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1.
In this paper,we explore possible conflict between morphological and molecular interpretations of phylogenetic relationships within the well-known peritrichous genus Zoothamnium. On the basis of morphological evidence,for a long time this genus has been believed to be a well-defined monophyletic taxon. Nonetheless,Z oothamnium exhibits higher genetic diversity than the gross morphology of its species. Here,we used all available genetic information for the small subunit of ribosomal RNA(SSU r RNA) and internal transcribed spacer region(ITS1-5.8S-ITS2) for this genus to reconstruct phylogenies for four datasets(SSU rRNA,ITS1,ITS2,and ITS1-5.8S-ITS2) and a combined dataset(SSU rRNA+ITS1-5.8SITS2) using different phylogenetic methods and with consideration of the secondary structure of the genes. Confidence in phylogenetic tree selection was assessed with the approximately unbiased test. The molecular results showed both that Zoothamnium is more likely to be polyphyletic,and morphologically similar genera Zoothamnopsis and Myoschiston were always nested among Zoothamnium species. Accordingly,as with some other groups of ciliates,to understand more fully the correct phylogeny of Zoothamnium there remains a need for additional data from both morphological and molecular studies,covering additional Zoothamnium spp. and members of closely related genera(e.g. Zoothamnopsis,Myoschiston,and Epistylis). 相似文献
2.
The phylogeny of the oligotrich ciliates is currently a hot debate despite the availability of both morphological and molecular
data. In the present paper, further small subunit rRNA (SS rRNA) genes were analyzed from the Genera Omegastrombidium and Novistrombidium, as well as from Strombidium, and combined with three new SS rRNA sequences from Strombidium basimorphum, S. sulcatum population QD-1, and Novistrombidium testaceum population GD. The phylogenetic positions of these organisms were inferred using Bayesian inference, Maximum Likelihood,
and Maximum Parsimony methods. The main results are: (1) the SS rRNA gene sequence analyses match the recent findings about
the molecular evolution of oligotrichs, indicating that the family Strombidiidae is paraphyletic; (2) the Genus Omegastrombidium is separated from the Genus Strombidium, as shown in recent cladistic analyses; (3) morphospecies in Genus Novistrombidium, based on similarity of somatic ciliature, are separated from each other in all topological trees, indicating that this genus
could be a paraphyletic group; (4) the molecular data indicate a possibility of paraphyly for the genus Strombidium; and (5) the similarities of the SS rRNA gene of specimens identified as S. sulcatum and S. inclinatum are 99.8%–100%. However, present knowledge on the oligotrichs sensu stricto is still insufficient and further studies based
on both molecular and other technologies are required. 相似文献
3.
The 5.8S ribosomal DNA sequences (5.8S rDNA) and their flanking regions, internal transcribed spacer 1 and spacer 2 (ITS1
and ITS2) of three new isolates in genus Alexandrium (Alexandrium sp. qd1, Alexandrium sp. qd2, Alexandrium sp. gz) from China were amplified, sequenced, and subjected to phylogenetic analysis. Alexandrium sp. gz and Alexandrium sp. qd1 were grouped with high bootstrap values with four strains/species, i.e., A. catenella South Korea strain, A. catenella Japan strain, and two from China, Alexandrium sp. AC03 and Alexandrium sp. AN01 being proposed to be A. catenalla in a previous study. Then Alexandrium sp. gz and Alexandrium sp. qd1 were identified as Alexandrium catenella. As A. catenella was isolated from Qingdao and Guangzhou sea areas, it supposedly distributed at least in these two areas and was genetically
different. Alexandrium sp. qd2 differed greatly from species in Alexandrium. It clustered with Symbiodinium californium, Symbiodinium sp. G15 and Gymnodinium sp. Zhao 01 with 100% bootstrap value; so Alexandrium sp. qd2 affiliates to genus Symbiodinium, and is probably a free-living Symbiodinium species. 相似文献
4.
