Accurate species identification is a key component of biodiversity research.DNA barcoding is an effective molecular method used for fish species identification.We aimed to study the DNA barcoding of fish in Zhoushan c...Accurate species identification is a key component of biodiversity research.DNA barcoding is an effective molecular method used for fish species identification.We aimed to study the DNA barcoding of fish in Zhoushan coastal waters,explore the differences and applicability of two gene fragments(12S rRNA and COI)of DNA barcoding in fish species identification,and established a comprehensive fish barcoding reference database.Two hundred and eighty-seven captured fish samples from Zhoushan coastal waters were identified using morphological characteristics and DNA barcoding.A total of 26412S rRNA sequences(belonging to eight orders,31 families,55 genera,and 66 species)and 188 COI sequences(belonging to seven orders,30 families,48 genera,and 58 species)were obtained.The lengths of the 12S rRNA sequences ranged from 165 to 178 bp,and the guanine-cytosine(GC)content was 45.37%.The average 12S rRNA interspecific and intraspecific genetic distances(K2P)were 0.10%and 26.66%,respectively.The length of the COI sequence ranged 574–655 bp,and the content of GC was 45.97%.The average 12S rRNA interspecific and intraspecific genetic distances(K2P)were 0.16%and 27.45%,respectively.The minimum interspecific genetic distances of 12S rRNA and COI(1.23%and 1.86%)were both greater than their maximum intraspecific genetic distances(2.42%and 8.66%).Three molecular analyses(NJ tree,ABGD,and GMYC)were performed to accurately identify and delineate species.Clustering errors occurred when the 12S rRNA sequences were delimited using the NJ tree method,and the delimitation results of ABGD and GMYC are consistent with the final species identification results.Our results demonstrate that DNA barcoding based on 12S rRNA and COI can be used as an effective tool for fish species identification,and 12S rRNA has good application prospects in the environmental DNA(eDNA)metabarcoding of marine fish.展开更多
Zooplankton,a crucial component of urban wetland,are one of the effective bioindicators for monitoring the feeding stocks of organisms at higher trophic levels and assessing the ecological quality of ecosystems.Howeve...Zooplankton,a crucial component of urban wetland,are one of the effective bioindicators for monitoring the feeding stocks of organisms at higher trophic levels and assessing the ecological quality of ecosystems.However,information about the characteristics of epiphytic zooplankton community structure resulted from traditional methods is limited and hindered by the large amount of detritus and sludge attached to the macrophytes.We investigated the epiphytic zooplankton communities associated with macrophytes(Vallisneria,Nymphaea,and Thalia dealbata)in a subtropical wetland using as DNA markers of the 18 S rRNA gene and the mitochondrial cytochrome c oxidase subunit I(COI)gene.A total of 241 OTUs of zooplankton were obtained from COI amplicons,including 194 OTUs of Rotifera,22 of Cladocera,and 25 of Copepoda,while only 62 OTUs of zooplankton were obtained from 18 S rDNA amplicons including 34 OTUs of Rotifera and 28 of Copepoda.The zooplankton communities associated with the three macrophytes were similar,but they differed significantly from those in the open waters.However,there were no significant temporal differences among the zooplankton communities.Epiphytic zooplankton communities were dominated by littoral zooplankton such as Testudinella,Lecane,and Philodina.Microzooplankton,especially littoral species,utilize macrophytes as food sources and as refuges against predation.This further led to an increase inαandβdiversity of zooplankton communities in urban wetlands.Our result suggests that the joint use of multiple molecular markers could improve the taxonomic resolution and generate a comprehensive biodiversity profile of zooplankton.展开更多
Benthodytes tetrapapillata sp.nov.was collected from a seamount located on the Caroline Ridge at a depth of 2289 m,during the cruise of R/V Kexue in June 2019.We provided detailed descriptions of external and deposits...Benthodytes tetrapapillata sp.nov.was collected from a seamount located on the Caroline Ridge at a depth of 2289 m,during the cruise of R/V Kexue in June 2019.We provided detailed descriptions of external and deposits morphology.The phylogenetic analyses based on cytochrome c oxidase I(COI)and a concatenated dataset of 16S and COI genes showed that the new species belonged to Benthodytes that is not monophyletic.Both details of morphological comparisons and molecular analyses confirmed that Benthodytes tetrapapillata sp.nov.is a new psychropotid species.A state of main morphological characters in valid species of Benthodytes is also provided in this study.展开更多
