木本高山花卉马缨杜鹃的全基因组扫描分析

本研究采用高通量测序技术(Illumina Hiseq ~(TM)2000)首次对世界名贵园林花卉马缨杜鹃(Rhododendron delavayi)进行了基因组大小的测定,并评估了马缨杜鹃的GC含量、杂合率和序列重复度等信息参数,为马缨杜鹃全基因组测序策略的选择提供了有据参考。全基因组扫描结果如下:马缨杜鹃的基因组大小约为698 Mb,杂合率较高约为1.25%,GC含量约为39%,且具有一定的基因组序列重复度。研究表明:马缨杜鹃的全基因组测序分析不宜采用全基因组鸟枪法(WGS),可尝试WGS与fosmid或BAC-to-BAC相结合的测序策略,亦或采用杂合组装软件进行序列拼装,以提高全基因组序列的拼装质量。     

宽边黄粉蝶(Eurema hecabe)基因组Survey分析

宽边黄粉蝶(Eurema hecabe)是重要的传粉昆虫,广布于非洲热带区、东洋区、澳洲区及古北区东部,具有较高的学术价值和经济意义。为了深入研究其广泛适应性,确定适合该蝴蝶的全基因组的测序研究策略,我们首先做低覆盖度的基因组Survey测序,然后做大规模的全基因组深度测序。采用第二代高通量的测序技术作为该研究的研究方法,测定了宽边黄粉蝶基因组大小,并利用生物信息学方法估计该种的杂合率、重复序列和GC含量等基因组信息。结果表明:(1)宽边黄粉蝶的基因组大小估计为285.34 Mb,测序深度51×;(2)从K-mer分布曲线发现黄粉蝶基因组有明显的杂合峰,杂合率达1.97%,重复序列比例为35.37%。该研究结果对于揭示宽边黄粉蝶物种的起源和进化及适应性具有重要意义,为宽边黄粉蝶选择全基因组测序策略提供依据。     

崖壁植物太行菊与长裂太行菊全基因组大小及特征分析北大核心CSCD

太行菊(Opisthopappus taihangensis)、长裂太行菊(O.longilobus),为太行山特有多年生崖壁草本植物,菊科(Compositae)重要野生资源,具有较高的经济与生态价值。为确定适合两物种的全基因组测序策略,该研究利用流式细胞法和高通量测序技术,分析两物种基因组大小、杂合率、重复序列及GC含量等信息。结果表明:(1)流式细胞法估算太行菊基因组大小约为2.1 Gb,长裂太行菊基因组大小约为2.4 Gb。(2)高通量测序修正后太行菊基因组大小为3.13 Gb,重复序列比例为84.35%,杂合度为0.99%,GC含量为36.56%;长裂太行菊基因组为3.18 Gb,重复序列比例为83.83%,杂合度为1.17%,GC含量为36.62%。(3)初步组装后GC含量分布及平均深度存在异常,出现分层现象,可能是两物种基因组杂合率较高所致。综上结果表明,太行菊、长裂太行菊均属于高重复、高杂合、大基因组的复杂基因组,建议使用Illumina+PacBio测序组装策略,进行全基因组测序分析。     

罗汉果全基因组Survey分析

罗汉果是广西特有药用及甜料植物,其主要成分之一甜苷V作为天然、非糖甜味剂,具有广阔的开发前景,但罗汉果目前完全来自于栽培,适生区狭窄,连作障碍严重,加之含量低导致甜苷V生产成本居高不下,严重限制了其应用。为了减少盲目性,在大规模全基因组深度测序之前,先做低覆盖度的基因组Survey测序,评价基因组的大小及复杂程度,以确定适合该植物全基因组的测序研究策略。该研究采用第二代高通量测序技术(Illumina Hiseq TM 2000)首次测定了罗汉果基因组大小,并利用生物信息学方法估计罗汉果杂合率、重复序列和GC含量等基因组信息。结果表明:(1)获得了18.1 Gb罗汉果基因组测序数据,基因组大小估计为344.95 Mb左右,测序深度为52×;(2)从K-mer分布曲线发现罗汉果基因组有明显的杂合峰,杂合率达1.5%,基因组高杂合导致组装的结果中Contig N50和Scaffold N50的长度比预期的要短很多,还造成GC平均深度及含量分布明显异常,存在一个低深度分布区域。基因组主峰后面有微弱的重复峰,说明罗汉果存在较多的重复序列;(3)由于罗汉果存在高杂合率和重复序列较多的特点,该基因组测序分析仅采用全基因组鸟枪法(WGS)策略不合适,为了更好地对全基因组进行序列拼接和组装,可尝试结合采用Fosmid-to-Fosmid或BAC-to-BAC策略。该研究结果对于揭示罗汉果产量、有效成分含量、发育及抗病虫的分子机制,以及通过分子育种来提高甜苷V含量和降低生产成本具有重要意义,为全基因组测序策略的选择提供了依据。     

