基于叶绿体psaA和psbA基因的中国熊野藻属植物系统发育分析

以中国产熊野藻属Kumanoa的两个种, 绞扭熊野藻K. intorta (=绞扭串珠藻Batrachospermum intortum), 弯形熊野藻K. curvata (=弯形串珠藻B. curvatum)和其他6种淡水红藻为实验材料, 对其psaA和psbA基因进行扩增和测序, 并与GenBank中相近序列进行比对分析, 以贝叶斯法、最大似然法和邻接法分别构建了单基因和联合基因系统发育树. 结果表明, 3种方法构建的系统树具有相似的拓扑结构, 反映的系统发育关系基本一致, 熊野藻属中的两个种聚为一支, 与串珠藻属相分离, 支持该属的建立; 中国产的熊野藻属分子学研究结果与来自南美洲及澳洲的该属植物结果一致, 说明该属的建立具有广泛的地理适用性. 系统发育树聚类结果也明确反映了熊野藻属与串珠藻属较近的亲缘关系, 根据果胞枝形态特点, 推测熊野藻属进化地位晚于串珠藻属植物, 而早于顶丝藻目和红索藻目. 此外, 胶串珠藻与其他串珠藻组植物分离, 支持将其单独分组, 红索藻目植物与串珠藻目植物分离, 支持红索藻目的建立. 同时也表明psaA和psbA基因用于淡水红藻分析, 能够较好地反映其系统发育关系.       

串珠藻目植物的系统发育-基于rbcL序列的证据

世界范围内报道的全部串珠藻目种类均生活于淡水中,而在淡水红藻中,70%约有130种属于串珠藻目。研究以目前获取的来自世界各大洲串珠藻目植物43种的rbcL基因序列,结合其形态和生物地理特征,构建了该目的系统发育关系,以期探讨整个串珠藻目植物的系统发育关系及发生途径,进而为研究该目以至淡水红藻的起源提供基本资料。运用PAUP*4.0b10和MrBayes 3.0b4等软件对43种串珠藻目植物的叶绿体DNA rbcL基因序列进行系统发育分析,探讨了其主要分类群的系统演化关系。用最大简约法、邻接法和贝叶斯分析方法构建的系统树基本一致,结果显示:(1)基于分子数据分析结果显示,红索藻目植物均独立于串珠藻目植物,构成一个单独的分支,支持红索藻目的建立。(2)鱼子菜科属于串珠藻目植物中较为进化的类群。(3)串珠藻属扭曲组与杂生组的差异度较小,结合其形态特点,倾向于将杂生组并入扭曲组。(4)串珠藻科属于串珠藻目中最大的科,包括较多的种类,其系统关系也较为复杂。因此,串珠藻科系统发育关系的明确有待于进一步结合更多的分子数据和形态学特征加以分析研究。       

基于psaA和psbA基因的红索藻目系统发育研究

对红索藻目植物棘刺红索藻(Thorea hispida)的psaA和psbA基因进行扩增和测序,并与其它类群比对分析,分别用最大简约法、邻接法和贝叶斯法构建系统发育树。结果显示,psaA和psbA基因测得的序列片段分别为825和920 bp,psaA基因A、T、C、G碱基含量分别为29.9%、35.8%、16.5%和17.8%,psbA基因A、T、C、G碱基含量分别为27.5%、35.3%、16.8%和20.4%,两个基因A+T含量均高于C+G含量,说明两个基因在进化上均有碱基的偏好性。用3种方法所构建的系统树拓扑结构基本一致,红索藻目植物均聚合于一个分支,独立于其它类群,支持红索藻目为一独立的目。     

