A PCR based SNPs marker for specific characterization of English walnut (<Emphasis Type="Italic">Juglans regia</Emphasis> L.) cultivars

English walnut (Juglans regia L.) is the most economically important species from all the 21 species belonging to the genus Juglans and is an important and healthy food as well as base material for timber industry. The aim of this study was to develop a simple technique for specific characterization of English walnut using DNA method. The first and second internal transcribed spacers (ITS1 and ITS2) as well as the intervening 5.8S coding region of the rRNA gene for 18 cultivars of J. regia L. isolated from different geographic origins were characterized. The size of the spacers sequences ranged from 257 to 263 bases for ITS1 and from 217 to 219 bases for ITS2. Variation of GC contents has also been observed and scored as 55–56.7 and 57.1–58.9% for ITS1 and ITS2, respectively. This data exhibited the presence of polymorphism among cultivars. Alignment of the ITS1-5.8S-ITS2 sequences from 18 walnut cultivars showed that there were 244 single nucleotide polymorphisms (SNPs) and 1 short insertion–deletion (indel) at 5′ end ITS1. Amplification refractory mutation system strategy was successfully applied to the SNP markers of the ITS1 and ITS2 sequences for the fingerprinting analysis of 17 on 18 walnut cultivars. The prediction of ITS1 and ITS2 RNA secondary structure from each cultivar was improved by detecting key functional elements shared by all sequences in the alignments. Phylogenetic analysis of the ITS1-5.8S-ITS2 region clearly separated the isolated sequences into two clusters. The results showed that ITS1 and ITS2 region could be used to discriminate these walnut cultivars.     

NUCLEAR RIBOSOMAL DNA INTERNAL TRANSCRIBED SPACER REGIONS (ITS1 AND ITS2) DEFINE DISCRETE BIOGEOGRAPHIC GROUPS IN CLADOPHORA ALBIDA (CHLOROPHYTA)1

Nucleotide sequences of the nuclear ribosomal DNA internal transcribed spacers (ITS1 and ITS2), the 5.8S, and short stretches of the adjacent 18S and 26S coding regions were determined in isolates from four disjunct Cladophora albida (Huds.) Kütz. populations (NE-America, W-Europe, Japan, and W-Australia). The two Pacific isolates share nearly identical ITS sequences as do the two Atlantic isolates. In contrast, interoceanic comparisons exhibit a 21% sequence difference. Variation within ITS regions is useful for identification of population groups on a regional or oceanic scale. However, both spacers are characterized by numerous repeat motifs as well as point mutations, which result in alignment problems at the interspecific level within Cladophora.     

从ITS序列探讨猪苓与其伴生菌的亲缘关系

对猪苓菌丝、野生猪苓子实体、野生猪苓菌核和其伴生菌的 5.8SrDNA及其两侧的ITS 1区和ITS2区进行了序列分析。发现猪苓与其伴生菌的ITS序列同源性达 99.36% ,说明猪苓与其伴生菌有着极高的分子亲缘关系。     

Differentiation of two ovine Babesia based on the ribosomal DNA internal transcribed spacer (ITS) sequences

The first and second internal transcribed spacers (ITS1, ITS2) as well as the intervening 5.8S coding region of the rRNA gene for six Babesia spp. isolated from different geographic origins were characterized. Varying degrees of ITS1 and ITS2 intra- and inter-species sequence polymorphism were found among these isolates. Phylogenetic analysis of the ITS1-5.8S gene-ITS2 region clearly separated the isolates into two clusters. One held an unidentified Babesia sp. transmitted by Hyalomma anatolicum anatolicum. The second held five other isolates, which were considered to be Babesia motasi. Each Babesia species cluster possessed ITS1 and ITS2 of unique size(s) and species specific nucleotide sequences. The results showed that ITS1, ITS2 and the complete ITS1-5.8S-ITS2 region could be used to discriminate these ovine Babesia spp. effectively.     

Nucleotide sequence of the 17S–25S spacer region from rice rDNA

Summary The nucleotide sequence of a spacer region between rice 17S and 25S rRNA genes (rDNAs) has been determined. The coding regions for the mature 17S, 5.8S and 25S rRNAs were identified by sequencing terminal regions of these rRNAs. The first internal transcribed spacer (ITS1), between 17S and 5.8S rDNAs, is 194–195 bp long. The second internal transcribed spacer (ITS2), between 5.8S and 25S rDNAs, is 233 bp long. Both spacers are very rich in G+C, 72.7% for ITS1 and 77.3% for ITS2. The 5.8S rDNA is 163–164 bp long and similar in primary and secondary structures to other eukaryotic 5.8S rDNAs. The 5.8S rDNA is capable of interacting with the 5′ terminal region of 25S rDNA.     

