Xuan Yi

We have determined the complete chloroplast (cp) genome sequence of Cephalotaxus oliveri. The genome is 134,337 bp in length, encodes 113 genes, and lacks inverted repeat (IR) regions. Genome-wide mutational dynamics have been investigated through comparative analysis of the cp genomes of C. oliveri and C. wilsoniana. Gene order transformation analyses indicate that when distinct isomers are considered as alternative structures for the ancestral cp genome of cupressophyte and Pinaceae lineages, it is not possible to distinguish between hypotheses favoring retention of the same IR region in cupressophyte and Pinaceae cp genomes from a hypothesis proposing independent loss of IRA and IRB. Furthermore, in cupressophyte cp genomes, the highly reduced IRs are replaced by short repeats that have the potential to mediate homologous recombination, analogous to the situation in Pinaceae. The importance of repeats in the mutational dynamics of cupressophyte cp genomes is also illustrated by the accD reading frame, which has undergone extreme length expansion in cupressophytes. This has been caused by a large insertion comprising multiple repeat sequences. Overall, we find that the distribution of repeats, indels, and substitutions is significantly correlated in Cephalotaxus cp genomes, consistent with a hypothesis that repeats play a role in inducing substitutions and indels in conifer cp genomes.

BACKGROUND: Ferns have generally been neglected in studies of chloroplast genomics. Before this study, only one polypod and two basal ferns had their complete chloroplast (cp) genome reported. Tree ferns represent an ancient fern lineage that first occurred in the Late Triassic. In recent phylogenetic analyses, tree ferns were shown to be the sister group of polypods, the most diverse group of living ferns. Availability of cp genome sequence from a tree fern will facilitate interpretation of the evolutionary changes of fern cp genomes. Here we have sequenced the complete cp genome of a scaly tree fern Alsophila spinulosa (Cyatheaceae). RESULTS: The Alsophila cp genome is 156,661 base pairs (bp) in size, and has a typical quadripartite structure with the large (LSC, 86,308 bp) and small single copy (SSC, 21,623 bp) regions separated by two copies of an inverted repeat (IRs, 24,365 bp each). This genome contains 117 different genes encoding 85 proteins, 4 rRNAs and 28 tRNAs. Pseudogenes of ycf66 and trnT-UGU are also detected in this genome. A unique trnR-UCG gene (derived from trnR-CCG) is found between rbcL and accD. The Alsophila cp genome shares some unusual characteristics with the previously sequenced cp genome of the polypod fern Adiantum capillus-veneris, including the absence of 5 tRNA genes that exist in most other cp genomes. The genome shows a high degree of synteny with that of Adiantum, but differs considerably from two basal ferns (Angiopteris evecta and Psilotum nudum). At one endpoint of an ancient inversion we detected a highly repeated 565-bp-region that is absent from the Adiantum cp genome. An additional minor inversion of the trnD-GUC, which is possibly shared by all ferns, was identified by comparison between the fern and other land plant cp genomes. CONCLUSION: By comparing four fern cp genome sequences it was confirmed that two major rearrangements distinguish higher leptosporangiate ferns from basal fern lineages. The Alsophila cp genome is very similar to that of the polypod fern Adiantum in terms of gene content, gene order and GC content. However, there exist some striking differences between them: the trnR-UCG gene represents a putative molecular apomorphy of tree ferns; and the repeats observed at one inversion endpoint may be a vestige of some unknown rearrangement(s). This work provided fresh insights into the fern cp genome evolution as well as useful data for future phylogenetic studies.

A novel cuboid quadrifilar helical antenna (QHA) with polarization and pattern reconfigurabilities is presented. The proposed antenna consists of a reconfigurable radiator and a switchable feeding network. The radiator combines two individual QHAs in a cuboid, which can be alternatively activated. The feeding network provides switchable quadrature excitations to the radiator. By controlling the p-i-n diodes on the radiator and the feeding network, four working states including both polarization and pattern agilities are achieved. The polarization of the antenna can be switched between two orthogonal circular polarizations, and the radiation pattern can be changed between broadside and backfire modes. A prototype designed to operate at 0.9 GHz band is developed and measured. The measured results validated that the antenna achieved the four working states with stable wide-beam radiation patterns. Moreover, the proposed antenna obtained wide impedance and axial-ratio bandwidths (36.2% and 22%, respectively) in a compact size (0.26λ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> × 0.26λ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> × 0.25λ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> ). The proposed antenna which has attractive electrical characteristics can be applied to various wireless communications, e.g., RFID readers, subway, and railway communications.

We demonstrate an eight-channel reconfigurable optical filter on a silicon chip. It consists of cascaded microring resonators and integrated compact heaters. With an embedded Mach-Zehnder (MZ) arm coupling to a microring resonator, the important parameters of a filter such as center frequency, extinction ratio and bandwidth can be controlled simultaneously for purposes of filtering, routing and spectral shaping. Thus our device could potentially be useful in dense wavelength division multiplexing (DWDM) and radio frequency arbitrary waveform generation (RFAWG). Multichannel filter response was successfully tuned to match the International Telecommunication Unit (ITU) grid with 50, 100 and 200 GHz in channel spacing. Programmable channel selectivity was demonstrated by heating the MZ arm, and continuous adjustment of through-port extinction ratio from 0 dB to 27 dB was achieved. Meanwhile, the 3 dB bandwidth in the drop port changed from 0.12 nm to 0.16 nm. The device had an ultra-compact footprint (1200 microm x 100 microm) excluding the metal leads and contact pads, making it suitable for large scale integration.