Complete Reference Research Articles

Catalogue of phonon modes in several cuprate high-temperature superconductors from density functional theory

Cuprates are promising candidates for study in developing higher temperature superconductors. A thorough understanding of a material’s phonon modes enables further investigation of its emergent properties, however, no complete reference of the phonon modes exists. Here, using density functional theory, we evaluate the phonon frequencies and atomic displacements for La2CuO4, Bi2Sr2CuO6, and Bi2Sr2CaCu2O8, in their tetragonal structures. The phonon modes for all materials agree with those expected from space group symmetry and display instabilities corresponding to known low-temperature structural phase transitions.

A survey on face presentation attack detection mechanisms: hitherto and future perspectives.

The advances in human face recognition (FR) systems have recorded sublime success for automatic and secured authentication in diverse domains. Although the traditional methods have been overshadowed by face recognition counterpart during this progress, computer vision gains rapid traction, and the modern accomplishments address problems with real-world complexity. However, security threats in FR-based systems are a growing concern that offers a new-fangled track to the research community. In particular, recent past has witnessed ample instances of spoofing attacks where imposter breaches security of the system with an artifact of human face to circumvent the sensor module. Therefore, presentation attack detection (PAD) capabilities are instilled in the system for discriminating genuine and fake traits and anticipation of their impact on the overall behavior of the FR-based systems. To scrutinize exhaustively the current state-of-the-art efforts, provide insights, and identify potential research directions on face PAD mechanisms, this systematic study presents a review of face anti-spoofing techniques that use computational approaches. The study includes advancements in face PAD mechanisms ranging from traditional hardware-based solutions to up-to-date handcrafted features or deep learning-based approaches. We also present an analytical overview of face artifacts, performance protocols, and benchmark face anti-spoofing datasets. In addition, we perform analysis of the twelve recent state-of-the-art (SOTA) face PAD techniques on a common platform using identical dataset (i.e., REPLAY-ATTACK) and performance protocols (i.e., HTER and ACA). Our overall analysis investigates that despite prevalent face PAD mechanisms demonstrate potential performance, there exist some crucial issues that requisite a futuristic attention. Our analysis put forward a number of open issues such as; limited generalization to unknown attacks, inadequacy of face datasets for DL-models, training models with new fakes, efficient DL-enabled face PAD with smaller datasets, and limited discrimination of handcrafted features. Furthermore, the COVID-19 pandemic is an additional challenge to the existing face-based recognition systems, and hence to the PAD methods. Our motive is to present a complete reference of studies in this field and orient researchers to promising directions.

Review: The Transformation Of The Meaning Of Kebaya From National Clothing To A Media Of Self-Representation And Lifestyle

As a cultural product of the Indonesians, Kebaya has become a national dress that sticks with its philosophical principles and values. However, along with the times and the influence of popular culture, the kebaya changed its design lines. It caused a transformation of the meaning of the Indonesian national dress into a medium of self-representation and the lifestyle of modern women. This review aims to analyze the transformation of the meaning of kebaya as a medium of self-representation and lifestyle. The method used is a narrative review by analyzing several articles using the PRISMA method. The analysis results show that the kebaya, as Indonesia's national dress, has design characteristics, materials, and accessories that contain philosophical meanings that reflect the personality of Indonesian women. The design transformation of the traditional kebaya gave birth to a modern kebaya far from the standard of the conventional kebaya. Modern kebaya is interpreted as a symbol representing the wearer's self-image and social class. The modern kebaya, as a medium of self-image and social class, gives birth to a new lifestyle in society, namely a consumptive lifestyle, because someone will carry out consumption activities continuously without considering the use value of the item. Besides being able to complete references related to kebaya, the results of this review are also expected to be input for related parties to maintain the traditional kebaya standard and consider ethics in buying kebaya so as not to create a consumptive lifestyle.

An FMEA model for risk assessment of university sustainability: using a combined ITARA with TOPSIS-AL approach based neutrosophic sets.

