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The signal-to-noise ratio (SNR) of fiber-optic distributed acoustic sensing (DAS) systems based on Rayleigh backscattered (RBS) signals can be improved using point-backscattering-enhanced fiber (PBSEF). It is necessary to explore the methods to achieve stable and low noise demodulation for PBSEF-based DAS system. Driven by this, this work theoretically analyzes the effect of the phase and intensity noises on the PBSEF-based demodulated signal during averaging process. The results show that the phase noise has a weaker impact on the demodulated phase than the intensity noise. Based on this analysis, two methods, direct averaging and weighted averaging, for suppressing the noise level of DAS have been investigated and the optimal parameters are investigated. For both methods, simulation and experiments show the noise level suppression of 1.5 and 4.4 times, corresponding to the noise level reduction of 0.45 and 3.78 $\text{p}\varepsilon /\surd $ Hz, respectively. The relationship between the system noise level and the number of sampling points used in the demodulation is different for the two methods. The weighted-averaging method demonstrates superior performance for its higher stability. These conclusions provide significant theoretical basis and guidance for the development of practical high-performance DAS systems for field applications.

The measurement of acoustic signals at high frequencies with a large dynamic range remains a challenge for phase-demodulation-based fiber acoustic sensing systems due to the phase wrapping phenomenon. Here, an optical path difference (OPD)-assisted demodulation method aiming at breaking the limitations of phase demodulation is reported. By interrogating an imbalanced Michelson interferometer (IMI) with a frequency-modulated pulse light, a time-resolved interference spectrum is obtained and used for OPD demodulation. Theoretical analysis reveals that the variation amplitude of demodulated OPD signal not only is linearly dependent on the amplitude of the acoustic signal applied to the IMI, but also experiences a gain that is directly proportional to the signal frequency. Consequently, compensation of this gain introduces a noise suppression that favors high-frequency signals, resulting in a higher signal-to-noise ratio (SNR) at high frequencies. The method's capability for detecting both single-frequency and multi-frequency acoustic signals is demonstrated by simulations and experiments, and the results show that the upper-frequency limit of the proposed scheme is at least 40 times the limit of the phase demodulation method for an acoustic signal with an amplitude of 1.135 μϵ. The proposed method can be easily extended to distributed acoustic sensing systems and is of great potential to break the limitation of a restricted dynamic range encountered in traditional phase demodulation methods.

This article reports a multi-point curvature sensor system based on multiplexed optical fiber Fabry-Perot interferometric (FPI) sensor devices and a microwave photonics interrogation technique. The FPI sensor is fabricated with the assistance of a capillary tube, where a short section of the capillary is sandwiched between two single-mode fibers, forming the air-gap Fabry-Perot cavity. Bending of the FPI device leads to changes in the fringe contrast of its reflection spectrum. Based on the microwave photonics filtering technique, variations of the fringe contrast are encoded into the changes in the peak magnitude of the passband in the frequency response of the FPI device. By multiplexing such FPI devices with different cavity lengths, multi-point measurements of curvature can be realized by tracking changes in corresponding passbands in the frequency response of the system. The FPI curvature sensor is easy-to-manufacture and cost-effective, and the microwave photonics-based system provides an alternative and robust solution to interrogating the multiplexed FPI sensors for multi-point curvature sensing that could be desired in structural health monitoring, human-machine interface sensing, and other related fields.

Vibration sensing is vital in the health monitoring of critical structures such as aerospace engines. Although there are many mature vibration techniques in the market, there is still a lack of simple sensors suitable for high temperatures with a wide frequency range. In this article, we proposed a chirped pulse interferometer (CPI) empowered by a pair of gold-coated optical fiber partial reflectors. Information of the vibration is obtained by demodulating the phase change of the interference fringes from the reflection of the reflector pair. Both simulation and experimental results show that the CPI is reliable in detecting vibrations from 1 Hz to 30 kHz, with an operating temperature of up to 600 °C. Furthermore, the CPI was compared to a commercial accelerometer and a high-precision fiber Bragg grating (FBG) interrogator in the same testing environment. The results show that the difference in frequency response between CPI and the accelerometer is less than 1%, and the signal-to-noise ratio (SNR) of the signal detected by CPI is higher than that of the interrogator by more than 14 dB. The novel vibration detection system provides a sensitive and cost-effective vibration detection scheme with a wide frequency range, even at high temperatures. The simple structure makes it an attractive option for various applications.

