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1.
Front Plant Sci ; 12: 746771, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34745180

RESUMO

Cotton is one of the most important fiber crops globally. Despite this, various abiotic stresses, including drought, cause yield losses. We used transcriptome profiles to investigate the co-expression patterns of gene networks associated with drought stress tolerance. We identified three gene modules containing 3,567 genes highly associated with drought stress tolerance. Within these modules, we identified 13 hub genes based on intramodular significance, for further validation. The yellow module has five hub genes (Gh_A07G0563, Gh_D05G0221, Gh_A05G3716, Gh_D12G1438, and Gh_D05G0697), the brown module contains three hub genes belonging to the aldehyde dehydrogenase (ALDH) gene family (Gh_A06G1257, Gh_A06G1256, and Gh_D06G1578), and the pink module has five hub genes (Gh_A02G1616, Gh_D12G2599, Gh_D07G2232, Gh_A02G0527, and Gh_D07G0629). Based on RT-qPCR results, the Gh_A06G1257 gene has the highest expression under drought stress in different plant tissues and it might be the true candidate gene linked to drought stress tolerance in cotton. Silencing of Gh_A06G1257 in cotton leaves conferred significant sensitivity in response to drought stress treatments. Overexpression of Gh_A06G1257 in Arabidopsis also confirms its role in drought stress tolerance. L-valine, Glutaric acid, L-proline, L-Glutamic acid, and L-Tryptophan were found to be the most significant metabolites playing roles in drought stress tolerance. These findings add significantly to existing knowledge of drought stress tolerance mechanisms in cotton.

2.
J Nanobiotechnology ; 19(1): 382, 2021 Nov 22.
Artigo em Inglês | MEDLINE | ID: mdl-34809618

RESUMO

BACKGROUND: Inflammatory osteolysis, a major complication of total joint replacement surgery, can cause prosthesis failure and necessitate revision surgery. Macrophages are key effector immune cells in inflammatory responses, but excessive M1-polarization of dysfunctional macrophages leads to the secretion of proinflammatory cytokines and severe loss of bone tissue. Here, we report the development of macrophage-biomimetic porous SiO2-coated ultrasmall Se particles (porous Se@SiO2 nanospheres) to manage inflammatory osteolysis. RESULTS: Macrophage membrane-coated porous Se@SiO2 nanospheres(M-Se@SiO2) attenuated lipopolysaccharide (LPS)-induced inflammatory osteolysis via a dual-immunomodulatory effect. As macrophage membrane decoys, these nanoparticles reduced endotoxin levels and neutralized proinflammatory cytokines. Moreover, the release of Se could induce macrophage polarization toward the anti-inflammatory M2-phenotype. These effects were mediated via the inhibition of p65, p38, and extracellular signal-regulated kinase (ERK) signaling. Additionally, the immune environment created by M-Se@SiO2 reduced the inhibition of osteogenic differentiation caused by proinflammation cytokines, as confirmed through in vitro and in vivo experiments. CONCLUSION: Our findings suggest that M-Se@SiO2 have an immunomodulatory role in LPS-induced inflammation and bone remodeling, which demonstrates that M-Se@SiO2 are a promising engineered nanoplatform for the treatment of osteolysis occurring after arthroplasty.

3.
Theor Appl Genet ; 2021 Nov 22.
Artigo em Inglês | MEDLINE | ID: mdl-34811574

RESUMO

KEY MESSAGE: Rf candidate genes were related to the super D05_PPR-cluster and verified to be individually nonfunctional. Restorer of fertility (Rf) genes of cytoplasmic male sterility (CMS) is commonly found to be PPR (pentatricopeptide repeat) genes, which are mostly located in a cluster of PPR genes with high similarity. Here, Homocap-seq was applied to analyze PPR clusters in 'three lines,' and we found broad variations within the D05_PPR-cluster in a restorer line and deduced that the D05_PPR-cluster was associated with fertility restoration. Genetic mapping of Rf and Homocap-seq analysis of three genotypes in the F2 population validated that the D05_PPR-cluster was the origin of Rf. Three Rf candidates were cloned that were the most actively expressed genes in the D05_PPR-cluster in the restorer line as revealed by their high-depth amplicons. However, further transgenic experiments showed that none of the candidates could restore fertility of the CMS line independently. Then, the members of the brand-new super D05_PPR-cluster in the restorer line, containing 14 full-length PPRs and at least 13 PPR homologous sequences, were identified by long-read resequencing, which validated the effectiveness of variation and expression prediction of Homocap-seq. Additionally, we found that several PPR duplications, including 2 of the 3 Rf candidates, had undergone site-specific selection as potentially important anther development-associated genes. Finally, we proposed that multiple PPRs were coordinately responsible for the fertility restoration of the CMS line.