It is necessary to emphasize both the process and results of performance management to find the balance between quality and quantity needed to ensure the sustainable development of universities to make the best use of limited educational resources and meet the diverse needs of students. This study applies failure mode and effects analysis (FMEA) to analyze obstacles to university sustainability by constructing complete risk assessment modes and reference indicators. The neutrosophic set theory was incorporated into the FMEA to account for information uncertainty and asymmetry. A specialist team then evaluated the importance of the risk factors using neutrosophic indifference threshold-based attribute ratio analysis to determine objective weights for the risk factors. Furthermore, the neutrosophic technique for order preference by similarity to the ideal solution based on aspiration level (N-TOPSIS-AL) is employed to aggregate the total risk scores of the failure modes. Using neutrosophic sets to measure truth, falsity, and indeterminacy in the assessment significantly improve the adaptability of the fuzzy theory to real-world problems. The study results indicate that when assessing university affairs management and analyzing possible risks, priority must be given to the occurrence of risks and that the lack of educational facilities is the riskiest item in the specialist assessment. The proposed assessment model can be applied as a basis for university sustainability assessments to accelerate the development of other forward-looking approaches.

Complete Reference Genome Sequence of the Clinical Neisseria gonorrhoeae Strain H035, with Resistance to the Novel Antimicrobial Zoliflodacin, Identified in Japan in 2000.

Zoliflodacin is a promising novel antimicrobial in clinical development for treatment of gonorrhea; currently, it is in a global phase 3 randomized controlled clinical trial. High activity against global Neisseria gonorrhoeae strains has been shown. We present the complete reference genome of the zoliflodacin-resistant strain H035, which was identified in Japan in 2000.

Chromosome-scale genome assembly of the pink bollworm, Pectinophora gossypiella, a global pest of cotton.

The pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae), is a major global pest of cotton. Current management practices include chemical insecticides, cultural strategies, sterile insect releases, and transgenic cotton producing crystalline (Cry) protein toxins of the bacterium Bacillus thuringiensis (Bt). These strategies have contributed to the eradication of P. gossypiella from the cotton-growing areas of the United States and northern Mexico. However, this pest has evolved resistance to Bt cotton in Asia, where it remains a critical pest, and the benefits of using transgenic Bt crops have been lost. A complete annotated reference genome is needed to improve global Bt resistance management of the pink bollworm. We generated the first chromosome-level genome assembly for pink bollworm from a Bt-susceptible laboratory strain (APHIS-S) using PacBio continuous long reads for contig generation, Illumina Hi-C for scaffolding, and Illumina whole-genome re-sequencing for error correction. The pseudo-haploid assembly consists of 29 autosomes and the Z sex chromosome. The assembly exceeds the minimum Earth BioGenome Project quality standards, has a low error rate, is highly contiguous at both the contig and scaffold levels (L/N50 of 18/8.26 MB and 14/16.44 MB, respectively), and is complete, with 98.6% of lepidopteran single-copy orthologs represented without duplication. The genome was annotated with 50% repeat content and 14,107 protein-coding genes, further assigned to 41,666 functional annotations. This assembly represents the first publicly available complete annotated genome of pink bollworm and will serve as the foundation for advancing molecular genetics of this important pest species.

A high-quality reference genome of the kelp surfperch, Brachyistius frenatus (Embiotocidae), a wide-ranging Eastern Pacific reef fish with no pelagic larval stage.

