桃花水母

介绍了桃花水母的生活习性、形态、生理、分类、分布,讨论了桃花水母的研究意义及经济价值。     

中国桃花水母属的修订（淡水水母目，笑水母科）

作者对我国的桃花水母属Craspedacusta的2亚种和2变种重新通过形态学观察,并与国内外已发表的Craspeda-custa属7种相比较,其刺丝囊疣的形状和排列及生殖腺的形状和颜色均存在明显的差异。故认为此2亚种和2变种应提升为种,即信阳桃花水母Craspedacusta xinyangensis He,1980,杭州桃花水母Craspedacusta hangzhouensis He,1980、乐山桃花水母Craspedacusta kiatingi Gaw and Kung,1939和宜昌桃花水母Craspedacusta kawaii(Oka,1907)。本文将全世界11种桃花水母的形态特征作了比较并附以系统检索。     

我国桃花水母分布近况

桃花水母是世界的珍稀动物,它具有重要的学术价值和观赏价值.1880年首次在英国发现,订名为索氏桃花水母Craspedacusta sowerbyi Lankester 1880.1880～1939年共发现5种,1980年以后相继报道了6种.1959年台湾省台北市台湾师范大学校园一人工水池中发现桃花水母,共采得4个标本,作者订为一新种C. koui Shieh and Wang 1959.Kramp(1961)认为此非新种,乃为C.sowerbyi,这有待证实.作者在其论文中只称刺丝囊成丛,没描述刺丝囊疣的形状,对生殖腺的形状描述不清,未说明其颜色.为此,台湾的桃花水母难以鉴定.至于前苏联报道的一新种C.vovasi Naumov and Stepanjants 1971,共得16个标本,采自南Sakhalin的Bousset咸水湖.我们认为这不是淡水水母,应是一种海产的水螅水母.Stepanjants于1988年宣告此种无效,他认为此标本是Eperetmus typus Biglow 1915的一个新变种E.typus var.vovasi.因此,目前世界上桃花水母已记录11种,9种分布在我国.     

我国的桃花水母

2003年7月9日至10月16日于浙江省宁波市鄞州和象山分别采得多个桃花水母标本,经鉴定这两种桃花水母为信阳桃花水母。鉴于这几年,我国许多地方相继报道发现有桃花水母出没,在此基础上,参阅了我国在研究桃花水母方面的相关资料,介绍了目前我国关于桃花水母的研究现状, 并指出其研究价值所在,以期为今后桃花水母的研究提供参考依据。     

桃花水母生活史的实验观察

记录了中国产信阳桃花水母(Craspedacusta xinyangensis)的生活史及各阶段主要发育特征。25～28℃条件下,卵受精23h后发育成长0.14～0.21mm的圆棍状浮浪幼虫,养殖环境下,浮浪幼虫在水中漂浮3～5d后固定到人工玻璃底质上,3～4d后发育成长度0.3～0.6mm的螅状体。水螅体产生无纤毛的类浮浪幼虫形成新的螅状体。一个螅状体成熟后产生一个水母芽,新释放的幼水母具有16只触手。     

桃花水母

桃花水母是水螅纲有世代交替的一类淡水生活的刺胞动物。由于我国的秭归桃花水母的生境在三峡水库蓄水后将被淹没,它的生存受到各方的关注。近期媒体也做了较多的报道,为有利于读者了解这一方面的知识,介绍了桃花水母的螅状体和水母体的形态和生活习性,以及世代交替的情况,提出了有关对桃花水母的研究和保护的一些看法。     

安徽省桃花水母的初步研究

桃花水母属Craspedacusta隶属于刺胞动物门Cnidaria水螅纲Hydrozoa淡水水母目Limnomedusae笠水母科Olindiidae。我国的桃花水母种类丰富,分布广泛,近年来多地有新种和分布新纪录的报道。安徽曾发现桃花水母,但均未进行详细描述和研究。本文对采自安徽省金寨县梅河河谷水潭内的桃花水母进行了初步研究,依据其伞形、缘膜宽度、触手及平衡囊数目、刺丝囊疣形状和排列方式、生殖腺形状和颜色等形态特征对其进行初步的分类鉴定。结果表明,此次在金寨县发现的桃花水母更接近于宜昌桃花水母Craspedacusta kawaii Oka,1907。这是对安徽省发现的桃花水母首次进行较为明确的分类鉴定和初步的形态学研究。     

秭归桃花水母( Craspedacusta ziguiensis )

"春来桃花水,中有桃花鱼.浅白深红画不如,是花是鱼两不知".这首古诗中描述的比画还要美丽的"桃花鱼",实际上就是我们今天说的桃花水母.虽然早在1250年,我国对桃花水母及其生活习性就有详细的描述,但按照现代生物学概念命名的桃花水母却是在1880年. 由于这一类群有着数亿年的生存历史,是进化过程中的关键物种,桃花水母被认为有重要的保护价值.     

