中国、日本和澳大利亚珍珠贝的ITS 2序列特征分析

对中国、日本和澳大利亚的珍珠贝核糖体DNA第二内部转录间隔子(ITS2)的序列特征进行了分析。PCR扩增产物包括5.8S基因部分序列、ITS2基因和28S基因部分序列。去除引物序列后5.8S基因片段长64bp,ITS2长230～237bp,28S基因片段长249bp。共分析了16个基因型的序列特征,结果表明,5.8S和28S基因片段高度保守,仅28S有1个碱基位点突变;而ITS2变异大,237个比对位点中有20个位点发生突变,其中12个位点为缺失/插入突变,4个简约信息位点。在碱基组成中,5.8S和28S的GC含量(58.1%～59.4%)高于AT含量,也高于ITS2的GC含量(51.3%～52.0%),ITS2的GC含量与AT含量相差不大。碱基组成中5.8S的A碱基含量较低,28S的T碱基含量较低,存在较大的碱基偏倚性。3个地理群体内和群体间的遗传距离都很小(0.010～0.013),且相互重叠。从基因型数据看,3个群体既有各自独立的基因型,也有共享基因型。但从序列的碱基变异数据看,3个群体没有各自独有的突变位点。上述结果表明,3个地理群体既具有丰富的遗传多样性,又具有高度的遗传一致性,即亲缘关系近,可能存在基因交流,或者分化时间不长。丰富的遗传多样性有利于合浦珠母贝的遗传选育。     

Genetic structure of yellowback sea bream Dentex tumifrons in China inferred from AFLP data

ABSTRACT:   The resource of yellowback sea bream Dentex tumifrons has declined very quickly in China due to overfishing since the 1970s. In this study, a total of 122 wild samples of the yellowback sea bream from marine waters of Qingdao (QD), Zhoushan (ZS), Shenzhen (SZ), and Beihai (BH) were analyzed using amplified fragment length polymorphism (AFLP). A total of 265 putative loci were detected by five AFLP primer sets, 116 of which were polymorphic (43.8%). The locality with the highest proportion of polymorphic loci (PPL, 29.4%) and number of polymorphic loci (PL, 78) was ZS, whereas that with the lowest was BH, in which a PL of 64 and a PPL of 24.2% were detected. The locality with the highest Nei's gene diversity was also ZS with a value of 0.2237, whereas the locality with the lowest was BH with a value of 0.1905. Analysis of Wright's F _st indicated that there existed distinct genetic differentiation among four localities ( P  ≤ 0.001). It is speculated that there exist at least four distinct geographic subpopulations of the sea bream in Chinese waters. This research provides some of the first published AFLP data in the species.     

用AFLP方法分析中国对虾抗病选育群体的遗传变异

利用AFLP技术对连续4年选育的中国对虾抗白斑病毒群体进行了遗传分析,并比较了不同的数据处理方法对遗传学参数的影响。7个EcoRⅠ／MseⅠ引物组合共产生350个位点,其中202个为多态位点。4代群体的多态位点比例分别为：39．4286％,41．4286％,33．4286％,39．1429％,Nei基因多样性指数分别为：0．1197,0．1259,0．1133,0．1249;4代群体的Shannon多样性指数分别为0．1831,0．1917,0．1702,0．1896。遗传多样性水平除了第3代群体标本明显较低外,其它3代甚为接近,维持在一个恒定的水平。比较了Nei分析、Shannon信息指数分析、AMOVA分析得出的遗传学参数,建议AMOVA分析作为应用AFLP进行群体遗传学分析时首选的统计方法。在AFLP指纹图谱中发现共显性基因座,对其中1个基因座的两个AFLP片段进行了回收、克隆及测序。序列分析表明,多态性是由引物扩增区域内4个核苷酸的插入／缺失导致的,证明了AFLP标记并不完全是显性标记。实验表明AFLP技术灵敏度高,信息量大,适用于分析亲缘关系较近的个体或品系,在中国对虾分子标记辅助育种方面有应用潜力。     