The surfperches (family Embiotocidae) are a unique group of mostly marine fishes whose phylogenetic position within the Ovalentaria clade (Percomorpha) is still unresolved. As a result of their viviparity and lack of a dispersive larval stage, surfperches are an excellent model for the study of speciation, gene flow, and local adaptation in the ocean. They are also the target of an immensely popular recreational fishery. Very few high-quality molecular resources, however, are available for this group and only for a single species. Here, we describe a highly complete reference genome for the kelp surfperch, Brachyistius frenatus, assembled using a combination of short-read (Illumina, ~47× coverage) and long-read (Oxford Nanopore Technologies, ~27× coverage) sequencing. The 596 Mb assembly has a completeness level of 98.1% (BUSCO), a contig N50 of 2.6 Mb (n = 56), and a contig N90 of 406.6 kb (n = 293). Comparative analysis revealed a high level of synteny between B. frenatus and its close relative, Embiotoca jacksoni. This assembly will serve as a valuable molecular resource upon which future evolutionary dynamics research will build, such as the investigation of local adaptation and the genomic potential for climate adaptation in wild populations.

Comparative Genomics of Legionella pneumophila Isolates from the West Bank and Germany Support Molecular Epidemiology of Legionnaires’ Disease

Legionella pneumophila is an environmental bacterium and clinical pathogen that causes many life-threating outbreaks of an atypical pneumonia called Legionnaires' disease (LD). Studies of this pathogen have focused mainly on Europe and the United States. A shortage in L. pneumophila data is clearly observed for developing countries. To reduce this knowledge gap, L. pneumophila isolates were studied in two widely different geographical areas, i.e., the West Bank and Germany. For this study, we sequenced and compared the whole genome of 38 clinical and environmental isolates of L. pneumophila covering different MLVA-8(12) genotypes in the two areas. Sequencing was conducted using the Illumina HiSeq 2500 platform. In addition, two isolates (A194 and H3) were sequenced using a Pacific Biosciences (PacBio) RSII platform to generate complete reference genomes from each of the geographical areas. Genome sequences from 55 L. pneumophila strains, including 17 reference strains, were aligned with the genome sequence of the closest strain (L. pneumophila strain Alcoy). A whole genome phylogeny based on single nucleotide polymorphisms (SNPs) was created using the ParSNP software v 1.0. The reference genomes obtained for isolates A194 and H3 consisted of circular chromosomes of 3,467,904 bp and 3,691,263 bp, respectively. An average of 36,418 SNPs (min. 8569, max. 70,708 SNPs) against our reference strain L. pneumophila str. Alcoy, and 2367 core-genes were identified among the fifty-five strains. An analysis of the genomic population structure by SNP comparison divided the fifty-five L. pneumophila strains into six branches. Individual isolates in sub-lineages in these branches differed by less than 120 SNPs if they had the same MLVA genotype and were isolated from the same location. A bioinformatics analysis identified the genomic islands (GIs) for horizontal gene transfer and mobile genetic elements, demonstrating that L. pneumophila showed high genome plasticity. Four L. pneumophila isolates (H3, A29, A129 and L10-091) contained well-defined plasmids. On average, only about half of the plasmid genes could be matched to proteins in databases. In silico phage findings suggested that 43 strains contained at least one phage. However, none of them were found to be complete. BLASTp analysis of proteins from the type IV secretion Dot/Icm system showed those proteins highly conserved, with less than 25% structural differences in the new L. pneumophila isolates. Overall, we demonstrated that whole genome sequencing provides a molecular surveillance tool for L. pneumophila at the highest conceivable discriminatory level, i.e., two to eight SNPs were observed for isolates from the same location but several years apart.

Smart Biomimetic Nanozymes for Precise Molecular Imaging: Application and Challenges.

