棕囊藻北部湾株的18S rDNA分子鉴定

为研究北部湾棕囊藻(Phaeocystis)藻华的成因,采用PCR克隆了棕囊藻北部湾株核糖体18S r DNA序列。结果表明,棕囊藻北部湾株具有游动单细胞与群体结构两种形态;其18S r DNA序列和NCBI基因库中球形棕囊藻(Phaeocystis globosa)的同源性为99%~100%,在系统进化树上与不同海域来源的球形棕囊藻聚在一大分支上,且与球形棕囊藻间的遗传距离均小于其他种。首次从分子生物学上确定棕囊藻北部湾株为球形棕囊藻。     

Assessing the Biodiversity of Monoraphidium Using 18S rDNA Sequences

The taxonomy of the genus Monoraphidium is unclear due in part to the absence of morphological features to clearly distinguish one species from another. Phytoplankton samples collected from lakes in the Arrowwood National Refuge in eastern North Dakota were found to contain several morphological species of Monoraphidium. Eighteen Monoraphidium isolates were examined with light microscopy and six morphological species were identified. PCR–RFLP of the 18S rDNA was used to type the isolates. Following digestion by Hae III and Taq I, the 18S rDNA PCR–RFLP patterns indicated 10 different types. Presently, the 18S rDNA product is being sequenced for each of the 10 types. By examining morphological characters and 18S rDNA sequences, congruence between morphology and sequence data may be compared. Also, because there is a lack of morphological characters defining Monoraphidium species, diversity within the 18S rDNA sequences may aid in the taxonomy of the genus and its place within the Chlorococcales. Supported by National Science Foundation Grants MCB‐0084188 and DBI‐0070387.     

Subgenus Systematics of Acanthamoeba: Four Nuclear 18S rDNA Sequence Types

ABSTRACT Classification of Acanthamoeba at the subgenus level has been problematic, but increasing reports of Acanthamoeba as an opportunistic human pathogen have generated an interest in finding a more consistent basis for classification. Thus, we are developing a classification scheme based on RNA gene sequences. This first report is based on analysis of complete sequences of nuclear small ribosomal subunit RNA genes ( Rns ) from 18 strains. Sequence variation was localized in 12 highly variable regions. Four distinct sequence types were identified based on parsimony and distance analyses. Three were obtained from single strains: Type T1 from Acanthamoeba castellanii V006, T2 from Acanthamoeba palestinensis Reich, and T3 from Acanthamoeba griffini S-7. T4, the fourth sequence type, included 15 isolates classified as A. castellanii, Acanthamoeba polyphaga, Acanthamoeba rhysodes , or Acanthamoeba sp., and included all 10 Acanthamoeba keratitis isolates. Interstrain sequence differences within T4 were 0%–4.3%, whereas differences among sequence types were 6%–12%. Branching orders obtained by parsimony and distance analyses were inconsistent with the current classification of T4 strains and provided further evidence of a need to reevaluate criteria for classification in this genus. Based on this report and others in preparation, we propose that Rns sequence types provide the consistent quantititive basis for classification that is needed.     

基于5.8SrDNA序列论三白草科的系统发育

三白草科（Saururaceae)是古草本的一个核心类群,它的研究对被子植物起源和早期演化具有重要意义,本文采用最大简约法（maximum parsimony method)和邻接法（neighbor-joining method)等不同的分析方法,对三白草科及其外类群齐头绒（Zippelia begoniaefolia Blume)的5.85rDNA序列进行分析,得到一致的结论：Anemopsis最早从三白草科中分离出来,Saururus chinensis和S.cernuus是一对姐群,由于5.85rDNA序列的变异位点和信息位点相对比较少,Gymnotheca chinensis-G.involucrata-Houttuynia-Saururus之间难以通过5.8SrDNA序列的比较进行分辨。     

15 Phylogeny of the chlorophyta: inferences from 18S and 26S rDNA

Recent studies of the Chlorophyceae using 18S and 26S rDNA data in meta‐analysis have demonstrated the power of combining these two sets of rDNA data. Furthermore, the 26S rDNA data complement the more conserved 18S gene for many chlorophycean lineages. Consequently, this data approach was pursued in an expanded taxon‐sampling scheme for the Chlorophyta, with special reference to the classes Chlorophyceae and Trebouxiophyceae. Results of these new phylogenetic analyses identify Microspora sp. (UTEX LB 472) and Radiofilum transversale (UTEX LB 1252) as sister taxa which, in turn, form a basal clade in the Cylindrocapsa alliance (Treubaria, Trochiscia, Elakatothrix). The relative position of the “Cylindrocapsa” clade within the Chlorophyceae remains uncertain. The enhanced taxon‐sampling has not resolved the relative positions of the Oedogoniales, Chaetophorales or Chaetopeltidales. Furthermore, the Sphaeropleaceae are supported as members of the Sphaeropleales in only some analyses, raising concerns about the status of the order. Although based on a limited set of taxa (currently <10), a combined data approach reveals support for a monophyletic Trebouxiophyceae that includes the distinctive organisms, Geminella and Eremosphaera. The goal of a well‐resolved phylogeny for the Chlorophyta remains just that, a goal. Achieving that goal obviously will require additional taxon sampling in the Prasinophyceae and Ulvophyceae, as well as, the Trebouxiophyceae. Moreover, it is clear that other genes (e.g., cp‐atpB, cp‐rbcL, cp‐16S, mt‐nad5) will be needed to help address problems of resolution based on the rDNA data alone. Supported by NSF DEB 9726588 and DEB 0129030.     

