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1.
In this study, we integrated a DNA barcoding project with an ecological survey on intertidal polychaete communities and investigated
the utility of CO1 gene sequence as a DNA barcode for the classification of the intertidal polychaetes. Using 16S rDNA as
a complementary marker and combining morphological and ecological characterization, some of dominant and common polychaete
species from Chinese coasts were assessed for their taxonomic status. We obtained 22 haplotype gene sequences of 13 taxa,
including 10 CO1 sequences and 12 16S rDNA sequences. Based on intra- and inter-specific distances, we built phylogenetic
trees using the neighbor-joining method. Our study suggested that the mitochondrial CO1 gene was a valid DNA barcoding marker
for species identification in polychaetes, but other genes, such as 16S rDNA, could be used as a complementary genetic marker.
For more accurate species identification and effective testing of species hypothesis, DNA barcoding should be incorporated
with morphological, ecological, biogeographical, and phylogenetic information. The application of DNA barcoding and molecular
identification in the ecological survey on the intertidal polychaete communities demonstrated the feasibility of integrating
DNA taxonomy and ecology. 相似文献
2.
This study is part of the endeavor to construct a comprehensive DNA barcoding database for common seaweeds in China. Identifications of red seaweeds, which have simple morphology and anatomy, are sometimes difficult solely depending on morphological characteristics. In recent years, DNA barcode technique has become a more and more effective tool to help solve some of the taxonomic difficulties. Some DNA markers such as COI (cytochrome oxidase subunitⅠ) are proposed as standardized DNA barcodes for all seaweed species. In this study, COI, UPA (universal plastid amplicon, domain V of 23S rRNA), and ITS (nuclear internal transcribed spacer) were employed to analyze common species of intertidal red seaweeds in Qingdao (119.3 -121 E, 35.35 -37.09 N). The applicability of using one or a few combined barcodes to identify red seaweed species was tested. The results indicated that COI is a sensitive marker at species level. However, not all the tested species gave PCR amplification products due to lack of the universal primers. The second barcode UPA had effective universal primers but needed to be tested for the effectiveness of resolving closely related species. More than one ITS sequence types were found in some species in this investigation, which might lead to confusion in further analysis. Therefore ITS sequence is not recommended as a universal barcode for seaweeds identification. 相似文献
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A new identification method for five species of oysters in genus Crassostrea from China based on high-resolution melting analysis 总被引：2，自引：0，他引：2
The high phenotypic plasticity in the shell of oysters presents a challenge during taxonomic and phylogenetie studies of these economically important bivalves. However, because DNA can exhibit marked differences among morphologically similar species, DNA barcoding offers a potential means for oyster identification. We analyzed the complete sequences of the cytochrome oxidase subunit I （COI） of five common Crassostrea species in China （including Hong Kong oyster C. hongkongensis, Jinjiang oyster C. ariakensis, Portuguese oyster C. angulata, Kumamoto oyster C. sikamea, and Pacific oyster C. gigas） and screened for distinct fragments. Using these distinct fragments on a high-resolution melting analysis platform, we developed an identification method that does not rely on species-specific PCR or fragment length polymorphism and is efficient, reliable, and easy to visualize. Using a single pair of primers （Oyster- COI-1）, we were able to successfully distinguish among the five oyster species. This new method provides a simple and powerful tool for the identification of oyster species. 相似文献
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DNA barcoding provides accurate identification of zooplankton species through all life stages. Single-gene-targeted metagenomic analysis based on DNA barcode databases can facilitate longterm monitoring of zooplankton communities. With the help of the available zooplankton databases, the zooplankton community of the Changjiang (Yangtze) River estuary was studied using a single-gene-targeted metagenomic method to estimate the species richness of this community. A total of 856 mitochondrial cytochrome oxidase subunit 1 (cox1) gene sequences were determined. The environmental barcodes were clustered into 70 molecular operational taxonomic units (MOTUs). Forty-two MOTUs matched barcoded marine organisms with more than 90% similarity