DNA barcoding of Oryza: conventional,specific, and super barcodes

Key message

We applied the phylogenomics to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity.

Abstract

Rice (genus Oryza) is one of the most important crops in the world, supporting half of the world’s population. Breeding of high-yielding and quality cultivars relies on genetic resources from both cultivated and wild species, which are collected and maintained in seed banks. Unfortunately, numerous seeds are mislabeled due to taxonomic issues or misidentifications. Here, we applied the phylogenomics of 58 complete chloroplast genomes and two hypervariable nuclear genes to determine species identity in rice seeds. Twenty-one Oryza species were identified. Conspecific relationships were determined between O. glaberrima and O. barthii, O. glumipatula and O. longistaminata, O. grandiglumis and O. alta, O. meyeriana and O. granulata, O. minuta and O. malampuzhaensis, O. nivara and O. sativa subsp. indica, and O. sativa subsp. japonica and O. rufipogon. D and L genome types were not found and the H genome type was extinct. Importantly, we evaluated the performance of four conventional plant DNA barcodes (matK, rbcL, psbA-trnH, and ITS), six rice-specific chloroplast DNA barcodes (psaJ-rpl33, trnC-rpoB, rps16-trnQ, rpl22-rps19, trnK-matK, and ndhC-trnV), two rice-specific nuclear DNA barcodes (NP78 and R22), and a chloroplast genome super DNA barcode. The latter was the most reliable marker. The six rice-specific chloroplast barcodes revealed that 17% of the 53 seed accessions from rice seed banks or field collections were mislabeled. These results are expected to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity.

     

Transient silencing of VvCSN5 enhances powdery mildew resistance in grapevine (Vitis vinifera)

As one of the most economically important fruit crops in the world, the grapevine (Vitis vinifera) suffers significant yield losses from various pathogens including powdery mildew caused by Erysiphe necator. In contrast, several wild Chinese grapevines, including Vitis pseudoreticulata accession Baihe-35-1, are highly resistant to powdery mildew pathogens. Here, we identified a grapevine gene CSN5 (COP9 signalosome complex subunit 5), designated VvCSN5, that was differentially expressed between the resistant ‘Baihe-35-1’ and susceptible ‘Thompson Seedless’ during powdery mildew isolate Erysiphe necator NAFU1 infection. Moreover, transient silencing of VvCSN5 in ‘Thompson Seedless’ leaves enhanced resistance to En NAFU1. This resistance manifested in cell wall callose deposition at attempted infection sites and hypersensitive response-like cell death of penetrated epidermal cells. Several defense-related marker genes (VvPR1, VvPR3, VvPAD4, and VvRBOHD) had higher basal expression levels in VvCSN5-silenced leaves. In addition, we found the structure and activity of CSN5 promoters in ‘Thompson Seedless’ and ‘Baihe-35-1’ were different, which may have been behind their different resistances to powdery mildew infection. Taken together, these results implied that grapevine CSN5 plays an important role in the response to powdery mildew infection.

     

Vegetation recovery alters soil N status in subtropical karst plateau area: Evidence from natural abundance δ15N and δ18O

Plant and Soil - Forest recovery from disturbance can alter soil nitrogen (N) status as a result of complex interactions in plant-soil system. The δ15N and δ18O are indicators that...     

Rho-kinase inhibitor hydroxyfasudil protects against HIV-1 Tat-induced dysfunction of tight junction and neprilysin/Aβ transfer receptor expression in mouse brain microvessels

HIV-1 transactivator protein (Tat) induces tight junction (TJ) dysfunction and amyloid-beta (Aβ) clearance dysfunction, contributing to the development and progression of HIV-1-associated neurocognitive disorder (HAND). The Rho/ROCK signaling pathway has protective effects on neurodegenerative disease. However, the underlying mechanisms of whether Rho/ROCK protects against HIV-1 Tat-caused dysfunction of TJ and neprilysin (NEP)/Aβ transfer receptor expression have not been elucidated. C57BL/6 mice were administered sterile saline (i.p., 100 μL) or Rho-kinase inhibitor hydroxyfasudil (HF) (i.p., 10 mg/kg) or HIV-1 Tat (i.v., 100 μg/kg) or HF 30 min before being exposed to HIV-1 Tat once a day for seven consecutive days. Evans Blue (EB) leakage was detected via spectrophotometer and brain slides in mouse brains. The protein and mRNA levels of zonula occludens-1 (ZO-1), occludin, NEP, receptor for advanced glycation end products (RAGE), and low-density lipoprotein receptor-related protein 1 (LRP1) in mouse brain microvessels were, respectively, analyzed by Western blotting and quantitative real-time polymerase chain reaction (qRT-PCR) analyses. Exposure of the mice to HIV-1 Tat increased the amount of EB leakage, EB fluorescence intensity, blood–brain barrier (BBB) permeability, as well as the RAGE protein and mRNA levels, and decreased the protein and mRNA levels of ZO-1, occludin, NEP, and LRP1 in mouse brain microvessels. However, these effects were weakened by Rho-kinase inhibitor HF. Taken together, these results provide information that the Rho/ROCK signaling pathway is involved in HIV-1 Tat-induced dysfunction of TJ and NEP/Aβ transfer receptor expression in the C57BL/6 mouse brain. These findings shed some light on potentiality of inhibiting Rho/Rock signaling pathway in handling HAND.