New nanotechnologies for imaging molecules are widely being applied to visualize the expression of specific molecules (e.g., ions, biomarkers) for disease diagnosis. Among various nanoplatforms, nanozymes, which exhibit enzyme-like catalytic activities in vivo, have gained tremendously increasing attention in molecular imaging due to their unique properties such as diverse enzyme-mimicking activities, excellent biocompatibility, ease of surface tenability, and low cost. In addition, by integrating different nanoparticles with superparamagnetic, photoacoustic, fluorescence, and photothermal properties, the nanoenzymes are able to increase the imaging sensitivity and accuracy for better understanding the complexity and the biological process of disease. Moreover, these functions encourage the utilization of nanozymes as therapeutic agents to assist in treatment. In this review, we focus on the applications of nanozymes in molecular imaging and discuss the use of peroxidase (POD), oxidase (OXD), catalase (CAT), and superoxide dismutase (SOD) with different imaging modalities. Further, the applications of nanozymes for cancer treatment, bacterial infection, and inflammation image-guided therapy are discussed. Overall, this review aims to provide a complete reference for research in the interdisciplinary fields of nanotechnology and molecular imaging to promote the advancement and clinical translation of novel biomimetic nanozymes.

Microbial contamination and composition of oral samples subjected to clinical whole genome sequencing.

Biological material from the oral cavity is an excellent source of samples for genetic diagnostics. This is because collection is quick, easy-to-access, and non-invasive. We have set-up clinical whole genome sequence testing for patients with suspected hereditary disease. Beside the excellent quality of human DNA that can be isolated from such samples, we observed the presence of non-human DNA sequences at varying percentages. We investigated the proportion of non-human mapped reads (NHMR) sequenced from buccal swabs and saliva, the type of microbial genomes from which they were derived, and impact on molecular classification. Read sequences that did not map to the human reference genome were aligned to complete reference microbial reference sequences from the National Center for Biotechnology Information's (NCBI) RefSeq database using Kraken2. Out of 765 analyzed samples over 80% demonstrated more than 5% NHMRs. The majority of NHMRs were from bacterial genomes (average 69%, buccal swabs and 54% saliva), while the proportion of viruses was low, averaging 0.32% (buccal swabs) and 0.07% (saliva). We identified more than 30 different bacterial families of which Streptococcus mitis and Rothia mucilaginosa were the most common species. Importantly, the level of contamination did not impact the diagnostic yield.

Prevalence of Listeria monocytogenes, Salmonella spp., Shiga toxin-producing Escherichia coli, and Campylobacter spp. in raw milk in the United States between 2000 and 2019: A systematic review and meta-analysis

Raw (unpasteurized) milk is available for sale and direct human consumption within some states in the United States (US); it cannot be sold or distributed in interstate commerce. Raw milk may contain pathogenic microorganisms that, when consumed, may cause illness and sometimes may result in death. No comprehensive review for prevalence and levels of the major bacterial pathogens in raw milk in the US exists. The objective of the present research was to systematically review the scientific literature published from 2000 to 2019 to estimate the prevalence and levels of Listeria monocytogenes, Salmonella spp., Shiga toxin-producing Escherichia coli (STEC), and Campylobacter spp. in raw milk in the US. Peer-reviewed studies were retrieved systematically from PubMed®, Embase®, and Web of ScienceTM. The unique complete nonduplicate references were uploaded into the Health Assessment Work Collaborative (HAWC). Based on the selection criteria, twenty studies were included in the systematic review and meta-analysis. Comprehensive Meta-Analysis (CMA) was used for statistical analyses, specifically, random effects meta-analyses were used to synthesize raw bulk tank milk (BTM) and milk filters (MF) data. Data from studies using culture and non–culture-based detection methods were included. Forest plots generated in CMA (Biostat, Englewood, NJ) were used to visualize the results. The average prevalence (event rate) of L. monocytogenes, Salmonella spp., STEC, and Campylobacter spp. in raw BTM in the US was estimated at 4.3% (95% confidence intervals [CIs], 2.8–6.5%), 3.6% (95% CIs, 2.0–6.2%), 4.3% (95% CIs, 2.4–7.4%), and 6.0% (95% CIs, 3.2–10.9%), respectively. Estimated prevalence was generally larger in MF than in BTM. There was not enough data to perform a meta-analysis for the prevalence or levels of pathogens in raw milk from retail establishments or other milk categories.

Chromosome-Level Genome Assembly of the Cape Cliff Lizard (Hemicordylus capensis).

