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HU Jingjie WANG Xiaolong HU Xiaoli BAO Zhenmin 《中国海洋大学学报(英文版)》2006,5(1):12-20
Common carp expressed sequence tags （ESTs） were analyzed for the existence of microsatellites, or simple sequence repeats （SSRs）. In the NCBI dbEST database, a total of 10612 sequences were registered before December 31, 2004. A complete search of 2-6 nucleotide microsatellites resulted in the identification of 513 SSR-containing ESTs, accounting for 4.8% of the total. Cluster analysis indicated that 73 sequences of SSR-containing ESTs fell into 27 groups and the remaining 440 ESTs were independent. A total of 467 unique SSR-containing ESTs were identified. These EST-SSRs contained a vari- ety of simple sequence types, and di- and tri-nucleotide repeats were the most abundant, accounting for 42.1% and 27.9% of the whole, respectively. Of the dinucleotide repeats, CA/TG was the most abundant, followed by GA/TC. BLASTx search showed that 38.1% of the SSR loci could be associated with genes or proteins of known or unknown function. BLASTx searches of SSR-containing ESTs also showed high frequencies （98/179） of hits on zebrafish sequences. 相似文献
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The sea cucumber Apostichopus japonicus is a commercially and ecologically important species in China. A total of 3056 potential unigenes were generated after assembling 7597 A. japonicus expressed sequence tags (ESTs) downloaded from Gen-Bank. Two hundred and fifty microsatellite-containing ESTs (8.18%) and 299 simple sequence repeats (SSRs) were detected. The average density of SSRs was 1 per 7.403 kb of EST after redundancy elimination. Di-nucleotide repeat motifs appeared to be the most abundant type with a percentage of 69.90%. Of the 126 primer pairs designed, 90 amplified the expected products and 43 showed polymorphism in 30 individuals tested. The number of alleles per locus ranged from 2 to 26 with an average of 7.0 alleles, and the observed and expected heterozygosities varied from 0.067 to 1.000 and from 0.066 to 0.959, respectively. These new EST-derived microsatellite markers would provide sufficient polymorphism for population genetic studies and genome mapping of this sea cucumber species. 相似文献
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Nematode Diversity of Qingdao Coast Inferred from the 18S Ribosomal RNA Gene Sequence Analysis 总被引：1，自引：0，他引：1
SHEN Xiquan YANG Guanpin LIU Yongjian 《中国海洋大学学报(英文版)》2007,6(2):132-136
The 18S ribosomal DNA gene （18S rDNA） sequences （approxtmately 1300 bp in length） were amplified from the DNA extracted from the free-living marine nematodes collected from the inter-tidal sediment of Qingdao coast in bulk with nematode specific primers. The PCR products were cloned, re-amplified, digested with Rsa I and Hin61 restriction endonucleases and separated in agarose gel. Among 17 restriction fragment length types, types 1, 2 and 6 covered 61.2%, 14.4% and 9.3% of the clones analyzed, respectively, while the remaining 14 only covered 21 clones, which accounted for 15.1% of the total. Twenty-four representative clones were sequenced and phylogenetically analyzed by referring to those currently available in RDP and GenBank databases. Although it was hard to assign these sequences to known species or genera due to the lack of the 18S rDNA sequence data of known marine free-living nematodes, the obtained sequences were assigned to the nematodes of Adenophorea. Among them, twelve sequences were close to Pontonema vulgate and Adoncholaimus sp., four to Daptonema procerus and two （identical） to Enoplus brews. Our results showed that free-living marine nematode diversities could be determined by PCR retrieving and analysis of the 18S rDNA sequences and an 18S rDNA sequence could be assigned to a species or a genus only if the 18S rDNA sequences of the free-living marine nematodes were accumulated to some extent. 相似文献
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Microsatellites are a ubiquitous component of the eukaryote genome and constitute one of the most popular sources of molecular markers for genetic studies. However, no data are currently available regarding microsatellites across the entire genome in oysters, despite their importance to the aquaculture industry. We present the fi rst genome-wide investigation of microsatellites in the Pacifi c oyster Crassostrea gigas by analysis of the complete genome, resequencing, and expression data. The Pacifi c oyster genome is rich in microsatellites. A total of 604 653 repeats were identifi ed, in average of one locus per 815 base pairs(bp). A total of 12 836 genes had coding repeats, and 7 332 were expressed normally, including genes with a wide range of molecular functions. Compared with 20 different species of animals, microsatellites in the oyster genome typically exhibited 1) an intermediate overall frequency; 2) relatively uniform contents of(A)n and(C)n repeats and abundant long(C)n repeats(≥24 bp); 3) large average length of(AG)n repeats; and 4) scarcity of trinucleotide repeats. The microsatellite-fl anking regions exhibited a high degree of polymorphism with a heterozygosity rate of around 2.0%, but there was no correlation between heterozygosity and microsatellite abundance. A total of 19 462 polymorphic microsatellites were discovered, and dinucleotide repeats were the most active, with over 26% of loci found to harbor allelic variations. In all, 7 451 loci with high potential for marker development were identifi ed. Better knowledge of the microsatellites in the oyster genome will provide information for the future design of a wide range of molecular markers and contribute to further advancements in the fi eld of oyster genetics, particularly for molecular-based selection and breeding. 