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Cunningham C Hikima J Jenny MJ Chapman RW Fang GC Saski C Lundqvist ML Wing RA Cupit PM Gross PS Warr GW Tomkins JP 《Marine biotechnology (New York, N.Y.)》2006,8(5):521-533
Large-insert genomic bacterial artificial chromosome (BAC) libraries of two culturally and economically important oyster species,
Crassostrea virginica and C. gigas, have been developed as part of an international effort to develop tools and reagents that will advance our ability to conduct
genetic and genomic research. A total of 73,728 C. gigas clones with an average insert size of 152 kb were picked and arrayed representing an 11.8-fold genome coverage. A total of
55,296 clones with an average insert size of 150 kb were picked and arrayed for C. virginica, also representing an 11.8-fold genome coverage. The C. gigas and C. virginica libraries were screened with probes derived from selected oyster genes using high-density BAC colony filter arrays. The probes
identified 4 to 25 clones per gene for C. virginica and 5 to 50 clones per gene for C. gigas. We conducted a preliminary analysis of genetic polymorphism represented in the C. gigas library. The results suggest that the degree of divergence among similar sequences is highly variable and concentrated in
intronic regions. Evidence supporting allelic polymorphism is reported for two genes and allelic and/or locus specific polymorphism
for several others. Classical inheritance studies are needed to confirm the nature of these polymorphisms. The oyster BAC
libraries are publicly available to the research community on a cost-recovery basis at 相似文献
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Jenny MJ Chapman RW Mancia A Chen YA McKillen DJ Trent H Lang P Escoubas JM Bachere E Boulo V Liu ZJ Gross PS Cunningham C Cupit PM Tanguy A Guo X Moraga D Boutet I Huvet A De Guise S Almeida JS Warr GW 《Marine biotechnology (New York, N.Y.)》2007,9(5):577-591
The eastern oyster, Crassostrea virginica, and the Pacific oyster, C. gigas, are species of global economic significance as well as important components of estuarine ecosystems and models for genetic
and environmental studies. To enhance the molecular tools available for oyster research, an international group of collaborators
has constructed a 27,496-feature cDNA microarray containing 4460 sequences derived from C. virginica, 2320 from C. gigas, and 16 non-oyster DNAs serving as positive and negative controls. The performance of the array was assessed by gene expression
profiling using gill and digestive gland RNA derived from both C. gigas and C. virginica, and digestive gland RNA from C. ariakensis. The utility of the microarray for detection of homologous genes by cross-hybridization between species was also assessed
and the correlation between hybridization intensity and sequence homology for selected genes determined. The oyster cDNA microarray
is publicly available to the research community on a cost-recovery basis. 相似文献
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Simple sequence repeat (SSR) markers were developed from expressed sequence tags (ESTs) in the eastern oyster (Crassostrea virginica). ESTs of the eastern oyster were downloaded from GenBank and screened for SSRs with at least eight units of dinucleotide
or five units of tri-, tetra-, penta-, and hexa-nucleotide repeats. The screening of 9101 ESTs identified 127 (1.4%) SSR-containing
sequences. Primers were designed for 88 SSR-containing ESTs with good and sufficient flanking sequences. Polymerase chain
reaction (PCR) amplification was successful for 71 primer pairs, including 19 (27%) pairs that amplified fragments longer
than expected sizes, probably due to introns. Sixty-six pairs that produced fragments shorter than 800 bp were screened for
polymorphism in five oysters from three populations via polyacrylamide gels, and 53 of them (80%) were polymorphic. Fifty-three
polymorphic SSRs were labeled and genotyped in 30 oysters from three populations via an automated sequencer. Five of the SSRs
amplified more than two fragments per oyster, suggesting locus duplication. The remaining 48 SSRs had 2 alleles per individual,
