香花枇杷质体基因组序列密码子偏性分析

选取香花枇杷质体基因组进行密码子使用偏好性的生物信息学分析,用于理解其密码子使用偏性的主要原因,为今后该属植物基因的进化、起源以及转化体系中载体构建等方面研究提供借鉴。利用Codon W 1.4.2、SPSS statistics 17.0、Excel 2016和cusp等软件对筛选出的37条基因编码序列密码子进行最优密码子分析、中性绘图分析、ENC-plot和PR2-plot绘图分析。结果表明,ENC平均值为47.02;GC₃与GC₁、GC₂的相关性均不显著;GC_all为39.08%,GC₁（48.79%）>GC₂（40.18 %）>GC₃（28.44%）;RSCU>1的29个密码子中有28个以A或U结尾;PR2-plot绘图分析显示多数位点偏离中心,落于左下方位置;确定了UUU、UUG、CUU等15个最优密码子。香花枇杷叶绿体基因组中,同义密码子的使用偏性较弱（47.02）;密码子的第1、 2位碱基组成比较相似,但均不同于第3位;整体A、U含量大于C、G,末位碱基以A、U为主,且嘧啶的使用频率高于嘌呤;香花枇杷叶绿体基因组密码子的使用模式主要受到选择、突变的和其他因素的综合作用影响。     

肖蒲桃叶绿体基因组结构特征及系统发育关系

【目的】肖蒲桃(Syzygium acuminatissimum)是我国南方高价值的硬木树种之一,适宜作为行道树或园景树。研究揭示肖蒲桃叶绿体基因组的结构特征及系统发育关系,对蒲桃属甚至桃金娘科的分类学研究具有重要意义。【方法】使用CTAB法提取肖蒲桃叶片基因组DNA。利用Illumina HiSeq X TEN平台进行高通量测序,在SPAdes v3.13.0上组装叶绿体基因组,并通过GeSeq注释肖蒲桃的完整叶绿体基因组。分析了肖蒲桃叶绿体基因组的结构特征、序列特征及系统发育关系。【结果】肖蒲桃完整的叶绿体基因组长度为159 352 bp,共有109个基因,包括78个蛋白质编码基因、27个tRNA基因和4个r RNA基因,其中17个基因具有内含子;检测到21 379个密码子,其中丝氨酸密码子最丰富、蛋氨酸密码子最匮乏;检测到47个RNA可编辑位点,其中ndhB基因最多(10个);检测到48个长片段重复序列,其中18个正向重复、6个反向重复、22个回文重复和2个互补重复;检测到230个简单重复序列,其中绝大多数为单核苷酸(205个)。基因组比较分析结果表明,4个蒲桃属植物的IR边界有较小差异,核苷酸多样性高于0.015的区间有7个。系统发育分析结果表明,肖蒲桃与丁香蒲桃(S. aromaticum)关系密切。【结论】研究结果有助于开展后续的蒲桃属系统发育研究和物种鉴定工作。     

转基因植物中删除选择标记基因的研究进展

选择标记基因广泛应用于植物转基因工程中,然而这些基于除草剂和抗生素类抗性选择标记基因的利用,在转基因筛选和鉴定完成后功能多余。当前转基因植物的标记基因及相关产物对环境污染和食用安全的潜在影响,已经引起了人们的广泛关注。随着转基因技术的不断发展和人们对转基因植物和食品安全性的关注,删除转基因植物中的选择标记基因非常重要。文章着重讨论了植物转基因过程中,选择标记基因的利用,删除选择标记基因的几种方法,包括共转化法、位点特异性重组、染色体内重组、转座子介导的重组、删除叶绿体转化中选择标记基因,以及无选择标记基因植株的直接再生等。同时,还对这些技术的发展作了展望。     

茶树叶绿体基因组SNP分子标记的初步研究

传统的叶绿体基因分子标记在茶组植物分类系统研究中的应用价值相对有限,为了筛选可用于茶树鉴别与母系溯源的SNP（单核苷酸多态性）位点组合,将18个已报道的茶组植物叶绿体全基因组序列进行比对,通过设计通用引物,在169个茶树品种/品系中进行候选分子标记扩增与一代测序分析,筛选出16对引物,共含25个SNP位点可用于茶树品种母系溯源与鉴别分析。另外,将SNP位点组成的DNA指纹图谱结合茶树品种资源基本信息进行数字编码,最终形成由30位数字组成的茶树品种资源分子身份证,并构建相应的条形码和二维码用于品种识别。本研究数据为茶树品种的母本溯源与鉴别提供新的思路。     

