赤眼鳟线粒体NADH脱氢酶6基因克隆及序列特征分析

[目的]根据赤眼鳟线粒体NADH脱氢酶6（ND6）基因序列分析不同种鱼类的分子进化关系。[方法]根据其他鱼类的线粒体ND6基因及侧翼序列设计引物,采用PCR扩增并克隆、测序赤眼鳟ND6基因,通过MEGA4．0Neighbor—Joining法分析不同鱼类的进化关系。[结果]赤眼鳟（Squaliobarbus curriculus）线粒体基因组ND6基因序列长度为522bp,编码173个氨基酸。该基因碱基组成为：A41．5％、C32．7％、G12．4％、T13．4％,其中A＋T含量（54．9％）高于G＋C含量（45．1％）。将赤眼鳟ND6基因序列与GenBank中其他11种鱼类ND6基因序列进行比对发现,赤眼鳟ND6核酸序列与团头鲂的同源性最高,为90．8％;与红点鲑鱼的同源性最低,为73．0％。赤眼鳟ND6氨基酸序列与其他物种ND6氨基酸进行比对发现,赤眼鳟与团头鲂同源性最高,为98．3％;与大黄鱼的同源性最低,为75．7％。以ND6氨基酸序列采用NJ法构建12种鱼类的系统发生树基本反映了它们的种间、属间和科间的关系。[结论]首次得到了赤眼鳟线粒体ND6基因序列,并确定了赤眼鳟与其他11种鱼类的分子进化关系。     

胨冻样芽孢杆菌(Bacillus mucilaginosus YNUCC0001)絮凝剂生产、絮凝特性及其系统发育学分析

对BacillusmucilaginosusYNUCC000116SrDNA的1481bp片段与GenBank中最相似的16个分类单位进行了比较。UPGMA,NJ,ME和MP方法构建的系统发育树显示B.mucilaginosusYNUCC0001与B.mucilaginosusHSCC1605T、B.mucilaginosus1480D及Paenibacillussp.NBT形成一个单系群分支。在50L全自动发酵罐中30℃发酵52h后,菌株YNUCC0001产生的胞外生物多聚絮凝剂(EBF)达到最大产率(粘度:3420C.P.)。在pH4.0、用量为0.25mlL-1的条件下,这种EBF对高岭土悬浊液的絮凝活性最大(99.8%);121℃高压灭菌60min后絮凝活性维持在98.6%。Hg2+,Ca2+,Mg2+,K+,Zn2+对其絮凝活性有促进作用,而Fe3+、Al3+、EDTA和Cu2+则有强烈抑制。     

林麝肺成纤维细胞线粒体全基因组结构特征及遗传变异分析

林麝(Moschus berezovskii)是一种具有较高经济价值和药用价值的保护野生动物。为深入研究林麝线粒体基因组的结构特征及遗传变异,基于Illumina NovaSeq平台对林麝肺成纤维细胞FMD-C1线粒体进行全基因组测序,并进行特征注释、结构预测、序列分析和系统发育重建。结果显示,FMD-C1线粒体基因组序列全长为16 351 bp,共有13个蛋白编码基因(protein coding gene, PCG),22个tRNA,2个rRNA和两段非编码区,具有明显的AT偏好性。将序列上传至GenBank,登录号为MW879208。与NCBI上林麝的其余序列比对,FMD-C1的4个PCGs中检测出5个单氨基酸突变和3个插入氨基酸;D-loop区检测出19个差异碱基和2个碱基缺失。系统进化分析发现与林麝亲缘关系最近的是安徽麝。研究结果可为林麝的选育和遗传多样性保护提供参考依据,也为进一步探讨林麝肺部疾病线粒体水平的致病机制奠定基础。     