including 11 with null alleles. In the 30 oysters analyzed, the SSRs had an average of 9.3 alleles per locus, ranging from
2 to 24. Forty-three loci segregated in a family with 100 progeny, with nine showing significant deviation from Mendelian
ratios (three after Bonferroni correction). Seventy percent of the loci were successfully amplified in C. rhizophorae and 34% in C. gigas. This study demonstrates that ESTs are valuable resources for the development of SSR markers in the eastern oyster, and EST-derived
SSRs are more transferable across species than genomic SSRs. 相似文献
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The ridgetail white prawn Exopalaemon carinicauda is one of the most important commercial species in eastern China. However, little information of immune genes in E. carinicauda has been reported. To identify distinctive genes associated with immunity, an expressed sequence tag (EST) library was constructed from hemocytes of E. carinicauda. A total of 3411 clones were sequenced, yielding 2853 ESTs and the average sequence length is 436 bp. The cluster and assembly analysis yielded 1053 unique sequences including 329 contigs and 724 singletons. Blast analysis identified 593 (56.3%) of the unique sequences as orthologs of genes from other organisms (E-value < 1e-5). Based on the COG and Gene Ontology (GO), 593 unique sequences were classified. Through comparison with previous studies, 153 genes assembled from 367 ESTs have been identified as possibly involved in defense or immune functions. These genes are categorized into seven categories according to their putative functions in shrimp immune system: antimicrobial peptides, prophenoloxidase activating system, antioxidant defense systems, chaperone proteins, clottable proteins, pattern recognition receptors and other immune-related genes. According to EST abundance, the major immune-related genes were thioredoxin (141, 4.94% of all ESTs) and calmodulin (14, 0.49% of all ESTs). The EST sequences of E. carinicauda hemocytes provide important information of the immune system and lay the groundwork for development of molecular markers related to disease resistance in prawn species. 相似文献
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William F. Font 《Journal of invertebrate pathology》1980,36(1):41-47
The interactions of cellular and humoral factors of hemolymph of the American oyster, Crassostrea virginica, and several species of marine cercariae were studied. Attraction of hemocytes to dead but not to living cercariae was observed. Dead cercariae were encapsulated in vitro by oyster hemocytes. The plasma of C. virginica was apparently not toxic to the species of cercariae tested. 相似文献
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该研究以泸定百合(Lilium sargentiae Wilson)为材料,构建其组培苗经百合尖孢镰刀菌侵染后的叶片SSH文库,从中筛选镰刀菌枯萎病抗病相关基因。从正向SSH文库中随机挑取300个单克隆测序后得到280条ESTs,进行功能比对分析后,除去未知功能、沉冗蛋白以及无同源序列,得到有功能的ESTs共168条,其功能涉及信号传导、蛋白质合成与代谢、抗病与防御、物质与能量代谢、转录相关等多种途径,其中有31条ESTs与抗病防御相关。从抗病防御相关基因中选取8条ESTs:过氧化氢酶、ATP结合盒转运蛋白(ABC transporter)、Kunitz型胰蛋白酶抑制剂4(Kunitz trypsin inhibitor 4)、丝氨酸乙醛酸氨基转移酶、多聚泛素、脂氧合酶I(Lipoxygenase I)、丝氨酸/苏安酸蛋白激酶(Serine/Threonine-protein kinase)、抗坏血酸过氧化物酶(Arabidopsis thaliana),通过RTPCR对其表达情况进行分析,发现经镰刀菌诱导后均为上调表达,推测它们可能参与了泸定百合镰刀菌枯萎病的抗病反应途径。 相似文献
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Perkinsus marinus 《Fish & shellfish immunology》1996,6(8):581-597
The effects of extracellular products (ECP) and purified proteases from the protozoan parasitePerkinsus marinuson three host defence parameters (haemocyte motility, lysozyme and haemagglutinin) of the eastern oyster,Crassostrea virginica, were investigated. ECP with high proteolytic activities, as well as purified proteases, significantly decreased the random migration of haemocytes through micro-porous filters in Boyden chambers. Stimulation of haemocyte migration byP. marinuscells orP. marinuscell lysate was also dramatically reduced by ECP and purified proteases. Incubation of oyster plasma with ECP and purified proteases caused a significant decrease in lysozyme activity and also appeared to reduce haemagglutinin titres. These data suggest thatP. marinusECP, as well as the proteolytic fraction of the ECP, can modulate some defence parameters of oystersin vitro. 相似文献