灰飞虱类酵母型共生菌18S rDNA序列变异及系统发生

分离纯化了云南楚雄、宁夏银川、北京通县、上海七宝镇、四川西昌５个地区的灰飞虱体内类酵母型共生菌（Ｙｅａｓｔ－ｌｉｋｅ Ｓｙｍｂｉｏｎｔｓ,ＹＬＳ）,并对其１８ＳｒＤＡＮ的约６００ｂｐ的序列进行了测定。结合已有的序列,构建了不同宿主的ＹＬＳ的分子系统树。结果表明,灰飞虱的ＹＬＳ属于子囊菌亚门Ｐｙｒｅｎｏｍｙｃｅｔｅｓ纲,与此纲的Ｈ．ｃｈｒｙｓｏｓｐｅｒｍｕｓ亲缘关系最近。我国各地区及日本的灰飞虱体内     

Phylogeny of the Prolecithophora (Platyhelminthes) Inferred from 18S rDNA Sequences

Complete nuclear 18S rDNA sequences from 14 species of the Prolecithophora were obtained and used, in combination with literature data, to generate the first parsimony-based hypothesis of the phylogeny of the order Prolecithophora (Platyhelminthes). Bootstrap, parsimony jack-knife, and Bremer support values were computed and compared. The monophyly of the Prolecithophora sensu stricto and the family Plagiostomidae is strongly supported. The taxa Separata, Combinata, and Plagiostomum are shown to be nonmonophyletic. Cylindrostomidae and Ulianinidae are transferred to Pseudostomidae. The Urastomidae is not part of the Prolecithophora.     

The Palaeoptera Problem: Basal Pterygote Phylogeny Inferred from 18S and 28S rDNA Sequences

Monophyly of the pterygote insects is generally accepted, but the relationships among the three basal branches (Odonata, Ephemeroptera and Neoptera) remain controversial. The traditional view, to separate the pterygote insects in Palaeoptera (Odonata + Ephemeroptera) and Neoptera, based on the ability or inability to fold the wings over the abdomen, has been questioned. Various authors have used different sets of morphological characters in support of all three possible arrangements of the basal pterygote branches. We sequenced 18S and 28S rDNA from 18 species of Odonata, 8 species of Ephemeroptera, 2 species of Neoptera, and 1 species of Archaeognatha in our study. The new sequences, in combination with sequences from GenBank, have been used in a parsimony jackknife analysis resulting in strong support for a monophyletic Palaeoptera. Morphological evidence and the phylogenetic implications for understanding the origin of insect flight are discussed.     

178 Molecular Systematics of the Ulvellaceae (Ulvales, Ulvophyceae) Inferred from Nuclear and Chloroplast DNA Sequences

The traditional use of thallus morphology to define lineages within the Ulvophyceae proved problematic because parallelism and convergence obscured natural relationships. The advent of transmission electron microscopy led to a re-evaluation of groups on the basis of zoid characters. Within TEM-defined lineages, the Ulotrichales and Ulvales were considered closely related orders, and molecular evidence has substantiated this hypothesis. In our molecular systematic studies of ulvophyceous green algae, we have broadened taxon sampling among these two orders. We show that the Ulvales and Ulotrichales are indeed monophyletic orders. However, the phylogenetic placement of species in the genera Bolbocoleon, Ctenocladus, Phaeophila, Pseudendoclonium and Acroblaste indicates that one or more additional lineages, placed between Ulvales and Ulotrichales in gene sequence trees, must be recognized. These species may constitute a separate order (Ctenocladales) consisting of multiple families. Our findings will be compared with taxonomic concepts based on morphological criteria.     