Hybrid maize displays superior heterosis and contributes over 30% of total worldwide cereal production. However, the molecular mechanisms of heterosis remain obscure. Here we show that structural variants (SVs) between the parental lines have a predominant role underpinning maize heterosis. De novo assembly and analyses of 12 maize founder inbred lines (FILs) reveal abundant genetic variations among these FILs and, through expression quantitative trait loci and association analyses, we identify several SVs contributing to genomic and phenotypic differentiations of various heterotic groups. Using a set of 91 diallel-cross F1hybrids, we found strong positive correlations between better-parent heterosis of the F1hybrids and the numbers of SVs between the parental lines, providing concrete genomic support for a prevalent role of genetic complementation underlying heterosis. Further, we document evidence that SVs in both ZAR1and ZmACO2contribute to yield heterosis in an overdominance fashion. Our results should promote genomics-based breeding of hybrid maize.

Bivalvesare species-rich mollusks with prominent protective roles in coastal ecosystems. Across these ancient lineages, colony-founding larvae anchor themselves either by byssus production or by cemented attachment. The latter mode of sessile life is strongly molded by left-right shell asymmetryduring larval development of Ostreoida oysterssuch as Crassostrea hongkongensis. Here, we sequenced the genome of C. hongkongensisin high resolution and compared it to reference bivalve genomes to unveil genomic determinants driving cemented attachment and shell asymmetry. Importantly, loss of the homeobox gene Antennapedia(Antp) and broad expansion of lineage-specific extracellular gene families are implicated in a shift from byssal to cemented attachment in bivalves. Comparative transcriptomic analysis shows a conspicuous divergence between left-right asymmetrical C. hongkongensisand symmetrical Pinctada fucatain their expression profiles. Especially, a couple of orthologous transcription factor genes and lineage-specific shell-related gene families including that encoding tyrosinases are elevated, and may cooperatively govern asymmetrical shell formation in Ostreoida oysters.

A special open-cavity Mach–Zehnder salinity sensor is presented and verified in this Letter, which has obvious advantages in salinity sensitivity and loss. The open-cavity structure is composed of a short section of etched double-side hole fiber spliced between a pair of multimode fibers and connected in series between a pair of single-mode fibers, which is the SMF-MMF-etched DSHF-MMF-SMF structure proposed in the paper. According to the experiment results, when the cavity length is about 100 µm, the salinity sensitivity of the sensing probe can reach 2 nm/‰, and its refractive index (RI) sensitivity can be more than 10,000 nm/RIU, while having a low loss of ${-}{15}\;{\rm dB}$ and a detection limit of 0.23‰. Based on its characteristics, the sensor is a prospective online monitor of ocean salinity. At the same time, it also provides a low-cost way to construct an open cavity instead of femtosecond inscribing.

Rye is a valuable food and forage crop, an important genetic resource for wheat and triticale improvement and an indispensable material for efficient comparative genomic studies in grasses. Here, we sequenced the genome of Weining rye, an elite Chinese rye variety. The assembled contigs (7.74 Gb) accounted for 98.47% of the estimated genome size (7.86 Gb), with 93.67% of the contigs (7.25 Gb) assigned to seven chromosomes. Repetitive elements constituted 90.31% of the assembled genome. Compared to previously sequenced Triticeae genomes, Daniela, Sumayaand Sumanaretrotransposons showed strong expansion in rye. Further analyses of the Weining assembly shed new light on genome-wide gene duplications and their impact on starch biosynthesis genes, physical organization of complex prolamin loci, gene expression features underlying early heading trait and putative domestication-associated chromosomal regions and loci in rye. This genome sequence promises to accelerate genomic and breeding studies in rye and related cereal crops.

Allotetraploid cotton species (Gossypium hirsutumand Gossypium barbadense) have long been cultivated worldwide for natural renewable textile fibers. The draft genome sequences of both species are available but they are highly fragmented and incomplete1–4. Here we report reference-grade genome assemblies and annotations for G. hirsutumaccession Texas Marker-1 (TM-1) and G. barbadenseaccession 3–79 by integrating single-molecule real-time sequencing, BioNano optical mapping and high-throughput chromosome conformation capture techniques. Compared with previous assembled draft genomes1,3, these genome sequences show considerable improvements in contiguity and completeness for regions with high content of repeats such as centromeres. Comparative genomics analyses identify extensive structural variations that probably occurred after polyploidization, highlighted by large paracentric/pericentric inversions in 14 chromosomes. We constructed an introgression line population to introduce favorable chromosome segments from G. barbadenseto G. hirsutum, allowing us to identify 13 quantitative trait loci associated with superior fiber quality. These resources will accelerate evolutionary and functional genomic studies in cotton and inform future breeding programs for fiber improvement.

