Phylogenetic relationships of some spirurine nematodes (Nematoda: Chromadorea: Rhabditida: Spirurina) parasitic in fishes inferred from SSU rRNA gene sequences

Abstract: Small subunit rRNA sequences were obtained from 38 representatives mainly of the nematode orders Spirurida (Camallanidae, Cystidicolidae, Daniconematidae, Philometridae, Physalopteridae, Rhabdochonidae, Skrjabillanidae) and, in part, Ascaridida (Anisakidae, Cucullanidae, Quimperiidae). The examined nematodes are predominantly parasites of fishes. Their analyses provided well-supported trees allowing the study ofphylogenetic relationships among some spirurine nematodes. The present results support the placement of Cucullanidae at the base of the suborder Spirurina and, based on the position of the genus Philonema (subfamily Philoneminae) forming a sister group to Skrjabillanidae (thus Philoneminae should be elevated to Philonemidae), the paraphyly of the Philometridae. Comparison of a large number of sequences of representatives of the latter family supports the paraphyly of the genera Philometra, Philometroides and Dentiphilometra. The validity of the newly included genera Afrophilometra and Caranginema is not supported. These results indicate geographical isolation has not been the cause of speciation in this parasite group and no coevolution with fish hosts is apparent. On the contrary, the group of South-American species ofAlinema, Nilonema and Rumai is placed in an independent branch, thus markedly separated from other family members. Molecular data indicate that the skrjabillanid subfamily Esocineminae (represented by Esocinema bohemicum) should be either elevated to the rank of an independent family or Daniconematidae (Mexiconema africanum) should be decreased to Daniconematinae and transferred to the family Skrjabillanidae. Camallanid genera Camallanus and Procamallanus, as well as the subgenera Procamallanus and Spirocamallanus are confirmed to be paraphyletic. Paraphyly has also been found within Filarioidea, Habronematoidea and Thelazioidea and in Cystidicolidae, Physalopteridae and Thelaziidae. The results of the analyses also show that Neoascarophis, Spinitectus and Rhabdochona are monophyletic, in contrast to the paraphyletic genus Ascarophis. They further confirm the independence of two subgenera, Rhabdochona and Globochona, in the genus Rhabdochona. The necessity of further studies of fish-parasitizing representatives of additional nematode families not yet studied by molecular methods, such as Guyanemidae, Lucionematidae or Tetanonematidae, is underscored.     

Phylogenetic analysis of elongation factor Tu gene of phytoplasmas from Japan

The elongation factor Tu (tuf) gene from nine Japan phytoplasma isolates was amplified with the polymerase chain reaction, and the DNA sequences of the tuf gene were determined. The tuf gene from 14 phytoplasma isolates, including reference isolates and other bacteria, were phylogenetically analyzed. A nucleotide sequence of the tuf gene among seven aster yellows group (16Sr I-B and I-D) phytoplasmas had 97%–100% similarity, and the tuf gene of two phytoplasmas of the X-disease group (16Sr III-B) had 99% similarity. The tuf genes had lower homology than did the 16S rRNA gene in the phytoplasma groups. A phylogenetic tree of amino acid sequences of the tuf gene was nearly equal to that of the 16S rRNA gene but differed somewhat from the tree based on the 16S rRNA gene in that paulownia witches broom (PaW: 16Sr I-D) and American aster yellows (AAY: 16Sr I-B) were in a subclade.The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession numbers AB095495, AB095667, AB095668, AB095669, AB095670, AB095671, AB095672, AB095673 and AB095674     

Phylogenetic analysis of Trypanosomatina (Protozoa: Kinetoplastida) based on minicircle conserved regions

Phylogenetic relationships within the suborder Trypanosomatina were inferred from the kinetoplast DNA minicircle conserved region sequences. Trees built using distance-matrix (Neighbor-Joining) and maximum parsimony methods showed that the minicircle conserved regions (CRs) provide a sensitive and specific molecular marker suitable for phylogenetic analyses of subspecies and strains of trypanosomatid flagellates, as testified by the subdivision of the genus Leishmania into the subgenera Leishmania. Viannia and Sauroleishmania. However, since Phytomonas and monogenetic parasites of insects represent the earliest diverging groups, the CRs do not seem to be useful for inference of relationships among major lineages of the order Kinetoplastida.     