相似文献
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Introduced species may outcompete or hybridize with native species, resulting in the loss of native biodiversity or even alteration of ecosystem processes. In this study, we reported an alien distromatic Ulva species, which was found in an embayment（Holly Pond） connected with Long Island Sound, USA. The morphological and anatomical observations in combination with molecular data were used for its identification to species. Anatomy of collected specimens showed that the cell shape in rhizoidal and basal regions was round and the marginal teeth along the basal and median region were not found. These characteristics were primarily identical to the diagnostic characteristics of Ulva laetevirens Areschoug（Chlorophyta）. The plastid-encoding tufA and nucleus-encoding ITS1 were used for its molecular identification. Phylogenetic analysis for the tufA gene placed the specimens from Holly Pond in a well-supported clade along with published sequences of U. laetevirens identified early without any sequence divergence. In ITS tree, the sample also formed well-supported clades with the sequences of U. laetevirens with an estimated sequence divergence among the taxa in these clades as low as 1%. These findings confirmed the morpho-anatomical conclusion. Native to Australia, this species was reported in several countries along the Mediterranean coast after the late of 1990 s. This is the first time that U. laetevirens is found in the northeast coast of United States and the second record for Atlantic North America. 相似文献
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《中国海洋大学学报(英文版)》2015,(6)
Toll-like receptor(TLR) signaling pathway plays a pivotal role in the innate immune system. Studies on TLR signaling pathway genes in Zhikong scallop(Chlamys farreri) have mainly focused on sequence analysis and expression profiling, no research has been carried out on their localization. The chromosomal position of TLR signaling pathway genes can be valuable for assemblying scallop genome and analysizing gene regulatory networks. In the present study, five key TLR signaling pathway genes(Cf TLR, Cf Myd88, Cf TRAF6, Cf NFκB, and Cf IκB) containing bacterial artificial chromosomes(BACs) were isolated and physically mapped through fluorescence in situ hybridization on five non-homologous chromosome pairs, showing a similar distribution to another five model species. The isolation and mapping of these key immune genes of C. farreri will aid to the research on innate immunity, assignment of interested genes to chromosomes, and integration of physical, linkage and cytogenetic maps of this species. 相似文献
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Chunmei Li Xubo Wang Quanqi Zhang Zhigang Wang Jie Qi Qilin Yi Zhipeng Liu Yanan Wang Haiyang Yu 《中国海洋大学学报(英文版)》2012,11(1):32-44
Major histocompatibility complex class II antigens are important in vertebrate immune system.In the present study,the full cDNA sequence of class II A gene was synthesized by RACE-PCR from half-smooth tongue sole(Cynoglossus semilaevis),and its open reading frame(ORF) polymorphism was studied.The whole cDNA sequence was 992 bp in length,including the ORF with 717 bp.Twenty-five alleles were identified and clustered into two distinct groups according to the specific nucleotides/amino acids in specific positions.Eleven alleles belonged to Cyse-DAA while fourteen alleles belonged to Cyse-DBA.Four Cyse-DAA alleles were observed in one individual,and three to five Cyse-DBA alleles were observed in each of the three detected individuals,which indicated that at least two loci existed in each gene.Moreover,in order to study the function of the alleles in resistance to infection,200 individuals were intraperitoneally injected with Vibrio anguillarum and the first 20 dead individuals and 20 surviving ones were selected for genotype analysis.Fifty-six alleles were identified among the 40 individuals.Twenty-nine alleles belonged to Cyse-DAA and the other 27 alleles belonged to Cyse-DBA.Eighteen alleles were selected for studying their function in resistance to infection.Alleles Cyse-DAA*0201,Cyse-DAA*1101,Cyse-DBA*0401,Cyse-DBA*1102,Cyse-DBA*1801 and Cyse-DBA*2201 were identi-fied only in surviving individuals,while alleles Cyse-DAA*0901,Cyse-DBA*1101 and Cyse-DBA*1401 occurred more frequently in dead individuals.This study confirmed the existence and polymorphism of two class II A genes as well as the relationship between alleles of class II A genes and disease susceptibility/resistance in half-smooth tongue sole. 相似文献