Phylogenetic Analysis of the Genus Bifidobacterium and Related Genera Based on 16S rDNA Sequences

The 16S rRNA gene sequences were determined for type strains of 21 Bifidobacterium species. A phylogenetic tree was constructed using the determined sequences and sequences from DNA databases, which contain the sequences of 11 type strains of Bifidobacterium species and 11 strains of related genera. All species of the genus Bifidobacterium and Gardnerella vaginalis ATCC 14018 belonged to a cluster phylogenetically distinct from the other genera. The cluster was divided into two subclusters: subcluster 1 composed of most species of Bifidobacterium and G. vaginalis, and subcluster 2 consisting of two species, B. denticolens and B. inopinatum; both of which were isolated from human dental caries. In the genus Bifidobacterium, four groups of species are known to be moderately to highly related by DNA-DNA hybridization. The four groups of species exhibited more than 99% similarity among their 16S rDNA sequences within each group. These results indicated that species with around 99% or more similarity in their 16S rDNA sequences should be confirmed for species identities.     

短裙竹荪和白鬼笔18S rDNA部分序列及其系统学意义

以短裙竹荪 [Dictyophoraduplicata(Bosc.)Fisch.]和白鬼笔 (PhallusimpudicusL.:Pers)作为鬼笔目 (Phal lales)的代表种 ,将其部分 1 8SrDNA序列与担子菌门 (Basidiomycota)其他科目 1 2个代表种已知的相关序列进行对比分析 ,以接合菌总状毛霉 (MucorracemosusFres.)为外类群构建系统树 ,探讨鬼笔目在系统分类学中的地位及其亲缘关系。结果表明 ,鬼笔目中竹荪属 (Dictyophora)与鬼笔属 (Phallus)的关系最为密切 ;其次它们与笼头菌科 (Clathraceae)的三叉鬼笔属 (Pseudocolus)关系较近 ,这与传统形态学分类系统一致。此外 ,鬼笔目与J櫣ｌｉｃｈ分类系统中的钉菇目 (Gomphales)、高腹菌目 (Gautieriales)、枝瑚菌目 (Ramariales)及鸡油菌目 (Cantharel lales)的关系较其他目更为密切 ,而与牛肝菌目 (Boletales)和腹菌类的马勃目 (Lycoperdales)及硬皮马勃目 (Scle rodermatales)的亲缘关系则相对较远。这一结果支持了Kirk等将钉菇目、高腹菌目和枝瑚菌目划为鬼笔目的分类观点。     

18S rDNA sequences and the holometabolous insects

The Holometabola (insects with complete metamorphosis: beetles, wasps, flies, fleas, butterflies, lacewings, and others) is a monophyletic group that includes the majority of the world's animal species. Holometabolous orders are well defined by morphological characters, but relationships among orders are unclear. In a search for a region of DNA that will clarify the interordinal relationships we sequenced approximately 1080 nucleotides of the 5' end of the 18S ribosomal RNA gene from representatives of 14 families of insects in the orders Hymenoptera (sawflies and wasps), Neuroptera (lacewing and antlion), Siphonaptera (flea), and Mecoptera (scorpionfly). We aligned the sequences with the published sequences of insects from the orders Coleoptera (beetle) and Diptera (mosquito and Drosophila), and the outgroups aphid, shrimp, and spider. Unlike the other insects examined in this study, the neuropterans have A-T rich insertions or expansion regions: one in the antlion was approximately 260 bp long. The dipteran 18S rDNA evolved rapidly, with over 3 times as many substitutions among the aligned sequences, and 2-3 times more unalignable nucleotides than other Holometabola, in violation of an insect-wide molecular clock. When we excluded the long-branched taxa (Diptera, shrimp, and spider) from the analysis, the most parsimonious (minimum-length) trees placed the beetle basal to other holometabolous orders, and supported a morphologically monophyletic clade including the fleas+scorpionflies (96% bootstrap support). However, most interordinal relationships were not significantly supported when tested by maximum likelihood or bootstrapping and were sensitive to the taxa included in the analysis. The most parsimonious and maximum-likelihood trees both separated the Coleoptera and Neuroptera, but this separation was not statistically significant.(ABSTRACT TRUNCATED AT 250 WORDS)     

Phylogenetic Relationships Among Xiphinema and Xiphidorus Nematode Species from Brazil Inferred from 18S rDNA Sequences

Maximum likelihood trees produced from 18S rDNA sequences separated 14 Xiphinema and five Xiphidorus nematode species from Brazil into distinct groups that concurred with their current morphological taxonomic status. Species belonging to the X. americanum group (X. brevicolle, X. diffusum, X. oxycaudatum, and X. peruvianum) formed a single group that was clearly separated from the other Xiphinema species. As with previous taxonomic studies that noted only minor morphological differences between putative X. americanum group species, separation of these species based upon 18S rDNA sequences was inconclusive. Thus it is probable that instead of comprising distinct species, the X. americanum group may in fact represent numerous morphotypes with large inter- and intra- population morphological variability that may be environmentally driven. Within the cluster representing non X. americanum group species, there was little statistical support to clearly separate species. However, three subgroups, comprising (i) the X. setariae/vulgare complex, (ii) X. ifacolum and X. paritaliae, and (iii) X. brasiliense and X. ensiculiferum were well resolved.     