中国熊野藻属植物系统发育分析——基于叶绿体UPA序列

以中国产的6种熊野藻属(Kumanoa)和串珠藻属(Batrachospermum)植物为材料,测定其UPA序列,并在GenBank中下载相关基因序列,通过贝叶斯法、最大似然法和邻接法构建系统发育树,分析其系统发育。结果显示,UPA序列核苷酸变异位点占序列长度的43.1%,其中简约信息位点占序列长度的31.1%,种间差异度为0~1.81%,属间差异度大于4.19%,可以作为分子标记用于系统发育分析。中国产熊野藻属的两个种和来自世界范围内的多数该属种类聚为一大支,支持该属的建立。基于UPA序列的地理起源分析显示,两属的祖先分布区节点主要在北美洲和大洋洲,然后向其它地区扩散,熊野藻属向外扩散后,在南美洲分布较为集中。     

10种棘豆属植物的trnL-F序列及其分子系统学研究

选择内蒙古27个样地采集的10种棘豆属植物54个单株,提取样品的基因组DNA,对其叶绿体trnL-F序列进行扩增、测序,所得序列利用ClustalX软件进行对位排列,并用MEGA5.0软件采用最大似然法构建系统发育树,以探讨棘豆属的种间关系与系统进化.结果显示:(1)10种棘豆属trnL-F的变异位点54个,信息位点46个,种间碱基差异百分率为1.9％,GC含量变化范围在30.69％～31.50％之间.(2)棘豆属与黄芪属各为一支,自展支持率达99％,支持棘豆属植物为单系起源.(3)系统树中小花棘豆的样本自成一支,为相对独立进化;多叶棘豆、砂珍棘豆和黄毛棘豆的样本相互混杂,表明亲缘关系很近,从而支持《内蒙古植物志》将三者归入真棘豆亚属轮叶棘豆组的观点.(4)刺叶柄棘豆的样本不同样地形成2个分支,对其亚属水平上的分类需进一步探讨.(5)缘毛棘豆与阴山棘豆的样本聚成一支,支持将二者归入矮生棘豆组.研究表明,trnL-F序列可为棘豆属下种间系统发育关系研究提供分子证据.     

基于ITS序列分析探讨杜鹃属映山红亚属的组间关系

以叶状苞亚属的叶状苞杜鹃为外类群,以杜鹃属映山红亚属（subg.Tsutsusi)2组12种杜鹃和羊踯躅亚属（subg.Pentanthera）3种4种杜鹃的ITS区（包括5.8S rDNA)的序列了系统学分析。3个亚属的ITS区序长度范围为642－645bp。排序后ITS区的序列长度为653个位点,gap做缺失处理时,变异位点和信息位点分别占6．58％和3．68％。运用PAUP4．0软件分析,获得15个最简树,步长为75,一致性指数（CI）和维持性指数（RI）值分别为0．9333和0．9515,利用15个最简约树获取严格一致树,结果表明：1）映山红亚属为一单系类群,其内部支持率为81％;2）不支持将R.ashiroi独立成假映山红组,也不支持将R.tashiroi并入映山红组,而支持将R.tashiroi并入轮生叶组中的观点;3）支持将R.tsusiophyllum并入映山红组中的观点;4）大字杜鹃的系统位置还需进一步的研究。     

冬季赤水河流域刚毛藻多样性调查及系统发育分析

研究于2019年冬季对赤水河流域开展刚毛藻多样性调查, 共设计采样点38个, 覆盖赤水河上、中、下游。调查发现: 21个采样位点分布有刚毛藻目藻类, 其中19个位点有刚毛藻分布。基于核糖体小亚基(SSU rDNA)、核糖体大亚基(LSU rDNA)和内转录间隔区(ITS)对采集样品进行系统发育分析, 结果显示: (1)赤水河流域刚毛藻多样性较高, 且该流域上、中、下游均有刚毛藻分布; (2)目前淡水刚毛藻类群包含至少10个支系, 赤水河流域采集到的刚毛藻覆盖其中6个支系(分别是clade 1、clade 2、clade 4、clade 7、clade 9和clade 10); (3)相比基于SSU+LSU双分子标记构建的系统进化树, 基于SSU+ITS+LSU三分子标记构建的进化树各支系支持度更高, 可以较有效地将淡水刚毛藻不同支系区分开来。研究较好地展示了冬季赤水河流域刚毛藻的广泛分布及其分子多样性, 丰富了中国淡水丝状绿藻的分类研究, 也为赤水河段的水生态环境保护提供了基础数据支持。     

