基于ITS序列探讨荻属及其近缘植物的系统发育关系

荻属是禾本科的一个小属,其分类地位存在争议。通过测定和从Gen Bank中提取荻属Triarrhena及其近缘植物的ITS序列,以芦苇Phragmites australis为外类群,采用MP(maximum parsimony)和NJ(neighbor-joining)分析方法进行了系统发育分析,这两种方法得到的系统发育树基本相同。荻属和芒属Miscauthus的种类形成一个单系类群;河八王Narenga porphyrocoma与芒属和荻属的植物聚在一起并构成姐妹群;白茅Imperata cylindrica与斑茅Saccharum arundinaceum聚成一小支并构成姐妹群,白茅与荻属的关系较远;荻属植物归并到芒属更为合理,不支持将荻属置入白茅属或另立一属的观点。斑茅与白茅、河八王及蔗茅Erianthus fulvus系统发育关系较近,而与滇蔗茅E.rockii及甘蔗属的竹蔗Saccharum sinense、甘蔗S.officinarum、细秆甘蔗S.barberi和甜根子草S.spontaneum的关系较远。甘蔗属、河八王属及蔗茅属关系复杂,还需要进一步研究。     

绣球属(Hydrangea L.)植物分子系统学及系统发育分析

该研究基于对绣球属(Hydrangea L.)的大尺度取样,选取国内外61种绣球属和近缘属植物,分别基于核基因片段(ITS)和叶绿体基因片段(rbcL,trnL-F,atpB)重建了绣球属及其近缘种属的系统发育关系。结果表明:(1)核基因与叶绿体基因树之间在树形上没有明显的冲突,进而基于核基因和叶绿体基因联合数据重建了绣球属及其近缘种属的系统发育关系。(2)基于联合数据构建的系统树确认了2个大分支,并得到了果实顶端截平与否这一形态学证据的强力支持;每个大分枝又分为4个类群,共确定了8个类群。部分类群也得到了广义宏观形态性状的支持,如第1类群得到了叶形、花粉以及种子形态的支持。因此,该系统发育关系的重建对于全面理解绣球属及其近缘种属的演化关系具有重要的启发。     

基于DNA条形码的半夏属及其伪品分子鉴别

利用DNA条形码技术对半夏属及其伪品进行分子鉴定, 研究半夏属药用植物鉴定的新方法。该实验使用matK序列对半夏(Pinellia ternata)及其伪品进行扩增测序, 结合GenBank数据库数据, 分析ITS、ITS2、psbA-trnH、rbcL和matK各序列的种内与种间变异及barcoding gap, 并采用最近距离法(nearest distance)和相似性搜索算法(BLAST1)评价不同序列的鉴定能力。结果显示, matK序列的种间变异最大, rbcL序列的种内变异最小; rbcL序列的种内和种间遗传变异重叠比例最小, 其次为matK序列; 各序列的Neighbor Joining树均可明显地将不同种分开。实验结果表明, 利用DNA条形码能够准确地鉴别半夏属药用植物及其伪品, matK和rbcL序列为鉴别半夏属及其伪品的较理想条形码组合。该研究为半夏属植物的分子鉴别提供了科学依据与新的思路。     

甘蔗属种及其近缘属种蔗茅的全基因组密码子偏好性分析

【目的】为解析甘蔗基因组的密码子使用特征,提高异源基因在甘蔗中的表达效率。【方法】以已发布的甘蔗属种（热带种LA-purple、割手密NP-X和AP85-441）及其近缘属种蔗茅（Yunnan2009-3）基因组为数据,利用Python、CodonW1.4.2进行密码子偏好性分析,同时通过中性绘图、ENC-plot、PR2-plot等分析探讨密码子偏好性形成的影响因素,并结合转录组测序数据分析密码子偏好性参数与基因表达水平的相关性。最后,基于RSCU均值与7个主要模式生物种（玉米、高粱、水稻、拟南芥、烟草、大肠杆菌、酿酒酵母）的密码子使用模式进行比较分析。【结果】显示热带种、割手密和蔗茅的基因组都富含GC,平均GC含量为56.3%,且GC3>GC1>GC2,倾向于使用以G/C结尾的密码子,平均ENC值为48.45,偏好性较低。中性绘图、ENC-plot和PR2-plot分析表明它们的密码子偏好性受到自然选择、突变压力等多种因素的共同影响,其中自然选择占主导作用。相关性分析表明密码子偏好性参数与基因实际的转录表达水平存在显著相关性,但相关性不强。根据RSCU和?RSCU值,确...     

