猪差异表达EST的组织表达谱分析

表达序列标签是一种快捷、高效的揭示基因组信息的方法。本研究以蓝塘猪与大白猪差异表达的5条EsT在各组织中的表达情况为目的．采用大白猪、蓝塘猪为实验材料，从成年种猪的10个组织中提取总RNA；运用RT—PCR方法分析，结果显示5条EST在猪的多数组织中均有表达；同源性比对后发现，在5条差异显示cDNA中，EST1、EST2与已知序列无同源性；电子表达谱分析表明EST1、EST2、EST4及ESt5在骨骼肌、肝脏组织中有表达。这为进一步研究该EST的功能奠定基础。     

泥蚶Smad1/5基因cDNA全全长克隆及时空表达特征分析

为了研究Smad1/5基因在泥蚶生长、发育过程中的调控作用,本文利用SMART RACE方法克隆得到泥蚶Smad1/5基因（Tg-Smad1/5）的cDNA全长序列,该序列全长2 424 bp,开放阅读框有1 386 bp,编码462个氨基酸。Tg-Smad1/5蛋白与合浦珠母贝Smad5、太平洋牡蛎Smad5和大西洋舟螺Smad1的同源性分别达到了92.3%,91.2%和80.4%,与脊椎动物的同源性都在70%以上;该蛋白包含MH1和MH2区两个较为保守的结构域,此结构与高等动物Smad1和Smad5蛋白极为相似,表明该基因在物种进化过程中比较保守。利用qRT-PCR技术,研究了Smad1/5基因在泥蚶6个组织和9个发育时期中的表达情况,结果显示,Tg-Smad1/5基因在泥蚶成贝6个组织中均有表达,而在斧足中的表达量最高,极显著地高于其他组织;在各发育时期中,Tg-Smad1/5表达量随发育进程呈逐渐升高的趋势,在眼点幼虫期达到最高,极显著高于其他时期,而在变态至稚贝时,表达量又极显著地下降。研究结果表明,Tg-Smad1/5具有类似于高等动物的分子结构,并在泥蚶不同组织、不同发育时期表达有所差异,这为进一步研究该基因在贝类中的功能和作用机制奠定了重要基础。     

草鱼NADPH氧化酶2个调节亚基cDNA的克隆及表达特征

为了解草鱼(Ctenopharyngodon idellus)NADPH多酶复合体的基因结构及其在机体的防御体系中的功能,利用RT-PCR结合RACE-PCR的方法,克隆草鱼NADPH氧化酶的2个调节亚基p40phox和p47phox的cDNA,对其编码的氨基酸序列进行了同源性比较和功能域分析,同时对这两个亚基在草鱼不同组织中的差异性表达进行分析。结果显示:p47phox亚基cDNA序列全长为1 589 bp,开放阅读框长度为1 233 bp,编码410个氨基酸;p40phox亚基cDNA序列全长为2 103 bp,开放阅读框为1 068 bp,编码355个氨基酸。这两个亚基编码的氨基酸序列与其他鱼类的同源性在68%~96%,具有其它鱼类类似的PX,SH3,PB1和PC功能域。组织差异性表达分析结果表明:2个调节亚基在草鱼胸腺、心脏、头肾、鳃、肠、肝、肾、脾和皮肤组织中均有表达,在不同组织中的表达强度略有差异,在心脏、胸腺中表达水平最高,在肝脏中表达水平较低,但是不同组织之间的表达水平差异不显著(P>0.05)。     

