di-nucleotide repeat motifs (75.2%), followed by tri- (20.4%), tetra- (3.8%), penta- (0.5%), and hexanucleotide (0.2%) repeats. In total, 1546 SSR markers were validated to be amplified, and 721 of these were identified as polymorphic SSR markers. Fifty polymorphic SSR markers were randomly selected for the identification of the genetic diversity of the 14 red swamp crayfish populations in China. The expected and observed heterozygosity and polymorphism information content were 0.39, 0.30, and 0.29, respectively, on average. The results indicated a medium genetic diversity among the 14 investigated populations. These probably cluster into three genetic populations. The current study provides abundant genetic markers and information on the 14 populations, which can be helpful for genetic diversity estimation and molecular breeding of the red swamp crayfish.
Heterotrimeric Heme Activator Protein (HAP) family genes are involved in the regulation of flowering in plants. It is not clear how many HAP genes regulate heading date in rice. In this study, we identified 35 HAP genes, including seven newly identified genes, and performed gene duplication and candidate gene-based association analyses. Analyses showed that segmental duplication and tandem duplication are the main mechanisms of HAP gene duplication. Expression profiling and functional identification indicated that duplication probably diversifies the functions of HAP genes. A nucleotide diversity analysis revealed that 13 HAP genes underwent selection. A candidate gene-based association analysis detected four HAP genes related to heading date. An investigation of transgenic plants or mutants of 23 HAP genes confirmed that overexpression of at least four genes delayed heading date under long-day conditions, including the previously cloned Ghd8/OsHAP3H. Our results indicate that the large number of HAP genes in rice was mainly produced by gene duplication, and a few HAP genes function to regulate heading date. Selection of HAP genes is probably caused by their diverse functions rather than regulation of heading.
Viral infectious diseases are a devastating and continuing threat to human and animal health. Receptor binding is the key step for viral entry into host cells. Therefore, recognizing viral receptors is fundamental for understanding the potential tissue tropism or host range of these pathogens. The rapid advancement of single-cell RNA sequencing (scRNA-seq) technology has paved the way for studying the expression of viral receptors in different tissues of animal species at single-cell resolution, resulting in huge scRNA-seq datasets. However, effectively integrating or sharing these datasets among the research community is challenging, especially for laboratory scientists. In this study, we manually curated up-to-date datasets generated in animal scRNA-seq studies, analyzed them using a unified processing pipeline, and comprehensively annotated 107 viral receptors in 142 viruses and obtained accurate expression signatures in 2 100 962 cells from 47 animal species. Thus, the VThunter database provides a user-friendly interface for the research community to explore the expression signatures of viral receptors. VThunter offers an informative and convenient resource for scientists to better understand the interactions between viral receptors and animal viruses and to assess viral pathogenesis and transmission in species. Database URL: https://db.cngb.org/VThunter/.
Barley occupies the widest ecological area among the major cereal crops, thereby generating a high potential for adaptive genetic diversity against various environmental factors. Colored barley such as black grain barley has been suggested to result from environmental adaptation to biotic and abiotic stresses. Using one double haploid population (433 lines), plus three F5 recombinant inbred line (RIL) populations (1,009 lines), the black lemma and pericarp (Blp) gene was mapped between two Insertion/deletion (Indel) markers MC_1570156 and MC_162350 with a physical distance of 0.807 Mb, containing 21 annotated genes in the mapped interval. Whole-genome re-sequencing was performed on two Tibetan wild barley lines (X1 and W1) with black grain phenotype. The probable candidate genes for Blp were discussed based on gene functional annotation and gene sequence variation analyses. Thirteen polymorphic Indel markers covering the target genetic region were used to analyze 178 barley accessions including 49 black husk entries. Genotype-based clustering analyses showed that the black landraces of different geographical background may have evolved from a single origin. Our study represents a significant improvement on the genetic mapping of Blp and would facilitate future study on the characterization of the genetic basis underlying this interesting agronomic trait.
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