4.
Zhongguo Xiu Fu Chong Jian Wai Ke Za Zhi ; 35(10): 1221-1226, 2021 Oct 15.
Artigo em Chinês | MEDLINE | ID: mdl-34651472

RESUMO

Lower limb alignment and soft tissue balance are important factors affecting patient satisfaction, clinical functional outcome, and prosthetic long-term survival rate after total knee arthroplasty (TKA). Robot-assisted TKA (rTKA) has the advantages of achieving precise osteotomy and soft tissue balance. However, rTKA under the guidance of classic mechanical alignment principles does not significantly improve the functional outcome after operation. The new TKA alignment principles, such as kinematic alignment (KA) and functional alignment (FA), can better consider the patient's own knee joint morphology and kinematic characteristics, which may help improve the clinical results of TKA. With the help of more objective and accurate soft tissue balance assessment tool such as pressure sensors, KA and FA have been proven to better achieve soft tissue balance. rTKA can achieve non-neutral alignment goals such as KA or FA more accurately and reproducibly. The use of these lower limb alignment and soft tissue balancing strategies will be expected to further increase the patients' satisfaction rate after rTKA.


Assuntos
Artroplastia do Joelho , Prótese do Joelho , Osteoartrite do Joelho , Robótica , Fenômenos Biomecânicos , Humanos , Articulação do Joelho/cirurgia , Extremidade Inferior , Osteoartrite do Joelho/cirurgia
6.
J Agric Food Chem ; 2021 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-34523915

RESUMO

Nanozymes as a cost-effective and robust enzyme mimic have attracted widespread attention in the development of novel analytical methods. Herein, a new nanozyme-enhanced surface-enhanced Raman scattering (SERS) immunoassay platform was successfully developed using a peroxidase-mimicking nanozyme to replace the natural enzymes as a catalytic label of the enzyme-linked immunosorbent assay for the detection of allergy proteins. In this platform, the peroxidase-mimicking nanozymes as a catalytic label could catalyze the oxidation of the Raman-inactive reporter [i.e., leucomalachite green (LMG)] to generate Raman-active malachite green (MG) with H2O2. Moreover, the produced MG Raman signal was further enhanced by the formed Raman "hot spot" through MG-induced gold nanoparticle aggregation, which could be recorded by a portable Raman spectrometer. On this basis, the established nanozyme-enhanced SERS immunoassay showed improved accuracy, high sensitivity, and good selectivity and was used for accurate quantification of α-lactalbumin (α-LA). With this method, α-LA could be detected with a limit of detection as low as 0.01 ng/mL. Moreover, the method was also verified by performing in food samples and showed satisfactory recoveries and high reliability. This study not only provides insight into the use of a nanozyme to establish new analytical methods but also broadens the applications of nanozymes in a food safety assay.

7.
Adv Mater ; 33(44): e2104410, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34486185

RESUMO

Metabolic homeostasis is vital for individual cells to keep alive. Stronger metabolic homeostasis allows bacteria to survive in vivo and do persistent harm to hosts, which is especially typical in implant-associated infection (IAI) with biofilm intervention. Herein, based on the competitive role of selenium (Se) and sulfur (S) in bacteria metabolism as congeners, a congener-induced sulfur-related metabolism interference therapy (SMIT) eradicating IAI is proposed by specific destruction of bacteria metabolic homeostasis. The original nanodrug manganese diselenide (MnSe2 ) is devised to generate permeable H2 Se in bacteria, triggered by the acidic microenvironment. H2 Se, the congener substitution of H2 S, as a bacteria-specific intermediate metabolite, can embed itself into the H2 S-utilization pathway and further alternatively disrupt the downstream sulfur-related metabolism state inside bacteria. A proteomic study indicates ribosome-related proteins are heavily downregulated and the basic metabolic pathways are mainly disordered after SMIT, revealing the destruction of bacteria metabolic homeostasis. The efficiency of SMIT is significantly promoted with the mild temperature sensitization provided by the photothermal treatment (PTT) of MnSe2 nanoparticles, verified by the proteomic study and the anti-IAI effect in vitro and in vivo. With the intelligent nanodrug, a PTT-promoted SMIT strategy against IAI is provided and a new insight into the interference design toward metabolic homeostasis with biochemical similarity is demonstrated.