The sea star Asterias amurensis is widely viewed as a severe“marine pest”because of its broad feeding habits.Over the past few decades,A.amurensis undergoes massive and sporadic population outbreaks worldwide,causin...The sea star Asterias amurensis is widely viewed as a severe“marine pest”because of its broad feeding habits.Over the past few decades,A.amurensis undergoes massive and sporadic population outbreaks worldwide,causing extensive economic and ecological losses to the local aquaculture industry and marine ecosystem.Understanding the genetic diversity and population structure of A.amurensis can provide vital information for resource management.By analyzing the polymorphism of the mitochondrial cytochrome C oxidase subunit I(COI)gene and ten simple sequence repeat(SSR)microsatellites markers,the genetic diversity and population structure of A.amurensis of four populations along the northern coast of China was uncovered.A total of 36 haplotypes were identified,and a main haplotype was found in four populations.The Qingdao(QD)population displayed the highest genetic diversity among all the populations.The AMOVA and pairwise F_(st)showed that there was small but statistically significant population differentiation among the four populations,especially between QD and Weihai(WH).Moreover,the principal component analysis(PCA)and admixture analysis showed that several individuals in Yantai(YT)and Dalian(DL)had little genetic association with other individuals.Overall,this study provided useful information of the genetic diversity and population structure of A.amurensis and will contribute to the resource management of A.amurensis in China.展开更多
Hyalomma anatolicum, Hyalomma asiaticum and Hyalomma detritum are wide-spread tick vectors in China. They could transmit a great variety of serious animal and human pathogens, which are great threats to the health of ...Hyalomma anatolicum, Hyalomma asiaticum and Hyalomma detritum are wide-spread tick vectors in China. They could transmit a great variety of serious animal and human pathogens, which are great threats to the health of human beings and the safety of stockbreeding. Most of them are distributed in Xinjiang and Inner Mongolia, and they share similar morphologies. This study is to establish a method for identifying H. anatolicum, H. asiaticum and H. detritum with molecular markers and to revealing the phylogenetic relationship of these ticks. Ticks were collected from domestic animals in Xinjiang and Inner Mongolia autonomous regions and classified by morphological characters. 16S rRNA and mitachondrial cytochrome oxidase subunit I gone （CO1） of ticks were amplified by PCR and subsequently sequenced. Phylogenetic trees were constructed by MEGA 5.0 and Mrbayes 3.2. On the 16S rRNA-based phylogenetic tree, H. anatolicum and H. aisaticum were clustered together with their respective classes. H. detritum was clustered with their respective class and the H. anatolicum, H. asiaticum formed distinct branches on the phylogenetic trees based on the COL The method based on morphology that combined with molecular 16S rRNA and COl seemed a simple and accurate method for species identification of H. anatolicum, H. asiaticum and H. detritum. n展开更多
基金Supported by the Zhejiang Provincial Key Research and Development Program (No.2021C02047)。
文摘Accurate species identification is a key component of biodiversity research.DNA barcoding is an effective molecular method used for fish species identification.We aimed to study the DNA barcoding of fish in Zhoushan coastal waters,explore the differences and applicability of two gene fragments(12S rRNA and COI)of DNA barcoding in fish species identification,and established a comprehensive fish barcoding reference database.Two hundred and eighty-seven captured fish samples from Zhoushan coastal waters were identified using morphological characteristics and DNA barcoding.A total of 26412S rRNA sequences(belonging to eight orders,31 families,55 genera,and 66 species)and 188 COI sequences(belonging to seven orders,30 families,48 genera,and 58 species)were obtained.The lengths of the 12S rRNA sequences ranged from 165 to 178 bp,and the guanine-cytosine(GC)content was 45.37%.The average 12S rRNA interspecific and intraspecific genetic distances(K2P)were 0.10%and 26.66%,respectively.The length of the COI sequence ranged 574–655 bp,and the content of GC was 45.97%.The average 12S rRNA interspecific and intraspecific genetic distances(K2P)were 0.16%and 27.45%,respectively.The minimum interspecific genetic distances of 12S rRNA and COI(1.23%and 1.86%)were both greater than their maximum intraspecific genetic distances(2.42%and 8.66%).Three molecular analyses(NJ tree,ABGD,and GMYC)were performed to accurately identify and delineate species.Clustering errors occurred when the 12S rRNA sequences were delimited using the NJ tree method,and the delimitation results of ABGD and GMYC are consistent with the final species identification results.Our results demonstrate that DNA barcoding based on 12S rRNA and COI can be used as an effective tool for fish species identification,and 12S rRNA has good application prospects in the environmental DNA(eDNA)metabarcoding of marine fish.