缢蛏β-ACTIN-1基因的分子特性及其表达分析

为研究缢蛏功能基因的表达调控,利用SMART cDNA文库构建试剂盒成功构建了缢蛏肝脏组织的标准化cDNA文库。对随机选取的5 679个克隆进行随机测序,比对、筛选出2条β-actin同源序列,对其中一条EST序列两端进行扩增、测序,然后进行5′RACE(rapid amplification of cDNA ends,RACE)扩增、测序,拼接得到全长cDNA序列,命名为β-ACTIN 1。该序列全长为1 552 bp,包括73 bp的5′非翻译区和348 bp的3′非翻译区,以及1 131 bp的开放阅读框。阅读框共编码376个氨基酸,推算分子量约为41.95 ku,理论等电点为5.23。与其他7种软体动物的氨基酸序列进行比对发现,β-ACTIN 1基因的氨基酸序列中Ile179、Glu229、Ser232、Pro236、Ile248、Asn272、Cys273、Val283、Ser320、Ser325、Val330、Pro339等12个氨基酸残基具有特异性;同时发现缢蛏β-ACTIN 1氨基酸序列与其他软体动物的相似性高达97%以上。系统进化分析显示,缢蛏首先与软体动物聚在一起,然后与节肢动物聚在一起,再依次与鱼类、两栖类、哺乳类聚在一起。荧光定量PCR检测结果显示,β-ACTIN 1基因在缢蛏各组织中的表达及鳗弧菌诱导后的表达均不稳定,不适合作为内参基因。     

半滑舌鳎HIRA基因部分cDNA序列克隆及表达分析

为研究HIRA基因在半滑舌鳎胚胎发育中的作用及其组织差异表达,以半滑舌鳎为研究对象,采用同源克隆策略从其精巢中分离了长度为764bp的HIRA部分cDNA序列,该片段编码254个氨基酸,具有5个wD结构域。对氨基酸进行比较发现,半滑舌鳎HIRA与比较物种的氨基酸序列具有很高的同源性,与红鳍东方纯亲缘关系最近。实时定量PCR分析发现,HIRA mRNA在多细胞期到原肠胚期的表达量较高,表明HIRA对胚胎发育起重要作用;HIRA在不同组织中表达差异显著,其中在性腺中表达最高,推测HIRA在维持性腺的功能方面有一定作用。     

合浦珠母贝C-型凝集素基因的序列特征和功能分析

通过EST筛选结合重测序法获得合浦珠母贝一种C-型凝集素cDNA的全长序列(命名为PoLEC1)。PoLEC1全长988 bp,5′-UTR为33 bp,3′-UTR为101 bp,开放阅读框为864 bp,编码287个氨基酸,分子量为31.68 ku,理论等电点约5.83。预测的氨基酸序列中含有信号肽(Met¹-Ser¹⁹)和糖结合位点。同源性分析结果表明,PoLEC1与其它物种C-型凝集素的的糖识别结构域序列的同源性在18.8%~28.6%,相似性在28.9%~50.0%之间。进化树分析结果表明,PoLEC1与栉孔扇贝聚为一支。组织表达分析表明,PoLEC1 mRNA在消化腺、外套膜、性腺、闭壳肌、肠、鳃和血淋巴组织均有表达,在消化腺中的表达分析表明,经溶藻弧菌刺激后2 h表达显著下调,而在4和24 h后表达显著上调。利用PoLEC1成熟肽构建原核表达载体,在大肠杆菌中进行重组表达。制备包涵体后,用IDA HisBind 树脂纯化得到单一的重组蛋白,凝菌试验表明该蛋白对大肠杆菌有明显的凝集作用。     

团头鲂促肾上腺皮质激素释放激素受体基因序列特征及表达分析

促肾上腺皮质激素释放激素受体(corticotropin-releasing hormone receptor,CRHR)是鱼类下丘脑–垂体–头肾调控轴上的重要应激调节因子。本研究通过c DNA末端快速扩增(RACE)技术成功克隆出团头鲂(Megalobrama amblycephala)CRHR1 m RNA全长序列,应用生物信息学方法对其序列特征进行解析;同时采用荧光定量PCR技术分析了团头鲂CRHR1的组织分布图谱及外源性皮质醇注射模拟应激处理下团头鲂CRHR1 m RNA的表达变化。研究结果表明,CRHR1 m RNA序列开放阅读框(open reading frame,ORF)为1290 bp,编码429个氨基酸。团头鲂CRHR1氨基酸序列与鲤科鱼类的CRHR1氨基酸序列同源性最高;该受体具有7次横跨膜结构和氨基端激素受体结构域。CRHR1在垂体中表达量最高,其次为下丘脑,在心脏、肝、脾等组织中表达丰度较低。经外源性皮质醇注射后,实验组血糖和血清皮质醇显著高于对照组,在处理2 h后达到峰值;实验组血清ACTH水平与对照组差异总体不显著,但呈现先升高后下降。应激处理后,CRHR1转录水平在4种组织中的表达变化存在差异;垂体中CRHR1在早期出现明显的表达抑制,在下丘脑中则呈现先缓慢升高后缓慢下降的趋势,而心脏和头肾中CRHR1在早期则表现出表达迅速上调而后缓慢下降的趋势。本研究进一步丰富了CRHR在鱼类研究方面的基础资料,为鱼类应激调控提供了理论基础。     