8.
Patient Prefer Adherence ; 15: 1785-1793, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34429590

RESUMO

Background: To transfer a paper-version Chinese and Western medication adherence scale for CKD into an electronic scale, and evaluate its validity, internal consistency and clinical implementation, and assess whether the transition is feasible in clinic. Methods: We built an e-version Chinese and Western medication adherence scale based on the Wen-JuanXing platform. CKD subjects' responses were applied to test the scale's validity and internal consistency. We retested some of the participants two weeks later randomly. We also tested the clinical application. Results: Of the 434 recruited patients, 228 responded. In exploratory factor analysis (EFA), the Kaiser-Meyer-Olkin (KMO) measure of sampling adequacy = 0.8 and Bartlett's approx. Chi-Square = 1340.0 (df = 105, p < 0.001). We extracted four common factors which could explain 61.47% of the variance. However, Item 15 "Have you changed a traditional Chinese medicine prescription yourself within the past month?" had factor loading = 0.3 and measure of sampling adequacy (MSA) = 0.5, meaning we could not enter it into the factor analysis. The internal consistency reliability for medication adherence was 0.9, with a Guttman split-half coefficient = 0.5 and a Spearman-Brown coefficient = 0.6. Cronbach's α was 0.9, 0.4 and 0.5 for the knowledge, belief and behavior domains, respectively. The correlation coefficient r of the test-retest reliability was -0.8 and was -0.8, 0.4, -0.3 in the knowledge, belief and behavior domains, respectively. Patients with comorbidities were more likely to respond. We detected no other significant differences in the clinical profiles between respondents and non-respondents. Conclusion: The e-version Chinese and Western medication adherence scales have undesirable construct validity and internal consistency. Thus, caution is needed in transitioning the paper-version scale into an e-version.

9.
Neurochem Res ; 46(12): 3213-3221, 2021 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-34406548

RESUMO

In numerous studies, microRNAs (miRNAs) have been authenticated to play vital roles in the pathophysiology of neuropathic pain and other neurological diseases. In our study, we focused on evaluating miR-378 and its potential effects in neuropathic pain development, as well as the underlying molecular mechanisms. Primarily, a chronic sciatic nerve injury (CCI) rat model was established. Next, reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was employed to measure the expression levels of miR-378 and EZH2 mRNA; the EZH2 protein expression levels were detected by western blot. A luciferase activity assay monitored the interaction of miR-378 and EZH2. Mechanical and thermal hyperalgesia was also performed to quantitate the effects of overexpression of miR-378 or EZH2 on the CCI rats. We found that miR-378 was down-regulated in the CCI rats, and the overexpression of miR-378 produced significant relief in their pain management. EZH2 was the downstream gene of miR-378 and was negatively regulated by miR-378. The up-regulation of EZH2 reduced the inhibitory effects of miR-378 on the development of neuropathic pain in the CCI rats. miR-378 acts as an inhibitor in the progression of neuropathic pain via targeting EZH2; the miR-378/EZH2 axis may be a novel target for the diagnosis and therapy of neuropathic pain in clinical treatment.