Hybridization drives rapid speciation by shaping novel genotypic and phenotypic profiles. Genomic incompatibility and transcriptome shock have been observed in hybrids, although this is rarer in animals than in plants. Using the newly sequenced genomes of the blunt snout bream (Megalobrama amblycephala[BSB]) and the topmouth culter (Culter alburnus[TC]), we focused on the sequence variation and gene expression changes in the reciprocal intergeneric hybrid lineages (F1–F3) of BSB × TC. A genome-wide transcriptional analysis identified 145–974 expressed recombinant genes in the successive generations of hybrid fish, suggesting the rapid emergence of allelic variation following hybridization. Some gradual changes of gene expression with additive and dominance effects and various cisand transregulations were observed from F1to F3in the two hybrid lineages. These asymmetric patterns of gene expression represent the alternative strategies for counteracting deleterious effects of the subgenomes and improving adaptability of novel hybrids. Furthermore, we identified positive selection and additive expression patterns in transforming growth factor, beta 1b (tgfb1b), which may account for the morphological variations of the pharyngeal jaw in the two hybrid lineages. Our current findings provide insights into the evolution of vertebrate genomes immediately following hybridization.

The ancestors of Gossypium arboreumand Gossypium herbaceumprovided the A subgenome for the modern cultivated allotetraploid cotton. Here, we upgraded the G. arboreumgenome assembly by integrating different technologies. We resequenced 243 G. arboreumand G. herbaceumaccessions to generate a map of genome variations and found that they are equally diverged from Gossypium raimondii. Independent analysis suggested that Chinese G. arboreumoriginated in South China and was subsequently introduced to the Yangtze and Yellow River regions. Most accessions with domestication-related traits experienced geographic isolation. Genome-wide association study (GWAS) identified 98 significant peak associations for 11 agronomically important traits in G. arboreum. A nonsynonymous substitution (cysteine-to-arginine substitution) of GaKASIII seems to confer substantial fatty acid composition (C16:0 and C16:1) changes in cotton seeds. Resistance to fusarium wilt disease is associated with activation of GaGSTF9expression. Our work represents a major step toward understanding the evolution of the A genome of cotton. The authors report an improved genome assembly of G. arboretumand resequencing of 243 diploid cotton accessions. GWAS and QTL-seq identify a number of candidate loci that associate with seed oil content, disease resistance and yield traits in cotton.

Brassica species, including crops such as cabbage, turnip and oilseed, display enormous phenotypic variation. Brassica genomes have all undergone a whole-genome triplication (WGT) event with unknown effects on phenotype diversification. We resequenced 199 Brassica rapa and 119 Brassica oleracea accessions representing various morphotypes and identified signals of selection at the mesohexaploid subgenome level. For cabbage morphotypes with their typical leaf-heading trait, we identified four subgenome loci that show signs of parallel selection among subgenomes within B. rapa, as well as four such loci within B. oleracea. Fifteen subgenome loci are under selection and are shared by these two species. We also detected strong subgenome parallel selection linked to the domestication of the tuberous morphotypes, turnip (B. rapa) and kohlrabi (B. oleracea). Overall, we demonstrated that the mesohexaploidization of the two Brassica genomes contributed to their diversification into heading and tuber-forming morphotypes through convergent subgenome parallel selection of paralogous genes.

The Brassica genus encompasses three diploid and three allopolyploid genomes, but a clear understanding of the evolution of agriculturally important traits via polyploidy is lacking. We assembled an allopolyploid Brassica juncea genome by shotgun and single-molecule reads integrated to genomic and genetic maps. We discovered that the A subgenomes of B. juncea and Brassica napus each had independent origins. Results suggested that A subgenomes of B. juncea were of monophyletic origin and evolved into vegetable-use and oil-use subvarieties. Homoeolog expression dominance occurs between subgenomes of allopolyploid B. juncea, in which differentially expressed genes display more selection potential than neutral genes. Homoeolog expression dominance in B. juncea has facilitated selection of glucosinolate and lipid metabolism genes in subvarieties used as vegetables and for oil production. These homoeolog expression dominance relationships among Brassicaceae genomes have contributed to selection response, predicting the directional effects of selection in a polyploid crop genome.