Comparison of two short DNA barcoding loci (COI and COII) and two longer ribosomal DNA genes (SSU & LSU rRNA) for specimen identification among quarantine root-knot nematodes (Meloidogyne spp.) and their close relatives

Root-knot nematodes (Meloidogyne spp.) are important pests of numerous crops worldwide. Some members of this genus have a quarantine status, and accurate species identification is required to prevent further spreading. DNA barcoding is a method for organism identification in non-complex DNA backgrounds based on informative motifs in short DNA stretches (≈600 bp). As part of the EU 7th Framework project QBOL, 15 Meloidogyne species were chosen to compare the resolutions offered by two typical DNA barcoding loci, COI and COII, with the distinguishing signals produced by two ribosomal DNA genes (small and large subunit rDNA; SSU?≈?1,700 and LSU?≈?3,400 bp). None of the four markers distinguished between the tropical species Meloidogyne incognita, M. javanica and M. arenaria. Taking P ID (Liberal) values ≥0.93 as a measure for species delimitation, the four mtDNA and rDNA markers performed well for the tropical Meloidogyne species complex, M. enterolobii, M. hapla, and M. maritima. Within cluster III A (Holterman et al. Phytopathology, 99, 227–235, 2009), SSU rDNA did not offer resolution at species level. Both mtDNA loci COI and COII did, whereas for LSU rDNA a longer fragment (≥700 bp) is required. The high level of mitochondrial heteroplasmy recently reported for M. chitwoodi (Humphreys-Pereira and Elling Nematology, 15, 315–327, 2013) was not found in the populations under investigation, suggesting this could be a regional phenomenon. For identification of RKNs, we suggest the combined use of SSU rDNA with one of three other markers presented here.     

不同地区辣椒疫霉菌遗传多样性的RAPD分析

 通过利用12个十碱基随机引物对来自我国7个不同地理区域的56个辣椒疫霉菌株进行RAPD分析,探索了我国主要辣椒种植区间的辣椒疫霉菌的遗传分化关系。结果表明:1)受试56个菌株共产生70条谱带,其中多态性为56条,占80%,说明我国主要辣椒种植区的辣椒疫霉菌具有较丰富的遗传多样性;2)根据引物扩增的DNA指纹图谱,运用UPGMA分析法,以遗传相似系数0.6为阈值,将供试56个菌株划分为8个基因型(I、II、III、IV、V、VI、VII、VIII),发现除少数来自相近地理海拔的绝大多数菌株被划分为同一个基因型外,其它不同地理区域的菌株基因型的划分与地理来源无直接的关系。在此基础上,结合我国不同地理区域辣椒疫霉病发生情况,提出我国辣椒疫霉菌基因型的划分除少数与地理区域有关外,其它绝大多数地区的辣椒疫霉菌基因型的划分与地理来源无直接的相关性。     

Phylogenetic analysis of partial sequences from Fig mosaic virus isolates in Turkey

Fig mosaic virus (FMV), which was described recently, is the only characterized causal agent of fig mosaic disease (FMD). It has six RNA segments and belongs to the Bunyaviridae family. In order to determine the genetic diversity of Turkish FMV isolates, the most common fig cultivars showing FMD symptoms were collected from different fig-growing provinces of Turkey. Nucleoprotein (Np) and Glycoprotein (Gp) gene-specific primers of FMV were used for RT-PCR analysis. According to RT-PCR results, 71 of 90 samples from 20 different cultivars and unknown fig seedlings were found to be infected by FMV. Among them, 41 isolates were sequenced and subjected to phylogenetic analyses based on the partial Gp and Np sequences at the amino acid level by the neighbor-joining method. The isolates showed more than 80% identity with reference FMV isolates (Acc. nos. FM991954.1 and FM864225.2). Based on phylogenetic analysis, the sequences clustered into two main groups for Np and Gp regions. Significant relationships between FMV isolates based on geographic origin and cultivars were not observed.     

Molecular characterisation and diagnostics of some Longidorus species (Nematoda: Longidoridae) from Russia and other countries using rRNA genes

The needle nematodes of the genus Longidorus can cause diseases of various crops and trees, and are comprised of more than 150 valid species. Eleven valid and six unidentified species of the genus Longidorus collected in different regions of Russia, two states of USA, Germany, New Zealand and Ukraine were molecularly characterized using analysis of the partial 18S rRNA and the D2–D3 expansion segments of the 28S rRNA gene sequences. Fifty-four partial 28S rRNA and fifteen partial 18S rRNA gene sequences were obtained for the present study. Using molecular criteria, we confirmed the morphological identification and distinguished between the following species: L. aetnaeus, L. africanus, L. andalusicus, L. artemisiae, L. caespiticola, L. distinctus, L. elongatus, L. euonymus, L. intermedius, L. leptocephalus and L. lignosus. Two longidorid populations from Russia and four from California were not identified to a species level. We obtained the full length D2–D3 of 28S rRNA gene sequence from several freshly-collected L. artemisiae samples. We confirmed the identity of the D2 region of 28S rRNA gene sequence with a short D2 of 28S rRNA gene fragment sequence previously obtained from formalin-fixed nematodes embedded in the L. artemisiae paratype slides. Longidorus lignosus was molecularly characterized and L. aetnaeus was reported from Russia for the first time. PCR-D2-D3-RFLP diagnostic profiles generated by five restriction enzymes: AluI, HinfI, Bsp143I, Tru1I and RsaI are presented for sixteen Longidorus species.     