10.
Front Bioeng Biotechnol ; 9: 675093, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34249882

RESUMO

Background The medial-pivot (MP) prosthesis was developed to produce more physiological postoperative knee kinematics and better patient satisfaction than traditional prostheses, but outcomes are inconsistent in different studies of Caucasian patients. This study aimed to investigate the postoperative patient satisfaction and in vivo knee kinematics of the MP and posterior-stabilized (PS) prosthesis during gait activity in Chinese patients. Methods A retrospective analysis of 12 patients was received for this study in each MP group and PS group. Patient-reported satisfaction level and Forgotten Joint Score (FJS) were evaluated with questionnaires. A dual fluoroscopic imaging system was used to investigate in vivo knee kinematics of MP and PS total knee arthroplasty (TKA) during treadmill walking at a speed of 0.4 m/s. Results Comparable promising patient satisfaction and overall FJS (MP 60.7 ± 15.35 vs. PS 51.3 ± 17.62, p = 0.174) were found between the MP and PS groups. Peak flexion appeared at around 70% of gait cycle with values of 52.4 ± 7.4° for MP and 50.1 ± 3.6° for PS groups (no difference). Both groups maintained a stable position at the stance phase and began to translated anteriorly at toe-off with an amount of 4.5 ± 2.3 mm in the MP and 6.6 ± 2.7 mm in the PS (p = 0.08) group until late swing. The range of this external rotation motion was 5.9 ± 4.8 and 6.2 ± 4.1° (p = 0.79) for the MP and PS, respectively. Conclusion A similar knee kinematics pattern characterized by a loss of early-stance knee flexion and femoral rollback during walking was observed in the MP and PS TKAs. Our study confirmed similar effectiveness of MP TKA compared to PS TKA in Chinese patients, while the change of knee kinematics of both implants during slow walking should be noted.

11.
Genomics ; 113(5): 3405-3414, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34311045

RESUMO

Structural variations (SVs) are recognized to have an important role in transcriptional regulation, especially in the light of resolved 3D genome structure using high-throughput chromosome conformation capture (Hi-C) technology in mammals. However, the effect of SVs on 3D genome organization in plants remains rarely understood. In this study, we identified 295,496 SVs and 5251 topologically associating domains (TADs) in two diploid and two tetraploid cottons. We observed that approximately 16% of SVs occurred in TAD boundary regions that were called boundary affecting-structural variations (BA-SVs), and had a large effect on disrupting TAD organization. Nevertheless, SVs preferred occurring in TAD interior instead of TAD boundary, probably associated with the relaxed evolutionary selection pressure. We noticed the biased evolution of the At and Dt subgenomes of tetraploid cottons, in terms of SV-mediated disruption of 3D genome structure relative to diploids. In addition, we provide evidence showing that both SVs and TAD disruption could lead to expression difference of orthologous genes. This study advances our understanding of the effect of SVs on 3D genome organization and gene expression regulation in plants.

12.
Sci Total Environ ; 794: 148388, 2021 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-34217078

RESUMO

The SAR has the ability of all-weather and all-time data acquisition, it can penetrate the cloud and is not affected by extreme weather conditions, and the acquired images have better contrast and rich texture information. This paper aims to investigate the use of an object-oriented classification approach for flood information monitoring in floodplains using backscattering coefficients and interferometric coherence of Sentinel-1 data under time series. Firstly, the backscattering characteristics and interference coherence variation characteristics of SAR time series are used to analyze whether the flood disaster information can be accurately reflected and provide the basis for selecting input classification characteristics of subsequent SAR images. Subsequently, the contribution rate index of the RF model is used to calculate the importance of each index in time series to convert the selected large number of classification features into low dimensional feature space to improve the classification accuracy and reduce the data redundancy. Finally, the SAR image features in each period after multi-scale segmentation and feature selection are jointly used as the input features of RF classification to extract and segment the water in the study area to monitor floods' spatial distribution and dynamic characteristics. The results showed that the various attributes of backscatter coefficients and interferometric coherence under time series could accurately correspond with the actual flood risk, and the combined use of backscattering coefficient and interferometric coherence for flood extraction can significantly improve the accuracy of flood information extraction. Overall, the object-based random forest method using the backscattering coefficient and interference coherence of Sentinel-1 time series for flood extraction advances our understanding of flooding's temporal and spatial dynamics, essential for the timely adoption of adaptation and mitigation strategies for loss reduction.