水稻MYB-MYC基因家族的全基因组鉴定、系统进化和表达模式分析

为了挖掘水稻MYB-MYC基因的功能,通过生物信息学手段对水稻MYB-MYC基因家族进行基因组水平的鉴定,并对其系统进化及表达模式进行分析。本研究在水稻中鉴定到17个MYB-MYC基因,根据系统进化树将它们划分为2个亚家族,不同亚组具有特异的保守基序和基因结构。通过对水稻MYB-MYC基因复制事件的分析发现水稻MYB-MYC基因共产生6个基因复制。此外,转录组数据分析发现水稻MYB-MYC基因在不同组织都存在表达且响应不同非生物胁迫。本试验为水稻MYB-MYC基因功能的研究提供了初步的理论基础。     

叶绿体基因组及其在樟科植物系统发育研究中的应用

樟科植物是被子植物中一个较大的木本植物类群,也是一个较为古老的类群,集轻工业、食用、材用、药用、观价值赏于一身,在我国林业史和园林史上占有重要地位。植物的系统发育研究可在阐明物种之间亲缘关系的同时,挖掘它们的共同祖先以及它们在进化过程中的分化和演化路径,揭示生物种群和物种的多样性及其时空分布。在概述樟科植物和叶绿体基因组的基础上,分析了利用叶绿体基因组对樟科植物进行系统发育研究的相关进展,以期为樟科植物的相关研究提供参考。     

Identification and characterization of a tospovirus causing chlorotic ringspots on <Emphasis Type="Italic">Phalaenopsis</Emphasis> orchids

A putative virus-induced disease showing chlorotic ringspots on leaves of Phalaenopsis orchids has been observed in Taiwan for several years. A virus culture, 91-orchid-1, isolated from a Phalaenopsis orchid bearing chlorotic ringspot symptoms was established in Chenopodium quinoa and Nicotiana benthamiana, and characterized serologically and biologically. The virus reacted slightly with the antiserum of Watermelon silver mottle virus (WSMoV) but not with those of Tomato spotted wilt virus (TSWV), Impatiens necrotic spot virus (INSV) and Groundnut ringspot virus (GRSV). Isometric particles measuring about 70–100 nm were observed. Inoculation with isolated virus was conducted to confirm that 91-orchid-1 is the causal agent of chlorotic ringspot disease of Phalaenopsis orchids. To determine the taxonomic relationships of the virus, the conserved region of L RNA and the complete nucleocapsid gene (N gene) were cloned and sequenced. The sequence of conserved region of L RNA shares 83.8, 82.5, 64.4 and 64.9% nucleotide identities and 96.5, 97.7, 67.3 and 67.6% amino acid identities with those of Peanut bud necrosis virus (PBNV), WSMoV, TSWV and INSV, respectively, indicating that 91-orchid-1 is a tospovirus related to WSMoV. The complete nucleotide sequence of the N gene determined from a cDNA clone was found to be 828 nucleotides long encoding 275 amino acids. Sequence analyses of the N gene showed that 91-orchid-1 is an isolate of Capsicum chlorosis virus (CaCV) which has been reported to infect tomato and capsicum plants in Australia and Thailand. 91-orchid-1 is therefore designated as CaCV-Ph. To our knowledge, this is the first formal report of a tospovirus infecting Phalaenopsis orchids.     

Identification of mangrove endophytic fungus 1403 (Fusarium proliferatum) based on morphological and molecular evidence

A mangrove endophytic fungus 1403 isolated from the South China Sea Coast, which is able to produce griseofulvin and anthracenediones under submerged fermentation, was compared with Fusarium genus with the similar morphological characters such as elongated, microconidium-producing conidiophores, ovoid microconidia and straight to slightly curved macroconidia. It was found that the fungus 1403 resembles pathogenic F. verticillioides (teleomophy Gibberella moniliforme) in the production of false head or chains and abundant microconidia on the aerial mycelium, but different in the occasional formation of polyphialides with relatively long as well as short monophialides, in its typical coiled hyphae and mycelia fusion. Through maximum Parsimony and Bayesian analyses, the fungus 1403 was further compared with some similar Fusarium species. The results indicated that this endophyte was identified as Fusarium proliferatum based on the analyses of partial 18S and 28S rDNA genes, ITS region, and EF-1α gene. Foundation project: This research was supported partly by the Guangzhou Natural Science Foundation (Grant No. 2007Z3-EO581), the Guangdong Provincial Natural Science Foundation (Grant No. 2007A0200300001-7; 05003268), the Chinese High-Tech 863 Project (Grant No. 2006AA09Z422), and the National Natural Science Foundation of China (Grant No. 20572136)     