干旱胁迫对3种苹果属植物叶片解剖结构、微形态特征及叶绿体超微结构的影响

采用树脂包埋块半薄/超薄切片技术,通过光镜（LM）、扫描电镜（SEM）和透射电镜（TEM）方法,研究了轻度、中度和严重干旱胁迫对楸子（Malus prunifolia）、新疆野苹果（M. sieversii）和平邑甜茶（M. hupehensis）叶片组织解剖结构、表皮微形态特征（气孔密度、大小及角质层厚度）及叶绿体超微结构的影响。光镜观察结果表明,与对照相比,干旱胁迫条件下3种苹果属植物叶片厚度、栅栏组织厚度及叶肉组织结构紧密度（CTR）都显著减小（P＜0.05）,而海绵组织厚度与叶肉组织结构疏松度（SR）均显著增加（P＜0.05）。扫描电镜观察结果显示,3种苹果属植物幼叶气孔密度在干旱胁迫下显著增大（P＜0.05）,而气孔宽度、开张比及其开张度明显下降。透射电镜观察结果表明,在干旱胁迫下,楸子和新疆野苹果上下角质层厚度逐渐增加,而平邑甜茶的随干旱胁迫程度增加呈先增后减的变化;在轻度和中度水分胁迫下,叶绿体膨胀变形,淀粉粒变小消失,基粒片层排列松散减少,类囊体腔扩大;在严重胁迫条件下,叶绿体膨胀近圆形,叶绿体膜破裂,类囊体严重泡化开始解体。与平邑甜茶相比,严重水分胁迫下楸子和新疆野苹果叶绿体超微结构损伤较小,能较好地保持细胞结构的完整性。     

大豆专用肥对轮作,连作大豆叶片超微结构的影响

本文通过透射电镜观察了常规施肥与施用大豆专用复肥对轮作。连作大豆叶片超微结构的影响。结果发现，大豆连作导致叶绿体基粒片层结构破坏，淀粉粒积累，基粒片层结构出现“空隙区”。与常规施肥相比，施用复肥增强了轮作，连作大豆叶片叶绿体基粒片层结构的完整性，增加了基粒数量和基粒片层数，为促进大豆叶片的光合作用创造了条件，相关分析表明，叶绿体基粒片层数与大豆植株营养生长呈显著正相关。     

用改进的高盐低pH法分离和纯化棉花叶绿体及叶绿体DNA

报道了用改进的高盐低ｐＨ法分离和纯化棉花叶绿体及叶绿体ＤＮＡ的实验过程，即先在高盐（离子强度）介质下，通过ｐＨ值变换，多次洗涤的方法去除叶绿体表面的静电附着杂质，得到纯净的叶绿体；然后氯仿抽提纯化ＤＮＡ；最后采用界面针挑法得到高纯度的ｃｐＤＮＡ。实验过程中针对棉花的特点，采用ＰＶＰ排除棉酚和丹宁的干扰，用ＤＩＥＣＡ抑制酚氧化酶活性，并对实验细节作了较大改进。得到的ＤＮＡ可满足酶切、ＰＣＲ等分子生物学分析。     

Production and genetic evaluation of interspecific hybrids within the genus Sambucus

Attempts were made to produce hybrids among various Sambucus species in order to change the plant structure of S. nigra, a medicinal plant of increasing agricultural importance. The first successful genetic recombination, involving four species, was conducted after the introduction of S. javanica from a South Pacific island. A series of genetic analyses of the involved species and some relatives was performed in order to obtain reliable data on genetic similarity among parental species and to confirm the hybrid nature of putative hybrids. The nuclear 2C DNA content revealed by flow cytometry of nine species showed limited variation, the greatest being in S. nigra (28.6 pg) and the smallest in S. caerulea (23.9 pg). Maximum parsimony analysis of seven Sambucus species was used to form two dendrograms, one based on the sequenced nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) region and the other based on the cpDNA trnT‐trnF region. The results showed similar clustering into distinct groups; on both dendrograms S. nigra and S. javanica ES were closely related. Analysis of hybrid origin was based on the sequenced cpDNA region, genome size differences and PCR–RFLP analysis of the nrDNA ITS region. The seed parent and maternal origin of cpDNA was confirmed for all hybrids, while the pollen parent was confirmed in 21 of 22 putative hybrid plants tested.     

Identification of the Putative Cytoplasmic Donor of a CMS System in Brassica juncea

Chloroplast (cp) and mitochondrial (mt) DNA restriction profiles of a cytoplasmic male sterile (CMS) line of Brassica juncea and its maintainer line were compared and found to be markedly different. Comparison of cpDNA restriction profiles of fifty different species of genus Brassica and some allied genera showed that the cpDNA profiles of CMS lines were similar to that of B. tournefortii for twenty different restriction endonucleases. This CMS system is thus not of spontaneous origin as reported earlier, but is alloplasmic in nature. Comparison of restriction profiles of mtDNA of B. tournefortii and CMS lines revealed some differences which might either be due to changes in DNA pattern during the transfer, or, due to the cytoplasm coming from a B. tournefortii line different from the one used in this study.     

Indica-japonica differentiation in Chinese rice landraces

Summary Ninety Chinese rice landraces were examined with special reference to the indica-japonica differentiation in terms of traditional criteria, isozyme analysis and PCR analysis of the chloroplast DNA (cpDNA). Cultivars were separated into indica and japonica defined by a discriminant function (Z) based on key characters, as well as by isozyme genotypes. Most indica landraces had chloroplast DNAs with a deletion at the Pst-12 fragment, while most japonica landraces had cpDNAs without the deletion. Two traditionally recognized varietal groups in China, keng and hsien, corresponded largely to the respective japonica and indica revealed in our study. The results obtained in this study showed good agreement for classification of indica and japonica types by the three methods: discriminant analysis by Z value, isozyme analysis, and PCR analysis for cpDNA.