LEUNIG regulates AGAMOUS expression in Arabidopsis flowers

LEUNIG was identified in a genetic screen designed to isolate second-site enhancer mutations of the floral homeotic mutant apetala2-1. leunig mutations not only enhance apetala2, but by themselves cause a similar but less-pronounced homeotic transformation than apetala2 mutations. leunig flowers have sepals that are transformed toward stamens and carpels, and petals that are either staminoid or absent. In situ hybridization experiments with leunig mutants revealed altered expression pattern of the floral homeotic genes APETALA1, APETALA3, PISTILLATA, and AGAMOUS. Double mutants of leunig and agamous exhibited a phenotype similar to agamous single mutants, indicating that agamous is epistatic to leunig. Our analysis suggests that a key role of LEUNIG is to negatively regulate AGAMOUS expression in the first two whorls of the Arabidopsis flower

Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development

Length distribution of small RNAs derived from lncRNAs. Figure S2. Characterization of strawberry lncRNAs. Figure S3. Heatmaps showing tissue-specific expression patterns of lncRNAs. Figure S4. Expression correlations between lncRNAs and the adjacent PC genes. Figure S5. Negative correlations of lncRNA expression with PC genes across the genome. (PDF 12315 kb

Simple allele-discriminating PCR for cost-effective and rapid genotyping and mapping

<p>Abstract</p> <p>Background</p> <p>Single nucleotide polymorphisms (SNPs) are widely observed between individuals, ecotypes, and species, serving as an invaluable molecular marker for genetic, genomic, ecological and evolutionary studies. Although, a large number of SNP-discriminating methods are currently available, few are suited for low-throughput and low-cost applications. Here, we describe a genotyping method named Simple Allele-discriminating PCR (SAP), which is ideally suited for the small-scale genotyping and gene mapping routinely performed in small to medium research or teaching laboratories.</p> <p>Results</p> <p>We demonstrate the feasibility and application of SAP to discriminate wild type alleles from their respective mutant alleles in <it>Arabidopsis thaliana</it>. Although the design principle was previously described, it is unclear if the method is technically robust, reliable, and applicable. Three primers were designed for each individual SNP or allele with two allele-discriminating forward primers (one for wild type and one for the mutant allele) and a common reverse primer. The two allele-discriminating forward primers are designed so that each incorporates one additional mismatch at the adjacent (penultimate) site from the SNP, resulting in two mismatches between the primer and its non-target template and one mismatch between the primer and its target template. The presence or absence of the wild type or the mutant allele correlates with the presence or absence of respective PCR product. The presence of both wild type-specific and mutant-specific PCR products would indicate heterozygosity. SAP is shown here to discriminate three mutant alleles (<it>lug-3</it>, <it>lug-16</it>, and <it>luh-1</it>) from their respective wild type alleles. In addition, the SAP principle is shown to work in conjunction with fluorophore-labeled primers, demonstrating the feasibility of applying SAP to high throughput SNP analyses.</p> <p>Conclusion</p> <p>SAP offers an excellent alternative to existing SNP-discrimination methods such as Cleaved Amplified Polymorphic Sequence (CAPS) or derived CAPS (dCAPS). It can also be adapted for high throughput SNP analyses by incorporating fluorophore-labeled primers. SAP is reliable, cost-effective, fast, and simple, and can be applied to all organisms not limited to <it>Arabidopsis thaliana</it>.</p

TSO1 functions in cell division during Arabidopsis flower development

We describe an Arabidopsis mutant, tso1, which develops callus-like tissues in place of floral organs. The tso1 floral meristem lacks properly organized three cell layers, and the nuclei of these cells are irregular in size and shape. Further analyses reveal partially formed cell walls and increased DNA ploidy in tso1 floral meristem cells, indicating defects in mitosis and cytokinesis. Our finding that TSO1 is required for organ formation in floral tissues but not in other tissues indicates that TSO1 may encode a floral-specific cell division component, or that TSO1 function is redundant in nonfloral tissues

Pyrite cloning: a single tube and programmed reaction cloning with restriction enzymes

Insertion of engineered DNA fragments into bacterial vectors is the foundation of recombinant DNA technology, yet existing methods are still laborious, require many steps, depend on specific vector configuration, or require expensive reagents. We have developed a method, called “Pyrite” cloning that combines the traditional restriction enzyme digestion and ligation reaction in a single tube and uses a programmed thermocycler reaction, allowing rapid and flexible cloning in a single tube. After the Pyrite reaction and transformation, approximately 50% colonies contain the expected insert, which can be easily and quickly determined by colony PCR or blue-white colony screening. We also demonstrated that Pyrite cloning can be applied for different cloning purposes. The Pyrite cloning method reported here is a single tube and programmed reaction cloning with restriction enzymes. Compared to other cloning methods, Pyrite cloning is flexible, inexpensive, simple, and highly efficient.https://doi.org/10.1186/s13007-018-0359-