Squamates represent a highly diverse and species-rich vertebrate group that is remarkably understudied from a genomic perspective. A scarcity of genomic data is particularly evident for scincomorph lizards, which encompass over 10% of all living squamates, and for which high-quality genomic resources are currently lacking. To address this knowledge gap, we present the first chromosome-level reference genome for this group, generated from a male Cape cliff lizard (Hemicordylus capensis), using highly accurate PacBio HiFi long-read sequencing data, long-range Omni-C chromosomal conformation capture data and transcriptomic data for annotation. The rHemCap1.1 genome assembly spans 2.29 Gb, with a scaffold N50 of 359.65 Mb, and includes 25,300 protein-coding genes, with a BUSCO completeness score of 95.5% (sauropsida_odb10). We have generated the most contiguous and complete chromosome-level squamate reference genome assembly publicly available to date. Furthermore, we used short-read resequencing of 35 males and females and applied a differential coverage approach to infer the sex-determination system of the species, which was previously unknown. Our results suggest this species has XX/XY sex chromosomes, representing the first evidence of sex determination in the family Cordylidae. This reference genome will help to establish this species as an evolutionary model for studying variation in body armor, a key trait in cordylids and other squamate groups. Lastly, this is the first squamate reference genome from a continental African species and, as such, represents a valuable resource not only for further evolutionary research in cordylids but also in closely related groups.

Determination of Complete Blood Count Reference Intervals by an Indirect Method for Newborns, Adults, and Geriatric Ages.

The availability of a reliable reference interval is crucial for clinical decision-making. Correctly defined reference intervals for different age groups are currently unavailable for many parameters. Our study aimed to determine the complete blood count reference intervals in our region from newborn to geriatric ages with an indirect method. The study was carried out at Marmara University Pendik E&R Hospital Biochemistry Laboratory between January 2018 and May 2019 using the laboratory information system data. The complete blood count (CBC) measurements were performed by Unicel DxH 800 Coulter Cellular Analysis System (Beckman Coulter, FL, USA). A total of 14,014,912 test results belonging to infants, children, adolescents, adults, and geriatric ages were collected. We analyzed 22 CBC parameters, and an indirect method was used for reference interval determination. Data were analyzed according to the Clinical and Laboratory Standards Institute (CLSI) C28-A3 guideline for defining, establishing, and verifying reference intervals in the clinical laboratory. We have established reference intervals from newborn to geriatric ages for 22 hematology parameters [hemoglobin (Hb), hematocrit (Hct), red blood cell (RBC), mean red cell volume (MCV), mean red cell hemoglobin (MCH), mean red cell hemoglobin concentration (MCHC), red cell distribution width (RDW), white blood cell (WBC) count, WBC differentials, including percentages and absolute counts, platelet count, platelet distribution width (PDW), mean platelet volume (MPV) and plateletcrit (PCT)]. Our study showed that reference intervals established with data obtained from clinical laboratory databases are comparable to those created using direct methods.

An Efficient Ontology Based Machine Learning for Classifying High Definition Satellite Images (Chandrayaan-3)

The analysis of satellite images to determine the kind of land, forest cover, plant type, and other aspects of a particular image has become a standard practice. Object-based image classification for land-cover mapping with remote-sensing data has received a lot of interest in recent years. Several researches have looked into a range of sensors, feature extraction, classifiers, and other important elements throughout the last decade. These data, however, have yet to be gathered into a complete reference on the implications of different guided object-based land-cover categorization methods. To solve this issue, we provide an ontology-based conceptual UKNN classification algorithm in this study. We create an 18-field database from the rit18 database's qualitative and quantitative data in this research. Instead of unexplainable characteristics provided by a CNN, this proposed study uses an ontology-based methodology framework to enable picture classification using features extracted from hyper spectral image data. The image is initially given a Gaussian filter. The suggested UNet K nearest neighbours (UKNN) classifier is utilised to translate the ontology components into image-based parameters, which are then used to improve the classification process. When a typical support vector machine (SVM) is compared to UKNN, we find that UKNN outperforms SVM in classification accuracy

