Improving the ostrich genome assembly using optical mapping data

BACKGROUND: The ostrich (Struthio camelus) is the tallest and heaviest living bird. Ostrich meat is considered a healthy red meat, with an annual worldwide production ranging from 12,000 to 15,000 tons. As part of the avian phylogenomics project, we sequenced the ostrich genome for phylogenetic and comparative genomics analyses. The initial Illumina-based assembly of this genome had a scaffold N50 of 3.59 Mb and a total size of 1.23 Gb. Since longer scaffolds are critical for many genomic analyses, particularly for chromosome-level comparative analysis, we generated optical mapping (OM) data to obtain an improved assembly. The OM technique is a non-PCR-based method to generate genome-wide restriction enzyme maps, which improves the quality of de novo genome assembly. FINDINGS: In order to generate OM data, we digested the ostrich genome with KpnI, which yielded 1.99 million DNA molecules (>250 kb) and covered the genome at least 500×. The pattern of molecules was subsequently assembled to align with the Illumina-based assembly to achieve sequence extension. This resulted in an OM assembly with a scaffold N50 of 17.71 Mb, which is 5 times as large as that of the initial assembly. The number of scaffolds covering 90% of the genome was reduced from 414 to 75, which means an average of ~3 super-scaffolds for each chromosome. Upon integrating the OM data with previously published FISH (fluorescence in situ hybridization) markers, we recovered the full PAR (pseudoatosomal region) on the ostrich Z chromosome with 4 super-scaffolds, as well as most of the degenerated regions. CONCLUSIONS: The OM data significantly improved the assembled scaffolds of the ostrich genome and facilitated chromosome evolution studies in birds. Similar strategies can be applied to other genome sequencing projects to obtain better assemblies

Temporal genomic evolution of bird sex chromosomes

BACKGROUND: Sex chromosomes exhibit many unusual patterns in sequence and gene expression relative to autosomes. Birds have evolved a female heterogametic sex system (male ZZ, female ZW), through stepwise suppression of recombination between chrZ and chrW. To address the broad patterns and complex driving forces of Z chromosome evolution, we analyze here 45 newly available bird genomes and four species’ transcriptomes, over their course of recombination loss between the sex chromosomes. RESULTS: We show Z chromosomes in general have a significantly higher substitution rate in introns and synonymous protein-coding sites than autosomes, driven by the male-to-female mutation bias (‘male-driven evolution’ effect). Our genome-wide estimate reveals that the degree of such a bias ranges from 1.6 to 3.8 among different species. G + C content of third codon positions exhibits the same trend of gradual changes with that of introns, between chrZ and autosomes or regions with increasing ages of becoming Z-linked, therefore codon usage bias in birds is probably driven by the mutational bias. On the other hand, Z chromosomes also evolve significantly faster at nonsynonymous sites relative to autosomes (‘fast-Z’ evolution). And species with a lower level of intronic heterozygosities tend to evolve even faster on the Z chromosome. Further analysis of fast-evolving genes’ enriched functional categories and sex-biased expression patterns support that, fast-Z evolution in birds is mainly driven by genetic drift. Finally, we show in species except for chicken, gene expression becomes more male-biased within Z-linked regions that have became hemizygous in females for a longer time, suggesting a lack of global dosage compensation in birds, and the reported regional dosage compensation in chicken has only evolved very recently. CONCLUSIONS: In conclusion, we uncover that the sequence and expression patterns of Z chromosome genes covary with their ages of becoming Z-linked. In contrast to the mammalian X chromosomes, such patterns are mainly driven by mutational bias and genetic drift in birds, due to the opposite sex-biased inheritance of Z vs. X. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12862-014-0250-8) contains supplementary material, which is available to authorized users

Transcriptomic Response of Wolf Spider, \u3cem\u3ePardosa pseudoannulata\u3c/em\u3e, to Transgenic Rice Expressing \u3cem\u3eBacillus thuringiensis\u3c/em\u3e Cry1Ab Protein

Background: Bacillum thuringiensis (Bt) toxin produced in Cry1-expressing genetically modified rice (Bt rice) is highly effective to control lepidopteran pests, which reduces the needs for synthetic insecticides. Non-target organisms can be exposed to Bt toxins through direct feeding or trophic interactions in the field. The wolf spider Pardosa pseudoannulata, one of the dominant predators in South China, plays a crucial role in the rice agroecosystem. In this study, we investigated transcriptome responses of the 5th instar spiders fed on preys maintained on Bt- and non-Bt rice. Results: Comparative transcriptome analysis resulted in 136 differentially expressed genes (DEGs) between spiderlings preying upon N. lugens fed on Bt- and non-Bt rice (Bt- and non-Bt spiderlings). Functional analysis indicated a potential impact of Bttoxin on the formation of new cuticles during molting. GO and KEGG enrichment analyses suggested that GO terms associated with chitin or cuticle, including “chitin binding”, “chitin metabolic process”, “chitin synthase activity”, “cuticle chitin biosynthetic process”, “cuticle hydrocarbon biosynthetic process”, and “structural constituent of cuticle”, and an array of amino acid metabolic pathways, including “alanine, asparatate and glutamate metabolism”, “glycine, serine and theronine metabolism”, “cysteine and methionine metabolism”, “tyrosine metabolism”, “phenylalanine metabolism and phenylalanine”, and “tyrosine and tryptophan biosynthesis” were significantly influenced in response to Cry1Ab. Conclusions: The Cry1Ab may have a negative impact on the formation of new cuticles during molting, which is contributed to the delayed development of spiderlings. To validate these transcriptomic responses, further examination at the translational level will be warranted

