基于cpDNA和ITS序列对庭藤复合群的居群遗传学研究

采用2个叶绿体基因组片段(ndh J-trn F和trn D-trn T)和核基因组ITS序列对分布于中国东部和相邻地区的庭藤复合群(Indigofera decora complex)的24个居群进行分析,探讨该复合群的遗传多样性、单倍型分布、遗传结构和居群历史动态。cp DNA和ITS序列分析表明,庭藤复合群的单倍型多样性较高,而总体遗传多样性偏低(cp DNA片段:Hd=0.778,π=0.00123;ITS:Hd=0.909,π=0.01290);皖浙地区居群的遗传多样性相对较高,推测其可能是该复合群遗传多样性的分布中心。遗传变异主要存在于复合群居群间,种内居群间遗传分化较大(cp DNA片段:FST=0.848;ITS:FST=0.787);基因流较小(cp DNA片段:Nm=0.228;ITS:Nm=0.241),主要是地理隔离(遗传漂变)或生境片段化促进了物种形成;复合群的不同物种间存在由基因渐渗引起的单倍型共享现象,可能是种间不完全的生殖隔离所致。花木蓝的居群单独聚为一枝,且与其他种无共享单倍型,因此应保留花木蓝种的分类地位,而其他种的分类地位有待进一步研究。     

濒危植物宽叶羌活天然居群cpDNA非编码区多态性分析

采用叶绿体DNA非编码区直接测序的方法,对青海、甘肃、四川3个省区内濒危植物宽叶羌活14个天然居群的遗传多样性和遗传结构进行了研究,以明确其遗传背景,为宽叶羌活的保护提供理论依据。结果表明:(1)14个居群138个个体的序列长度介于509~515bp;碱基组成A+T含量较高(平均67.6%)。(2)根据序列的核苷酸变异共鉴定出31个单倍型,其中9种单倍型(H5、H1、H9、H10、H16、H17、H19、H20、H22)为居群所共享,而且单倍型H5分布最广、在10个群体的67个个体中检测到,占总样品数的48.56%。(3)14个居群宽叶羌活具有高水平单倍型多样性(Hd=0.750 3)和较高水平核苷酸多样性(Pi=0.007 11),但31个单倍型没有按地理分布形成明显的族群,各地理单元中的单倍型相互混杂,没有明显的地理分化模式。(4)AMOVA分析、居群间分化度(FST=0.602 4)分析和基因流(Nm=0.330)分析的结果一致,表明宽叶羌活大部分遗传变异(60.24%)发生在居群间,居群间的基因流较低,群体间变异是宽叶羌活的主要变异来源。(5)14个居群的遗传距离在0.000~0.007,平均为0.003,表明居群间的亲缘关系较远,且居群间的遗传距离与地理距离之间无显著相关关系(P=0.143),说明宽叶羌活居群遗传变异的分布没有明显的地理趋势。研究认为,宽叶羌活居群间高的遗传变异可能是由基因流受阻、遗传漂变、地理隔离造成的,并提出了对该物种遗传多样性的保护策略。     

濒危植物长柄扁桃的遗传变异格局研究

该研究基于ITS1-ITS4序列对濒危植物长柄扁桃(Amygdalus pedunculata)自然分布区内的8个居群,105个个体的遗传多样性及遗传结构进行了分析,以明确长柄扁桃的地理分布及其遗传多样性特征。结果表明:(1)ITS1-ITS4序列长度583bp,变异位点13个,共定义了8个单倍型;居群间总的遗传多样性(hT)为0.727,居群内平均遗传多样性(hS)为0.564,各居群单倍型多样性、核酸多样性的变化范围分别为0.182~0.636、0.000 6~0.006 3。(2)AMOVA分析表明,33.65%的遗传变异来自居群间,而66.35%的遗传变异来自居群内;居群间平均基因流(Nm)为0.986,居群间遗传分化系数NSTGST(GST=0.225,NST=0.362,P0.05),表明长柄扁桃居群间存在不十分显著的遗传分化,但谱系地理结构显著;中性检验和错配分布曲线表明,居群自然分布区内的长柄扁桃没有经历明显的近期扩张。(3)单倍型网络和最大似然树都表明:内蒙古和陕西的长柄扁桃居群分别聚为2个明显的分支。     

