Genome‐wide mutations induced by ethyl methanesulfonate (EMS) and gamma irradiation in the tomato Micro‐Tom genome were identified by a whole‐genome shotgun sequencing analysis to estimate the ...spectrum and distribution of whole‐genome DNA mutations and the frequency of deleterious mutations. A total of ~370 Gb of paired‐end reads for four EMS‐induced mutants and three gamma‐ray‐irradiated lines as well as a wild‐type line were obtained by next‐generation sequencing technology. Using bioinformatics analyses, we identified 5920 induced single nucleotide variations and insertion/deletion (indel) mutations. The predominant mutations in the EMS mutants were C/G to T/A transitions, while in the gamma‐ray mutants, C/G to T/A transitions, A/T to T/A transversions, A/T to G/C transitions and deletion mutations were equally common. Biases in the base composition flanking mutations differed between the mutagenesis types. Regarding the effects of the mutations on gene function, >90% of the mutations were located in intergenic regions, and only 0.2% were deleterious. In addition, we detected 1 140 687 spontaneous single nucleotide polymorphisms and indel polymorphisms in wild‐type Micro‐Tom lines. We also found copy number variation, deletions and insertions of chromosomal segments in both the mutant and wild‐type lines. The results provide helpful information not only for mutation research, but also for mutant screening methodology with reverse‐genetic approaches.
The complex and coordinated regulation of flowering has high ecological and agricultural significance. The maturity locus E1 has a large impact on flowering time in soybean, but the molecular basis ...for the E1 locus is largely unknown. Through positional cloning, we delimited the E1 locus to a 17.4-kb region containing an intron-free gene ( E1 ). The E1 protein contains a putative bipartite nuclear localization signal and a region distantly related to B3 domain. In the recessive allele, a nonsynonymous substitution occurred in the putative nuclear localization signal, leading to the loss of localization specificity of the E1 protein and earlier flowering. The early-flowering phenotype was consistently observed in three ethylmethanesulfonate-induced mutants and two natural mutations that harbored a premature stop codon or a deletion of the entire E1 gene. E1 expression was significantly suppressed under short-day conditions and showed a bimodal diurnal pattern under long-day conditions, suggesting its response to photoperiod and its dominant effect induced by long day length. When a functional E1 gene was transformed into the early-flowering cultivar Kariyutaka with low E1 expression, transgenic plants carrying exogenous E1 displayed late flowering. Furthermore, the transcript abundance of E1 was negatively correlated with that of GmFT2a and GmFT5a , homologues of FLOWERING LOCUS T that promote flowering. These findings demonstrated the key role of E1 in repressing flowering and delaying maturity in soybean. The molecular identification of the maturity locus E1 will contribute to our understanding of the molecular mechanisms by which a short-day plant regulates flowering time and maturity.
Abstract
The draft genome sequence of a wild rose (Rosa multiflora Thunb.) was determined using Illumina MiSeq and HiSeq platforms. The total length of the scaffolds was 739,637,845 bp, consisting of ...83,189 scaffolds, which was close to the 711 Mbp length estimated by k-mer analysis. N50 length of the scaffolds was 90,830 bp, and extent of the longest was 1,133,259 bp. The average GC content of the scaffolds was 38.9%. After gene prediction, 67,380 candidates exhibiting sequence homology to known genes and domains were extracted, which included complete and partial gene structures. This large number of genes for a diploid plant may reflect heterogeneity of the genome originating from self-incompatibility in R. multiflora. According to CEGMA analysis, 91.9% and 98.0% of the core eukaryotic genes were completely and partially conserved in the scaffolds, respectively. Genes presumably involved in flower color, scent and flowering are assigned. The results of this study will serve as a valuable resource for fundamental and applied research in the rose, including breeding and phylogenetic study of cultivated roses.
Dynamic projection mapping is an interactive display technology, which is capable with multiplayers with naked eyes for augmented reality. However, the fixed and shallow depth-of-field of the ...projector optics limits its potential applications. In this work, a high-speed projection mapping method with a dynamic focal tracking technology based on a variable focus lens will be illustrated. The proposed system included a high-speed variable focus lens, a high-speed camera, and a high- speed projector, so that the depth and rotation information would be detected and then served as feedback to correct the focal length and update the projection information in real time. As a result, the information would be well-focused projected even on a 3D dynamic moving object. The response speed of the high-speed prototype could reach around 5 ms, and the dynamic projection range covered from 0.5 to 2.0 m.