基于psbA-trnH序列的十种棘豆属植物分子系统学研究

选择内蒙古28个样地采集的10种棘豆属植物56个单株,提取样品的基因组DNA,对其叶绿体psbA．trnH序列进行扩增、测序,所得序列利用ClustalX软件进行对位排列,并用MEGA5．0软件采用最大似然法构建系统发育树。结果显示：（1）10种棘豆属psbA．trnH序列的变异位点50个,信息位点36个,种间碱基差异百分率为3．4％,GC含量变化范围在23．18％～25．72％之间。（2）棘豆属与黄芪属各为一支,自展支持率达99％,这10种棘豆属植物可能为单系起源。（3）系统树中小叶小花棘豆与小花棘豆的样本独立成一支,支持将小叶小花棘豆作为小花棘豆的变种来处理。（4）多叶棘豆、砂珍棘豆和黄毛棘豆的样本相互混杂,表明亲缘关系很近,支持《内蒙古植物志》将三者归入真棘豆亚属轮叶棘豆组的观点。（5）缘毛棘豆与薄叶棘豆的样本聚成一支。支持将二者归入矮生棘豆组。研究表明,psbA-trnH序列可为棘豆属下种间系统发育关系研究提供分子证据。     

基于28S rDNA序列的鞘藻目系统发育研究

作者进行了较广泛的样品采集,通过实验分离纯化培养得到多个鞘藻目种类的株系,并采用PCR技术新获得鞘藻目2属8个种类的部分28S rDNA序列,连同GenBank中的另两条序列,分析的物种涵盖了鞘藻目中的每个属。通过比较分析绿藻纲中包括此10条序列的共36个种类的同一基因序列,并选取Trebouxiophyceae中的椭圆小球藻（Chlorella ellipsoidea）和Fusochloris perforata作外类群,运用多种方法构建分子系统树,包括邻接法（Neighbor-Joining）、最大简约法（Maximum Parsimony）和Bayesian方法。3种方法所得的结果非常相似,在形态上就在整个绿藻中界限分明的鞘藻目从分子水平上再次证明为单系起源的类群;构建的系统发育树还在一定程度上表明毛鞘藻属处于鞘藻目内三个属中较分离的位置,而枝鞘藻属与鞘藻属植物并无明显界限。     

基于rbcL序列探讨荨麻科植物的系统发育关系

对苎麻属4个种的rbcL序列进行了PCR扩增和T/A克隆产物的序列测定.扩增出长度为1370bp的rbcL序列.从GenBank中选取荨麻科8个属的rbcL序列,将所有物种的rbcL序列排序后,总长度约为1 428bp.其中保守位点1 263个,变异住点165个,信息位点71个.利用MEGA3.1软件构建荨庥科植物的MP和NJ系统树,并根据rbcL区碱基序列的差异计算种间的遗传距离,从而进一步探讨荨麻科植物之间的亲缘关系.其中,赤车属、锥头麻属、藤麻属、楼梯草属和冷水花属聚为一支,具有较近的亲缘关系;墙草属、单蕊麻属和苎麻属聚为另一组;而荨麻属植物在一级分支中就与荨麻科其他属植物分开,说明该属与其他属的亲缘关系较远.     