Bivalvesare species-rich mollusks with prominent protective roles in coastal ecosystems. Across these ancient lineages, colony-founding larvae anchor themselves either by byssus production or by cemented attachment. The latter mode of sessile life is strongly molded by left–right shell asymmetryduring larval development of Ostreoida oysterssuch as Crassostrea hongkongensis. Here, we sequenced the genome of C. hongkongensisin high resolution and compared it to reference bivalve genomes to unveil genomic determinants driving cemented attachment and shell asymmetry. Importantly, loss of the homeobox gene antennapedia (Antp) and broad expansion of lineage-specific extracellular gene families are implicated in a shift from byssal to cemented attachment in bivalves. Evidence from comparative transcriptomics shows that the left–right asymmetrical C. hongkongensisplausibly diverged from the symmetrical Pinctada fucatain expression profiles marked by elevated activities of orthologous transcription factors and lineage-specific shell-related gene families including tyrosinases, which may cooperatively govern asymmetrical shell formation in Ostreoida oysters.

Cultivated chrysanthemum (Chrysanthemum× morifoliumRamat.) is a beloved ornamental crop due to the diverse capitula types among varieties, but the molecular mechanism of capitulum development remains unclear. Here, we report a 2.60 Gb chromosome-scale reference genome of C. lavandulifolium,a wild Chrysanthemumspecies found in China, Korea and Japan. The evolutionary analysis of the genome revealed that only recent tandem duplications occurred in the C. lavandulifoliumgenome after the shared whole genome triplication (WGT) in Asteraceae. Based on the transcriptomic profiling of six important developmental stages of the radiate capitulum in C. lavandulifolium, we found genes in the MADS-box, TCP, NACand LOBgene families that were involved in disc and ray floret primordia differentiation. Notably, NAMand LOB30homologs were specifically expressed in the radiate capitulum, suggesting their pivotal roles in the genetic network of disc and ray floret primordia differentiation in chrysanthemum. The present study not only provides a high-quality reference genome of chrysanthemum but also provides insight into the molecular mechanism underlying the diverse capitulum types in chrysanthemum.

In the canonical version of evolution by gene duplication, one copy is kept unaltered while the other is free to evolve. This process of evolutionary experimentation can persist for millions of years. Since it is so short lived in comparison to the lifetime of the core genes that make up the majority of most genomes, a substantial fraction of the genome and the transcriptome may—in principle—be attributable to what we will refer to as “evolutionary transients”, referring here to both the process and the genes that have gone or are undergoing this process. Using the rice gene set as a test case, we argue that this phenomenon goes a long way towards explaining why there are so many more rice genes than Arabidopsisgenes, and why most excess rice genes show low similarity to eudicots.

In the canonical version of evolution by gene duplication, one copy is kept unaltered while the other is free to evolve. This process of evolutionary experimentation can persist for millions of years. Since it is so short lived in comparison to the lifetime of the core genes that make up the majority of most genomes, a substantial fraction of the genome and the transcriptome may—in principle—be attributable to what we will refer to as “evolutionary transients”, referring here to both the process and the genes that have gone or are undergoing this process. Using the rice gene set as a test case, we argue that this phenomenon goes a long way towards explaining why there are so many more rice genes than Arabidopsisgenes, and why most excess rice genes show low similarity to eudicots.

This publisher’s note contains corrections to Opt. Lett.46, 2714 (2021).OPLEDP0146-959210.1364/OL.428001

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Brassica rapacomprises several important cultivated vegetables and oil crops. Current reference genome assemblies of Brassica rapaare quite fragmented and not highly contiguous, thereby limiting extensive genetic and genomic analyses. Here, we report an improved assembly of the B. rapagenome (v3.0) using single-molecule sequencing, optical mapping, and chromosome conformation capture technologies (Hi-C). Relative to the previous reference genomes, our assembly features a contig N50 size of 1.45 Mb, representing a ~30-fold improvement. We also identified a new event that occurred in the B. rapagenome ~1.2 million years ago, when a long terminal repeat retrotransposon (LTR-RT) expanded. Further analysis refined the relationship of genome blocks and accurately located the centromeres in the B. rapagenome. The B. rapagenome v3.0 will serve as an important community resource for future genetic and genomic studies in B. rapa. This resource will facilitate breeding efforts in B. rapa, as well as comparative genomic analysis with other Brassicaspecies.

Following publication of this article, the authors have corrected 426 chimeric scaffolds in this genome (total scaffold number 10,684). The genome assembly has now been improved as V1.5, and the updated genome assembly is available to be downloaded from http://brassicadb.org/brad/datasets/pub/Genomes/Brassica_juncea/V1.5/.