     

Salidroside Inhibits Reactive Astrogliosis and Glial Scar Formation in Late Cerebral Ischemia via the Akt/GSK-3β Pathway

Neurochemical Research - Cerebral ischemia leads to reactive astrogliosis and glial scar formation. Glial scarring can impede functional restoration during the recovery phase of stroke. Salidroside...     

抑咽侧体素基因在大猿叶虫生殖滞育准备中的功能分析

【目的】本研究旨在明确大猿叶虫Colaphellus bowringi促咽侧体素(allatotropin, AT)和抑咽侧体素(allatostatin, AST)基因的分子特征,分析其在该虫生殖和滞育过程中的表达差异,并探究其在大猿叶虫生殖滞育准备中的功能。【方法】利用前期建立的大猿叶虫转录组数据库,鉴定大猿叶虫CbAT和CbASTs基因序列并克隆其开放阅读框(ORFs),并对其序列进行生物信息学分析;通过qRT-PCR技术检测CbAT和CbASTs在大猿叶虫注定滞育和注定非滞育雌蛹和雌成虫头部的表达模式;对注定滞育大猿叶虫2日龄雌蛹进行CbAST-B, CbAST-C以及CbAST-B+CbAST-C RNAi试验后,检测4日龄雌成虫保幼激素(juvenile hormone, JH)信号基因以及卵黄原蛋白基因的表达量变化。【结果】鉴定并克隆了大猿叶虫的一个促咽侧体素基因CbAT(GenBank登录号: MT977128)及两个抑咽侧体素基因CbAST-B(GenBank登录号: MT977126)和CbAST-C(GenBank登录号: MT977127),其开放阅读框分别长408, 600和303 bp。通过氨基酸序列比对和系统进化分析发现,CbAT, CbAST-B和CbAST-C均与鞘翅目昆虫的同源蛋白聚在一支,在进化上表现出较高保守性。qRT-PCR检测发现,CbAT基因在注定滞育与注定非滞育2日龄雌蛹到4日龄雌成虫头部中始终无表达差异;而CbAST-B和CbAST-C基因分别自雌成虫1和2日龄开始在注定滞育雌成虫头部显著高表达,且在注定滞育和注定非滞育个体中的差异表达状态一直持续到滞育准备期结束。在注定滞育2日龄雌蛹中沉默CbAST-B, CbAST-C以及同时沉默CbAST-B和CbAST-C后,检测4日龄雌成虫头部的干扰效率发现,CbAST-B和CbAST-C的表达均受到显著抑制,干扰效率达70%以上。在去除触角的头部中,JH合成途径基因AACT, FPPS和JHAMT以及脂肪体中JH应答基因Kr-h1和JHE1的表达在dsCbAST-B, dsCbAST-C和dsCbAST-B+dsCbAST-C处理组中均被显著上调,脂肪体中卵黄原蛋白基因Vg1和Vg2的表达也被显著上调。【结论】CbAT基因可能并非造成大猿叶虫产卵前期与滞育准备期保幼激素信号产生差异的主要原因,而在生殖滞育准备期CbAST-B和CbAST-C抑制了JH的合成,进而抑制Vgs的表达以促进滞育的发生。本研究进一步揭示了昆虫生殖滞育准备期保幼激素信号的上游调控机制,有助于进一步理解昆虫对环境的季节性适应策略,为挖掘害虫防治的新靶标提供了新的指导和借鉴。     

长足大竹象消化道不同分段菌群异质性及竹木质纤维素降解能力

【目的】长足大竹象Cyrtotrachelus buqueti消化道共生菌群参与了竹纤维素的降解。本研究旨在揭示长足大竹象幼虫消化道不同分段共生菌群异质性及木质纤维素的降解能力。【方法】通过对16S rRNA测序对长足大竹象幼虫消化道分段口器(YB)、前肠(YFG)、中肠(YMG)和后肠(YHG)进行菌群组成分析及功能预测;分析各消化道分段核心属细菌基因组中碳水化合物活性酶(carbohydrate active enzyme, CAZy)基因,预测木质纤维素降解能力;应用口器混合菌(MPJ)、前肠混合菌(FJ)、中肠混合菌(MJ)和后肠混合菌(HJ)悬液体外降解竹笋粉,检测共生菌群的木质纤维素的降解能力。【结果】长足大竹象幼虫消化道菌群多样性分析显示,YFG, YMG和YHG的菌群多样性大于YB,YFG的菌群物种多样性最高,而YB最低。YFG, YMG和YHG样本中厚壁菌门(Firmicutes)、拟杆菌门(Bacteroidetes)和变形菌门(Proteobacteria)相对丰度最高,而YB中变形菌门(Proteobacteria)、厚壁菌门(Firmicutes)和放线菌门(Actinobacteria)相对丰度最高。核心属细菌基因组CAZy基因分析表明长足大竹象幼虫消化道中大多数细菌基因组中存在丰富的CAZy基因,且在拟杆菌属Bacteroides细菌基因组中尤为明显,预示其与木质纤维素的降解密切相关。体外降解竹笋粉实验结果表明,长足大竹象幼虫MPJ, FJ, MJ和HJ对竹笋粉纤维素的降解率分别为21.7%, 39.9%, 44.2%和21.0%,对半纤维素降解率分别为72.7%, 52.3%, 65.7%和61.5%,对木质素降解率分别为20.5%, 41.3%, 39.9%和37.9%。【结论】长足大竹象幼虫的消化道菌群的异质性可以影响木质纤维素降解能力,因而这些菌群可以作为分离高效木质纤维素降解菌的重要来源之一。本研究为竹生物质的工业转化利用提供部分参考信息。     