Re-annotation of the woodland strawberry (Fragaria vesca) genome

Fragaria vesca is a low-growing, small-fruited diploid strawberry species commonly called woodland strawberry. It is native to temperate regions of Eurasia and North America and while it produces edible fruits, it is most highly useful as an experimental perennial plant system that can serve as a model for the agriculturally important Rosaceae family. A draft of the F. vesca genome sequence was published in 2011 [Nat Genet 43:223,2011]. The first generation annotation (version 1.1) were developed using GeneMark-ES+[Nuc Acids Res 33:6494,2005]which is a self-training gene prediction tool that relies primarily on the combination of ab initio predictions with mapping high confidence ESTs in addition to mapping gene deserts from transposable elements. Based on over 25 different tissue transcriptomes, we have revised the F. vesca genome annotation, thereby providing several improvements over version 1.1. The new annotation, which was achieved using Maker, describes many more predicted protein coding genes compared to the GeneMark generated annotation that is currently hosted at the Genome Database for Rosaceae (http://www.rosaceae.org/). Our new annotation also results in an increase in the overall total coding length, and the number of coding regions found. The total number of gene predictions that do not overlap with the previous annotations is 2286, most of which were found to be homologous to other plant genes. We have experimentally verified one of the new gene model predictions to validate our results. Using the RNA-Seq transcriptome sequences from 25 diverse tissue types, the re-annotation pipeline improved existing annotations by increasing the annotation accuracy based on extensive transcriptome data. It uncovered new genes, added exons to current genes, and extended or merged exons. This complete genome re-annotation will significantly benefit functional genomic studies of the strawberry and other members of the Rosaceae.https://doi.org/10.1186/s12864-015-1221-

Calibrating the absorption imaging of cold atoms under high magnetic fields

We develop a theoretical model for calibrating the absorption imaging of cold atoms under high magnetic fields. Comparing to zero or low magnetic fields, the efficiency of the absorption imaging becomes lower while it requires an additional correction factor to obtain the absolute atom number under the Beer-Lambert law. Our model is based on the rate equations and can account many experimental imperfections such as Zeeman level crossing, failures of hyperfine structures, off-resonant couplings, and low repumping efficiency, etc. Based on this method, we can precisely calculate the correction factor for atom number measurement without any empirical or fitting parameters. Meanwhile, we use a cold-atom apparatus of rubidium-85 to experimentally verify our model. Besides these, we find our work can also serve as a benchmark to measure the polarization impurity of a circular-polarized laser beam with high sensitivities. We believe this work will bring convenience for most of cold-atom experiments using absorption imaging.Comment: 9 pages, 5 figure

Distinct double flower varieties in Camellia japonica exhibit both expansion and contraction of C-class gene expression

Double flower domestication is of great value in ornamental plants and presents an excellent system to study the mechanism of morphological alterations by human selection. The classic ABC model provides a genetic framework underlying the control of floral organ identity and organogenesis from which key regulators have been identified and evaluated in many plant species. Recent molecular studies have underscored the importance of C-class homeotic genes, whose functional attenuation contributed to the floral diversity in various species. Cultivated Camellia japonica L. possesses several types of double flowers, however the molecular mechanism underlying their floral morphological diversification remains unclear. In this study, we cloned the C-class orthologous gene CjAG in C. japonica. We analyzed the expression patterns of CjAG in wild C. japonica, and performed ectopic expression in Arabidopsis. These results revealed that CjAG shared conserved C-class function that controls stamen and carpel development. Further we analyzed the expression pattern of CjAG in two different C. japonica double-flower varieties, `Shibaxueshi’ and `Jinpanlizhi’, and showed that expression of CjAG was highly contracted in `Shibaxueshi’ but expanded in inner petals of `Jinpanlizhi’. Moreover, detailed expression analyses of B- and C-class genes have uncovered differential patterns of B-class genes in the inner organs of `Jinpanlizhi’. These results demonstrated that the contraction and expansion of CjAG expression were associated with the formation of different types of double flowers. Our studies have manifested two different trajectories of double flower domestication regarding the C-class gene expression in C. japonica.https://doi.org/10.1186/s12870-014-0288-

Independent mutations in a single locus, the transcriptional factor MYB10, control natural variation in fruit color among Fragaria species

External and internal fruit color are important traits in strawberry (Fragaria spp.) breeding programs, where different preferences are sought depending on whether the fruits are produced for fresh consumption or processing. Therefore, there is a great interest in the development of predictive markers that effectively speed the development of new cultivars with increased consumer acceptance and/or which address processed fruit industry´s preferences. In order to identify loci controlling fruit color variation, two mapping populations were generated: one crossing diploid F. vesca parentals and another interspecific population between two octoploid species: the cultivated and the Chilean strawberry, F. x ananassa and F. chiloensis. Both populations allowed the detection of a QTL spanning a region of the F. vesca linkage group 1 (LG I) that includes the MYB10 gene, a known key regulator of anthocyanin biosynthesis. Mapping by sequencing in the F. vesca population revealed an LTR retrotransposon inserted in the third exon of FvMYB10, which produces a premature stop codon, and co-segregates with white fruits in the entire population. Genotyping by Sanger sequencing of additional white-fruited F. vesca accessions resulted in the identification of another three independent mutations in MYB10, two of them not previously described1. In octoploid strawberry, a mayor QTL on LG I-3 controls about 55% variation in internal flesh color and is associated with an insertion in the promoter region of FcMYB10. Similar insertions have been detected in other F. chiloensis accessions bearing white fruits. In all cases, transient over-expression of FvMYB10 restored anthocyanin biosynthesis and red color in fruit flesh and skin, indicating that lack of function of MYB10 was the underlying cause of white fruits in all analyzed cases