基金Supported by the Guangzhou Municipal Science and Technology Project(No.202201010592)the Fundamental Research Funds for the Central Public Welfare Research Institutes(No.PM-zx 703-202305-165)。
文摘Zooplankton,a crucial component of urban wetland,are one of the effective bioindicators for monitoring the feeding stocks of organisms at higher trophic levels and assessing the ecological quality of ecosystems.However,information about the characteristics of epiphytic zooplankton community structure resulted from traditional methods is limited and hindered by the large amount of detritus and sludge attached to the macrophytes.We investigated the epiphytic zooplankton communities associated with macrophytes(Vallisneria,Nymphaea,and Thalia dealbata)in a subtropical wetland using as DNA markers of the 18 S rRNA gene and the mitochondrial cytochrome c oxidase subunit I(COI)gene.A total of 241 OTUs of zooplankton were obtained from COI amplicons,including 194 OTUs of Rotifera,22 of Cladocera,and 25 of Copepoda,while only 62 OTUs of zooplankton were obtained from 18 S rDNA amplicons including 34 OTUs of Rotifera and 28 of Copepoda.The zooplankton communities associated with the three macrophytes were similar,but they differed significantly from those in the open waters.However,there were no significant temporal differences among the zooplankton communities.Epiphytic zooplankton communities were dominated by littoral zooplankton such as Testudinella,Lecane,and Philodina.Microzooplankton,especially littoral species,utilize macrophytes as food sources and as refuges against predation.This further led to an increase inαandβdiversity of zooplankton communities in urban wetlands.Our result suggests that the joint use of multiple molecular markers could improve the taxonomic resolution and generate a comprehensive biodiversity profile of zooplankton.
基金Supported by the National Key Research and Development Program of China (No.2021YFE0193700)the Strategic Priority Research Program of the Chinese Academy of Sciences (No.XDB42000000)+3 种基金the National Natural Science Foundation of China (No.41930533)the Biological Resources ProgramChinese Academy of Sciences (No.KFJ-BRP-017-38)the Major Scientific and Technological Projects of Hainan Province (No.ZDKJ2021036)。
文摘Benthodytes tetrapapillata sp.nov.was collected from a seamount located on the Caroline Ridge at a depth of 2289 m,during the cruise of R/V Kexue in June 2019.We provided detailed descriptions of external and deposits morphology.The phylogenetic analyses based on cytochrome c oxidase I(COI)and a concatenated dataset of 16S and COI genes showed that the new species belonged to Benthodytes that is not monophyletic.Both details of morphological comparisons and molecular analyses confirmed that Benthodytes tetrapapillata sp.nov.is a new psychropotid species.A state of main morphological characters in valid species of Benthodytes is also provided in this study.
基金Supported by the International Science Partnership Program of the Chinese Academy of Sciences(No.133137KYSB20200002)the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDA23050304)the Natural Science Foundation of Shandong Province(Nos.ZR2021MC151,ZR2021QD158)。
文摘The sea star Asterias amurensis is widely viewed as a severe“marine pest”because of its broad feeding habits.Over the past few decades,A.amurensis undergoes massive and sporadic population outbreaks worldwide,causing extensive economic and ecological losses to the local aquaculture industry and marine ecosystem.Understanding the genetic diversity and population structure of A.amurensis can provide vital information for resource management.By analyzing the polymorphism of the mitochondrial cytochrome C oxidase subunit I(COI)gene and ten simple sequence repeat(SSR)microsatellites markers,the genetic diversity and population structure of A.amurensis of four populations along the northern coast of China was uncovered.A total of 36 haplotypes were identified,and a main haplotype was found in four populations.The Qingdao(QD)population displayed the highest genetic diversity among all the populations.The AMOVA and pairwise F_(st)showed that there was small but statistically significant population differentiation among the four populations,especially between QD and Weihai(WH).Moreover,the principal component analysis(PCA)and admixture analysis showed that several individuals in Yantai(YT)and Dalian(DL)had little genetic association with other individuals.Overall,this study provided useful information of the genetic diversity and population structure of A.amurensis and will contribute to the resource management of A.amurensis in China.
基金Supported by National Key Technology Research and Development Program ofChina(2012BAK11B04)
文摘Hyalomma anatolicum, Hyalomma asiaticum and Hyalomma detritum are wide-spread tick vectors in China. They could transmit a great variety of serious animal and human pathogens, which are great threats to the health of human beings and the safety of stockbreeding. Most of them are distributed in Xinjiang and Inner Mongolia, and they share similar morphologies. This study is to establish a method for identifying H. anatolicum, H. asiaticum and H. detritum with molecular markers and to revealing the phylogenetic relationship of these ticks. Ticks were collected from domestic animals in Xinjiang and Inner Mongolia autonomous regions and classified by morphological characters. 16S rRNA and mitachondrial cytochrome oxidase subunit I gone （CO1） of ticks were amplified by PCR and subsequently sequenced. Phylogenetic trees were constructed by MEGA 5.0 and Mrbayes 3.2. On the 16S rRNA-based phylogenetic tree, H. anatolicum and H. aisaticum were clustered together with their respective classes. H. detritum was clustered with their respective class and the H. anatolicum, H. asiaticum formed distinct branches on the phylogenetic trees based on the COL The method based on morphology that combined with molecular 16S rRNA and COl seemed a simple and accurate method for species identification of H. anatolicum, H. asiaticum and H. detritum. n