Phylogenetic Position of the Phacotaceae Within the Chlamydophyceae as Revealed by Analysis of 18S rDNA and rbcL Sequences

Four genera of the Phacotaceae (Phacotus, Pteromonas, Wislouchiella, Dysmorphococcus), a family of loricated green algal flagellates within the Volvocales, were investigated by means of transmission electron microscopy and analysis of the nuclear encoded small-subunit ribosomal RNA (18S rRNA) genes and the plastid-encoded rbcL genes. Additionally, the 18S rDNA of Haematococcus pluvialis and the rbcL sequences of Chlorogonium elongatum, C. euchlorum, Dunaliella parva, Chloromonas serbinowii, Chlamydomonas radiata, and C. tetragama were determined. Analysis of ultrastructural data justified the separation of the Phacotaceae into two groups. Phacotus, Pteromonas, and Wislouchiella generally shared the following characters: egg-shaped protoplasts, a single pyrenoid with planar thylakoid double-lamellae, three-layered lorica, flagellar channels as part of the central lorica layer, mitochondria located in the central cytoplasm, lorica development that occurs in mucilaginous zoosporangia that are to be lysed, and no acid-resistant cell walls. Dysmorphococcus was clearly different in each of the characters mentioned. Direct comparison of sequences of Phacotus lenticularis, Pteromonas sp., Pteromonas protracta, and Wislouchiella planctonica revealed DNA sequence homologies of ≥98.0% within the 18S gene and 93.9% within the rbcL gene. D. globosus was quite different from these species, with a maximum of 92.9% homology in the 18S rRNA and ≤86.6% in the rbcL gene. It showed major similarities to the 18S rDNA of Dunaliella salina, with 95.3%, and to the rbcL sequence of Chlamydomonas tetragama, with 90.3% sequence homology. Additionally, the Phacotaceae sensu stricto exclusively shared 10 (rbcL: 4) characters which were present neither in other Chlamydomonadales nor in Dysmorphococcus globosus. Different phylogenetic analysis methods confirmed the hypothesis that the Phacotaceae are polyphyletic. The Phacotaceae sensu stricto form a stable cluster with affinities to the Dunaliellaes and possibly Haematococcus pluvialis. Dysmorphococcus globosus represented an independent lineage that is possibly related to Chlamydomonas moewusii and C. tetragama. Received: 9 June 1997 / Accepted: 17 October 1997     

Molecular Phylogeny of the Family Ophryscolecidae (Ciliophora,Litostomatea) Inferred from 18S rDNA Sequences

The 18S rDNA was used to infer oral ciliature patterns of evolution within the family Ophryoscolecidae, with the addition of five new sequences of ciliates from the genus Ostracodinium. Our data confirmed the monophyly of the subfamilies Entodiniinae and Ophryoscolecinae, but more analysis would be required for the definition of the status of the subfamily Diplodiniinae. The oral infraciliature patterns reflect evolutionary divergence in the family Ophryscolecidae, observing monophyly on Entodinium‐type, Diplodinium‐type, Ostracodinium‐type, Epidinium‐type, and Ophryoscolex‐type. The ancestral infraciliature of Entodinium‐type cannot be proven, however, the position of Entodinium‐type showed closer of Diplodinium‐type than Ophryoscolex‐type, corroborating previous studies using morphological characters. The observed inconsistencies reflect the need to increase the number of 18S rDNA sequences to family Ophryoscolecidae and investigate the evolution of this group using other molecular markers.     

基于18S rDNA序列的蝽次目(半翅目：异翅亚目)

利用18SrDNA分子约1 912 bp的序列对蝽次目21个科53个种进行系统发育分析。运用MP法、ML法和NJ法分析后的结果表明:蝽次目的单系性得到很高的支持;扁蝽总科成为毛点类的姐妹群;毛点类基本确定为两大分支:一支包含蝽总科和红蝽总科;另一支主要由长蝽总科、缘蝽总科和南蝽总科组成;长蝽总科和缘蝽总科都是多系;长蝽总科中,跷蝽科和皮蝽科的关系最近,构成姐妹群,位于整个毛点类的基部;与长蝽总科中另外两个科长蝽科和地长蝽科的关系很远。说明利用18SrDNA分子对研究蝽次目的系统发育关系是适合的,能够重建蝽次目;扁蝽总科和蝽总科单系性的结果与形态学的研究以及Li et al (2005)的研究一致;但较Li et al(2005)的研究更进一步把红蝽总科从广义的缘蝽总科中分出来;并建议皮蝽科作为一个独立的总科更合适。