and were assigned to either the species (similarity>96%) or genus level (similarity<96%). Sibling species could also be distinguished. Many species that were overlooked by morphological methods were identified by molecular methods, especially gelatinous zooplankton and merozooplankton that were likely sampled at different life history phases. Zooplankton community structures differed significantly among all of the samples. The MOTU spatial distributions were influenced by the ecological habits of the corresponding species. In conclusion, single-gene-targeted metagenomic analysis is a useful tool for zooplankton studies, with which specimens from all life history stages can be identified quickly and effectively with a comprehensive database. 相似文献
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【目的】了解巨砺属牡蛎的系统关系和种类区分。【方法】对我国沿海分布的7种巨砺属牡蛎(香港牡蛎、有明牡蛎、熊本牡蛎、岩牡蛎、艾氏牡蛎、太平洋牡蛎、葡萄牙牡蛎)的线粒体DNA片段(COI、12S、16S和tRNAs),以及核糖体RNA基因转录间隔子序列(ITS-1、ITS-2和ITS)进行分子系统学研究。【结果】无论种间或种内,tRNAs序列差异最大,亚种内TS1序列差异最大;tRNAs和COI序列较其它序列变异更快,种间变异与种内变异之间有明显的条形码间隙;12S、16S、ITS和ITS2的种间变异与种内变异无重叠及条形码间隙;ITS1的种间变异与种内变异出现重叠。在亚种层面,12S、ITS、ITS1和ITS2的亚种间变异与亚种内变异出现重叠;16S的亚种间变异与亚种内变异无重叠及条形码间隙;tRNAs与COI序列亚种间变异与亚种内变异之间有明显的条形码间隙,有利于区分亚种。【结论】tRNAs和COI序列可用于种及亚种的鉴定。 相似文献
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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
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《中国海洋大学学报(英文版)》2019,(6)
Nassarius causes many poisonings in China and other Asian countries. The toxicity of Nassarius is related to species and populations. However, the molecular assignment of different toxic Nassarius samples is still unclear, which deteriorates the poisoning. Our study combined toxicity, toxin detection and multiple genes DNA barcoding to assign the various toxic Nassarius species and populations from China coast. The toxicity test indicated that different Nassarius species and different populations within one Nassarius species had different toxicity. Based on High Performance Liquid Chromatography, the toxin was confirmed to be TTX. The toxin content varied in different samples. The COI, 16 S and ITS sequences revealed different toxic Nassarius species as monophyletic clades. All the samples tested have been assigned to species level. However, the different toxic populations within N. succinctus, N. variciferus and N. semiplicata did not form separated clades, and the toxic and nontoxic species did not form two clades separately. Our study constructed the relationship between toxicity and taxonomy assignment of different toxic Nassarius samples based on toxicity detection and multiple gene DNA barcoding, which provides the basis for controlling poisoning and studying the toxin-resistance difference in Mollusca. It is also indicated that the toxicity of Nassarius is really related with species at the genetic level, but not absolutely related with populations. 相似文献
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《中国海洋大学学报(英文版)》2021,(4)
The dried shellfish products with rich nutrients and low-calorie content are favorite food in China, especially in coastal areas. However, the species of dried shellfish products in the market are usually unknown, as the taxonomic features were removed during the production process. This study described the application of DNA barcoding technique to the identification of 100 dried shellfish(scallop, squid, octopus and cuttlefish) products in markets. Samples were authenticated by comparing mitochondrial cytochrome oxidase subunit I(COI) gene and 16 S ribosomal RNA(16 S rRNA) gene sequences with public reference taxonomic databases. The results showed that all the 100 products can be identified at species level. Sixty four scallop adductor products were processed using the bay scallop, Argopecten irradians, and one was from Portuguese oyster, Crassostrea angulata. All the 27 squid, 2 cuttlefish and 6 octopus products were produced by the Jumbo flying squid, Dosidicus gigas. The neighbour-joining tree is in agreement with the results of DNA barcoding analysis. The 64 scallop samples formed one A. irradians cluster, leaving Sca65 clustered with the reference oyster sequence C. angulata(MH997922). All the 35 cephalopod(squid, octopus and cuttlefish) samples formed a D. gigas cluster. This investigation revealed a low variety of dried shellfish products sold on the market, and highlighted the high rate of mislabeling and species substitution. Our present work provides a practical method for tracing and authenticating shellfish products. 相似文献
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为鉴定鱼肚的正品来源,运用一对特异性引物扩增并测定10 个不同价格（700～1 500 元/kg）鱼肚样本的线粒体DNA 细胞色素c 氧化酶Ⅰ（cox1）约660 bp 的序列.通过BLASTN 比对DNA 序列同源度,判定鱼肚所属种类分别为鲈形目石首鱼科（Sciaenidae）、马鲅科（Eleutheronema）、笛鲷科（Lutjanidae）、带鱼科（Trichiuridae）.cox1 条码序列获取便捷,基于此条码序列的物种鉴定技术可用于鱼肚种类鉴别. 相似文献
11.