甘薯属耐盐植物马鞍藤基因组大小及特征分析

马鞍藤(Ipomoea pes-caprae(L.)R. Br.)是甘薯的近缘野生种之一,为热带、亚热带海滩生长的多年生藤蔓植物,作为沿海地区的园林绿化植物之一,具有较强的耐盐性。马鞍藤基因组学的研究可为耐盐甘薯种质创制提供信息参考。本试验调查了马鞍藤基因组大小和特征概况,为后续全基因组精细图谱绘制打下基础。研究以已知基因组大小的三裂叶薯(Ipomoea triloba L.)为对照,运用流式细胞术对马鞍藤基因组大小进行初步预估;使用二代高通量测序技术(Illumina Hiseq2500)对马鞍藤基因组进行survey评估,测序深度30×,利用生物信息学方法估算马鞍藤GC含量(即鸟嘌呤和胞嘧啶所占比例)、杂合率、重复序列等基因组概况。结果表明:流式细胞术估算马鞍藤基因组大小为1012.704±17.37 Mb;经全基因组Survey测定获得马鞍藤有效数据为21.71 Gb,基因组大小经修正后估算为1041.65 Mbp;通过K-mer分布曲线估算马鞍藤基因组中重复序列所占比率为74.52%,杂合率为0.99%;经初步组装后,GC平均深度及含量分布存在异常,出现分层的现象,这可能与马鞍藤基因组杂合率较高有关。本试验首次报导甘薯属耐盐植物马鞍藤基因组大小及特征信息,为马鞍藤进一步的全基因组深度测序和甘薯耐盐基因挖掘打下基础。     

基于流式细胞术和K-mer分析的银缕梅属(Parrotia C.A.Mey.)植物基因组大小测定

金缕梅科(Hamamelidaceae)银缕梅属(Parrotia C.A.Mey.)仅包含银缕梅(Parrotia subaequalis(H.T.Chang)R.M.Hao&H.T.Wei)和波斯铁木(Parrotia persica(DC.)C.A.Mey.)两种落叶阔叶乔木,其中银缕梅是我国华东地区特有的Ⅰ级濒危珍稀保护植物,属东亚第三纪孑遗成分;其姊妹种波斯铁木则间断分布于伊朗北部,属北极第三纪孑遗植物类群。本研究首次利用流式细胞术和K-mer分析方法对银缕梅属两姊妹种的基因组大小进行了测定,建立和优化了以萝卜(Raphanus sativus L.‘Saxa’)为内标、WPB(Woody plant buffer)为细胞核解离液的两种植物单倍体基因组的DNA含量(DNA C值)流式测定的适宜体系,旨在为金缕梅科银缕梅属植物的全基因组测序、基因组学研究、种质资源开发和利用以及物种保育等提供前期基础数据参考;同时也可为金缕梅科其他属、种的基因组大小测定提供借鉴。主要研究结果如下:(1)通过流式测定银缕梅基因组大小约为971.45±13.91 Mb,波斯铁木基因组大小约为890.52±24.69 Mb;(2)K-mer分析估测银缕梅基因组大小为951.70 Mb,杂合率为1.740%,重复序列比例为77.50%;波斯铁木基因组大小为858.50 Mb,杂合率为0.695%,重复序列占74.30%;(3)银缕梅属于高杂合和高重复基因组,波斯铁木则属于微杂合和高重复基因组。本研究的结果为银缕梅属植物后续基于DNA三代高通量测序技术的全基因组测序、组装及去冗余处理等工作提供了重要的数据参考。     

基于Survey分析的濒危植物四合木基因组研究

评价濒危植物四合木（Tetraenamongolica）基因组的大小及复杂程度,开展基因组研究可揭示四合木的超旱生机制,进一步挖掘其特色基因资源。为更好破解四合木的全基因组信息,采用第二代高通量测序技术的基因组Survey分析技术开展四合木基因组大小估测研究,并利用生物信息学方法估计了四合木杂合率、重复序列和GC含量等基因组信息。结果表明：四合木基因组大小为1 079.25 Mb,修正后的基因组大小为1 065.84 Mb,杂合率为0.76%,重复序列比例为75.25%,GC含量为33.57%。在经过四合木基因组初步组装后,获得3 502 126条contigs,总计682 Mb,其N50为187 bp,推测四合木基因组属于同源四倍体复杂基因组,全基因组测序组装难度较大。由于四合木的高杂合率,后续可采用第三代高通量测序技术（单分子测序）同时结合染色质区域捕获技术,有望最终获得高质量的四合木全基因图谱。     