中国桃花水母属的修订(淡水水母目,笠水母科)

作者对我国的桃花水母属Craspedacusta的2亚种和2变种重新通过形态学观察,并与国内外已发表的Craspeda-custa属7种相比较,其刺丝囊疣的形状和排列及生殖腺的形状和颜色均存在明显的差异.故认为此2亚种和2变种应提升为种,即信阳桃花水母Craspedacusta xinyangensis He,1980,杭州桃花水母Craspedacusta hangzhouensis He,1980、乐山桃花水母Craspedacusta kiatingi Gaw and Kung,1939和宜昌桃花水母Craspedacusta kawaii(Oka,1907).本文将全世界11种桃花水母的形态特征作了比较并附以系统检索.     

桃花水母及其生态学研究进展

桃花水母是一种濒临绝迹、古老而珍稀的腔肠动物,已有数亿年以上的生存历史,是地球上最低等级的无脊椎动物,是腔肠动物中生活于淡水中的仅有种类,是进化过程中的关键物种,具有极高的生态和人文价值,重要的学术价值和观赏价值。由于三峡水库的蓄水,桃花水母的生境将惨遭淹没,桃花水母濒临灭绝,这一珍贵物种的灭绝,不仅是世界物种多样性的损失,也是我国古代记载的“桃花鱼”这一文化资源的永久丧失。由于桃花水母较为罕见和出现时间极短,人们对其知之甚少,故本文从其生物学特性、出现时间、种类、分布以及研究现状等方面对桃花水母进行了较为系统的概述,提出了保护和研究桃花水母的科学意义并指出了今后研究的方向。     

Extensive pyrosequencing reveals frequent intra-genomic variations of internal transcribed spacer regions of nuclear ribosomal DNA

Background

Internal transcribed spacer of nuclear ribosomal DNA (nrDNA) is already one of the most popular phylogenetic and DNA barcoding markers. However, the existence of its multiple copies has complicated such usage and a detailed characterization of intra-genomic variations is critical to address such concerns.

Methodology/Principal Findings

In this study, we used sequence-tagged pyrosequencing and genome-wide analyses to characterize intra-genomic variations of internal transcribed spacer 2 (ITS2) regions from 178 plant species. We discovered that mutation of ITS2 is frequent, with a mean of 35 variants per species. And on average, three of the most abundant variants make up 91% of all ITS2 copies. Moreover, we found different congeneric species share identical variants in 13 genera. Interestingly, different species across different genera also share identical variants. In particular, one minor variant of ITS2 in Eleutherococcus giraldii was found identical to the ITS2 major variant of Panax ginseng, both from Araliaceae family. In addition, DNA barcoding gap analysis showed that the intra-genomic distances were markedly smaller than those of the intra-specific or inter-specific variants. When each of 5543 variants were examined for its species discrimination efficiency, a 97% success rate was obtained at the species level.

Conclusions

Identification of identical ITS2 variants across intra-generic or inter-generic species revealed complex species evolutionary history, possibly, horizontal gene transfer and ancestral hybridization. Although intra-genomic multiple variants are frequently found within each genome, the usage of the major variants alone is sufficient for phylogeny construction and species determination in most cases. Furthermore, the inclusion of minor variants further improves the resolution of species identification.     

Functional analysis of internal transcribed spacer 2 of Saccharomyces cerevisiae ribosomal DNA.

Using the previously described "tagged ribosome" (pORCS) system for in vivo mutational analysis of yeast rDNA, we show that small deletions in the 5'-terminal portion of ITS2 completely block maturation of 26 S rRNA at the level of the 29 SB precursor (5.8 S rRNA-ITS2-26 S rRNA). Various deletions in the 3'-terminal part, although severely reducing the efficiency of processing, still allow some mature 26 S rRNA to be formed. On the other hand, none of the ITS2 deletions affect the production of mature 17 S rRNA. Since all of the deletions severely disturb the recently proposed secondary structure of ITS2, these findings suggest an important role for higher order structure of ITS2 in processing. Analysis of the effect of complete or partial replacement of S. cerevisiae ITS2 with its counterpart sequences from Saccharomyces rosei or Hansenula wingei, points to helix V of the secondary structure model as an important element for correct and efficient processing. Direct mutational analysis shows that disruption of base-pairing in the middle of helix V does not detectably affect 26 S rRNA formation. In contrast, introduction of clustered point mutations at the apical end of helix V that both disrupt base-pairing and change the sequence of the loop, severely reduces processing. Since a mutant containing only point mutations in the sequence of the loop produces normal amounts of mature 26 S rRNA, we conclude that the precise (secondary and/or primary) structure at the lower end of helix V, but excluding the loop, is of crucial importance for efficient removal of ITS2.     