Motion Kinematics Analysis of a Horse Inspired Terrain-Adaptive Unmanned Vehicle With Four Hydraulic Swing Arms

All terrain vehicles (ATV) perform tasks in unstructured environments where the advanced adaptive ability of rigid terrain has become a key factor. In this article, we propose a novel horse inspired all terrain eight-wheeled vehicle with four swing arms for transportation in the mountain battlefield. The mechanism structure and system configuration of the ATV are designed based on the horse leg kinematics analysis. In order to analyze the obstacle surmounting strategy of the ATV, the kinematics model and the center of gravity of the ATV are represented. A model reference adaptive control method is proposed for the hydraulic attitude control system. Then the model for obstacle surmounting is proposed for dynamics performance and geometric kinematics. Additionally, the simulation is executed in Adams to verify the analysis and strategy. Finally, the experiment is demonstrated for climbing a vertical wall, which is a challenging and typical terrain of the mountain battlefield

Anisotropic elastic constants calculation of stainless steel cladded layers of pressure vessel steel plate

Cladding stainless steel layer on the inner surface of ferrite pressure vessel is a common method to improve the corrosion resistance and save the economic cost. However, the movement of heat source and temperature gradient in the process of cladded welding will lead to the anisotropy of cladded layer material. When measuring the residual stress of pressure vessel steel plate with stainless steel cladded layers (SSCL) by contour method, it is necessary to know the elastic mechanical properties of stainless steel cladded layers accurately. The assumption of transversely isotropy (TI) was employed, and the relationship between the material compliance matrix and the elastic modulus of transversely isotropic material was utilized. Based on the elastic modulus of each cladded layer and the whole steel plate from the longitudinal direction (0°) until the transverse direction (90°) measured by the experiment, the independent constants S11, S13, S33 and S44 in the compliance matrix of each cladded layer and the whole steel plate were obtained by regression analysis method. Furthermore, by using the relationship between the independent constants of the stiffness matrix of the transversely isotropic material and the single crystal material, the independent constant S12 in the compliance matrix of each stainless steel cladded layer and the whole steel plate were obtained. And then the independent constants of the stiffness matrix of each cladded layer and the whole steel plate were acquired. Hence, a method for calculating the anisotropic elastic constants of the stainless steel cladded layer and the whole steel plate was proposed. The results will provide material data support for measuring residual stress of pressure vessel steel plate with stainless steel cladded layers by contour method

Local injection therapy for carpal tunnel syndrome: a network meta-analysis of randomized controlled trial

Objective: Clinical research has shown that local injections for carpal tunnel syndrome reduce the symptoms of patients and enhance their quality of life considerably. However, there are several therapy options, and the optimal choice of regimen remains uncertain. Therefore, we comprehensively evaluated the variations in clinical efficacy and safety of several medications for treating carpal tunnel syndrome.Methods: Computer searches of Embase, PubMed, Cochrane Library, and Web of Science databases were used to collect articles of randomized controlled trials on local injections for treating carpal tunnel syndrome from database creation till 10 June 2023. Two researchers independently screened the literature, extracted information, evaluated the risk of bias in the included studies, and performed network Meta-analysis using Stata 17.0 software. Drug efficacy was assessed using symptom severity/function and pain intensity. Surface under the cumulative ranking curve (SUCRA) ranking was used to determine the advantage of each therapy.Results: We included 26 randomized controlled trials with 1896 wrists involving 12 interventions, such as local injections of corticosteroids, platelet-rich plasma, 5% dextrose, progesterone, and hyaluronidase. The results of the network meta-analysis showed the following: (i) symptom severity: at the 3-month follow-up, D5W combined with splinting (SUCRA = 95%) ranked first, and hyaluronidase (SUCRA = 89.6%) at 6 months; (ii) functional severity: either at the 3-month follow-up (SUCRA = 89.5%) or 6 months (SUCRA = 83.6%), iii) pain intensity: 5% dextrose in water combined with splinting was the most effective at the 3-month (SUCRA = 85%) and 6-month (SUCRA = 87.6%) follow-up.Conclusion: Considering the combination of symptoms/function and pain intensity, combining 5% dextrose in water with splinting is probably the treatment of choice for patients with carpal tunnel syndrome. It is more effective than glucocorticoids and no adverse effects have been observed.Systematic Review Registration:https://www.crd.york.ac.uk/PROSPERO/, identifier CRD42022370525