大麻状罗布麻的全基因组分析和SSR标记开发

大麻状罗布麻是重要的经济和生态作物,由于基因组数据匮乏和分子标记少而限制其遗传研究工作的开展。本研究利用Illumina测序平台对大麻状罗布麻的基因组大小进行测定,通过生物信息学方法对其基因组杂合度和重复序列等基本信息进行预估,并做了基因组的初步组装,在此基础上对其基因组序列进行了SSR查找。研究结果表明,总测序量为31.94 Gb,测序质量正常(Q20≥90%,Q30≥85%),与NCBI核苷酸数据库(NT)比对显示样本不存在外源污染;K-mer分析(K=17)结果显示,大麻状罗布麻基因组大小为239.02 Mbp,杂合率为0.56%,重复序列占全基因组比例为36.72%,初步预估大麻状罗布麻基因组为复杂基因组;采用K-mer=41进行基因组初步组装,共获得273336条contigs,N50为3838 bp,总长为222723253 bp,进一步将contigs进行连接、延长,组装得到224587条scaffolds,N50为6421 bp,总长为226378236 bp;此外,对基因组数据进行SSR分子遗传标记分析,共鉴定出117511个SSR,不同类型核苷酸重复差异较大,单核苷酸重复最多,六核苷酸重复最少。该研究为后续全基因组de novo测序及组装策略提供依据。     

印度血桐与中平树基因组调查及SSR分子标记分析

印度血桐与中平树是大戟科血桐属植物,该属植物具有多种药用价值,被广泛应用于民间医学中许多疾病的治疗,这两种植物种子中含有的神经酸也引起了研究者的高度关注。为确定适合印度血桐与中平树的全基因组测序研究策略,该研究采用二代高通量测序技术,结合生物信息学的方法首次测定了印度血桐与中平树的基因组大小、杂合率、重复率等基因组信息并初步分析了两种材料的SSR序列特征。结果表明:(1)印度血桐与中平树的基因组大小分别为986.84和946.23 M。(2)印度血桐与中平树的杂合率分别为0.75%和0.65%,重复序列比例分别为73.02%和71.5%。(3)通过对2种材料基因组序列的SSR特征分析,在印度血桐中共鉴定了4 499 185个SSR,在中平树中共鉴定了4 969 098个SSR。该研究结果为印度血桐与中平树SSR分子标记的筛选、开发以及全基因组深度测序提供了理论指导。     

蒙古沙冬青基因组调查及SSR分析

蒙古沙冬青是第三纪冰川孑遗物种,具有极强的耐逆性,是研究植物耐逆分子机制的良好材料。利用高通量测序技术和生物信息学工具预测蒙古沙冬青的基因组大小及杂合度,进行SSR分子遗传标记的初步鉴定。蒙古沙冬青基因组大小约为812 Mb,杂合率为0.506%,基因组杂合度较高。对基因组进行拼接,进行SSR分子遗传标记分析,共鉴定183 102个SSR,不同类型核苷酸重复差异较大,其中,二核苷酸重复中的AT/TA含量最高,四核苷酸重复最少,共占总数的1.48%。     

A Unique Protease Cleavage Site Predicted in the Spike Protein of the Novel Pneumonia Coronavirus (2019-nCoV) Potentially Related to Viral Transmissibility

正Dear Editor,In December 2019, a novel human coronavirus caused an epidemic of severe pneumonia(Coronavirus Disease 2019,COVID-19) in Wuhan, Hubei, China(Wu et al. 2020; Zhu et al. 2020). So far, this virus has spread to all areas of China and even to other countries. The epidemic has caused 67,102 confirmed infections with 1526 fatal cases     

Curcuminoids as inhibitors of thioredoxin reductase: A receptor based pharmacophore study with distance mapping of the active site

Curcumin is the yellow pigment of turmeric that interacts irreversibly forming an adduct with thioredoxin reductase (TrxR), an enzyme responsible for redox control of cell and defence against oxidative stress. Docking at both the active sites of TrxR was performed to compare the potency of three naturally occurring curcuminoids, namely curcumin, demethoxy curcumin and bis-demethoxy curcumin. Results show that active sites of TrxR occur at the junction of E and F chains. Volume and area of both cavities is predicted. It has been concluded by distance mapping of the most active conformations that Se atom of catalytic residue SeCYS498, is at a distance of 3.56 from C13 of demethoxy curcumin at the E chain active site, whereas C13 carbon atom forms adduct with Se atom of SeCys 498. We report that at least one methoxy group in curcuminoids is necessary for interation with catalytic residues of thioredoxin. Pharmacophore of both active sites of the TrxR receptor for curcumin and demethoxy curcumin molecules has been drawn and proposed for design and synthesis of most probable potent antiproliferative synthetic drugs.     