禾谷缢管蚜RpGST1基因的克隆、序列分析及原核表达

为揭示禾谷缢管蚜耐药性的分子机理,采用RT-PCR方法克隆了禾谷缢管蚜谷胱甘肽-S-转移酶(glutathione S-transferases,GSTs)的cDNA序列,命名为RpGST1(GenBank登录号KP192850),并构建原核表达载体pET32-RpGST1,对RpGST1基因进行原核表达、SDS-PAGE和Western blotting检测。结果显示,禾谷缢管蚜RpGST1基因的编码区长651 bp,编码216个氨基酸,分子量约为24.06 kD,理论等电点为6.20;RpGST1基因在大肠杆菌中成功表达出一个分子量约为45 kD的融合蛋白,与预测的融合蛋白分子量大小一致。通过克隆RpGST1基因的cDNA序列并进行序列比对分析,表明构建了GST基因的原核表达载体并成功表达。     

烟粉虱MED隐种蜕皮激素受体基因cDNA克隆、转录与组织表达

蜕皮激素受体(ecdysone receptor,Ec R)是调控昆虫蜕皮、变态和生殖等过程中基因表达的重要调控因子。为研究Ec R在烟粉虱Bemisia tabaci生长发育中的作用,利用RT-PCR和RACE等技术扩增了烟粉虱MED隐种Ec R基因的c DNA全长序列,并利用实时荧光定量PCR技术检测其在烟粉虱不同发育时期相对表达量的变化。Bt Ec R c DNA序列全长2 844 bp,含有一个1 518 bp的开放阅读框,共编码505个氨基酸,预测蛋白分子量为56 k D,等电点为6.43,含有特殊结构功能域:DNA结合域(DBD_Ec R)和配体结合域(LBD_Ec R),该序列编码的蛋白质序列与其它已报道的昆虫Ec R蛋白序列具有很高的相似性,命名为Bt Ec R(Gen Bank登录号:KR534774)。Bt Ec R在MED隐种若虫、雌成虫各发育时期均有表达,若虫期在伪蛹前期达到最高值,成虫期呈现先升高后降低的趋势,且在羽化后第7天达到最高值,约为羽化第1天的23倍。研究结果为揭示Bt Ec R在烟粉虱整个生长发育过程中的作用提供了重要依据。     

草地螟触角普通气味结合蛋白基因的克隆及序列分析

利用RT-PCR结合RACE技术克隆了编码草地螟(Loxostege sticticalis)触角中一种普通气味结合蛋白的基因。序列分析表明,成熟蛋白的序列中含有阅读框序列,推导的氨基酸序列与已报道的11种鳞翅目昆虫普通气味结合蛋白Ⅰ比较,平均相似度在62.3%左右,并拥有气味结合蛋白的典型结构特征。该基因归属于普通气味结合蛋白Ⅰ基因亚族。因此将它命名为LstiGOBP1。     

中国霸王属植物在世界该属中的系统发育地位与形态性状进化研究

通过PCR扩增和测序,得到了中国霸王属种类的rbc L和trn L-F基因片段序列数据,同时在网络数据库获得了南非、纳米比亚、澳大利亚和中亚地区的霸王属种类的rbc L和trn L-F片段,构建系统发育树,并且对霸王属系统发育信号和31个形态性状进行分析。结果显示:1中国霸王属种类聚为一大类,与南非和纳米比亚霸王属形成姐妹分支;2霸王属植物的生命周期、叶排列、叶形状及株高等8个性状具有明显的系统发育信号,其次,中国霸王属植物的萼片长度、萼片宽度、果实长度、茎性质和叶片结构等10个性状与国外霸王属有显著的差异,这与中国霸王属在该属系统发育树中形成单源分支相吻合。     