A phylogenetic study ofPolygonum sect.Tovara (Polygonaceae) based on ITS sequences of nuclear ribosomal DNA

Polygonum sect.Tovara comprises three morphologically very similar species;P. virginianum,P. filiforme, andP. neofiliforme. Sequences of internal transcribed spacers (ITSs) of nuclear ribosomal DNA of these were determined to examine phylogenetic relationships and the levels of differentiation among them. The size of ITS 1 was 241 bp inP. filiforme andP. neofiliforme, and 242 bp inP. virginianum. The size of ITS 2 was 243 bp, and that of the 5.8S rRNA coding region was 163 bp. The ITS sequences clearly separate North AmericanP. virginianum from the eastern Asian species. Nucleotide divergence between them ranges from 3.3% to 3.8% for ITS 1 and from 9.3% to 10.7% for ITS 2. The molecular data also revealed that two eastern Asian species are closely related but should be treated as distinct species.     

Diversity of the rDNA ITS haplotypes of the nematodes Haemonchus contortus (Trichostrongyloidea, Rhabditida) of the same host

Specimens sampled in Central Mongolia have been examined for the intraspecific polymorphism of the nucleotide sequences of ribosomal DNA internal transcribed spacers (ITS1 + 5.8S + ITS2) of the parasitic nematode Haemonchus contortus. A considerable diversity of haplotypes differing in the nucleotide composition of this DNA region has been observed. The phylogenetic relationships between the haplotypes detected in Central Mongolia and the corresponding sequences from other parts of the nematode distribution area (deposited with the NCBI GenBank) have been analyzed. Significantly different sequences have been found along with the haplotypes already observed in H. contortus or differing from them by one-two nucleotides.     

亚稀褶黑菇和稀褶黑菇的ITS序列分析

对亚稀褶黑菇和稀褶黑菇的ITS全序列进行了测定和比较,首次报道了亚稀褶黑菇的ITS1和5.8S区域.在ITS区域中,不同采集地的亚稀褶黑菇与稀褶黑菇的5.8S rDNA具有100%的同源性,而两侧ITS之间表现出种内和种间的多态性,种内的差异均不超过5%,种间的差异达10%左右.ITS序列分析方法可以作为两者的鉴定方法.     

亚稀褶黑菇和稀褶黑菇的ITS序列分析

对亚稀褶黑菇和稀褶黑菇的ITS全序列进行了测定和比较,首次报道了亚稀褶黑菇的ITS1和5.8S区域。在ITS区域中,不同采集地的亚稀褶黑菇与稀褶黑菇的5.8S rDNA具有100%的同源性,而两侧ITS之间表现出种内和种间的多态性,种内的差异均不超过5%,种间的差异达10%左右。ITS序列分析方法可以作为两者的鉴定方法。     

First report on the occurrence of Theileria sp. OT3 in China

Theileria sp. OT3 was firstly detected and identified from clinically healthy sheep in Xinjiang Uygur Autonomous Region of China (XUAR) through comparing the complete 18S rDNA gene sequences available in GenBank database and the phylogenetic status based on the internal transcribed spacers (ITS1, ITS2) as well as the intervening 5.8S coding region of the rRNA gene by the methods of a partitioned multi-locus analysis in BEAST and Maximum likelihood analysis in PhyML. Moreover, the findings were confirmed by the species-specific PCR for Theileria sp. OT3 and the prevalence of Theileria sp. OT3 was 14.9% in the north of XUAR. This study is the first report on the occurrence of Theileria sp. OT3 in China.     

Heterogeneity of the yeasts Zygowilliopsis californica: Z. californica var. dimennae comb. nov., stat. nov. and Z. californica var. fukushimae comb. nov., stat. nov.

A significant heterogeneity of the species Zygowilliopsis californica was revealed using RFLP-analysis of the PCR-amplified rDNA fragment spanning the 5.8S rRNA gene and the internal transcribed spacers ITS1 and ITS2. Phylogenetic analysis of the nucleotide sequences of ITS1 and ITS2 rDNA differentiated three varieties: Z. californica var. californica, Z. californica var. dimennae, and Z. californica var. fukushimae. The most variable was the ITS2 region, where 7–26 nucleotide substitutions were revealed. The varieties formed semisterile hybrids with meiotic segregation of control markers. The limits of the phylogenetic species concept are discussed.     

应用5.8S rDNA及ITS区序列分析链格孢种级分类*

对9个链格孢小孢子种和3个大孢子种共20个链格孢菌株的5.8S rDNA及其两侧的ITS1区和ITS2区进行了序列分析。聚类分析结果表明形态差异大的种可以明确加以区分,而供试的9个小孢子种之间差异很小,不能根据对所选区段的序列分析加以区分。传统分类上的滨菊链格孢不属于Alternaria, 其分类地位需进一步研究。     

Nucleotide sequences of the 5.8S rRNA gene and internal transcribed spacer regions in carrot and broad bean ribosomal DNA

Summary Nucleotide sequences of the first and second internal transcribed spacers (ITS1 and ITS2, respectively) of ribosomal DNA (rDNA) from two dicot plants, carrot and broad bean, were determined. These sequences were compared with those of rice, a monocot plant, and other eukaryotic organisms. Both types of ITS region in some species of Angiospermae were the shortest among all eukaryotes so far examined and showed a wide range of variation in their G+C content, in contrast to a general trend toward very high G+C content in animals. Phylogenetic relationships of plants with animals and lower eukaryotes were considered using the nucleotide sequences of carrot and broad bean 5.8S rDNA that were determined in the present study, together with that of wheat 5.8S rRNA, which has been reported previously.     