Ulvacean green seaweeds are common worldwide; they formed massive green tides in the Yellow Sea in recent years, which caused
marine ecological problems as well as a social issue. We investigated two major genera of the Ulvaceae, Ulva and Enteromorpha, and collected the plastid rbcL and nuclear ITS sequences of specimens of the genera in two sides of the Yellow Sea and analyzed them. Phylogenetic trees
of rbcL data show the occurrence of five species of Enteromorpha (E. compressa, E. flexuosa, E. intestinalis, E. linza and E. prolifera) and three species of Ulva (U. pertusa, U. rigida and U. ohnoi). However, we found U. ohnoi, which is known as a subtropical to tropical species, at two sites on Jeju Island, Korea. Four ribotypes in partial sequences
of 5.8S rDNA and ITS2 from E. compressa were also found. Ribotype network analysis revealed that the common ribotype, occurring in China, Korea and Europe, is connected
with ribotypes from Europe and China/Japan. Although samples of the same species were collected from both sides of the Yellow
Sea, intraspecific genetic polymorphism of each species was low among samples collected worldwide. 相似文献
5.
The systematic classification of the Eucheumatoideae is difficult because of their variable morphology and interpretation of reproductive structures. Kappaphycus and Eucheuma specimens cultivated on the Hainan and Fujian coast of China were introduced from Vietnam, the Philippines and Indonesia. Combined with morphological characteristics, all Kappaphycus and Eucheuma cultivated strains were identified by internal transcribed spacer (ITS) sequences. The phylogenetic tree was constructed using neighbor-joining and maximum likelihood methods. The results indicate that different ITS sequence lengths occurred in the different genera and species. An obvious difference in morphology could be found in the protuberance shape between Kappaphycus and Eucheuma. The protuberance in Eucheuma was thorn-like and in Kappaphycus was wartlike or papillate. Their ITS sequence lengths differed significantly in nucleotide variation rates up to 58.55%-63.90%. All nucleotide variations occurred in the ITS1 and ITS2 regions except for five nucleotide transversions in the 5.8S rDNA region. In addition, the difference was at the branches among congeneric species. Kappaphycus sp. had branches with small buds, while K. alvarezii did not have such a feature. The nucleotide variation rates varied from 7.02% to 7.48% among species; within the same species of the clades it was <1.20%. Eucheumatoideae algae cultivated in China consisted of three clades, K. alvarezii, Kappaphycus sp., and E. denticulatum. The results indicate that ITS sequence analysis was an effective way for identification of interspecies and intraspecies phylogenetic relationships and might provide a clue for molecular identification of algal Eucheumatoideae. 相似文献
6.
Genus Nassarius contains many subgenera, such as Zeuxis, Telasco, Niotha, Varicinassa, Plicarcularia, Nassarius s. str. and Reticunassa. On the basis of morphological characteristics of the shell and radula and sequences of mitochondrial cytochrome oxidase
subunit I (COI) and 16S rRNA genes, Nassarius specimens collected from the South China Sea were identified and phylogenetically analyzed. Although Nassarius sp. and Nassarius (Varicinassa) variciferus were morphologically different in their shells, few variations were found among their radular teeth and sequences of mtCOI
and mt16S RNA genes. Therefore, Nassarius sp. should be classified as N. (Varicinassa) variciferus. Nassarius (Zeuxis) sp. has only a subtle difference from Nassarius (Zeuxis) algidus on the shell, but it shows obvious differences in radular teeth and DNA sequence, indicating that they are two distinct species.
Sequence divergence of mtCOI and mt16S RNA genes within Nassarius species was much lower than that between species, suggesting that these two genes are suitable for Nassarius species identification. Phylogenetic analysis (neighbor-joining and maximum parsimony) based on mtCOI and mt16S rRNA genes
revealed the presence of two groups in genus Nassarius and a closest relationship between subgenera Zeuxis and Telasco. Species of subgenus Plicarcularia did not form a single clade. The molecular phylogeny was not congruent with the previous morphological phylogeny. The subgeneric
divisions of genus Nassarius appear to be uncertain and unreliable. 相似文献
7.
Based on the sequence data of the nuclear ribosomal DNA internal transcribed spacer (ITS) 1, 5.8 S, and ITS 2, the molecular
phylogeny was analyzed on Ulvaceae species collected from Qingdao coasts in summer of 2007, including 15 attached Ulva and Enteromorpha samples from 10 locations and 10 free-floating Enteromorpha samples from seven locations. The result supported the monophyly of all free-floating Enteromorpha samples, implying the unialgal composition of the free-floating Enteromorpha, and the attached Ulvaceae species from Qingdao coasts were grouped into other five clades, suggesting that they were not
the biogeographic origin of the free-floating Enteromorpha in that season.
Supported by NSFC (40506030); the Innovative Key Project of the Chinese Academy of Sciences (KZCX2-YW-209); Science & Technology
Project of Qingdao City (06-2-2-12-JCH) 相似文献
8.
