High-performance Ge/Si electro-absorption optical modulator up to 85°C and its highly efficient photodetector operation.

We studied a high-speed Ge/Si electro-absorption optical modulator (EAM) evanescently coupled with a Si waveguide of a lateral p-n junction for a high-bandwidth optical interconnect over a wide range of temperatures from 25 °C to 85 °C. We demonstrated 56 Gbps high-speed operation at temperatures up to 85 °C. From the photoluminescence spectra, we confirmed that the bandgap energy dependence on temperature is relatively small, which is consistent with the shift in the operation wavelengths with increasing temperature for a Ge/Si EAM. We also demonstrated that the same device operates as a high-speed and high-efficiency Ge photodetector with the Franz-Keldysh (F-K) and avalanche-multiplication effects. These results demonstrate that the Ge/Si stacked structure is promising for both high-performance optical modulators and photodetectors integrated on Si platforms.

Genome analyses reveal the hybrid origin of the staple crop white Guinea yam (Dioscorea rotundata).

White Guinea yam (Dioscorea rotundata) is an important staple tuber crop in West Africa. However, its origin remains unclear. In this study, we resequenced 336 accessions of white Guinea yam and compared them with the sequences of wild Dioscorea species using an improved reference genome sequence of D. rotundata In contrast to a previous study suggesting that D. rotundata originated from a subgroup of Dioscorea praehensilis, our results suggest a hybrid origin of white Guinea yam from crosses between the wild rainforest species D. praehensilis and the savannah-adapted species Dioscorea abyssinica We identified a greater genomic contribution from D. abyssinica in the sex chromosome of Guinea yam and extensive introgression around the SWEETIE gene. Our findings point to a complex domestication scenario for Guinea yam and highlight the importance of wild species as gene donors for improving this crop through molecular breeding.

Multimode-based polarization independent WDM devices using different order modes for TE and TM polarizations.

Multimode based polarization independent (PI) wavelength division multiplexing (WDM) devices are proposed and experimentally demonstrated. The key concept is to utilize two different order modes for the orthogonal polarizations, ith-order mode for TE and jth-order mode for TM (i ≠ j) polarization respectively to extend the flexibility for designing devices. PI coupler composed of a multimode directional coupler and mode converters is introduced as a basic device. Then, we apply PI coupler to Mach Zehnder interferometer (MZI) and Bragg grating bandpass filters. PI MZI is achieved by optimizing the combination of two phase shifters in the interferometer arms. PI bandpass uses 3dB-PI coupler and polarization rotate Bragg gratings that induce mode coupling between the polarizations. Each device showed good matching in the spectrum between TE and TM polarizations in term of operation wavelength. The proposed concept can be a promising approach to realize PI WDM functions without introducing polarization diversity scheme in which a polarization beam splitter, two devices designed for each polarization and a polarization beam combiner are required.

High-speed Ge/Si electro-absorption optical modulator in C-band operation wavelengths.

We studied a high-speed electro-absorption optical modulator (EAM) of a Ge layer evanescently coupled with a Si waveguide (Si WG) of a lateral pn junction for high-bandwidth optical interconnect. By decreasing the widths of selectively grown Ge layers below 1 µm, we demonstrated a high-speed modulation of 56 Gbps non-return-to-zero (NRZ) and 56 Gbaud pulse amplitude modulation 4 (PAM4) EAM operation in the C-band wavelengths, in contrast to the L-band wavelengths operations in previous studies on EAMs of pure Ge on Si. From the photoluminescence and Raman analyses, we confirmed an increase in the direct bandgap energy for such a submicron Ge/Si stack structure. The operation wavelength for the Ge/Si stack structure of a Ge/Si EAM was optimized by decreasing the device width below 1-µm and setting the post-growth anneal condition, which would contribute to relaxing the tensile-strain of a Ge layer on a Si WG and broadening the optical bandwidths for Franz-Keldysh (FK) effect with SiGe alloy formation.

45-degree curved micro-mirror for vertical optical I/O of silicon photonics chip.

The broadband vertical optical inputs/outputs (I/Os) of silicon (Si) photonics pose significant challenges in terms of practical applications. Herein, we worked on a vertical optical I/O using a 45° curved micro-mirror. To verify the optical coupling characteristics, a simulation was conducted. As a result, efficient broadband optical coupling with various types of single-mode optical fibers was obtained owing to its lens function. An integration technology of the curved mirror was also developed based on the semiconductor manufacturing process. A curved micro-mirror with a spherical surface was obtained, and the vertical optical I/O with its lens function was demonstrated experimentally.

Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination.

BACKGROUND: Root and tuber crops are a major food source in tropical Africa. Among these crops are several species in the monocotyledonous genus Dioscorea collectively known as yam, a staple tuber crop that contributes enormously to the subsistence and socio-cultural lives of millions of people, principally in West and Central Africa. Yam cultivation is constrained by several factors, and yam can be considered a neglected "orphan" crop that would benefit from crop improvement efforts. However, the lack of genetic and genomic tools has impeded the improvement of this staple crop. RESULTS: To accelerate marker-assisted breeding of yam, we performed genome analysis of white Guinea yam (Dioscorea rotundata) and assembled a 594-Mb genome, 76.4% of which was distributed among 21 linkage groups. In total, we predicted 26,198 genes. Phylogenetic analyses with 2381 conserved genes revealed that Dioscorea is a unique lineage of monocotyledons distinct from the Poales (rice), Arecales (palm), and Zingiberales (banana). The entire Dioscorea genus is characterized by the occurrence of separate male and female plants (dioecy), a feature that has limited efficient yam breeding. To infer the genetics of sex determination, we performed whole-genome resequencing of bulked segregants (quantitative trait locus sequencing [QTL-seq]) in F1 progeny segregating for male and female plants and identified a genomic region associated with female heterogametic (male = ZZ, female = ZW) sex determination. We further delineated the W locus and used it to develop a molecular marker for sex identification of Guinea yam plants at the seedling stage. CONCLUSIONS: Guinea yam belongs to a unique and highly differentiated clade of monocotyledons. The genome analyses and sex-linked marker development performed in this study should greatly accelerate marker-assisted breeding of Guinea yam. In addition, our QTL-seq approach can be utilized in genetic studies of other outcrossing crops and organisms with highly heterozygous genomes. Genomic analysis of orphan crops such as yam promotes efforts to improve food security and the sustainability of tropical agriculture.