Apostichopus japonicus(Holothuroidea,Echinodermata) is an ecological and economic species in East Asia.Conventional biometric monitoring method includes diving for samples and weighing above water,with highly variable in weight measurement due to variation in the quantity of water in the respiratory tree and intestinal content of this species.Recently,video survey method has been applied widely in biometric detection on underwater benthos.However,because of the high flexibility of A.japonicus body,video survey method of monitoring is less used in sea cucumber.In this study,we designed a model to evaluate the wet weight of A.japonicus,using machine vision technology combined with a support vector machine(SVM) that can be used infield surveys on the A.japonicus population.Continuous dorsal images of free-moving A.japonicus individuals in seawater were captured,which also allows for the development of images of the core body edge as well as thorn segmentation.Parameters that include body length,body breadth,perimeter and area,were extracted from the core body edge images and used in SVM regression,to predict the weight of A.japonicus and for comparison with a power model.Results indicate that the use of SVM for predicting the weight of 33 A.japonicus individuals is accurate(R~2=0.99) and compatible with the power model(R~2=0.96).The image-based analysis and size-weight regression models in this study may be useful in body weight evaluation of A.japonicus in lab and field study. 相似文献
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利用随机扩增多态DNA(RAPD)技术分别分析了五岛西部日本鲐、东海西部日本鲐和澳洲鲐三群体的样本,共产生226个分子标记,其中143个为多态性标记,多态百分率达到63.3%,每条引物产生的平均标记数为7.29。五岛西部日本鲐、东海西部日本鲐和澳洲鲐群体内遗传相似度分别为0.949、0.877和0.936,而群体间遗传距离依次为:五岛西部日本鲐-东海西部日本鲐(0.2357)<东海西部日本鲐-澳洲鲐(0.3030)<五岛西部日本鲐-澳洲鲐(0.3528),五岛西部日本鲐与东海西部日本鲐个体在UPGMA系统树独立聚类为两个类群,初步支持东、黄海的日本鲐存在东海西部和五岛西部的两个种群的观点。Shannon多样性指数表明,其遗传多样性大小依次为东海西部日本鲐、澳洲鲐、五岛西部日本鲐。 相似文献
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On October 1, 2009, sixteen dolphins were obtained from fishermen by incidental catching in the Yellow Sea, China. As the dolphins' skin color was ambiguous, morphological parameters were measured, and mitochondrial DNA cytochrome b(Cyt b) gene sequence was studied to identify the species. Morphological characteristics were consistent with Pantropical spotted dolphins, S tenella attenuata. Furthermore, a partial mitochondrial DNA cytochrome b(Cyt b) gene sequence as long as 328-bp was studied by extracting genomic DNA from the skins, and six haplotypes were detected in the sixteen dolphins. By comparing homologous sequences available in Gen Bank(www.ncbi.nlm.nih.gov), all the six haplotypes had maximal genetic similarity with Pantropical spotted dolphin. Eight species of cetacean(whales and dolphins) are now recognised in the Yellow Sea. To the best of our knowledge, this is the first record of Pantropical spotted dolphins from this region. Despite this species being listed as a Grade II National Key Protected Animal since 1988, little is known of its biology in Chinese waters. We recommend remedial research be undertaken to ensure appropriate management. 相似文献
14.
Yingchun Lv Rong Zheng Tao Zuo Yuming Wang Zhaojie Li Yong Xue Changhu Xue Qingjuan Tang 《中国海洋大学学报(英文版)》2014,13(5):825-829
Sea cucumbers are traditional marine food and Chinese medicine in Asia. The rapid expansion of sea cucumber market has resulted in various problems, such as commercial fraud and mislabeling. Conventionally, sea cucumber species could be distinguished by their morphological and anatomical characteristics; however, their identification becomes difficult when they are processed. The aim of this study was to develop a new convenient method of identifying and distinguishing sea cucumber species. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of mitochondrial cytochrome oxidase I gene (COI) was used to identifing five sea cucumber species (Apostichopus japonicus, Cucumaria frondosa, Thelenota ananas, Parastichopus californicus and Actinopyga lecanora). A 692 bp fragment of COI was searched for BamHI, KpnI, PstI, XbaI and Eco31I restriction sites with DNAMAN 6.0, which were then used to PCR-RFLP analysis. These five sea cucumber species can be discriminated from mixed sea cucumbers. The developed PCR-RFLP assay will facilitate the identification of sea cucumbers, making their source tracing and quality controlling feasible. 相似文献
15.