禾谷孢囊线虫(Heterodera avenae)纤维素结合 蛋白基因(Ha-cbp-1)的克隆和序列分析

 禾谷孢囊线虫(Heterodera avenae)是中国小麦上的重要病原线虫。纤维素结合蛋白基因是一种重要的植物线虫寄生和致病相关基因。用同源克隆的方法从禾谷孢囊线虫寄生前二龄幼虫中克隆出一种纤维素结合蛋白新基因Ha-cbp-1（GenBank 注册号GQ178086）cDNA序列。Ha-cbp-1基因cDNA包含1个开放阅读框,编码131个氨基酸残基的蛋白质,预测蛋白由1个长度为18氨基酸残基的信号肽和1个纤维素结合区域（CBD）组成。Ha-cbp-1的基因组DNA序列含有2个内含子。预测的禾谷孢囊线虫纤维素结合蛋白（HA-CBP-1）序列与大豆孢囊线虫纤维素结合蛋白（HG-CBP-1）序列有60%的同一性和76%的相似性,与甜菜孢囊线虫纤维素结合蛋白（HS-CBP-1）序列有60%的同一性和75%的相似性。本研究首次从禾谷孢囊线虫中成功克隆出CBP蛋白基因。     

Phylogenetic characterization of a microsporidium (Nosema sp.) isolated from the mulberry pest, Hemerophila atrilineata

Microsporidia are a group of obligate intracellular unicellular eukaryotes that can parasitize a wide variety of other eukaryotes ranging from protists to invertebrates and vertebrates. In this study, we examined the microsporidium Nosema sp. isolated from the mulberry pest, Hemerophila atrilineata Butler, 1881, named herein "Nosema sp. HA". The fresh spores were long oval in shape, 3.8 +/- 0.4 microm in length and 1.9 +/- 0.3 microm in width. Analysis of tissue infection of silkworm, Bombyx mori Linnaeus, 1758, indicated that the midgut, Malpighian tubules, muscle, fat body, silk glands, hemocytes, nerve tissue and gonads of silkworm were infected with Nosema sp. HA. The complete rRNA gene sequence of this microsporidium contained 4 305 base pairs (GenBank Accession JN882299), including the large subunit rRNA (2492 bp), the internal transcribed spacer (187 bp), the small subunit rRNA (1232 bp), the intergenic spacer (279 bp) and the 5S region (115 bp). The organization of the rRNA gene is 5'-LSU-ITS-SSU-IGS-5S-3'. Phylogenetic analysis, comparison of sequence identities and the arrangement in the rRNA gene subunits suggested that this isolate is separate from other Nosema species.     

Two new species of protogyrodactylus (Monogenoidea: Dactylogyridae) from the gills of Gerres nigri (Teleostei: Gerreidae) from Senegal

Protogyrodactylus ethiopicus sp. n. and P. kritskyi sp. n. are described from the gills of Gerres nigri Günther (Gerreidae, Perciformes) captured from the estuary of the Sine-Saloum River (Senegal, West Africa). These new species differ from previously described species within the genus by a mid- or dextro-ventral vaginal opening (dextral in all other species). They are part of a morphological species group within Protogyrodactylus Johnston et Tiegs, 1922 that has the tip of the superficial root of the ventral anchor resembling a hook and two anterior projections on the anterior margin of the ventral bar. Protogyrodactylus ethiopicus differs from the remaining species in this group mainly by the morphology of the base of the male copulatory organ (MCO), which is disk-shaped, and the shape of the anterior projections of the ventral bar (round in the new species and relatively elongate in the other species of the group). The other new species, P. kritskyi, differs from all others in the same morphological group in having a MCO with a greatly expanded base that bears a heel-like subterminal sclerotization.     

In vitro secretion of metabolic end-products by piscine haemoflagellates Cryptobia salmositica and C. bullocki (Kinetoplastida: Bodonidae) and the relationship of these products to the pH in the medium.

Pathogenic and nonpathogenic strains of Cryptobia salmositica Katz, 1951 and C. bullocki Strout, 1965 produced hydrogen peroxide, pyruvate and lactate under in vitro conditions in Minimum Essential Medium (MEM). As parasite number increased, the phenol red in the medium changed from red to yellow. This change was not associated with a decrease in pH, or an increase in pyruvate or lactate, but was correlated with an increased secretion of hydrogen peroxide. Parasites incubated at 10 degrees C in medium at pH 6.0, 6.5, 7.0 and 7.3 were active for about I week with decreasing activity in the absence of serum. Parasites in saline (pH 6.0, 6.5, 7.0 and 7.3) were nonmotile within 24 h and were dead in about 1 week. This suggests that these Cryptobia spp. are sensitive to changes in pH and require medium which is buffered, either with serum or Hepes.