栉孔扇贝wnt4基因cDNA克隆及表达分析

由栉孔扇贝(Chlamys farreri)转录组数据库获得wnt4基因的一段表达序列标签(EST)序列,利用SMART-RACE技术克隆了wnt4基因cDNA全长序列,该序列长1 239 bp,其中开放阅读框为1 068 bp,可以编码355个氨基酸,推导的氨基酸序列含有WNT家族特有序列,且与沙蚕(Platynereis dumerilii)、海胆(Heliocidariserythrogramma)、人(Homo sapiens)等物种WNT4同源性都在60%以上。半定量RT-PCR结果显示,除肾脏外,wnt4基因在栉孔扇贝的精巢、卵巢、闭壳肌、肝胰腺、鳃、外套膜组织中均有表达,但表达量较低。定量RT-PCR结果表明:wnt4基因在成熟期的精卵巢中表达量最高,增殖期和休止期表达量次之,生长期表达量最低;整个生殖周期中精巢表达量高于卵巢。该基因在栉孔扇贝多个组织中的表达特性,暗示其参与了多样的生物学过程;在性腺中的表达特征表明其可能参与两性性腺的发育并在生殖细胞成熟过程中发挥作用。     

草鱼APN基因的克隆及表达特征

氨肽酶N(APN)是肽酶M1家族的成员之一,在蛋白质的消化中发挥重要作用。采用同源克隆和RACE技术首次克隆草鱼APN基因的全长cDNA序列。该cDNA全长为3258bp,包含27bp的5UTR序列,552bp的3UTR序列,2679bp开放阅读框,编码892个氨基酸;草鱼与斑马鱼基因同源性和编码氨基酸同源性分别为81.5%和75.4%,与其他动物同源性分别为58.8%～61.2%和54.3%～60.2%。经预测,其编码蛋白的分子量为100.61ku,等电点为5.14,该蛋白具有与哺乳动物十分相似的1个螺旋跨膜结构,但跨膜区氨基酸同源性较低;系统进化分析表明,草鱼APN基因与斑马鱼的亲缘关系最近;利用Real-timePCR技术检测了该基因的发育表达,结果显示草鱼出膜4d后APNmRNA表达量相对稳定;APN在草鱼前肠、中肠和后肠均有较高的表达量,以前肠组织表达量最高;昼夜节律研究发现,肠道APN基因06:00-18:00的表达量较18:00-06:00高。     

草鱼PGC-1α基因的表达及饲喂n-3 HUFAs对其影响

获得了草鱼过氧化物酶体增殖物激活受体γ辅助活化因子1α(PGC-1α)部分cDNA序列(GenBank注册号为HM015283),并进行了序列同源性分析;采用实时定量反转录聚合酶链式反应(qRT-PCR)方法,检测了PGC-1α基因在草鱼不同组织的表达状况;研究了投喂高不饱和脂肪酸(HUFAs)对草鱼肝胰脏PGC-1α基因时序表达的影响。结果显示,所获得的草鱼PGC-1α基因部分cDNA序列长度为612bp,与人、牛、小鼠、斑马鱼和金鱼等动物的同源性为75%～97%;该基因在草鱼肝胰脏、肾脏、肌肉、心脏、鳃等10个组织中均有表达,其中在肾脏和心脏中表达丰度最高,在精巢和脾脏中表达丰度最低;草鱼摄食HUFAs饲料后第7天PGC-1α基因的表达水平极显著升高,随后又迅速下降。研究首次克隆得到草鱼PGC-1α基因部分cDNA序列,并发现该基因在草鱼能量代谢水平高的组织中表达较高,且其表达受到HUFAs的调控,其时序表达模式为先升高,然后恢复到正常水平。     