Assuntos
Desastres , Inundações , Monitoramento Ambiental , Radar , Tempo (Meteorologia)
13.
J Orthop Surg Res ; 16(1): 438, 2021 Jul 07.
Artigo em Inglês | MEDLINE | ID: mdl-34233695

RESUMO

BACKGROUND: Medial open wedge high tibial osteotomy (OWHTO) may result in lower limb discrepancy (LLD), and some patients experience uncomfortable symptoms. Studies have found that the degree of LLD is one but not the only high-risk factor for inducing symptoms. The main purpose of this study is to explore the risk factors for symptomatic LLD. METHODS: Sixty-four patients who underwent OWHTO in our hospital between June 2018 and January 2020 were included in the study. Changes in tibia length, lower limb length, femorotibial angle (FTA), LLD, and KOOS score were evaluated before and 1 year after surgery. Questionnaire was used to investigate whether patients had uncomfortable symptoms of LLD after surgery. Binary logistic regression was applied to analyze the risk factors of symptomatic LLD. RESULTS: There were 18 patients with subjective LLD uncomfortableness, 13 of them were occasional and 5 were frequent. Patients had a mean correction angle of 11.7° ± 4.6°, with a mean increase in tibial length of 6.0 ± 3.5 mm, lower limb length of 7.5 ± 2.3 mm, and LLD of 6.9 ± 4.2 mm at 1 year post-operation. Preoperative and postoperative changes in tibia length and lower limb length were statistically significant (P < 0.0001).There were statistically significant differences in pain, symptoms, ADL, sports/recreations, QOL of KOOS subclassification before and after surgery (P < 0.0001). Binary logistic regression revealed that age ≥ 55, BMI ≥ 28, and LLD ≥ 10 mm were high-risk factors for symptomatic LLD (P = 0.031, OR = 4.82; P = 0.012, OR = 6.251; P = 0.006, OR = 6.836). CONCLUSION: Patients with age ≥ 55, BMI ≥ 28, and postoperative LLD ≥ 10 mm are more likely to develop symptomatic LLD. Older or heavier patients, who are expected to have an LLD greater than 10 mm after OWHTO should be fully informed of the possibility of postoperative LLD symptoms.


Assuntos
Desigualdade de Membros Inferiores/etiologia , Osteoartrite do Joelho/cirurgia , Osteotomia/métodos , Dor Pós-Operatória/etiologia , Complicações Pós-Operatórias/etiologia , Tíbia/cirurgia , Adulto , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Medição da Dor , Fatores de Risco
14.
Bone Joint J ; 103-B(5): 923-930, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33934659

RESUMO

AIMS: As a proven and comprehensive molecular technique, metagenomic next-generation sequencing (mNGS) has shown its potential in the diagnosis of pathogens in patients with periprosthetic joint infection (PJI), using a single type of specimen. However, the optimal use of mNGS in the management of PJI has not been explored. In this study, we evaluated the diagnostic value of mNGS using three types of specimen with the aim of achieving a better choice of specimen for mNGS in these patients. METHODS: In this prospective study, 177 specimens were collected from 59 revision arthroplasties, including periprosthetic tissues, synovial fluid, and prosthetic sonicate fluid. Each specimen was divided into two, one for mNGS and one for culture. The criteria of the Musculoskeletal Infection Society were used to define PJI (40 cases) and aseptic failure (19 cases). RESULTS: The sensitivity and specificity of mNGS in the diagnosis of PJI were 95% and 94.7%, respectively, for all types of specimen. The sensitivity and specificity were 65% and 100%, respectively, for periprosthetic tissues, 87.5% and 94.7%, respectively, for synovial fluid, and 92.5% and 94.7%, respectively, for prosthetic sonicate fluid. The mNGS of prosthetic sonicate fluid outperformed that for other types of specimen in the rates of detection of pathogens (84.6%), sequencing reads (> ten-fold) and the rate of genome coverage (> five-fold). CONCLUSION: mNGS could serve as an accurate diagnostic tool in the detection of pathogens in patients with a PJI using three types of specimen. Due to its superior perfomance in identifying a pathogen, mNGS of prosthetic sonicate fluid provides the most value and may partly replace traditional tests such as bacteriological culture in these patients. Cite this article: Bone Joint J 2021;103-B(5):923-930.