DNA条形码在中国金合欢属中的应用

根据形态特征难以准确地辨别金合欢属植物,DNA条形码技术提供了一种准确地鉴定物种的方法。本文利用条形码技术对中国金合欢属物种的序列(psbA trnH、matK、rbcL和ITS)及其不同组合进行比较,通过计算种内和种间变异进行barcoding gap分析,运用Wilcoxon秩和检验比较不同序列的变异性,构建系统树。结果表明：4个片段均存在barcoding gap,ITS序列种间变异率较psbA trnH、rbcL和matK序列有明显优势,单片段ITS正确鉴定率最高,ITS+rbcL片段联合条码的正确鉴定率最高,因此我们认为ITS片段或条形码组合ITS+rbcL是金合欢属的快速鉴别最理想的条码。     

蒟蒻薯属 (薯蓣科) 植物DNA条形码研究

蒟蒻薯属（Tacca）植物种间在形态上差别不大,导致分类上存在一定的困难。DNA条形码是一种利用短的DNA标准片段来鉴别和发现物种的方法。本研究利用核基因ITS片段和叶绿体基因trnH psbA, rbcL, matK片段对蒟蒻薯属6个种的DNA条形码进行研究,对4个DNA片段可用性,种内种间变异,barcode gap进行了分析,采用Tree based和BBA两种方法比较不同序列的鉴定能力。结果显示：单片段ITS正确鉴定率最高,片段组合rbcL+matK正确鉴定率最高。支持CBOL植物工作组推荐的条码组合rbcL+matK可作为蒟蒻薯属物种鉴定的标准条码,建议ITS片段作为候选条码。丝须蒟蒻薯Tacca integrifolia采自西藏的居群与马来西亚居群形成了2个不同的遗传分支,且两者在形态上也存在一定的差异,很可能是一个新种。     

梅花草属叶绿体基因组进化分析

叶绿体基因组序列变异和基因组成等特征可有效反映植物类群间的系统发育和进化关系。本研究利用Illumina高通量测序平台对梅花草属（Parnassia）及其近缘属5种植物的叶绿体基因组进行测序和组装,同时基于已发表的近缘种叶绿体基因组信息,对梅花草属叶绿体基因组结构特征、序列遗传变异和蛋白编码基因密码子偏好性比对分析。结果显示：梅花草属叶绿体基因组整体结构较为保守,均为四分体结构;梅花草多个基因出现假基因化,而本属其他物种叶绿体基因组成一致,均编码115个基因;与近缘属物种相比,本属所有物种均丢失rpl16基因的内含子;蛋白质编码基因的非同义/同义替代率比值较低,叶绿体基因可能经历纯化选择作用;密码子偏好性聚类结果与蛋白编码序列重建的系统发育关系结果一致。本研究表明选择压力可能在梅花草属叶绿体基因组蛋白编码基因进化过程中发挥作用,有助于进一步理解梅花草属植物的进化和适应机制。     

蒟蒻薯属(薯蓣科)植物DNA条形码研究

蒟蒻薯属(Tacca)植物种间在形态上差别不大,导致分类上存在一定的困难.DNA条形码是一种利用短的DNA标准片段来鉴别和发现物种的方法.本研究利用核基因ITS片段和叶绿体基因trn H-psbA,rbcL,matK片段对蒟蒻薯属6个种的DNA条形码进行研究,对4个DNA片段可用性,种内种间变异,barcode gap进行了分析,采用Tree-based和BBA两种方法比较不同序列的鉴定能力.结果显示:单片段ITS正确鉴定率最高,片段组合rbcL+matK正确鉴定率最高.支持CBOL植物工作组推荐的条码组合rbcL+matK可作为蒟蒻薯属物种鉴定的标准条码,建议ITS片段作为候选条码.丝须蒟蒻薯Tacca integrifolia采自西藏的居群与马来西亚居群形成了2个不同的遗传分支,且两者在形态上也存在一定的差异,很可能是一个新种.     