Strong Labeling of Sound Events Using Crowdsourced Weak Labels and Annotator Competence Estimation

Crowdsourcing is a popular tool for collecting large amounts of annotated data, but the specific format of the strong labels necessary for sound event detection is not easily obtainable through crowdsourcing. In this work, we propose a novel annotation workflow that leverages the efficiency of crowdsourcing weak labels, and uses a high number of annotators to produce reliable and objective strong labels. The weak labels are collected in a highly redundant setup, to allow reconstruction of the temporal information. To obtain reliable labels, the annotators' competence is estimated using MACE (Multi-Annotator Competence Estimation) and incorporated into the strong labels estimation through weighing of individual opinions. We show that the proposed method produces consistently reliable strong annotations not only for synthetic audio mixtures, but also for audio recordings of real everyday environments. While only a maximum 80% coincidence with the complete and correct reference annotations was obtained for synthetic data, these results are explained by an extended study of how polyphony and SNR levels affect the identification rate of the sound events by the annotators. On real data, even though the estimated annotators' competence is significantly lower and the coincidence with reference labels is under 69%, the proposed majority opinion approach produces reliable aggregated strong labels in comparison with the more difficult task of crowdsourcing directly strong labels.

Establishment of Complete Capillary Blood Counts Reference Intervals for Young Children in Local Area, China.

Blood count reference intervals are important to diagnose diseases and assess overall health, especially for young children. Although, in 2021, the National Health Commission of the People's Republic of China issued "Reference intervals of blood cell analysis for children (WS/T 779-2021)", these RIs may not suitable for small children all over the country due to racial, lifestyle, and geographical differences. The aim of this study was to establish and validate locally determined hematological reference intervals among young children in Nantong district and compare them with WS/T 779-2021 and American data. The reference sample consisted of 4,758 apparently healthy small children aged from age 28 days to 3 years according to the EP28-A3c guideline issued by the Clinical and Laboratory Standards Institute (CLSI). Capillary blood samples collected in K2-EDTA anticoagulant tubes analyzed by standard procedures. Statistical analysis was based on the guidelines of the CLSI. Pediatric reference intervals for 18 capillary complete blood count (CCBC) parameters were established for young children. WBC and differentials did not differ by gender in the combined analysis of all data, but showed some variations among different age groups, especially for NE and LYM. RIs of RBC value, MCV, and MCH were established, especially with regard to the difference among different age and gender groups. An overall increasing trend of PLT value was observed in children with no obvious difference between boys and girls. Further validation with 1,136 healthy subjects demonstrated that the verified proportions of our study were within 90.11% - 100%. RIs determined in the present study were more concentrated than WS/T 779-2021, with slight differences in the upper and bottom boundaries. Establishing appropriate region-specific reference intervals for pediatrics is essential. This study offers local reference intervals of CCBC values for young children and could be used as a benchmark for similar populations in the Yangtze River Delta economic region.

Comprehensive variant discovery in the era of complete human reference genomes.

Comprehensive variant discovery in the era of complete human reference genomes.

Gear Wheel Finishing with Abrasive Brushing Tools to Improve the Surface Quality of Tooth Flanks for the Industrial Application

A high surface quality of tooth flanks can improve the service life and the performance of gears, as well as reduce acoustic emissions. However, high demands on the gear geometry pose a challenge for the finishing of tooth flank surfaces because the dimensional accuracy that can be achieved with modern grinding processes must not be impaired by the finishing process. A preceding study has shown fundamentally that profiled abrasive brushing tools can be used to improve the quality of individual tooth flank surfaces. Due to the integration into the grinding machine, it represents a promising alternative to common finishing applications. Before the process can be used in an industrial environment, process reliability and tool life must be examined. For this purpose, complete reference gearwheels (39 × 10) were finished with the brushing tools. It could be shown that the surface roughness can be reliably reduced by ΔRa ≈ 0.2 µm by using a single brush for an entire gearwheel without changing the gear geometry. In addition to the influence of the tool specifications on the work result, the influence of the initial roughness after grinding was considered in particular. It was found that the achievable surface roughness depends significantly on the depth of the grinding grooves, as these are retained as desired, while the roughness peaks are fully smoothed. Furthermore, a device for the machine-integrated profiling and dressing of brushing tools was successfully designed, implemented, and tested.