罗非鱼3个养殖群体的遗传多样性及特异性AFLP标记研究

对不同来源的养殖群体进行种质鉴定,探索在种苗阶段即区分新吉富罗非鱼（New GIFT strain Oreochromis niloticus）、吉诺玛罗非鱼（GenoMar strain O．niloticus）和奥杂罗非鱼（0．niloticus♀×O．aureus♂）3个养殖群体具有重要的意义。笔者选取了5对AFLP（amplified fragment length polymorphism）引物组合对3个罗非鱼养殖群体共60尾个体进行比较分析,引物组合E—ACA／M—CAT表现出较好的区分能力,有7条标记的分布在群体间表现出“有和无”的差别,引物组合E—ACA／M—CAG的扩增图谱中有2条带表现出“有和无”的差别。遗传多样性方面,平均基因多样性在新吉富罗非鱼和吉诺玛罗非鱼分别为0．1605和0．1595,而在奥尼罗非鱼为0．2214,多态位点百分数和Shannnon多样性指数也表现出相近的变化趋势。分析表明新吉富罗非鱼群体在遗传上已较为稳定,吉诺玛罗非鱼遗传多样性偏低。     

基于线粒体 Cyt b 和 ITS1 部分序列分析鲭科鱼类分子系统进化关系

鲭科(Scombridae)由15属51种表层洄游性海洋鱼类组成,广泛分布于热带和亚热带海域,是重要的经济鱼类。目前关于鲭科鱼类系统发生学的研究主要基于形态学特征。为了从分子水平上阐明鲭科鱼类的分类与系统进化关系,本研究扩增了鲭科7种鱼类的线粒体细胞色素b(Cyt b)基因1个含311个碱基的序列区和转录间隔区1(ITS1)的1个含644～692个碱基的序列区。采用多个生物软件对序列碱基组成进行分析,计算了Kimura-2parameter遗传距离、转换/颠换比等遗传信息指数。Cyt b和ITS1序列4种碱基平均含量分别是:A为22.8%、G为16.4%、C为31.2%、T为29.5%和A为13.5%、G为31.3%、C为38.7%、T为16.5%。基于Cyt b计算的鲭科鱼类种间遗传距离为0.0065～0.3335,平均遗传距离为0.1689;基于ITS1计算的金枪鱼族鱼类种间遗传距离为0.0032～0.2668,平均遗传距离为0.2025。Cyt b和ITS1序列的转换/颠换比分别为1.8和0.9。以竹荚鱼(Trachurus trachurus)和花鲈(Lateolabrax japonicus)为外群,并结合GenBank上鲭科24种鱼类的同源序列,构建NJ、ML和ME系统树。研究结果确认了金枪鱼属处于系统进化树的顶端,代表着最新演化的种类,是鲭科中最繁盛的一属,也是目前系统发育的高峰。所有分子系统树都表明鲣属、鲔属和舵鲣属显示与金枪鱼属很近的亲缘关系,它们均归入金枪鱼族。然而,研究结果与形态学上将金枪鱼属分为2个亚属的分类结果存在分歧。同时,本研究关于狐鲣属、平鲣属、刺鲅属和双线鲅属进化地位上的结果也不同于形态学的结果。故鲭科鱼类客观、科学的分类地位还需通过形态学、生态学和分子生物学的深入研究加以确认。     

Identification of razor clams <Emphasis Type="Italic">Ensis arcuatus</Emphasis> and <Emphasis Type="Italic">Ensis siliqua</Emphasis> by PCR-RFLP analysis of ITS1 region

ABSTRACT:   Ensis arcuatus and Ensis siliqua are the most economically important species of razor clams in the European Union. Due to similarities between their shell morphology, and the differing retail value, these species are often misidentified. Therefore, it is necessary to develop an appropriate protocol to allow accurate differentiation between these species of razor clam in order to protect consumer rights, avoid commercial fraud (whether intentional or unintentional), and to enforce labeling and safety regulations. With the aim of developing a rapid and reliable method of differentiation, individuals of E. arcuatus and of E. siliqua were examined by polymerase chain reaction restriction fragment polymorphism (PCR–RFLP) using the internal transcribed spacer region 1 (ITS1). A species-specific restriction endonuclease pattern was found with the enzyme Ksp I for both species, allowing their exact identification. Thus, this work provides a simple, reliable and rapid protocol for accurate discrimination between E. arcuatus and E. siliqua , which proves useful for traceability and enabling the enforcement of labeling regulations.