中国秋海棠属（秋海棠科）植物的DNA条形码评价

秋海棠属植物种类繁多,形态变异多样,导致种类的系统放置混乱,近缘种类鉴定困难。利用DNA条形码实现物种快速准确的鉴定技术具有不受形态特征约束的优势,为秋海棠属植物的分类鉴定提供了新的方法。本研究选择4个DNA条形码候选片段（rbcL,matK,trnH-psbA,ITS）对中国秋海棠属26种136个个体进行了分析。结果显示：叶绿体基因rbcL,matK和trnH-psbA种内和种间变异小,对秋海棠属植物的鉴别能力有限：ITS／ITS2种内和种间变异大,在本研究中物种正确鉴定率达到100％／96％,可考虑作为秋海棠属DNA条形码鉴定的候选片段。研究结果支持中国植物条形码研究组建议将核基因ITS／ITS2纳人种子植物DNA条形码核心片段中的观点。     

基于5个基因片段的野胡麻属系统位置研究

对单种属野胡麻属(原隶属于广义玄参科)及其可能近缘类群广泛取样,选择合适外类群,通过对4个叶绿体基因联合数据(trnL-F、rps16、rbcL、rps2)、核基因ITS片段、叶绿体基因与核基因ITS片段联合数据,进行最大简约法和贝叶斯法分析,探讨野胡麻属在科级系统位置及其与近缘类群系统发育关系。结果表明,所有系统树都支持野胡麻属先和肉果草属构成姐妹群关系,叶绿体基因联合系统树支持率分别为97%[Bootstrap(BS)]和100%[Posterior probability(PP)];ITS系统树支持率分别为99%(BS)和100%(PP);叶绿体基因和ITS联合系统树支持率均为100%(BS和PP)。野胡麻属、肉果草属与通泉草属一起构成一单系群,叶绿体基因联合系统树、ITS系统树、叶绿体基因和ITS联合系统树的支持率均为100%(BS和PP)。形态学证据也支持野胡麻属、肉果草属和通泉草属这3个属的近缘关系。本研究结果支持单种属野胡麻属隶属于透骨草科的通泉草亚科,与肉果草属亲缘关系最近,这两个属进而与通泉草属近缘,可能隶属于通泉草属内,与岩白翠亲缘关系较近,也可能与通泉草属互为姐妹群关系。     

Testing for endemism, genotypic diversity and species concepts in Antarctic terrestrial microalgae of the Tribonemataceae (Stramenopiles, Xanthophyceae)

The genetic diversity of all available culture strains of the Tribonemataceae ( Stramenopiles , Xanthophyceae ) from Antarctica was assessed using the chloroplast-encoded psbA /rbcL spacer region sequences, a highly variable molecular marker, to test for endemism when compared with their closest temperate relatives. There was no species endemic for Antarctica, and no phylogenetic clade corresponded to a limited geographical region. However, species of the Tribonemataceae may have Antarctic populations that are distinct from those of other regions because the Antarctic strain spacer sequences were not identical to sequences from temperate regions. Spacer sequences from five new Antarctic isolates were identical to one or more previously available Antarctic strains, indicating that the Tribonemataceae diversity in Antarctic may be rather limited. Direct comparisons of the spacer sequences and phylogenetic analyses of the more conserved rbcL gene revealed that current morphospecies were inadequate to describe the actual biodiversity of the group. For example, the genus Xanthonema , as currently circumscribed, was paraphyletic. Fortunately, the presence of distinctive sequence regions within the psbA/rbcL spacer, together with differences in the rbcL phylogeny, provided significant autoapomorphic criteria to re-define the Tribonemataceae species.     