Molecular phylogeny in Indian Citrus L. (Rutaceae) inferred through PCR-RFLP and trnL-trnF sequence data of chloroplast DNA

The taxonomy and phylogeny of Indian Citrus is revisited using PCR-RFLP of the trnD-trnT and rbcL-ORF 106 regions as well as sequence data analysis of the trnL-trnF intergenic spacer region of cpDNA. The study was based on 50 accessions of Citrus genotypes, collected from wild, semi-wild and domesticated stocks. Of the 13 restriction enzymes (RE) used for restriction digestion of the polymerase chain reaction (PCR) amplicons, four (Hinf I, Msp I, Alu I, Hae III) generated 47 restriction fragments, of which 24 (51%) were polymorphic. PCR-RFLP data showed a genetic distance ranging from 0 to 0.79 among 50 accessions of Citrus, and a cluster analysis, based on Neighbor-Joining (NJ) method, placed all the accessions in eight major clusters. Analysis of trnL-trnF sequences from 23 representative accessions of Citrus showed a pair-wise sequence divergence rate in the range of 0–0.064. NJ, minimum evolution (ME) and maximum parsimony (MP) analyses of trnL-trnF sequences produced phylogenetic trees, which placed all the 23 accessions in five clusters. PCR-RFLP analysis resulted in a well resolved phylogenetic tree with branches supported by moderate to high bootstrap values, while the trnL-trnF sequence-based trees showed only moderate to low bootstrap support for the internal tree branches, indicating uncertain origin of some Citrus genotypes. This study shows that the trnL-trnF spacer sequence data can detect genetic variation in Indian Citrus genotypes, but the utility of the data in inferring phylogeny at intra and inter-specific levels is limited probably by factors such as hybridization, bud mutations, apomixis and polyploidy. However, PCR-RFLP and trnL-trnF data supported the recognition of C. maxima, C. medica, and C. reticulata as the basal species of edible Citrus.     

基于叶绿体rRNA ITS序列的兰科植物系统发育关系分析

叶绿体DNA(Chloroplast DNA,cpDNA)中的反向重复序列中的非编码区对于陆生植物的进化研究非常有指导意义,被越来越广泛的应用在不同的分类阶元的系统研究中.该研究在叶绿体rRNA ITS 序列的保守区设计引物,PCR扩增得到450 bp左右的叶绿体rRNA从4.5 S到5 S的片段,扩增产物直接测序,进而依据叶绿体rRNA ITS基因序列分析了兰科植物(Orchidaceae)的33个品种材料(12个兰属品种,14个兜兰属品种,7个石斛属品种)间的亲缘关系.通过最简约性分析产生的叶绿体rRNA ITS系统树表明,石斛属和兜兰属为两个自然类群,兰属可能为一多源组.兰属的碧玉兰位于系统树的基部,构成其余各种的姐妹支.兜兰属的白花兜兰、麻栗坡兜兰独立于属内其他种而自成一支.由于兰科植物叶绿体rRNA ITS序列变异率较低,最简约分析产生的分支得不到Bootstrap分析的高度支持,各亚属之间的关系也不明确.对兰科植物系统发育关系的研究尚需要更多的证据.     

利用ITS序列和trnL-F序列探讨赖草属6个物种的系统发育关系

本研究克隆了赖草属6个物种Leymus karelinii,L.angustus,L.racemosus,L.arenarius,L.triticoides和L.ambiguus的ITS序列和trnL-F序列,并选用3个新麦属物种的ITS序列和27个小麦族二倍体物种的trnL-F序列,均以Bromus catharticus为外类群,用最大简约法构建系统发育树。结果发现:不同组的赖草属物种分别聚在一起;赖草属植物与新麦草属植物亲缘关系较近;新麦草属植物是这6个赖草属物种的母本来源。