Assuntos
Artroplastia de Quadril , Metagenômica/métodos , Infecções Relacionadas à Prótese/genética , Infecções Relacionadas à Prótese/microbiologia , Idoso , Artroplastia do Joelho , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Estudos Prospectivos , Reoperação , Sensibilidade e Especificidade
15.
Mater Sci Eng C Mater Biol Appl ; 124: 112069, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33947562

RESUMO

Peri-implant infection after hip and knee arthroplasty is a common and serious complication. Titanium (Ti), polyethylene (PE), and Al2O3 materials used as joint prosthesis materials have good biocompatibility and mechanical strength but no antibacterial effect. This study aimed to provide a theoretical basis for the design and manufacture of joint prosthesis materials with antibacterial effect. We applied a coating of gentamicin-silk protein (GS-Silk) on the surface of these materials. We characterized the Ti, PE, and Al2O3 materials coated with GS-Silk (experimental group) and performed in vivo and in vitro experiments to test antibacterial activity. Scanning electron microscopy confirmed successful GS-Silk coating, and infrared spectroscopy confirmed successful loading of gentamicin onto the three materials. Nanoscratch test proved that the GS-Silk coating is relatively reliable on the surface of these three materials. The antibacterial effect of the coating in vitro and in vivo was verified by performing bacteriostatic ring test in vitro, bacterial adhesion test, and subendothelial implant infection test. We demonstrated that GS-Silk coating can effectively load gentamicin onto Ti, PE, and Al2O3 materials and change the gentamicin release rate with a change in the solution pH to achieve intelligent release. The GS-Silk coating is relatively reliable on the surface of these three materials. Ti, PE, and Al2O3 materials coated with GS-Silk have good antibacterial ability, both in vivo and in vitro.


Assuntos
Gentamicinas , Titânio , Antibacterianos/farmacologia , Materiais Revestidos Biocompatíveis/farmacologia , Gentamicinas/farmacologia , Polietileno , Seda , Propriedades de Superfície , Titânio/farmacologia
16.
BMC Plant Biol ; 21(1): 229, 2021 May 22.
Artigo em Inglês | MEDLINE | ID: mdl-34022812

RESUMO

BACKGROUND: Casein kinase I (CKI) is a kind of serine/threonine protein kinase highly conserved in plants and animals. Although molecular function of individual member of CKI family has been investigated in Arabidopsis, little is known about their evolution and functions in Gossypium. RESULTS: In this study, five cotton species were applied to study CKI gene family in cotton, twenty-two species were applied to trace the origin and divergence of CKI genes. Four important insights were gained: (i) the cotton CKI genes were classified into two types based on their structural characteristics; (ii) two types of CKI genes expanded with tetraploid event in cotton; (iii) two types of CKI genes likely diverged about 1.5 billion years ago when red and green algae diverged; (iv) two types of cotton CKI genes which highly expressed in leaves showed stronger response to photoperiod (circadian clock) and light signal, and most two types of CKI genes highly expressed in anther showed identical heat inducible expression during anther development in tetraploid cotton (Gossypium hirsutum). CONCLUSION: This study provides genome-wide insights into the evolutionary history of cotton CKI genes and lays a foundation for further investigation of the functional differentiation of two types of CKI genes in specific developmental processes and environmental stress conditions.


Assuntos
Caseína Quinase I/genética , Evolução Molecular , Gossypium/genética , Proteínas de Plantas/genética , Caseína Quinase I/metabolismo , Genoma de Planta , Gossypium/crescimento & desenvolvimento , Gossypium/metabolismo , Proteínas de Plantas/metabolismo
17.
Mol Biol Evol ; 38(9): 3621-3636, 2021 Aug 23.
Artigo em Inglês | MEDLINE | ID: mdl-33973633

RESUMO

Transposable element (TE) amplification has been recognized as a driving force mediating genome size expansion and evolution, but the consequences for shaping 3D genomic architecture remains largely unknown in plants. Here, we report reference-grade genome assemblies for three species of cotton ranging 3-fold in genome size, namely Gossypium rotundifolium (K2), G. arboreum (A2), and G. raimondii (D5), using Oxford Nanopore Technologies. Comparative genome analyses document the details of lineage-specific TE amplification contributing to the large genome size differences (K2, 2.44 Gb; A2, 1.62 Gb; D5, 750.19 Mb) and indicate relatively conserved gene content and synteny relationships among genomes. We found that approximately 17% of syntenic genes exhibit chromatin status change between active ("A") and inactive ("B") compartments, and TE amplification was associated with the increase of the proportion of A compartment in gene regions (∼7,000 genes) in K2 and A2 relative to D5. Only 42% of topologically associating domain (TAD) boundaries were conserved among the three genomes. Our data implicate recent amplification of TEs following the formation of lineage-specific TAD boundaries. This study sheds light on the role of transposon-mediated genome expansion in the evolution of higher-order chromatin structure in plants.