Genes expressed in Japanese flounder <Emphasis Type="Italic">Paralichthys olivaceus</Emphasis> spleen: analysis of genes involved in immune function

ABSTRACT:   Expressed sequence tag (EST) analysis is an efficient tool for gene discovery and for profiling gene expression. A cDNA library developed from messenger RNA of the Japanese flounder, Paralichthys olivaceus spleen was constructed by directional cloning, in order to isolate functional genes involved in immunity in fish. A total of 1010 ESTs from the library were sequenced and compared with sequences in the GenBank database. Of the 1010 ESTs, 618 ESTs (61%) were identified as being homologous with known genes from many organisms by BLAST searches, whereas 392 (39%) appeared to be unknown and are likely to represent newly described genes. Of the identified genes, 105 (17%) encoded proteins associated with cell/organism defence and homeostasis. Of these 105 genes, 21 were identified for the first time in Japanese flounder. These included macrophage inflammatory protein (MIP)-3 α, granulin-A, novel immune-type receptor (NITR), interferon regulatory factor (IRF)-10, presenilin-like protein-2, and antizyme inhibitor. A comparison of ESTs derived from spleen, kidney, liver and leukocytes suggested that expression of immune-related genes in different tissues, organs, or cells are different.     

Characterization and genomic annotation of polymorphic EST‐SSR loci in Litopenaeus vannamei shrimp

In the present work, EST‐SSR (expressed sequence tag‐simple sequence repeat) loci were obtained by screening 45 000 ESTs from the Pacific white shrimp Litopenaeus vannamei, which was available in a database of the ShEST (Shrimp EST Genome Project) consortium. Fifty‐two of 600 EST‐SSR loci were selected. From this total, 21 EST‐SSRs were polymorphic among 40 individuals and had their gene products ascribed. Two to 20 alleles per locus were detected and the observed heterozygosity ranged from 0.15 to 0.86. Eight loci presented a significant heterozygote deficit after the Bonferroni correction, which was attributed to null alleles. Seven loci were able to have their protein products, molecular functions and biological processes determined. Our results are promising for future studies that relate the levels of these gene polymorphisms with different biological responses to stress in aquaculture.     

Analysis of immune-relevant genes expressed in red sea bream (Chrysophrys major) spleen

Expressed sequence tag (EST) analysis is an efficient tool for gene discovery and for profiling gene expression. In order to isolate functional genes involved in immunity in fish, a cDNA library was constructed from red sea bream (Chrysophrys major) spleen by unidirectional cloning. A total of 2010 ESTs from the library was sequenced and compared with sequences in the GenBank database. Of the 2010 ESTs, 320 ESTs (15.9%) were identified as orthologs of known gene from other organisms by BLAST searches, whereas 1690 ESTs (84.1%) appeared to be unknown and are likely to represent newly described genes. These identified clones were derived from at least 81 genes, which were categorized into eight categories: 9 in cell structure/motility (11.1%), 14 in metabolism (17.3%), 8 in cell defense/immunity (10%), 5 in cell division (6.2%), 7 in cell signal transduction/communication (8.6%), 30 in gene/protein expression (37%), 5 hemoglobin (6.2%) and 3 genes lacking enough information to be classified (3.7%). Several important cDNAs involved in immune functions, such as immunoglobulin light chain (IgL), MHC class II, MHC class IIβ and RAP2c, were identified in red sea bream and compared for their structure with those from other organisms. Alignment showed that the red sea bream IgL precursor was closer to that of spotted wolfish than to that of yellowtail, Europe sea bass, orange spotted grouper, Atlantic salmon, channel catfish, fugu and sterlet. Phylogenetic analysis indicated that the red sea bream MHC II and MHC IIβ were more related to those from striped sea bass than to those from cichlid, flounder, salmonids, zebrafish and carp. High identity (over 92%) in deduced amino acid sequence of RAP2c between red sea bream and mammals implied that RAP2c gene was highly conserved during evolution.     