基于cpDNA非编码序列的北沙柳遗传多样性分析

为揭示北沙柳(Salix psammophila)的遗传多样性、遗传结构及分化特征,利用叶绿体非编码区序列(trnL-trnF和trnD-trnT)对分布于毛乌素沙地和库布齐沙漠的16个北沙柳居群(339个个体)进行了遗传研究,为北沙柳种子资源库遗传管理、遗传改良、遗传育种及品种选育提供理论依据。结果表明:(1)经trnL-trnF和trnD-trnT片段联合比对获得了1811 bp序列,共有12个核苷酸变异位点(8个简约信息位点,4个变异位点),得到16个单倍型。(2)单倍型多样性指数(Hd)为0.737,核苷酸多样性指数(π)为0.00107;且单倍型H3的分布在所有居群中位于单倍型网络图中心,其余单倍型随机分布于各个居群。(3)AMOVA分析表明,北沙柳cpDNA的变异主要来源于居群内(91.16%),居群间遗传分化程度中等(FST=0.08837),各居群间的基因交流非常频繁(Nm=2.58);遗传分化系数NST(0.085)显著大于GST(0.056,0.01相似文献   

中国近海细鳞鯻线粒体控制区的遗传多样性

通过线粒体控制区序列的分析,研究采自中国南海及东海5个群体102尾细鳞鯻的遗传多样性。发现在962 bp序列中有205个变异位点,其中135个为简约信息位点,共定义102个单倍型。中国近海细鳞鯻总体呈现出较高的遗传多样性特征(Hd=1.000,Pi=0.022),其中博鳌最高(Hd=1.000,Pi=0.028),平潭最低(Hd=1.000,Pi=0.014)。不同地理群体间无明显分化,基因交流频繁(Fst=-0.014—0.041,P0.05);中性检验均为显著负值,推测在16.9万年—5.06万年前,即中-晚更新世出现种群扩张。系统邻接树和单倍型网络图均出现3个显著分化的谱系(谱系间Fst=0.508—0.698,P0.001;净遗传距离Da=0.024—0.031),且各谱系中均有不同地理来源的群体。3个谱系间分歧时间大约在1.07百万年—0.24百万年前,推测可能是更新世冰期边缘海的出现导致群体隔离而产生分化。谱系A(Lineage A)包含85.3%的个体,其总体遗传多样性较高(Hd=1.000,Pi=0.012),其中平潭最高(Hd=1.000,Pi=0.014),合浦最低(Hd=1.000,Pi=0.010);群体间Fst在-0.021—0.068之间,P0.005;AMOVA分析显示只有1.97%的变异来自于种群间,表明群体间也无明显分化;中性检验均为显著负值,推测在25.4万年—7.6万年前出现种群扩张。中国近海细鳞鯻主要受到中-晚更新世海侵和海退的影响而出现种群扩张使得谱系间发生二次接触,最终形成具有显著谱系结构但无地理分化的情况。     

长江中游鳊群体的遗传多样性

采用线粒体DNA(mt DNA)细胞色素b基因(cytb)和控制区序列,分析长江中游宜都、沙市、燕窝、团风等4个产卵场鳊种群的遗传多样性和遗传结构。结果表明:长江中游鳊群体cytb序列共检出82个多态位点,86种单倍型,平均单倍型多样性指数(Hd)和核苷酸多样性指数(Pi)分别为0.930和0.00244;控制区序列共检出变异位点46个,单倍型76种,Hd指数和Pi指数分别为0.972和0.00505;构建的单倍型网络结构和分子方差分析(AMOVA)显示,4个群体的遗传变异绝大部分来自群体内部,群体间无显著遗传分化;群体间的分化指数(FST)、平均基因流(Nm)和平均K2-P遗传距离均表明,4个鳊地理群体间存在广泛的基因交流,未发生明显群体遗传分化;中性检验表明,鳊历史上发生了群体扩张,扩张时间在第四纪冰期后期。     