Genome analysis of the foxtail millet pathogen Sclerospora graminicola reveals the complex effector repertoire of graminicolous downy mildews.

BACKGROUND: Downy mildew, caused by the oomycete pathogen Sclerospora graminicola, is an economically important disease of Gramineae crops including foxtail millet (Setaria italica). Plants infected with S. graminicola are generally stunted and often undergo a transformation of flower organs into leaves (phyllody or witches' broom), resulting in serious yield loss. To establish the molecular basis of downy mildew disease in foxtail millet, we carried out whole-genome sequencing and an RNA-seq analysis of S. graminicola. RESULTS: Sequence reads were generated from S. graminicola using an Illumina sequencing platform and assembled de novo into a draft genome sequence comprising approximately 360 Mbp. Of this sequence, 73% comprised repetitive elements, and a total of 16,736 genes were predicted from the RNA-seq data. The predicted genes included those encoding effector-like proteins with high sequence similarity to those previously identified in other oomycete pathogens. Genes encoding jacalin-like lectin-domain-containing secreted proteins were enriched in S. graminicola compared to other oomycetes. Of a total of 1220 genes encoding putative secreted proteins, 91 significantly changed their expression levels during the infection of plant tissues compared to the sporangia and zoospore stages of the S. graminicola lifecycle. CONCLUSIONS: We established the draft genome sequence of a downy mildew pathogen that infects Gramineae plants. Based on this sequence and our transcriptome analysis, we generated a catalog of in planta-induced candidate effector genes, providing a solid foundation from which to identify the effectors causing phyllody.

Inducible Transposition of a Heat-Activated Retrotransposon in Tissue Culture.

A transposition of a heat-activated retrotransposon named ONSEN required compromise of a small RNA-mediated epigenetic regulation that includes RNA-directed DNA methylation (RdDM) machinery after heat treatment. In the current study, we analyzed the transcriptional and transpositional activation of ONSEN to better understand the underlying molecular mechanism involved in the maintenance and/or induction of transposon activation in plant tissue culture. We found the transposition of heat-primed ONSEN during tissue culture independently of RdDM mutation. The heat activation of ONSEN transcripts was not significantly up-regulated in tissue culture compared with that in heat-stressed seedlings, indicating that the transposition of ONSEN was regulated independently of the transcript level. RdDM-related genes were up-regulated by heat stress in both tissue culture and seedlings. The level of DNA methylation of ONSEN did not show any change in tissue culture, and the amount of ONSEN-derived small RNAs was not affected by heat stress. The results indicated that the transposition of ONSEN was regulated by an alternative mechanism in addition to the RdDM-mediated epigenetic regulation in tissue culture. We applied the tissue culture-induced transposition of ONSEN to Japanese radish, an important breeding species of the family Brassicaceae. Several new insertions were detected in a regenerated plant derived from heat-stressed tissues and its self-fertilized progeny, revealing the possibility of molecular breeding without genetic modification.

Screening of rice mutants with improved saccharification efficiency results in the identification of CONSTITUTIVE PHOTOMORPHOGENIC 1 and GOLD HULL AND INTERNODE 1.

MAIN CONCLUSION: The screening of rice mutants with improved cellulose to glucose saccharification efficiency (SE) identifies reduced xylan and/or ferulic acid, and a qualitative change of lignin to impact SE. To ensure the availability of sustainable energy, considerable effort is underway to utilize lignocellulosic plant biomass as feedstock for the production of biofuels. However, the high cost of degrading plant cell wall components to fermentable sugars (saccharification) has been problematic. One way to overcome this barrier is to develop plants possessing cell walls that are amenable to saccharification. In this study, we aimed to identify new molecular factors that influence saccharification efficiency (SE) in rice. By screening 22 rice mutants, we identified two lines, 122 and 108, with improved SE. Reduced xylan and ferulic acid within the cell wall of line 122 were probable reasons of improved SE. Line 108 showed reduced levels of thioglycolic-released lignin; however, the amount of Klason lignin was comparable to the wild-type, indicating that structural changes had occurred in the 108 lignin polymer which resulted in improved SE. Positional cloning revealed that the genes responsible for improved SE in 122 and 108 were rice CONSTITUTIVE PHOTOMORPHOGENIC 1 (OsCOP1) and GOLD HULL AND INTERNODE 1 (GH1), respectively, which have not been previously reported to influence SE. The screening of mutants for improved SE is an efficient approach to identify novel genes that affect SE, which is relevant in the development of crops as biofuel sources.

Silicon wire waveguide TE0/TE1 mode conversion Bragg grating with resonant cavity section.

Silicon wire waveguide TE0/TE1 mode conversion Bragg grating can be used in wavelength add/drop and polarization rotation Bragg diffraction. The device can implement many filtering functionalities required in wavelength division multiplexing optical communications. In this paper we describe TE0/TE1 mode conversion Bragg grating device incorporating resonant cavity section to obtain narrow transmission wavelength peak. Theoretical calculation agreed with measured wavelength response.