Identification of four scallop species using PCR and restriction analysis of the ribosomal DNA internal transcribed spacer region

Polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis of the ribosomal DNA region spanning the 5.8S RNA gene and the 2 flanking internal transcribed spacers (ITSs) was performed to establish DNA-based molecular markers for the identification of the scallops Aequipecten opercularis, Chlamys distorta, Mimachlamys varia, and Pecten maximus. Chlamys distorta was distinguished simply by ITS size. Species-specific restriction patterns were found with the restriction enzyme AluI, and also with SmaI for A. opercularis and M. varia. When ITS sizes and the RFLPs obtained with SmaI were combined, the 4 scallops were also differentiated. Additional species-specific RFLPs were revealed after ITS-2 PCR amplification and subsequent digestion with Hsp92II. Using this marker, canned scallops were identified. Thus this work provides a simple, reliable, and rapid method for the identification of scallops that can be used when species-specific morphologic characteristics are removed or when specimens are small in size.     

The internal transcribed spacer of nuclear ribosomal DNA in the gymnosperm Gnetum

We analyze the structure of the internal transcribed spacers ITS1 and ITS2 of the nuclear ribosomal DNA in the gymnosperm Gnetum, using a phylogenetic framework derived mainly from an intron in the nuclear low-copy LEAFY gene. Gnetum comprises 25-35 species in South America, Africa, and Asia, of which we sampled 16, each with two to six clones. Criteria used to assess ITS functionality were highly divergent nucleotide substitution, GC content, secondary structure, and incongruent phylogenetic placement of presumed paralogs. The length of ITS1 ranged from 225 to 986 bp and that of ITS2 from 259 to 305 bp, the largest ranges so far reported from seed plants. Gnetum ITS1 contains two informative sequence motifs, but different from other gymnosperms, there are only few and short (7-13 bp) tandem repeats. Gnetum ITS2 contains two structural motifs, modified in different clades by shortening of stems and loops. Conspecific sequences grouped together except for two recombinant pseudogenes that had ITS1 of one clade and ITS2 of another. Most of the pseudogenic ITS copies, paralogs, and putative chimeras occurred in a clade that according to a fossil-calibrated chloroplast-DNA clock has an age of a few million years. Based on morphology and chromosome numbers, the most plausible causes of the observed high levels of ITS polymorphism are hybridization, allopolyploidy, and introgression.     

Soil microbial community analysis using two-dimensional polyacrylamide gel electrophoresis of the bacterial ribosomal internal transcribed spacer regions

Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of digested genomic DNA has been previously used in comparative genomics studies of closely related bacteria species. However, a two-dimensional gel electrophoresis approach for examining microbial community structures in environmental samples has not yet been developed. We determined that it is theoretically possible to separate internal transcribed spacer regions (ITS) of bacterial communities into hundreds of operational taxonomic units (OTUs) using 2D-PAGE. Application of 2D-PAGE for separating Bacterial ITS sequences that have been PCR-amplified from replicate soil samples taken from along a Zn gradient resulted in reproducible gels containing hundreds of spots. Clear differences in spot patterns were observed between soil samples that differed in both sampling location and Zn content. The number of OTUs detected using 2D-PAGE of ITS regions was much greater than that observed using Automated Ribosomal Internal Transcribed Spacer Analysis (ARISA), Terminal Restriction Fragment Length Polymorphism (T-RFLP), or Denaturing Gradient Gel Electrophoresis (DGGE). Principal Component Analysis (PCA) of community spot patterns resulted in similar groupings of samples as those obtained using other molecular methods, however, excised spots were found to contain a far lower diversity of different sequences than excised ITS bands of the same length, as determined by RFLP analysis of excision clone libraries and subsequent sequencing of DNA eluted from excised spots. This increase in resolution makes 2D-PAGE of Bacteria ITS fragments from complex microbial communities a viable method for detecting differences between highly similar communities, as well as in streamlining follow-on sequencing efforts by reducing the level of homoplasy (co-migration of heterogeneous sequences) often seen in band-based community fingerprinting methods.     

Molecular phylogenetic analysis of ixodid ticks based on the ribosomal DNA spacer, internal transcribed spacer 2, sequences

An internal transcribed spacer (ITS2) sequence between the 5.8S and 28S rRNA genes was used to estimate the phyletic relationships among Ixodes spp. tick vectors of Lyme disease-causing Borrelia spirochetes. Analysis indicates that Borrelia burgdorferi sensu lato species associated with Lyme disease are found mainly in ticks of the Ixodes ricinus species complex. Other closely related tick species are not known to transmit the Borrelia-that cause Lyme disease in humans, but they appear to have a specific association with other closely related Borrelia species. There is a high degree of concordance in the phylogenetics of Borrelia taxa and the phylogenetic relationships among Ixodes ticks.     