基于线粒体COⅡ基因的大豆蚜不同地理种群遗传分化研究

【目的】大豆蚜Aphis glycines逐渐成为栽培大豆上的世界性重要害虫,为明确大豆蚜不同地理种群的遗传分化及遗传多样性,本研究探讨其在中国的种群遗传变异。【方法】测定了采自7个省共14个地理种群339头大豆蚜的线粒体COⅡ基因的673 bp序列,利用Dna SP 5.0、Arlequin 3.5.1.2、Network4.6.1.3等软件对地理种群间的大豆蚜的遗传多样性、遗传分化程度及分子变异进行分析,并建立了单倍型网络图及单倍型系统进化树。【结果】在所分析的339个COⅡ序列中,共检测出7个单倍型,其中H1为各种群所共享。种群内遗传多样性较低(Hd=0.479±0.030,Pi=0.00166±0.00018),种群内遗传分化相对较大(Fst=0.1985),基因流水平较高(Nm=2.019)。中性检验结果不显著(Tajima’s D=﹣0.931,P>0.10,Fu’s Fs=0.220,P>0.10),说明中国地区大豆蚜在较近的历史时期内没有出现种群扩张现象。分子变异分析(AMOVA)结果表明,大豆蚜遗传变异主要来自种群内部(80.15%),而种群间未发生明显的遗传分化。根据各地理种群的单倍型建立的系统发育树、单倍型网络图表明,各单倍型散布在不同的地理种群中,无明显的地理分布格局。【结论】大豆蚜不同地理种群的遗传多样性不高,各种群的遗传距离与地理距离之间没有显著线性相关性,各种群间的基因交流并未受到地理距离的影响。     

中国甜菜夜蛾地理种群的遗传分化与基因流

【目的】为了明确我国甜菜夜蛾Spodoptera exigua地理种群间的遗传分化及基因流,阐明该种害虫在我国的种群历史动态。【方法】本研究对采自我国20个地理种群的529头甜菜夜蛾样品进行线粒体COI基因序列测定与分析,利用DnaSP 5.0和Arlequin 3.11软件分析种群间遗传多样性、遗传分化、基因流水平及分子变异,构建了单倍型系统发育树与单倍型网络图。【结果】在所分析的所有529个序列样本中,共检测出10个单倍型,其中Hap_1为所有种群所共享。总群体遗传多样性较低（Hd=0.257±0.025,Pi=0.0007±0.0001,Kxy=0.323）,群体间遗传分化较小（F_ST=0.211）,基因流水平较高（N_m=1.870）。AMOVA分析表明,甜菜夜蛾遗传变异主要来自种群内,种群间变异水平较低。各种群间遗传分化程度与地理距离无显著相关性（R²=0.005,P>0.05）。各单倍型相互散布在不同种群中,未形成明显系统地理结构。中性检验（Tajima’s D=-2.177, P<0.05; Fu’s F_S=-8.629, P<0.05)与错配分布分析表明,我国甜菜夜蛾种群曾经历种群近期扩张。【结论】研究结果揭示,甜菜夜蛾各种群间的基因交流并未受到地理距离的影响,验证了甜菜夜蛾具有高度的迁飞能力。     

云南西花蓟马rDNA-ITS2遗传多态性及其种群扩张

应用rDNA-ITS2基因序列对云南各地理种群西花蓟马Frankliniella occidentalis(Pergande)的遗传结构和遗传分化程度进行初步研究。经过比对112条序列,共发现了59个变异位点,定义了30种单倍型。云南省西花蓟马的单倍型多态性较高(Hd=0.90219),而核酸多态性较低(Pi=0.00891)。各地理种群西花蓟马的遗传分化指数Fst为0.00810,基因流Nm为30.61,表明各地理种群间遗传分化程度非常低,种群间存在充分的基因交流。对群体进行中性检验、错配分析表明西花蓟马群体曾经历过近期的种群扩张。分子方差分析(AMOVA)表明,云南西花蓟马的遗传变异主要来自于种群内部,种群间的遗传变异水平还非常低。从分子生物学的角度上也证实了西花蓟马近期入侵云南的事实。     