低温对麦红吸浆虫滞育解除及蜕皮激素受体基因EcR和热激蛋白基因Hsp70和Hsp90表达水平的影响

【目的】本研究旨在明确破茧率和破茧所需时间作为典型的专性幼虫期滞育昆虫麦红吸浆虫Sitodiplosis mosellana滞育解除指标的可行性,探讨蜕皮激素受体基因EcR和热激蛋白基因Hsp70和Hsp90在低温解除滞育中的作用。【方法】9月上旬采自田间的麦红吸浆虫滞育幼虫在低温(4℃)和自然变温处理不同时间(0~90 d)后转移至24℃化蛹,调查幼虫的破茧率、化蛹率及破茧和化蛹所需时间;采用qPCR技术分析4℃低温终止滞育并在24℃下恢复发育的幼虫EcR, Hsp70和Hsp90的mRNA水平。【结果】不同时间低温(4℃)和自然变温处理的麦红吸浆虫滞育幼虫破茧率和化蛹率以及破茧和化蛹所需时间均存在显著差异。未经低温(4℃)处理的幼虫在水分满足的条件下破茧率为71.3%,但均不能化蛹;低温(4℃)处理60 d内,随着处理时间的延长破茧率和化蛹率逐渐升高,破茧和化蛹所需时间逐渐缩短;与4℃低温处理30~60 d相比,自然变温处理30~60 d的幼虫化蛹率显著较低;4℃低温处理60 d和自然变温处理90 d后幼虫的化蛹率均超过91%。低温(4℃)处理显著提高了麦红吸浆虫幼虫EcR, Hsp70和Hsp90的表达量,其中处理30 d时其表达量最高,随着低温(4℃)处理时间的延长,表达量逐渐降低,大部分幼虫滞育解除后表达量趋于恒定。【结论】低温能显著促进麦红吸浆虫的滞育解除,效果优于9-10月自然变温;破茧率及破茧所需时间可作为评判麦红吸浆虫幼虫滞育强度的参考,但不能独立作为滞育解除的指标;EcR,Hsp70和Hsp90的表达水平与滞育强度密切相关,在麦红吸浆虫滞育解除中发挥潜在作用。     

NLRP3 regulates alveolar bone loss in ligature‐induced periodontitis by promoting osteoclastic differentiation

ObjectivesNLRP3 inflammasome is a critical part of the innate immune system and plays an important role in a variety of inflammatory diseases. However, the effects of NLRP3 inflammasome on periodontitis have not been fully studied.Materials and methodsWe used ligature‐induced periodontitis models of NLRP3 knockout mice (NLRP3^KO) and their wildtype (WT) littermates to compare their alveolar bone phenotypes. We further used Lysm‐Cre/Rosa^nTnG mouse to trace the changes of Lysm‐Cre⁺ osteoclast precursors in ligature‐induced periodontitis with or without MCC950 treatment. At last, we explored MCC950 as a potential drug for the treatment of periodontitis in vivo and in vitro.ResultsHere, we showed that the number of osteoclast precursors, osteoclast differentiation and alveolar bone loss were reduced in NLRP3^KO mice compared with WT littermates, by using ligature‐induced periodontitis model. Next, MCC950, a specific inhibitor of the NLRP3 inflammasome, was used to inhibit osteoclast precursors differentiation into osteoclast. Further, we used Lysm‐Cre/Rosa^nTnG mice to demonstrate that MCC950 decreases the number of Lysm‐Cre⁺ osteoclast precursors in ligature‐induced periodontitis. At last, treatment with MCC950 significantly suppressed alveolar bone loss with reduced IL‐1β activation and osteoclast differentiation in ligature‐induced periodontitis.ConclusionOur findings reveal that NLRP3 regulates alveolar bone loss in ligature‐induced periodontitis by promoting osteoclastic differentiation.     

Fitness of F1 hybrids between 10 maternal wild soybean populations and transgenic soybean

Transgenic Research - The releasing of transgenic soybeans (Glycine max (L.) Merr.) into farming systems raises concerns that transgenes might escape from the soybeans via pollen into...