The sporadotrichid ciliates are an especially diverse group. A number of investigators have studied the morphological, morphogenetic, and molecular relationships among members of this group. Despite this, a consistent classification is still lacking and several important questions about the phylogenetic relationships within this group remain unsolved. To improve our understanding of these relationships, we constructed phylogenetic trees using the nucleotide sequences of the small-subunit rRNA (SSrRNA) gene and amino acid sequences of actin I and α-tubulin. Analyses of SSrRNA gene sequences indicated that: 1) the Sporadotrichida sensu Lynn (2008) and the Oxytrichidae are polyphyletic; 2) the Uroleptus species, which are classified to urostylids, formed a sister group with the oxytrichids; 3) Halteria grandinella, which is grouped morphologically with oligotrich species, clustered within the oxytrichids. These results are congruent with previous studies based on SSrRNA gene sequences. However, the amino acid sequences of actin I and α-tubulin yielded different topologies. The main results are: 1) in all phylogenetic trees, the genus Oxytricha was paraphyletic; 2) Uroleptus was sister to a subset of Urostyla and Holosticha, albeit with low supporting values; 3) Halteria grandinella was separated distantly from the Oxytrichidae in trees inferred from actin I amino acid sequences but clustered with oligotrichids in the α-tubulin analysis. The inconsistency among the trees inferred from these different molecular markers may be caused by rapidly accumulated genetic characterizations of ciliates. Further studies with additional molecular markers and sampling of more taxa are expected to better address the relationships among sporadotrichids. 相似文献
9.
Green tides are caused by the proliferation of chlorophytes under suitable hydrographic conditions.These blooms lead to environmental degradation and negatively impact the waters and seagrass beds,as well as fishing and other recreational activities in the bay.A comprehensive ecological understanding of the bloom dynamics,including the origin and persistence,is needed to foster management decisions.The algae in the great majority of green tide blooms usually belong to two genera of Ulvophyceae,Ulva and Enteromorpha.Ulva has been observed more often in recent years.In China,green tides occurred for the first time in the middle area of the Yellow Sea in 2007,and a large-scale algae blooming broke out in the middle and southern areas of the Yellow Sea in late May 2008.We identified them as Ulva prolifera by comparative analysis of the rDNA internal transcribed spacer 1 (ITS1),5.8S and ITS2 sequences in combination with microscopic observation.Morphological differences were found between the free-floating algae and the attached thalli.Various reproduction patterns of the free-floating algae include sexual,asexual and vegetative propagations,which played important roles in the long-term green tide persistence in China.The ITS sequences of the blooming algae were identical to those of the samples from the Lianyungang sea area but were different from the attached samples from the Qingdao sea area.The results infer that the blooms are originated from other sea areas rather than from the local attached populations. 相似文献
10.
Batrachospermum arcuatum Kylin is typically dioecious,although some monoecious specimens have been collected from four locations in North China.In this study,B.arcuatum populations,including monoecious and dioecious thalli,were collected from seven stream segments.The nuclear DNA internal transcribed spacer(ITS)region was sequenced for the seven populations,and a phylogenetic tree was constructed using Bayesian inference to assess intraspecifi c relationships.A haplotype network was also created.The ITS region in B.arcuatum from North China comprised 822–853 bp,with 10 haplotypes detected from the seven locations.The results of this study support the inclusion of monoecious individuals in the species B.arcuatum. 相似文献
11.
We collected nine Enteromorpha specimens from the coast of Yantai and evaluated their diversity based on analyses of their ITS （internal transcribed spacer） and 5S rDNA NTS （non-transcribed spacer） sequences. The ITS sequences showed slight nucleotide divergences between Enteromorpha linza and Enteromorpha prolifera. In contrast, multiple highly variable regions were found in the ITS region of Enteromorpha flexuosa. In general, there were more variable sites in the NTS region than in the ITS region in the three species. The variations in 5S rDNA NTS sequences indicated that the molecular diversity of Enteromorpha from the coast of Yantai is very high. However, a phylogenetic tree constructed using 5S rDNA NTS sequence data indicated that genetic differences were not directly related to geographical distribution. 相似文献
12.