Molecular characterization and phylogenetic inferences of Dermanyssus gallinae isolates in Italy within an European framework

In order to investigate the genetic relationships between Dermanyssus gallinae (Metastigmata: Dermanyssidae) (de Geer) isolates from poultry farms in Italy and other European countries, phylogenetic analysis was performed using a portion of the cytochrome c oxidase subunit 1 (cox1) gene of the mitochondrial DNA and the internal transcribed spacers (ITS1+5.8S+ITS2) of the ribosomal DNA. A total of 360 cox1 sequences and 360 ITS+ sequences were obtained from mites collected on 24 different poultry farms in 10 different regions of Northern and Southern Italy. Phylogenetic analysis of the cox1 sequences resulted in the clustering of two groups (A and B), whereas phylogenetic analysis of the ITS+ resulted in largely unresolved clusters. Knowledge of the genetic make‐up of mite populations within countries, together with comparative analyses of D. gallinae isolates from different countries, will provide better understanding of the population dynamics of D. gallinae. This will also allow the identification of genetic markers of emerging acaricide resistance and the development of alternative strategies for the prevention and treatment of infestations.     

中药乌头及其近缘种的rDNA—ITS序列分析

运用PCR扩增产物直接测序的方法对云南、安徽的乌头及其近缘种植物的ITS区碱基序列测定。表明核糖体DNA中ITS区的完整序列（包括ITS1,ITS2和5．8s）,4种乌头属植物的ITS1序列长度为249bp,云南鸟头和安徽乌头及黄山鸟头ITS2序列长度为189bp,赣皖乌头ITS2序列长度为217bp。运用Mega2软件进行系统分析得到系统进化树。ITS序列特征是乌头鉴别的有效分子标记。     

罗氏沼虾缅甸野生原种rDNA-ITS区序列特征

对罗氏沼虾(Macrobrachium rosenbergii)内转录间隔区(internal transcribed spacer,ITS)全序列特征进行了分析.罗氏沼虾ITS1长度为1 070～1 150 bp,GC含量为51.4%～52.7%;5.8S长度一致为163bp,GC含量为55.2%;ITS2长度为48...     

Members of Sebacinales subgroup B form mycorrhizae with epiphytic orchids in a neotropical mountain rain forest

Previous investigations revealed that epiphytic orchids in a mountain rain forest in southern Ecuador formed mycorrhizae with diverse members of Tulasnellales. Using specific primers, we now show that the same orchids are also associated with Sebacinales. Ultrastructural observations confirmed the Sebacinales mycobionts in situ. Mycorrhizae of flowering individuals of Stelis hallii, S. superbiens, S. concinna and Pleurothallis lilijae were sampled in different forest types of the mountain rain forest of southern Ecuador along an altitudinal gradient between 1,850 and 2,100 m a.s.l. Phylogenetic analysis of fungal nuclear rDNA sequences coding for the ribosomal large subunit (nucLSU) showed the presence of eight sequence types based on proportional differences of <1% bp. All sequence types clustered in the Sebacinales subgroup B which also contained sequences of mycobionts from ericads and terrestrial orchids. Sequences of the nuclear rDNA 5.8S subunit, including parts of the internal transcribed spacers ITS1 and ITS2 (5.8-ITS) from the mycobionts of the epiphytic orchids, were distinct from published sequences of sebacinoid mycobionts of green terrestrial orchids and ericads. Sebacinales sequences from different epiphytic orchid species differed at least by 1% bp as was previously found for Tulasnella sequences. Sebacinales occurred less frequently and with a lower number of sequence types than Tulasnellales, but distribution along the altitudinal gradient was similar.     

PCR产物直接测序还是克隆测序?——密叶杉属rDNA ITS序列的测定方法

通过PCR产物直接测序和克隆测序对三种密叶杉属 (Athrotaxis)植物rDNA内转录间隔区 (ITS)及5 .8SrDNA序列进行了测定与分析。实验表明A .selaginoidesrDNA重复序列间的纯合程度很高 ,对PCR产物直接测序就可以测定其ITS区序列。而A .laxifolia、A .cupressoides的ITS1重复序列间的纯合程度较低 ,各重复单位间序列存在插入 /缺失 ,只有对PCR产物进行克隆测序才能确定其序列。A .laxi folia、A .cupressoides的ITS2区尽管也存在多态性 ,但不同重复序列的浓度比较平均 ,对PCR产物直接测序就可确定重复序列间的变异情况。本实验表明尽管是同一属的三种植物 ,但其rDNA重复序列间的纯合程度不同 ,同一植物ITS的不同区域 ,其重复序列间的纯合程度也不同 ,针对不同的ITS片段可采用不同的方法以测定其序列。