Phylogenetic relationships in Interfilum and Klebsormidium (Klebsormidiophyceae, Streptophyta)

Members of the genus Klebsormidium have cosmopolitan distribution and occur in a very wide range of freshwater and terrestrial habitats. Due to its simple filamentous morphology, this genus represents a taxonomically and systematically complex taxon in which phylogenetic relationships are still poorly understood. The phylogeny of Klebsormidium and closely related taxa was investigated using new ITS rRNA and rbcL sequences generated from 75 strains (isolated from field samples or obtained from culture collections). These sequences were analyzed both as single-marker datasets and in a concatenated dataset. Seven main superclades were observed in the analyses, which included sixteen well-supported clades. Some species of Klebsormidium, including the type species Klebsormidium flaccidum, were polyphyletic. Interfilum was recovered with high statistical support as sister taxon to a clade of Klebsormidium formed mainly by strains identified as K. flaccidum. Whereas some clades could be easily associated with described species, this was not possible for other clades. A new lineage of Klebsormidium, isolated from arid soils in southern Africa and comprising undescribed species, was discovered. Several morphological characters traditionally used for taxonomic purposes were found to have no phylogenetic significance and in some cases showed intra-clade variation. The capacity to form packet-like aggregates (typical of Interfilum), features of the morphology of the chloroplast and the type of habitat were the main phylogenetically relevant characters. Overall, Klebsormidium and Interfilum formed a more diverse algal group than was previously appreciated, with some lineages apparently undergoing active evolutionary radiation; in these lineages the genetic variation observed did not match the morphological and ecological diversity.     

Horizontal gene transfer of a plastid gene in the non-photosynthetic flowering plants Orobanche and Phelipanche (Orobanchaceae)

Plastid sequences are among the most widely used in phylogenetic and phylogeographic studies in flowering plants, where they are usually assumed to evolve like non-recombining, uniparentally transmitted, single-copy genes. Among others, this assumption can be violated by intracellular gene transfer (IGT) within cells or by the exchange of genes across mating barriers (horizontal gene transfer, HGT). We report on HGT of a plastid region including rps2, trnL-F, and rbcL in a group of non-photosynthetic flowering plants. Species of the parasitic broomrape genus Phelipanche harbor two copies of rps2, a plastid ribosomal gene, one corresponding to the phylogenetic position of the respective species, the other being horizontally acquired from the related broomrape genus Orobanche. While the vertically transmitted copies probably reside within the plastid genome, the localization of the horizontally acquired copies is not known. With both donor and recipient being parasitic plants, a possible pathway for the exchange of genetic material is via a commonly attacked host.     

Morphological convergence characterizes the evolution of Xanthophyceae (Heterokontophyta): evidence from nuclear SSU rDNA and plastidial rbcL genes

Xanthophyceae are a group of heterokontophyte algae. Few molecular studies have investigated the evolutionary history and phylogenetic relationships of this class. We sequenced the nuclear-encoded SSU rDNA and chloroplast-encoded rbcL genes of several xanthophycean species from different orders, families, and genera. Neither SSU rDNA nor rbcL genes show intraspecific sequence variation and are good diagnostic markers for characterization of problematic species. New sequences, combined with those previously available, were used to create different multiple alignments. Analyses included sequences from 26 species of Xanthophyceae plus three Phaeothamniophyceae and two Phaeophyceae taxa used as outgroups. Phylogenetic analyses were performed according to Bayesian inference, maximum likelihood, and maximum parsimony methods. We explored effects produced on the phylogenetic outcomes by both taxon sampling as well as selected genes. Congruent results were obtained from analyses performed on single gene multiple alignments as well as on a data set including both SSU rDNA and rbcL sequences. Trees obtained in this study show that several currently recognized xanthophycean taxa do not form monophyletic groups. The order Mischococcales is paraphyletic, while Tribonematales and Botrydiales are polyphyletic even if evidence for the second order is not conclusive. Botrydiales and Vaucheriales, both including siphonous taxa, do not form a clade. The families Botrydiopsidaceae, Botryochloridaceae, and Pleurochloridaceae as well as the genera Botrydiopsis and Chlorellidium are polyphyletic. The Centritractaceae and the genus Bumilleriopsis also appear to be polyphyletic but their monophyly cannot be completely rejected with current evidence. Our results support morphological convergence at any taxonomic rank in the evolution of the Xanthophyceae. Finally, our phylogenetic analyses exclude an origin of the Xanthophyceae from a Vaucheria-like ancestor and favor a single early origin of the coccoid cell form.     