DU Guoying WU Feifei MAO Yunxiang GUO Shenghua XUE Hongfan and BI Guiqi 《中国海洋大学学报(英文版)》2014,13(1):97-103
An assessment with assistance of DNA barcoding was conducted on green macroalgae in coastal zone around Qingdao, China, during the period of April–December, 2011. Three markers were applied in molecular discrimination, including the plastid elongation factor tufA gene, the internal transcribed spacer (ITS) region of the ribosomal cistron and rubisco large subunit gene 3′ regions (rbcL-3P). DNA barcoding discriminated 8 species, excluding species of genus Cladophora and Bryopsis due to failures in amplification. We ascertained and corrected 4 species identified by morphological methods for effectively assisting the classification. The gene tufA presented more advantages as an appropriate DNA marker with the strongest amplification success rate and species discrimination power than the other two genes. The poorest sequencing success largely handicapped the application of ITS. Samples identified by tufA and rbcL as Ulva flexuosa were clustered into the clade of U. prolifera by ITS in the neighbor-joining tree. Confusion with discrimination of the complex of U. linza, U. procera and U. prolifera (as the LPP complex) still existed for the three DNA markers. Based on our results, rbcL is recommended as a preferred marker for assisting tufA to discriminate green macroalgae. In distinguishing green-tide-forming Ulva species, the free-floating sample collected from the green tide in 2011 was proved to be identical with U. prolifera in Yellow Sea for ITS and rbcL genes. This study presents a preliminary survey of green macroalgae distributed in the coastal area around Qingdao, and proves that DNA barcoding is a powerful tool for taxonomy of green macroalgae. 相似文献
13.
In this report, complete mitochondrial genome sequences of Laminaria cultivation variety ‘Rongfu’ were obtained. The results showed the length of circular molecule of mtDNA was 37 638 bp (64.7%
A+T), encoding three rRNAs (23S, 16S and 5S), 25 tRNAs, 35 known mitochondrial proteins and 3 ORFs. Sequence alignment indicated
its mtDNA genome was very similar to that of Laminaria japonica. Phylogenetic trees inferred from concatenated 30 mitochondrial genes showed that ‘Rongfu’, Laminaria japonica, Laminaria longipedalis, Laminaria diabolica, Laminaria religiosa and Laminaria ochotensis clustered together. In addition, compared with mitochondrial genome of L. japonica, ‘Rongfu’ mtDNA lacked a non-coding region of 19 nucleotides, which was located between rRNA small subunit gene 3 (rps3) and rRNA small subunit gene 9 (rps9). Seven cultivation varieties of China were divided into two groups based on this non-coding region which was absent in
‘Rongfu’, ‘Fujian’ and ‘Sanhai’ while present in ‘Ailunwan’, ‘Dongfang No.2’, ‘Dongfang No.3’ and ‘Zaohoucheng’. So this variation
can be used in germplasm identification of cultivation variety. 相似文献
14.
A harmful algae bloom (HAB) is a dense aggregation of algae in a marine or aquatic environment that can result in significant
environmental problems. To forecast the occurrence of HAB, development of a rapid and precise detection method is urgently
required. In this study, two Skeletonema costatum-like diatoms (SK-1 and SK-2), were identified morphologically under a light microscope, and detected using fluorescent in situ hybridization (FISH). Strain SK-1 was isolated from a frequently HAB affected area of the East China Sea, and strain SK-2
from an aquatic farm in Qingdao, China. Fluorescent DNA probes were designed that were complementary to the ITS sequence (including
5.8S rDNA) of strain SK-1. After hybridization, strong green fluorescence was observed in cells of strain SK-1 under an epifluorescence
microscope; however, no such fluorescence was observed with strain SK-2, which indicates that probes hybridized only the DNA
of the target strain, SK-1, in species-specific manner, and that the two strains do not belong to a same species. This finding
was confirmed by ITS sequence analysis. The FISH technique used in this study was sensitive, simple, and rapid, and is a promising
tool for detecting target HAB species in natural environments. 相似文献
15.
Chlorophyta species are common in the southern and northern coastal areas of China. In recent years, frequent green tide incidents in Chinese coastal waters have raised concerns and attracted the attention of scientists. In this paper, we sequenced the 18S rDNA genes, the internal transcribed spacer (ITS) regions and the rbcL genes in seven organisms and obtained 536-566 bp long ITS sequences, 1 377-1 407 bp long rbcL sequences and 1 718-1 761 bp long partial 18S rDNA sequences. The GC base pair content was highest in the ITS regions and lowest in the rbcL genes. The sequencing results showed that the three Ulva prolifera (or U. pertusa) gene sequences from Qingdao and Nan’ao Island were identical. The ITS, 18S rDNA and rbcL genes in U. prolifera and U. pertusa from different sea areas in China were unchanged by geographic distance. U. flexuosa had the least evolutionary distance from U. californica in both the ITS regions (0.009) and the 18S rDNA (0.002). These data verified that Ulva and Enteromorpha are not separate genera. 相似文献
16.