Construction of a new complete growth reference for urban Chinese children

BackgroundGrowth chart is a valuable clinical tool to monitor the growth and nutritional status of children. A growth chart widely used in China is based on the merged data sets of national surveys in 2005. We aimed to establish an up-to-date, complete growth curve for urban Chinese children and adolescents with a full range of ages.MethodsUsing data collected in a large-scale, cross-sectional study (Prevalence and Risk factors for Obesity and Diabetes in Youth (PRODY), 2017–2019), we analyzed 201,098 urban children aged 3 to 18 years from 11 provinces, autonomous regions, and municipalities that are geographically representative of China. All participants underwent physical examinations. Sex-specific percentiles of height-for-age and weight-for-age were constructed by Generalized Additive Models for Location Scale and Shape (GAMLSS) model. We also compared the median values of height-for-age or weight-for-age between our growth chart and the established growth reference using Welch-Satterthwaite T-Test.ResultsConsistent with the established growth reference, we observed that the P50 percentile of height-for-age reached plateaus at the age of 15 years (172 cm) and 14 years (160 cm) for boys and girls, respectively. In addition, boys aged 10 ~ 14 years and girls aged 10 ~ 12 years exhibited the most dramatic weight difference compared to those of other age groups (19.5 kg and 10.3 kg, respectively). However, our growth chart had higher median values of weight-for-age and height-for-age than the established growth reference with mean increases in weight-for-age of 1.36 kg and 1.17 kg for boys and girls, respectively, and in height-for-age of 2.9 cm and 2.6 cm for boys and girls, respectively.ConclusionsOur updated growth chart can serve as a reliable reference to assess the growth and nutritional status in urban Chinese children throughout the entire childhood.

A long-read and short-read transcriptomics approach provides the first high-quality reference transcriptome and genome annotation for Pseudotsuga menziesii (Douglas-fir).

Douglas-fir (Pseudotsuga menziesii) is native to western North America. It grows in a wide range of environmental conditions and is an important timber tree. Although there are several studies on the gene expression responses of Douglas-fir to abiotic cues, the absence of high-quality transcriptome and genome data is a barrier to further investigation. Like for most conifers, the available transcriptome and genome reference dataset for Douglas-fir remains fragmented and requires refinement. We aimed to generate a highly accurate, and complete reference transcriptome and genome annotation. We deep-sequenced the transcriptome of Douglas-fir needles from seedlings that were grown under nonstress control conditions or a combination of heat and drought stress conditions using long-read (LR) and short-read (SR) sequencing platforms. We used 2 computational approaches, namely de novo and genome-guided LR transcriptome assembly. Using the LR de novo assembly, we identified 1.3X more high-quality transcripts, 1.85X more "complete" genes, and 2.7X more functionally annotated genes compared to the genome-guided assembly approach. We predicted 666 long noncoding RNAs and 12,778 unique protein-coding transcripts including 2,016 putative transcription factors. We leveraged the LR de novo assembled transcriptome with paired-end SR and a published single-end SR transcriptome to generate an improved genome annotation. This was conducted with BRAKER2 and refined based on functional annotation, repetitive content, and transcriptome alignment. This high-quality genome annotation has 51,419 unique gene models derived from 322,631 initial predictions. Overall, our informatics approach provides a new reference Douglas-fir transcriptome assembly and genome annotation with considerably improved completeness and functional annotation.