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Geetha Govind Harshavardhan Vokkaliga ThammeGowda Patricia Jayaker Kalaiarasi Dhanalakshmi Ramchandra Iyer Senthil Kumar Muthappa Sreenivasulu Nese Udaya Kumar Makarla 《Molecular genetics and genomics : MGG》2009,281(6):607-605
Peanut, found to be relatively drought tolerant crop, has been the choice of study to characterize the genes expressed under
gradual water deficit stress. Nearly 700 genes were identified to be enriched in subtractive cDNA library from gradual process
of drought stress adaptation. Further, expression of the drought inducible genes related to various signaling components and
gene sets involved in protecting cellular function has been described based on dot blot experiments. Fifty genes (25 regulators
and 25 functional related genes) selected based on dot blot experiments were tested for their stress responsiveness using
northern blot analysis and confirmed their nature of differential regulation under different field capacity of drought stress
treatments. ESTs generated from this subtracted cDNA library offered a rich source of stress-related genes including signaling
components. Additional 50% uncharacterized sequences are noteworthy. Insights gained from this study would provide the foundation
for further studies to understand the question of how peanut plants are able to adapt to naturally occurring harsh drought
conditions. At present functional validation cannot be deemed in peanut, hence as a proof of concept seven orthologues of
drought induced genes of peanut have been silenced in heterologous N. benthamiana system, using virus induced gene silencing method. These results point out the functional importance for HSP70 gene and key
regulators such as Jumonji in drought stress response.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
The nucleotide sequence reported in this paper has been submitted to (database) under accession numbers: Acc. No. EC268400–EC268685;
EC365167–EC365455.
An erratum to this article can be found at 相似文献
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Oyster (Crassostrea gigas) is widely distributed in coastal areas of world. We developed and evaluated simple sequence repeat (SSR) markers from expressed
sequence tags (ESTs) of C. gigas and to amplify EST-SSR in C. gigas. Characteristics of 11 EST-SSR loci were investigated using 45 C. gigas individuals. The number of alleles per locus ranged from two to thirteen. The observed heterozygosity (H
o) ranged from 0.0889 to 0.7333 and the expected heterozygosity (H
e) ranged from 0.0859 to 0.8981. Because of their high level of polymorphism, our 11 single-locus EST-SSR markers will be valuable
tools for research on mating system, population genetics and systemic evolution of oyster in the future. 相似文献
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Jenny MJ Ringwood AH Lacy ER Lewitus AJ Kempton JW Gross PS Warr GW Chapman RW 《Marine biotechnology (New York, N.Y.)》2002,4(1):81-93
A pilot program was initiated to identify genes from the American oyster, Crassostrea virginica, that are potentially involved in the stress response for use as bioindicators of exposure to environmental pollutants and
to toxic and infectious agents. A PCR-based method was used to construct cDNA libraries from pooled embryos and the hemocytes
of a single individual. A total of 998 randomly selected clones (expressed sequence tags, ESTs) were sequenced. Approximately
40% of the ESTs are novel sequences. Several potential biomarkers identified include an antimicrobial peptide, recognition
molecules (lectin receptors), proteinases and proteinase inhibitors, and a novel metallothionein. Diversity analysis shows
that 363 and 286 unique genes were identified from the hemocyte and embryo libraries, respectively, indicating that full-scale
EST collection is a valuable approach for the discovery of new genes of potential significance in the molluscan stress response.
Received May 11, 2001; accepted July 16, 2001 相似文献