Phylogeny of the sundews, Drosera (Droseraceae), based on chloroplast rbcL and nuclear 18S ribosomal DNA Sequences

The sundew genus Drosera consists of carnivorous plants with active flypaper traps and includes nearly 150 species distributed mainly in Australia, Africa, and South America, with some Northern Hemisphere species. In addition to confused intrageneric classification of Drosera, the intergeneric relationships among the Drosera and two other genera in the Droseraceae with snap traps, Dionaea and Aldrovanda, are problematic. We conducted phylogenetic analyses of DNA sequences of the chloroplast rbcL gene for 59 species of Drosera, covering all sections except one. These analyses revealed that five of 11 sections, including three monotypic sections, are polyphyletic. Combined rbcL and 18S rDNA sequence data were used to infer phylogenetic relationships among Drosera, Dionaea, and Aldrovanda. This analysis revealed that all Drosera species form a clade sister to a clade including Dionaea and Aldrovanda, suggesting that the snap traps of Aldrovanda and Dionaea are homologous despite their morphological differences. MacClade reconstructions indicated that multiple episodes of aneuploidy occurred in a clade that includes mainly Australian species, while the chromosome numbers in the other clades are not as variable. Drosera regia, which is native to South Africa, and most species native to Australia, were clustered basally, suggesting that Drosera originated in Africa or Australia. The rbcL tree indicates that Australian species expanded their distribution to South America and then to Africa. Expansion of distribution to the Northern Hemisphere from the Southern Hemispere occurred in a few different lineages.     

小麦及其相关物种rbcL基因序列的比较研究

用4个抗白粉病小麦品系构建了一个混合cDNA文库,从该文库中分离到一个新的小麦rbcL基因全长cDNA克隆。至此,已经有3个不同的小麦rbcL基因序列被报道,新rbcL基因cDNA与以前的2个序列分别有1个和3个碱基的差异。新的cDNA长1519bp(基因库查询号：AY328025)。同源性比较发现,新的小麦rbcL基因的cDNA序列与以前报告的小麦rbcL基因的cDNA序列(gi：344052)有一个碱基的差异,从而导致所编码的多肽在144位由Tyr变为Cys。进一步比较分析了在相关物种中rbcL基因的cDNA序列,结果显示,rbcL基因的编码区在不同属的物种间高度保守,并从分子水平表明小麦与大麦、新麦草、赖草、披碱草属等的亲源关系比与水稻、玉米等的近。     

Molecular phylogeny and evolution of the order Tribonematales (Heterokonta, Xanthophyceae) based on analysis of plastidial genes rbcL and psaA

Tribonematales is an order of filamentous algae in the class Xanthophyceae (Heterokonta). Few molecular studies, all with a limited taxon sampling, have previously investigated its evolutionary history and phylogenetic relationships. We sequenced the chloroplast-encoded rbcL and psaA genes of several tribonematalean species and of several coccoid and siphonous forms that previous studies revealed to be strictly related to Tribonematales. Multiple alignments included mostly new sequences obtained from 42 taxa. Phylogenetic reconstructions were performed using the maximum likelihood method. The rbcL and psaA data sets were analyzed independently and combined in a single multiple alignment. Neither rbcL nor psaA genes showed intraspecific sequence variation. The former proved to be a better diagnostic marker than the latter for characterization of species. We explored effects produced on phylogenetic outcomes by selected genes. Congruent results were obtained from analyses performed on single gene multiple alignments as well as on the combined data set. There is strong statistical support for trees that show several currently recognized taxonomic groups to be polyphyletic. The siphonous orders Botrydiales and Vaucheriales do not form a clade. Botrydiales and Tribonematales are polyphyletic as are the families Botrydiaceae, Centritractaceae and Tribonemataceae and the genera Xanthonema and Bumilleriopsis. We tentatively define new boundaries of the Tribonematales to include both coccoid and filamentous species having a bipartite cell wall and also the siphonous members of the genus Botrydium. Also, our results support morphological convergence at all taxonomic ranks in the evolution of the Xanthophyceae.     