新疆野苹果叶绿体DNA变异与遗传进化分析

利用4对叶绿体DNA引物对来源于新疆巩留、霍城和新源3个地区的242份新疆野苹果种质资源的4个非编码区trn H-psb A、trn S-trn G spacer+intron、trn T-5′trn L和5′trn L-trn F进行了扩增,基于4个叶绿体基因间区的序列变异,从母系遗传的角度评价了遗传变异和不同居群的遗传进化关系。结果表明:4个叶绿体DNA非编码区经测序、拼接、比对和合并之后的片段长度为3812 bp,共有171个多态性变异位点,其中包含6个单一突变位点、16个简约信息位点和149个插入-缺失位点。在242份新疆野苹果种质中,trn H-psb A、trn S-trn G spacer+intron、trn T-5′trn L和5′trn L-trn F区域的变异位点的数量分别为68个、25个、77个和1个,单倍型数量分别为36个、6个、6个和2个,合并之后的叶绿体DNA片段的单倍型为52个。核苷酸多样性和单倍型多样性最高的区域均为trn H-psb A(Hd=0.773,Pi=0.01982),最低的为5′trn L-trn F(Hd=0.025,Pi=0.00002)。242份新疆野苹果种质4个叶绿体DNA区域合并后的遗传多样性较高(Hd=0.806,Pi=0.00291)。Tajima′s D检验中,4个cpDNA区域合并后片段在P0.05水平上显著,4个cpDNA区域整体不遵循中性进化模型,自然选择的压力是新疆野苹果遗传进化的主要动力。新疆野苹果的遗传变异主要存在于居群内部,新疆巩留和新源居群间的遗传距离较近,与霍城居群间遗传距离相对较远,居群间的遗传分化与地理距离相关。3个地区的新疆野苹果各自经历着遗传分化但又存在频繁的基因交流,有向新疆新源的新疆野苹果演化的趋势。     

Recent advances in the study of Kaposi's sarcoma-associated herpesvirus replication and pathogenesis

It has now been over twenty years since a novel herpesviral genome was identified in Kaposi's sarcoma biopsies. Since then, the cumulative research effort by molecular biologists, virologists, clinicians, and epidemiologists alike has led to the extensive characterization of this tumor virus, Kaposi's sarcoma-associated herpesvirus(KSHV; also known as human herpesvirus 8(HHV-8)), and its associated diseases. Here we review the current knowledge of KSHV biology and pathogenesis, with a particular emphasis on new and exciting advances in the field of epigenetics. We also discuss the development and practicality of various cell culture and animal model systems to study KSHV replication and pathogenesis.     

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.     

The structure, reproduction and taxonomy of Vidalia and Osmundaria (Rhodophyta, Rhodomelaceae)

Comprises species occurring mostly in subtidal habitats in tropical, subtropical and warm-temperate areas of the world. An analysis of the type species, V. spiralis (Sonder) Lamouroux ex J. Agardh, a species from Australia, establishes basic characters for distinguishing species in the genus. These characters are (1) branching patterns of thalli, (2) flat blades that may be spiralled on their axis, (3) width of the blade, (4) primary or secondary derivation of sterile and fertile branchlets and (5) position of sterile and fertile branchlets on the thalli. Application of the latter two characters provides an important basic method for separation of species into three major groups. Osmundaria , a genus known only in southern Australia, was studied in relation to Vidalia , and its separation from the Vidalia assemblage is not accepted. Species of Vidalia therefore are transferred to the older genus name, Osmundaria. Two new species, Osmundaria papenfussii and Osmundaria oliveae are described from Natal. Confusion in the usage of the epithet, Vidalia fimbriala Brown ex Turner has been clarified, and Vidalia gregaria Falkenberg, described as an epiphyte on Osmundaria pro/ifera Lamouroux, is revealed to be young branches of the host, Osmundaria prolifera.     

New or rare chromosome counts in Artemisia L. (Asteraceae, Anthemideae) and related genera from Kazakhstan

Fifteen chromosome counts of six Artemisia taxa and one species of each of the genera Brachanthemum, Hippolytia, Kaschgaria, Lepidolopsis and Turaniphytum are reported from Kazakhstan. Three of them are new reports, two are not consistent with previous counts and the remainder are confirmations of very scarce (one to four) earlier records. All the populations studied have the same basic chromosome number, x = 9, with ploidy levels ranging from 2x to 6x. Some correlations between ploidy level, morphological characters and distribution are noted.