小麦抗白粉病相关基因GST克隆与表达

以从小麦抗白粉病相关基因差异表达分析中获得的EST-3 (Genbank序列号EX567360)为标签,采用电子克隆的方法对其进行延伸,并对电子克隆结果进行半定量RT-PCR验证,最后对白粉菌不同侵染时间进行了表达分析.经RT-PCR扩增,EST-3表达的带型变化趋势与其在抑制性消减杂交SSH-cDNA的差异显示情况一致,且RT-PCR获得的序列与电子克隆的序列一致性达98％.生物信息学分析表明,该序列是由875 bp核苷酸组成的,具有完整的开放阅读框架,编码蛋白为229个氨基酸,GenBank序列号JK841279,含有一个N端和C端谷胱甘肽硫转移酶结构域,该序列与小麦谷胱甘肽硫转移酶基因(GST)一致性较高,达97％.表达分析结果显示,白粉菌侵染24 h表达受到抑制,48 h开始表达,侵染72 h表达最强,96 h又开始下降,表明GST基因属于白粉菌诱导型相关基因,参与小麦对白粉病的应答反应.     

PHYLOGENETIC AFFINITIES OF “CHANTRANSIA” STAGES IN MEMBERS OF THE BATRACHOSPERMALES AND THOREALES (RHODOPHYTA)1

This study evaluated the phylogenetic relationship among samples of “Chantransia” stage of the Batrachospermales and Thoreales from several regions of the world based on sequences of two genes—the plastid‐encoded RUBISCO LSU gene (rbcL) and the nuclear SSU ribosomal DNA gene (SSU rDNA). All sequences of “Chantransia macrospora” were shown to belong to Batrachospermum macrosporum based on both molecular markers, confirming evidence from previous studies. In contrast, nine species are now associated with “Chantransia pygmaea,” including seven species of the Batrachospermales and two of the Thoreales. Therefore, the presence of “C. macrospora” in a stream can be considered reliable evidence that it belongs to B. macrosporum, whereas the occurrence of “C. pygmaea” does not allow the recognition of any particular species, since it is associated with at least nine species. Affinities of “Chantransia” stages to particular taxa were congruent for 70.5% of the samples comparing the rbcL and SSU analyses, which were associated with the same or closely related species for both markers. Sequence divergences have been reported in the “Chantransia” stage in comparison to the respective gametophyte, and this matter deserves further attention.     

A PROPOSAL FOR A NEW RED ALGAL ORDER,THE THOREALES1

Representatives of the freshwater red algal family Thoreaceae were studied to resolve their taxonomic and phylogenetic status. Three specimens of Nemalionopsis and five collections of Thorea were examined for pit plug ultrastructure and analyzed for the sequences of the genes coding for the large subunit of RUBISCO (rbcL) and the small subunit of rRNA (18S rRNA). The phylogenetic trees generated from the two genes, and a combined tree all showed the Thoreaceae to be contained in a well‐supported monophyletic clade that is separate from the other two families currently classified in the Batrachospermales, the Batrachospermaceae and the Lemaneaceae. In addition, secondary structure elements of the 18S rRNA gene were observed at positions 650 and 1145 (Escherichia coli numbering system) that are not present in other members of the Rhodophyta. The pit plugs of the gametophytic and chantransia stages of the Thoreaceae contain two cap layers, the outer one of which is typically plate‐like, though occasionally inflated ones have been seen. No pit plug cap membrane has been observed. These findings indicate the Thoreaceae has been misclassified in the Batrachospermales and should be placed in its own order, the Thoreales. This order is characterized by having freshwater representatives with multiaxial gametophytes, a uniaxial chantransia stage, and pit plugs with two cap layers, the outer one of which is usually plate‐like.     

Investigation of a freshwater acrochaetioid alga (Rhodophyta) with molecular and morphological methods

An enigmatic acrochaetioid alga was collected from Niangziguan spring in Shanxi Province, northern China. Morphological data indicated that this alga reproduces exclusively asexually by monosporangia and its morphological characteristics suggested that it might be referred to Audouinella heterospora. To ascertain its phylogenetic position, phylogenetic trees were reconstructed using partial sequences of the plastid‐encoded gene (rbcL) and the nuclear‐encoded gene (SSU rDNA) applying Bayesian inference (BI), maximum parsimony (MP) and maximum likelihood (ML). However, phylogenetic reconstructions showed that this acrochaetioid alga does not belong in a clade with the genus Audouinella, but forms a clade with Thorea hispida (Thoreales). Based on this analysis it is concluded that A. heterospora represents the ‘chantransia’ stage of T. hispida.     