Phylogenetics of Miscanthus,Saccharum and related genera (Saccharinae,Andropogoneae, Poaceae) based on DNA sequences from ITS nuclear ribosomal DNA and plastid trnLintron and trnL-F intergenic spacers

DNA sequences were used to assess the monophyly and inter-relationships of Miscanthus, Saccharum and related genera in the Saccharum complex. Three DNA regions were sequenced, including the trnL intron and the trnL-F intergenic spacer of the plastid genome and the ITS region of nuclear ribosomal DNA (nrDNA). Because it was more variable, the ITS region proved most suitable for phylogenetic reconstruction at this level, and the results indicate that Miscanthus s.l. and Saccharum s.l. are polyphyletic. A set of species from Saccharum section Ripidium (clade a) do not group closely with any members of Saccharum s.l.. A number of Miscanthus species from eastern or south-eastern Asia represent a monophyletic group with a basic chromosome number of 19 (clade b), but the other species from Africa and the Himalayas are clearly excluded. There is support for a monophyletic Saccharum s.s. clade including S. officinarum and S. spontaneum that is sister to Miscanthus s.s (clade c). There is no evidence to support the division of some Saccharum s.l. into the genera currently known as Erianthus and Narenga. Saccharum contortum (=Erianthus contortus), S. narenga (=Narenga porphyrocoma) and Erianthus rockii, group more closely with Miscanthus fuscus, a species from the Himalayas and also with the African Miscanthus s.l. species (=Miscanthidium, clade d). Electronic Publication     

The Evolutionary History of the Genus Acanthamoeba and the Identification of Eight New 18S rRNA Gene Sequence Types

ABSTRACT The 18S rRNA gene ( Rns ) phylogeny of Acanthamoeba is being investigated as a basis for improvements in the nomenclature and taxonomy of the genus. We previously analyzed Rns sequences from 18 isolates from morphological groups 2 and 3 and found that they fell into four distinct evolutionary lineages we called sequence types T1-T4. Here, we analyzed sequences from 53 isolates representing 16 species and including 35 new strains. Eight additional lineages (sequence types T5-T12) were identified. Four of the 12 sequence types included strains from more than one nominal species. Thus, sequence types could be equated with species in some cases or with complexes of closely related species in others. The largest complex, sequence type T4, which contained six closely related nominal species, included 24 of 25 keratitis isolates. Rns sequence variation was insufficient for full phylogenetic resolution of branching orders within this complex, but the mixing of species observed at terminal nodes confirmed that traditional classification of isolates has been inconsistent. One solution to this problem would be to equate sequence types and single species. Alternatively, additional molecular information will be required to reliably differentiate species within the complexes. Three sequence types of morphological group 1 species represented the earliest divergence in the history of the genus and, based on their genetic distinctiveness, are candidates for reclassification as one or more novel genera.     

The Relationship between Aleuritopteris humatifolia and A-chrysophylla Based on Three Chloroplast DNA Sequences Analyses

Total DNA from 27 species including Aleuritopteris humatifolia and Achrysophylla and related taxa was extracted in this research, and the rbcL, trnL F and matK sequences were amplified and sequenced. The sequences were aligned by ClustalX. The phylogenetic trees were constructed by Maximum parsimony methods and the intraspecific and interspecific genetic distance were computed in MEGA 60. The results showed as follows: no significant difference among rbcL, trnL F and matK sequences of one sample of Ahumatifolia and two samples of Achrysophy lla, and the maximum genetic distance between Ahumatifolia and Achrysophylla were less than the minimum genetic distance between Ahumatifolia and other closely related species. Therefore, our study support the taxonomic treatment of reducing Ahumatifolia to synonym of Achrysophylla based on our phylogenetic analysis combining the evidences from their morphological characters of blades, spores, indusia, and rhizome scales.