18.
BMC Genomics ; 22(1): 277, 2021 Apr 17.
Artigo em Inglês | MEDLINE | ID: mdl-33865322

RESUMO

BACKGROUND: Heterosis has been exploited for decades in different crops due to resulting in dramatic increases in yield, but relatively little molecular evidence on this topic was reported in cotton. RESULTS: The elite cotton hybrid variety 'Huaza Mian H318' (H318) and its parental lines were used to explore the source of its yield heterosis. A four-year investigation of yield-related traits showed that the boll number of H318 showed higher stability than that of its two parents, both in suitable and unsuitable climate years. In addition, the hybrid H318 grew faster and showed higher fresh and dry weights than its parental lines at the seedling stage. Transcriptome analysis of seedlings identified 17,308 differentially expressed genes (DEGs) between H318 and its parental lines, and 3490 extremely changed DEGs were screened out for later analysis. Most DEGs (3472/3490) were gathered between H318 and its paternal line (4-5), and only 64 DEGs were found between H318 and its maternal line (B0011), which implied that H318 displays more similar transcriptional patterns to its maternal parent at the seedling stage. GO and KEGG analyses showed that these DEGs were highly enriched in photosynthesis, lipid metabolic, carbohydrate metabolic and oxidation-reduction processes, and the expression level of these DEGs was significantly higher in H318 relative to its parental lines, which implied that photosynthesis, metabolism and stress resistances were enhanced in H318. CONCLUSION: The enhanced photosynthesis, lipid and carbohydrate metabolic capabilities contribute to the heterosis of H318 at the seedling stage, and establishes a material foundation for subsequent higher boll-setting rates in complex field environments.


Assuntos
Gossypium , Vigor Híbrido , Carboidratos , Expressão Gênica , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Gossypium/genética , Vigor Híbrido/genética , Fotossíntese/genética
19.
Genomics ; 113(4): 1999-2009, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-33915244

RESUMO

The high-quality reference-grade genome for Gossupium tomentosum can greatly promote the progress in biological research and introgression breeding for the mainly cultivated species, G. hirsutum. Here, we report a high-quality genome assembly for G. tomentosum by integrating PacBio and Hi-C technologies. Comparative genomic analysis revealed a large number of genetic variations. Two re-sequencing-based ultra-dense genetic maps were constructed which comprised 4,047,199 and 6,009,681 SNPs, 4120 and 4599 bins and covering 4126.36 cM and 4966.72 cM in the EMF2 (F2 from G. hirsutum × G. tomentosum) and GHF2 (F2 from G. hirsutum × G. barbadense). The EMF2 exhibited lower recombination rate at the whole-genome level as compared with GHF2. We mapped 22 and 33 QTL associated with crossover frequency and predicted Gh_MRE11 and Gh_FIGL1 as the candidate genes governing crossover in the EMF2 and GHF2, respectively. We identified 13 significant QTL that regulate the floral transition, and revealed that Gh_AGL18 was associated with the floral transition. Therefore, our study provides a valuable genomic resource to support a better understanding of cotton interspecific cross and recombination landscape for genetic improvement and breeding in cotton.

20.
Genome Biol ; 22(1): 119, 2021 04 23.
Artigo em Inglês | MEDLINE | ID: mdl-33892774

RESUMO

BACKGROUND: Millennia of directional human selection has reshaped the genomic architecture of cultivated cotton relative to wild counterparts, but we have limited understanding of the selective retention and fractionation of genomic components. RESULTS: We construct a comprehensive genomic variome based on 1961 cottons and identify 456 Mb and 357 Mb of sequence with domestication and improvement selection signals and 162 loci, 84 of which are novel, including 47 loci associated with 16 agronomic traits. Using pan-genome analyses, we identify 32,569 and 8851 non-reference genes lost from Gossypium hirsutum and Gossypium barbadense reference genomes respectively, of which 38.2% (39,278) and 14.2% (11,359) of genes exhibit presence/absence variation (PAV). We document the landscape of PAV selection accompanied by asymmetric gene gain and loss and identify 124 PAVs linked to favorable fiber quality and yield loci. CONCLUSIONS: This variation repertoire points to genomic divergence during cotton domestication and improvement, which informs the characterization of favorable gene alleles for improved breeding practice using a pan-genome-based approach.

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