17.
Eight hundred and thirty eight base pair fragment of mitochondrial COI gene of wild and cultured populations (CP1, CP4, CP5
and CP6) of Fenneropenaeus chinensis was amplified and sequenced. The A, T, G and C contents of the sequence were 235 bp (28.0%), 307 bp (36.6%), 138 bp (16.5%)
and 158 bp (18.9%), respectively. Furthermore, 556 bp fragment of the sequence was used to discuss the phylogenetic relationship
among 14 Penaeidae species using Alpheus armillatus as the outgroup. From the molecular phylogenetic tree constructed by neighbor-joining method, we obtained three large shrimp
groups: Farfantepenaeus, Litopenaeus and Fenneropenaeus group. The results also indicated that there were a closer genetic relationships between F. aztecus and F. paulensis, L. schmitti and L. setiferus, F. indicus and F. merguiensis, and the genus Farfantepenaeus was closer to Litopenaeus. 相似文献
18.
Li Jiasheng Peng Ying Zhang Shufei Liu Yifan Zhang Kun Chen Jian Zhang Hua Zhang Chi Liu Bingjian 《中国海洋湖沼学报》2023,41(1):267-279
The complete mitogenome of Parachiloglanis hodgarti was sequenced and characterized, which is the first mitogenome of the genus Parachiloglanis within Sisoridae. The mitogenome is 16 511-bp long and included 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and one control region. The genome composition was A+T biased (58.64%) and exhibited a positive AT-skew (0.095) and a negative GC-skew (?0.283). Compared with other Sisoridae fishes, the characteristics of nucleotide skews, codon usage, and amino acid usage of the P. hodgarti mitogenome are more similar to those of non-Glyptosternoid fishes. Furthermore, the phylogenetic trees show that Sisoridae fishes fall into four major clades and P. hodgarti (Clade I) is basal to the Sisoridae family, forming a sister clade to the Glyptosternoids (Clade IV). The topological structures constructed in this study raised doubts over the traditional classification system. These results will help better understand the features of the P. hodgarti mitogenome and provide a reference for further phylogenetic research on Sisoridae species.
相似文献19.
To evaluate the relationship between salinity tolerance and genetic diversity of plankton, we collected a wild species of
plankton from Taipingjiao, Qingdao. The fragment of ITS1-5.8S rDNA-ITS2 was extracted and sequenced. The results showed that
the plankton belongs to Oxyrrhis marina. The salinity tolerance of O. marina ranges from 4 to 60. Seven selected groups were built up to evaluate salinity tolerance and to assess genetic diversity by
RAPD. The salinity tolerance comparison revealed considerable differences among groups: the strains of O. marina in group 4 could survive under salinity from 4 to 32, while the strains selected for salinity 60 died under the salinity
lower than 16. Analysis of genetic diversity of the seven groups showed that the mean genetic diversity index value was 0.28,
but it was only 0.16 in selected group of 4 and was 0.24 for group 60. The result of AMOVA suggested a significantly positive
relationship between the salinity tolerance and genetic diversity of O. marina (P<0.01). This study indicates that consideration of intraspecific genetic divergence in O. marina might be indispensable when using it as a model in the study of salinity tolerance of wild plankton. 相似文献
20.
Sargassum muticum is one of the most abundant and conspicuous native macroalgae species on the northern coasts of China. It often forms large-scale seaweed beds in subtidal zones. This investigation was designed to understand the intraspecific genetic relationships of this alga based on samples collected from four northern coastal sites of China, and to evaluate gamete release and growth capacity in laboratory conditions. The nuclear internal transcribed spacer 2 （ITS2） sequences of 16 samples from four locations were identical. Based on cox3 gene and partial rbcLS operon sequences, intraspecific genetic variability was detected with three and two ribotypes, respectively. Temperature, not irradiance, was shown to significantly affect gamete release and fertilization. Elevated temperature and irradiance enhanced the growth of germlings and vegetative branchlets. Maximum growth rate of germlings was detected at 18-24℃and an irradiance of 60-100 μmol photons/（m^2.s）. Under ambient conditions （12-25℃ and 60-125 gmol photons/ （m2.s））, relative growth rate of young branchlets could reach 7.5%/d. 相似文献