Analysis of ribosomal DNA internal transcribed spacer sequences of the Leishmania donovani complex

To understand phylogenetic relationships of species and strains within the Leishmania donovani complex, we have analyzed the ribosomal DNA internal transcribed spacer (ITS) sequences of 27 Leishmania infantum, 2 Leishmania chagasi, 18 L. donovani and 5 Leishmania archibaldi strains of different zymodemes and geographical origin. Eight ITS sequence types were found. All detected sequence variation within ITS1 and ITS2 was based on 12 polymorphic microsatellites. The L. infantum strains from the Mediterranean region, China and L. chagasi from the New World formed a phylogenetic group well separated from the second main group including all strains from East Africa and India. Within the latter group three distinct phylogenetic subgroups could be differentiated: (1) L. donovani (Sudan/Ethiopia, China) + L. archibaldi (Sudan), (2) L. donovani (Sudan/Ethiopia) + L. infantum (Sudan) + L. archibaldi (Sudan/Ethiopia), and (3) L. donovani (Kenya, India). These groups are not consistent with previous species definitions based on isoenzyme analyses, e.g. L. infantum is polyphyletic and L. archibaldi is not supported as a distinct species. Two groups of Indian strains could be differentiated, one of which has an identical sequence type to the strains from Kenya. Three main lineages of strains can thus be differentiated in East Africa: two quite distantly related groups of strains from Sudan/Ethiopia, and a third group including all strains from Kenya, which is more closely related to part of the Indian strains than to any of the Sudanese/Ethiopian groups. The ITS sequence analysis presented here supports the need for revision of the taxonomy of the L. donovani complex.     

Evolutionary divergence of ribosomal internal transcribed spacer 2 in lizards

Internal transcribed spacers 1 and 2 (ITS1 and ITS2) are known to play an important role in rRNA maturation, yet the mechanism of their action is still not completely understood. Comparison of the ITS1 and ITS2 nucleotide sequences for various organisms reveals conserved regions, which are potentially involved in rRNA biogenesis, and yields new information about the evolutionary divergence of the corresponding region of the genome. The rDNA fragments containing ITS2 were amplified, cloned, and sequenced for three lizard species: Darevskia armeniaca, Lacerta strigata (Lacertidae), and Agama caucasia (Agamidae). The lizard ITS2 sequences were compared with their counterparts from other organisms and proved to contain not only universally conserved elements characteristic of the consensus secondary structure of vertebrate ITS2, but also lizard-specific regions. Comparison of the ITS2 size and the distribution of homologous regions for the two lizard families made it possible to assume that evolution of the modern species involved duplication of ITS2 in the genome of their common ancestor.     

A phylogeny of Apiaceae tribe Scandiceae: evidence from nuclear ribosomal DNA internal transcribed spacer sequences

The evolutionary relationships among members of Apiaceae (Umbelliferae) tribe Scandiceae and representatives of all major lineages of Apioideae (including putatively allied Caucalideae) identified in earlier molecular studies were inferred from nucleotide sequence variation in the internal transcribed spacer regions (ITS1 and ITS2) of nuclear ribosomal DNA. In all, 134 accessions representing 18 genera commonly treated in Scandiceae were analyzed. Phylogenies estimated using maximum parsimony and distance methods were generally similar and suggest that: (1) Scandiceae form a well-supported clade, consisting of the genera Anthriscus, Athamanta (in part), Balansaea, Chaerophyllum, Conopodium, Geocaryum, Kozlovia, Krasnovia, Myrrhis, Myrrhoides, Neoconopodium, Osmorhiza, Scandix, Sphallerocarpus, and Tinguarra; (2) Athamanta is polyphyletic, with A. della-cellae allied with Daucus and A. macedonica placed close to Pimpinella; and (3) Rhabdosciadium and Grammosciadium find affinity with the Aegopodium group of umbellifers, whereas the placement of the monotypic Molopospermum cannot be inferred because of its high sequence divergence. The genus Bubon has been restored with two new combinations, B. macedonicum subsp. albanicum and B. macedonicum subsp. arachnoideum. Scandiceae arise within paraphyletic Caucalideae, the latter comprising two major lineages whose relationships to Scandiceae are not clear. Therefore, a broad treatment of Scandiceae is proposed, with subtribes Scandicinae, Daucinae, and Torilidinae (the latter two representing the Daucus and Torilis subgroups, respectively, of recent molecular systematic investigations).     

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.