A molecular systematic investigation of the Acrochaetiales (Florideophycidae,Rhodophyta) and related taxa based on nuclear small-subunit ribosomal DNA sequence data

Small-subunit ribosomal DNA (SSU) sequences for 14 members of the rhodophyte order Acrochaetiales were used to generate phylogenetic trees to determine whether the Acrochaetiales is monophyletic and to assess the relationships of acrochaetioid algae to closely related taxa. Within the Acrochaetiales, two strongly supported groups are recognized: one group that includes, in addition to three other species, the type species of the genera Acrochaetium, Audouinella and Rhodochorton; and a second group that includes an unequivocal representative of Colaconema and nine additional species. The relationships of these groups with the Batrachospermales, Palmariales and Nemaliales were not resolved and the possibility that the Acrochaetiales is polyphyletic was not eliminated. Resolution of relationships for species within these groups was strong in only a few cases, with many of the phylogenetic issues at this level remaining equivocal. Our results do not position Camontagnea in the Acrochaetiales, as has recently been suggested, but strongly ally this genus to the family Rhodothamniellaceae of the Palmariales. The phylogenetic position of Rhododraparnaldia, an alga intermediate between the Acrochaetiales and Batrachospermales, remains unresolved. These molecular results provide a foundation for assessing the taxonomic significance of phenotypic characters (e.g. anatomy, life histories, morphology, phycoerythrin type and plastid details) variously considered taxonomically significant in the Acrochaetiales.     

Molecular phylogeny of onygenalean fungi based on small subunit ribosomal DNA (SSU rDNA) sequences

Phylogenetic analysis of nucleotide data from small subunit ribosomal DNA (SSU rDNA) sequences (ca. 1685 bp.) was performed on 19 taxa of the Onygenales and three related mitosporic fungi. Phylogenetic trees were constructed by the neighbor-joining method with the sequence data of related taxa obtained from DNA databases. The species in the Onygenales form two clusters and seven subclusters, and the tree topology reflects the traditional classification by Currah (1985) with some exceptions. The Myxotrichaceae is placed in the different lineage, separate from other plectomycetous taxa and among the Leotiales and the Erysiphales. Furthermore, two separate lineages in the Myxotrichaceae were found. Tree topology suggested the Onygenaceae is polyphyletic and composed of three subgroups; 1) most members of Onygenaceae, 2)Spiromastix warcupii, and 3) pathogenic dimorphic fungi classified inAjellomyces.     

应用ITS区序列对秋海棠属无翅组分类学问题的探讨

以侧膜组（Sect.Coeloecentrum)的Begonia cirrosa和单裂组（Sect.Reichenheimia)的B.henryi为外类群,对秋海棠属（Begonia L.)无翅组（Sect.Sphenanthera)9种2变种及秋海棠组（Sect.Begonia)4种进行了ITS区（包括5.8s rDNA)序列的测定。发现该属的ITS序列较一般类群要长一些,所测的序列长度变化范围为648－743bp。这些序列经Clustal X软件排序后序列总长为756个位点,gap做缺失处理时,变异位点和信息位点分别占26.41%和10.11%。运用PAUP4.0b8软件分析,获得6棵最大简约树,步长为286,一致性指数（CI）和维持性指数（RI）分别为0.8287和0.7841,利用6棵最简约树获取严格一致树,并作Bootstrap检测。结果表明：1.支持将原无翅组内子房3室的种类移入秋海棠组,而将子房4室的种保留,成立四室组（Sect.Sphenanthera);2.将B.tetragona作为B.acetosella的异名处理得到一定的支持;3.B.crassirostris的系统位置有待进一步的研究。