脊尾白虾血细胞ESTs的生物信息学与微卫星序列特征分析

对前期测序得到的脊尾白虾血细胞2853条EST序列进行了生物信息学和微卫星序列特征分析。EST序列拼接得到1053条Unigenes,包括329条Contigs和724条Singlets。BLAST分析表明,593(56.3%)条Uingenes与数据库中已知基因具有相似性。KEGG代谢途径分析表明,181条Unigenes映射到120条代谢途径。通过EST-SSR分析,共得到416条微卫星序列,检出率为14.58%。其中,两碱基重复序列374条,占89.90%,AG重复类型最多;三碱基35条,占8.41%,AAT重复类型最多;四碱基7条,占1.68%,AAGT重复类型最多。本研究可为脊尾白虾功能基因资源挖掘及分子标记筛选提供有效数据。     

Identification of enzyme genes in the liver of the Bleeker’s squid Loligo bleekeri by expressed sequence tag analysis

Expressed sequence tag (EST) analyses were performed with the aim of identifying enzyme genes in the liver of the Bleeker’s squid Loligo bleekeri. Of the 768 ESTs identified and sequenced, 669 were grouped into 324 clusters. Of these clusters, 123 comprising 245 ESTs were found to be homologous to genes reported to date. Among these, 43 clusters were annotated as enzymes according to the Enzyme Commission (EC) numbering system. Two EC groups, oxidoreductases and hydrolases, possessed a large number of ESTs. A cluster homologous to the glutathione peroxidase, an enzyme in the oxidoreductase group, contained 16 ESTs, which accounted for 2.4% of the total ESTs sequenced. There are three serine proteases, three cathepsins, two triacylgricerol lipases, and two chitinases among the clusters homologous to the enzymes in the hydrolase group. Since the squid liver functions in the digestive process, these enzymes would be involved in food digestion. Our data provide information on the various types of enzymes expressed in the squid liver and may provide a useful basis for further characterization of these enzymes.     

Characterization of 95 novel microsatellite markers for Zhikong scallop Chlamys farreri using FIASCO-colony hybridization and EST database mining

ABSTRACT:   In order to construct a simple sequence repeat (SSR)-based genetic linkage map and to promote molecular marker-assisted selection (MAS) in scallop breeding, the methods of Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO)-colony hybridization and expressed sequence tag (EST) database mining were modified and used to develop 95 novel microsatellite markers for Zhikong scallop. The SSR-enriched library constructed by the FIASCO method consisted of 830 clones, and 295 (35.5%) positive clones were identified after colony hybridization. One hundred and fifty clones were randomly sequenced and the results showed all clones contained at least one microsatellite. Of 91 primer pairs designed, 72 were amplified scorable polymerase chain reaction (PCR) products and 70 were polymorphic with the allele number range of 3–16 alleles/locus (average 7.0 alleles/locus). When EST database mining was performed, 66 microsatellites containing ESTs were identified from 3467 sequences deposited in GenBank. Based on cluster analysis of length and GC content of the flanking regions, 47 primer pairs were designed and 23 scorable EST SSRs were obtained. Compared with genomic SSRs developed in this study, EST SSRs showed lower genetic variability with an average of 4.2 alleles/locus. The results in the present study demonstrate that modified FIASCO-colony hybridization is an efficient and low-cost method for the isolation of large numbers of microsatellite markers for scallop species.     

Microarray analysis of differential utilization of plant-based diets by rainbow trout

Microarray analysis was conducted using liver samples from two families of rainbow trout that differed in their growth responses when compared between individuals fed a fishmeal or plant protein-based diet. Differential expression relating to dietary utilization between the two families found significant changes in expression of 33 expressed sequence tags (ESTs). Eight of the differentially expressed ESTs had identified mammalian homologs that had been previously researched with identified cellular interactions and functions. Utilizing pathway analysis software to analyze sequences annotated with known mammalian genes, we were able to map gene pathways and process interactions. From this information, we were able to infer that the metabolic changes associated with utilization of plant protein versus fishmeal were associated with differential regulation of genes related to cell oxidative stress, proliferation, growth and survival. Furthermore, we inferred from the changes we observed in immune response gene expression that ingestion of this plant-based diet upregulated the expression of genes involved in immunoregulatory processes.