《中国海洋湖沼学报》2021,(4)
Ichthyoplankton samples were collected from Changjiang(Yangtze) River estuary in May 2016.Species composition was studied by DNA barcoding and morphological identification.To make better use of the estuarine biotic integrity index(EBI) to assess the ecosystem health of the Changjiang River estuary over the past 30 years,we collected the data of a spring ichthyoplankton survey in the estuary from 1986 to 2016.The EBI was calculated using 12 evaluation metrics,namely,the number of total ichthyoplankton species,estuarine spawning species,estuarine nursery species,estuarine resident species,benthic species,pelagic species,and intolerant species,and the percentages of tolerant species,omnivores,insectivores,carnivores,and natural hybrid species.EBI was calculated in spring in four periods(1986,1999,2007,and 2016) by assigning points of 1,3 or 5,giving values of 50,38,36,and 32,respectively,corresponding to "Good", "Fair-Poor", "Fair-Poor",and "Poor" EBI levels,respectively.Changes in species composition were the primary reason for the significant decreases in EBI between 1986 and 1999,and for the large differences between 1986 and 2007 and between 2007 and 2016.The changes in species composition were influenced by declines in ichthyoplankton species,pollution sensitive species,estuarine nursery species and estuarine sedentary species,and an increase in pollution re sistant species.An analysis of EBI interdecadal variability showed that the health status of the Changjiang River estuary ecosystem over the last 3 0 years first declined and then stabilized at a lower level.This result further settled the argument for urgent protection and restoration of the Changjiang River estuary. 相似文献
16.
YU Shanshan KONG Xiaoyu LI Yulong and XU Hui Key Laboratory of Mariculture of Ministry of Education Ocean University of China Qingdao P. R. China 《中国海洋大学学报(英文版)》2007,(2)
The complete mitochondrial cytochrome oxidase subunit II (COII) gene of Penaeinae shrimp Fenneropenaeus chinen- sis was cloned and sequenced. The gene is 688 bp in length and codes for 229 amino acids. It shows 83.2%, 87.0% and 83.8% sequence similarity to Marsupenaeus japonicus, Penaeus monodon and Farfantepenaeus notialis, respectively. The A T content of the whole gene and that at the third position of codons are 64.7% and 78.2%, respectively. The phylogenetic relationship between F. chinensis and three other species representing genera Farfanatepenaeus, Marsupenaeus and Penaeus was analyzed. Results showed that the genetic distances among the four taxa ranged from 0.144 0 to 0.200 5, exceeding those estimated with COI and partial 16S rRNA gene sequences among Marsupenaeus, Litopenaeus and Melicertus, and being therefore larger than the value among subgenera. It has been suggested that the COII gene has a faster evolutionary rate than that of the COI gene and partial 16S rRNA gene and could be used for phylogenetic analysis at genus or species level. The results of the present study indicated that Farfantepenaeus, Fenneropenaeus, Marsupenaeus and Penaeus are at a higher phylogenetic level than subgenus, which supports the opinion of the elevation of phylogenetic status of the four subgenera to genus level. 相似文献
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Journal of Oceanology and Limnology - The kuruma shrimp Marsupenaeus japonicus is one of the most commercially important shrimp species in the world. Low salinity would affect the penetration and... 相似文献
20.
LIU Jinxian) ) GAO Tianxiang) WANG Yujiang) and ZHANG Yaping) ) The Key Laboratory of Mariculture Ministry of Education Ocean University of China Qingdao P.R.China ) Laboratory of Molecular Evolution Genome Diversity Kunming Institute of Zoology Chinese Academy of Sciences Kunming P. R. China 《中国海洋大学学报(英文版)》2005,4(1):85-88
1Introduction Japanese grenadier anchovy,Coilia ectenes Jordanet Seale(1905),is distributed in the northwest Pacif-ic.The congener,Osbeck's grenadier anchovy,Coil-ia mystus(Linnaeus,1758),is widely distributed inthe west Pacific.Both species inhabit coastal watersand estuaries and can reach up to rivers.The twospecies are important contributors to the coastal fish-eries of China(Zheng et al.,2003).Many studies on the fishery biology of the twospecies have been conducted(Zheng et al.,2003)… 相似文献