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Haiyang Yu Liming Jiang Wei Chen Xubo Wang Zhigang Wang Quanqi Zhang 《中国海洋大学学报(英文版)》2010,9(4):365-370
The expressed sequence tags (ESTs) of Japanese flounder, Paralichthys olivaceus, were selected from GenBank to identify simple sequence repeats (SSRs) or microsatellites. A bioinformatic analysis of 11111
ESTs identified 751 SSR-containing ESTs, including 440 dinucleotide, 254 trinucleotide, 53 tetranucleotide, 95 pentanucleotide
and 40 hexanucleotide microsatellites respectively. The CA/TG and GA/TC repeats were the most abundant microsatellites. AT-rich
types were predominant among trinucleotide and tetranucleotide microsatellites. PCR primers were designed to amplify 10 identified
microsatellites loci. The PCR results from eight pairs of primers showed polymorphisms in wild populations. In 30 wild individuals,
the mean observed and expected heterozygosities of these 8 polymorphic SSRs were 0.71 and 0.83 respectively and the average
PIC value was 0.8. These microsatellite markers should prove to be a useful addition to the microsatellite markers that are
now available for this species. 相似文献
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A complementary DNA (cDNA) library was constructed from half-smooth tongue sole spleen. A long-read expressed sequence tag
(EST) database was generated, containing 3100 cDNA clones, of which 220 clones were fully sequenced. A total of 1060 non-redundant
simple sequence repeats (SSRs) were obtained from the cDNA library. An average of 5 kb sequence generates 1 SSR in the half-smooth
tongue sole spleen cDNA library. The proportion of the SSR unit size was different in the cDNA library. The monomeric repeats
(51.4%) are the most abundant class of SSR in the dataset. The dimeric, trimeric, tetrameric and hexameric repeats are represented
in decreasing proportions of 27.2%, 16.0%, 2.8% and 1.9%, respectively. The frequency of pentameric repeats was observed the
least (only 0.7%). Most of the monomeric and dimeric repeats are distributed in 3′ and 5′ un-translation region. If translation
regions are considered merely, trimeric repeats are the highest, accounting for 57% of the total microsatellites. 相似文献
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LU Yongzhong ZHANG Xuecheng 《中国海洋大学学报(英文版)》2007,6(3):244-248
In order to investigate the regulation mechanism of the phycocyanin gene,a series of functional analyses of the upstream sequence of cpcB gene from Arthrospira platensis were conducted in E. coli with green fluorescent protein encoding gene(gfp) as the reporter. Results showed that the gfp gene could express at a high level under the promotion of the upstream sequence,suggesting the existence of some strong promoter elements in it. The expression of GFP was influenced by temperature. Higher temperature led to higher expression level. The bioinformatics analyses followed by mutation analyses on the secondary structure of translation ini-tiation region(TIR) revealed that RNA thermosensor might account for the temperature regulation. 相似文献
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LI Haitao YANG Guanpin SUN Ying WU Suihan ZHANG Xiufang 《中国海洋大学学报(英文版)》2007,6(2):167-174
The genus Cylindrotheca consists of a small group of marine diatoms with a few species described. Eleven isolates of diatoms identified as Cylindrotheca closterium morphologically were obtained from Jiaozhou Bay with their nuclear-encoded small-subunit ribosomal RNA （SSU rDNA） and chloroplast-encoded rbcL gene sequences determined in this study. Interestingly, very high sequence divergences of SSU rDNA and rbcL gene were found among these isolates, and numerous nucleotide variation of rbcL gene caused relatively few variation of deduced amino acid sequence. Phylogenetic analyses based on SSU rDNA and rbcL gene, respectively, grouped the isolates into 6 clades. Phylogenetic tree of SSU rDNA placed all the Cylindrotheca isolates together, separating them into two lineages clearly. LineageⅠ was composed of the eleven C. closterium isolates obtained in this study together with another C. closterium isolate, but some clades were not well supported. LineageⅠwas contained two C. closterium isolates and one C. fusiformis isolate. Phylogenetic analysis of rbcL gene also separated the Cylindrotheca isolates into two well-defined lineages. The eleven C. closterium isolates formed a lineage and all clades were supported strongly. Statistical comparisons of SSU rDNA indicated that the average distance within lineageⅠwas significantly higher than that of other microalgae species （P 〈0.01）. These results suggested the existence of cryptic species within C. closterium. 相似文献
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