Virtual reality (VR) and augmented reality (AR) are able to project virtual images to human eyes at a certain depth distance. This virtual image distance can be adjusted by controlling the diopter of ...the near-eye display. However, it is difficult to measure accurately and continuously since this virtual image distance spans a large range. In this work, we propose a method to accurately determine the virtual image distance of commercial VR/AR equipment. The measurement apparatus is built and calibrated to validate the feasibility. The focal distance of the focus-tunable lens can be automatically adjusted via a step motor by cooperating with the image sharpness analyzing program. Compared with other proposed methods, ours provides an effective means to achieve high accuracy, a wide and continuous testing range, and automatic evaluation of virtual image distance for compact near-eye displays.
Radish (Raphanus sativus L., n = 9) is one of the major vegetables in Asia. Since the genomes of Brassica and related species including radish underwent genome rearrangement, it is quite difficult to ...perform functional analysis based on the reported genomic sequence of Brassica rapa. Therefore, we performed genome sequencing of radish. Short reads of genomic sequences of 191.1 Gb were obtained by next-generation sequencing (NGS) for a radish inbred line, and 76,592 scaffolds of ≥ 300 bp were constructed along with the bacterial artificial chromosome-end sequences. Finally, the whole draft genomic sequence of 402 Mb spanning 75.9% of the estimated genomic size and containing 61,572 predicted genes was obtained. Subsequently, 221 single nucleotide polymorphism markers and 768 PCR-RFLP markers were used together with the 746 markers produced in our previous study for the construction of a linkage map. The map was combined further with another radish linkage map constructed mainly with expressed sequence tag-simple sequence repeat markers into a high-density integrated map of 1,166 cM with 2,553 DNA markers. A total of 1,345 scaffolds were assigned to the linkage map, spanning 116.0 Mb. Bulked PCR products amplified by 2,880 primer pairs were sequenced by NGS, and SNPs in eight inbred lines were identified.
Unlike other important Solanaceae crops such as tomato, potato, chili pepper, and tobacco, all of which originated in South America and are cultivated worldwide, eggplant (Solanum melongena L.) is ...indigenous to the Old World and in this respect it is phylogenetically unique. To broaden our knowledge of the genomic nature of solanaceous plants further, we dissected the eggplant genome and built a draft genome dataset with 33,873 scaffolds termed SME_r2.5.1 that covers 833.1 Mb, ca. 74% of the eggplant genome. Approximately 90% of the gene space was estimated to be covered by SME_r2.5.1 and 85,446 genes were predicted in the genome. Clustering analysis of the predicted genes of eggplant along with the genes of three other solanaceous plants as well as Arabidopsis thaliana revealed that, of the 35,000 clusters generated, 4,018 were exclusively composed of eggplant genes that would perhaps confer eggplant-specific traits. Between eggplant and tomato, 16,573 pairs of genes were deduced to be orthologous, and 9,489 eggplant scaffolds could be mapped onto the tomato genome. Furthermore, 56 conserved synteny blocks were identified between the two species. The detailed comparative analysis of the eggplant and tomato genomes will facilitate our understanding of the genomic architecture of solanaceous plants, which will contribute to cultivation and further utilization of these crops.
We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has ...undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.
In Batesian mimicry, animals avoid predation by resembling distasteful models. In the swallowtail butterfly Papilio polytes, only mimetic-form females resemble the unpalatable butterfly Pachliopta ...aristolochiae. A recent report showed that a single gene, doublesex (dsx), controls this mimicry; however, the detailed molecular mechanisms remain unclear. Here we determined two whole-genome sequences of P. polytes and a related species, Papilio xuthus, identifying a single ∼130-kb autosomal inversion, including dsx, between mimetic (H-type) and non-mimetic (h-type) chromosomes in P. polytes. This inversion is associated with the mimicry-related locus H, as identified by linkage mapping. Knockdown experiments demonstrated that female-specific dsx isoforms expressed from the inverted H allele (dsx(H)) induce mimetic coloration patterns and simultaneously repress non-mimetic patterns. In contrast, dsx(h) does not alter mimetic patterns. We propose that dsx(H) switches the coloration of predetermined wing patterns and that female-limited polymorphism is tightly maintained by chromosomal inversion.
The existing phase-shift methods are effective in achieving high-speed, high-precision, high-resolution, real-time shape measurement of moving objects; however, a phase-unwrapping method that can ...handle the motion of target objects in a real environment and is robust against global illumination as well is yet to be established. Accordingly, a robust and highly accurate method for determining the absolute phase, using a minimum of three steps, is proposed in this study. In this proposed method, an order structure that rearranges the projection pattern for each period of the sine wave is introduced, so that solving the phase unwrapping problem comes down to calculating the pattern order. Using simulation experiments, it has been confirmed that the proposed method can be used in high-speed, high-precision, high-resolution, three-dimensional shape measurements even in situations with high-speed moving objects and presence of global illumination. In this study, an experimental measurement system was configured with a high-speed camera and projector, and real-time measurements were performed with a processing time of 1.05 ms and a throughput of 500 fps.
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