Comparative morphology of the carpel in the Liliaceae: Hewardieae, Petrosavieae, and Tricyrteae

The young pistils in the melanthioid tribes, Hewardieae, Petrosavieae and Tricyrteae, are uniformly tricarpellate and syncarpous. They lack raphide idioblasts. All are multiovulate, with bitegmic ovules. The Petrosavieae are marked by the presence of septal glands and incomplete syncarpy. Tepals and stamens adhere to the ovary in the Hewardieae and the Petrosavieae but not in the Tricyrteae. Two vascular bundles occur in the stamens of the Hewartlieae and Tricyrtis latifolia. Ventral bundles in the upper part of the ovary of the Hewardieae are continuous with compound septal bundles and placental bundles in the lower part. Putative ventral bundles occur in the alternate position in the Tricyrteae and putative placental bundles in the opposite. position in the Petrosavieae. The dichtomously branched stigma in each carpel of the Tricyrteae is supplied by a bifurcated dorsal bundle.     

Enterovirus 71 3C proteolytically processes the histone H3 N-terminal tail during infection

Highlights
1. The N-terminal tail of histone H3 is specifically cleaved during EV71 infection.
2. Viral protease 3C is identified as a protease responsible for proteolytically processing the N-terminal H3 tail.
3. Our finding reveals a new epigenetic regulatory mechanism for Enterovirus 71 in virus-host interactions.     

Detection of EBV and HHV6 in the Brain Tissue of Patients with Rasmussen’s Encephalitis

Rasmussen’s encephalitis (RE) is a rare pediatric neurological disorder, and the exact etiology is not clear. Viral infection may be involved in the pathogenesis of RE, but conflicting results have reported. In this study, we evaluated the expression of both Epstein-Barr virus (EBV) and human herpes virus (HHV) 6 antigens in brain sections from 30 patients with RE and 16 control individuals by immunohistochemistry. In the RE group, EBV and HHV6 antigens were detected in 56.7% (17/30) and 50% (15/30) of individuals, respectively. In contrast, no detectable EBV and HHV6 antigen expression was found in brain tissues of the control group. The co-expression of EBV and HHV6 was detected in 20.0% (6/30) of individuals. In particular, a 4-year-old boy had a typical clinical course, including a medical history of viral encephalitis, intractable epilepsy, and hemispheric atrophy. The co-expression of EBV and HHV6 was detected in neurons and astrocytes in the brain tissue, accompanied by a high frequency of CD8⁺ T cells. Our results suggest that EBV and HHV6 infection and the activation of CD8⁺ T cells are involved in the pathogenesis of RE.     

Perinatal Vertical Transmission of Chikungunya Virus in Ruili,a Town on the Border between China and Myanmar

正Dear Editor,Chikungunya virus (CHIKV), an arbovirus in the family of Togaviridae, genus Alphavirus, is transmitted by the A.aegyptii or A. albopictus mosquito, and causes disease in humans characterized by fever, rash, and arthralgia (Silva and Dermody 2017; Suhrbier 2019). It was first reported in 1953 in Tanzania, and caused only a few outbreaks and sporadic cases in Africa and Asia in last century. However, in the epidemic in 2004, CHIKV acquired mutations that conferred enhanced transmission by the A. albopictus mosquito(Schuffenecker et al. 2006). Since then, it has successively caused outbreaks in Africa, the Indian Ocean, South East Asia, the South America, and Europe (Zeller et al. 2016).     

Development of a Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2

In conclusion, the novel visual RT-LAMP assay is a simple, rapid, and sensitive approach for detection of SARS-CoV-2, and it is ready for application in primary care and community hospitals or health care centers, and even patients' own houses in response to the current SARS-CoV-2 epidemic because the assay does not require sophisticated equipment and skilled personnel. Furthermore, it is also ready to be used in fields for screening samples from wild animals and environments to facilitate the identification of potential intermediate hosts that mediate the cross-species transmission of SARS-CoV-2 from bats to humans.