桃花水母的核糖体RNA基因ITS区序列分析及物种鉴定

利用PCR扩增和DNA测序技术,获得了青岛野外采集到的桃花水母(Craspedacusta)核糖体RNA基因ITS区序列。序列比对以及系统进化分析显示,在青岛采集到的桃花水母与索氏桃花水母(Craspedacusta sowerbyi)的ITS区序列相似度最高,同源性在93%以上;同时,在系统发育树中也与索氏桃花水母聚为一支。研究结果表明,青岛采集到的桃花水母为索氏桃花水母,这也是青岛地区桃花水母的新记录。     

黄渤海带鱼(Trichiurus lepturus)渔业生物学参考点估计研究

It is important to find a reliable method to estimate maximum sustainable yield(MSY) or total allowable catch(TAC) for fishery management, especially when the data availability is limited which is a case in China. A recently developed method(CMSY) is a data-poor method, which requires only catch data, resilience and exploitation history at the first and final years of the catch data. CMSY was used in this study to estimate the biological reference points for Largehead hairtail(Trichiurus lepturus, Temminck and Schlegel) in the Yellow Sea and Bohai Sea, based on the fishery data from China Fishery Statistical Year Books during 1986 to 2012. Additionally,Bayesian state-space Schaefer surplus production model(BSM) and the classical surplus production models(Schaefer and Fox) performed by software CEDA and ASPIC, were also projected in this study to compare with the performance of CMSY. The estimated MSYs from all models are about 19.7×104–27.0×104 t, while CMSY and BSM yielded more reasonable population parameter estimates(the intrinsic population growth rate and the carrying capacity). The biological reference points of B/BMSY smaller than 1.0, while F/FMSY higher than 1.0 revealed an over-exploitation of the fishery, indicating that more conservative management strategies are required for Largehead hairtail fishery.     

南极红藻Iridaea cordata和Curdiea racovitzae转录组分析及其极端光环境适应相关基因的挖掘

南极红藻具有重要的生态学功能和开发利用价值。南极极端环境赋予了其独特的生理耐受机制,也是发现新基因和代谢途径的理想材料。我们测序分析了南极产胶红藻Iridaea cordata (Turner) Bory和Curdiea racovitzae Hariot的转录组序列,并与其常温近缘种进行了比较,同时挖掘了其与光限制和强紫外线辐射等光环境适应相关的基因。I. cordata和C. racovitzae的转录组序列分别拼接成了14055条和12006条非冗余基因,平均长度分别为1473 bp和1448 bp。在I. cordata转录组中发现多条与绿藻基因同源的捕光复合物LHC基因Lhca2、Lhca6和Lhcb,并且在两种南极红藻中都各发现了1条编码结合岩藻黄质和Chl a/c蛋白的Lhcf基因,目前尚未在其他红藻中发现这类基因。光裂解酶修复紫外线诱导DNA损伤,在I. cordata的转录组序列中发现了6?4光裂解酶,光裂解酶CPD I和CPD II基因,而C. racovitzae转录组序列中仅找到了光裂解酶CPD II基因。尽管南极红藻中这些特有基因的功能有待进一步的验证,但是本文为后续研究红藻的南极极端光环境适应机制提供了方向。     

基于线粒体D-loop 基因探讨花鳗鲡的群体遗传多样性及其种群进化历史

通过测定花鳗鲡(Anguillia marmorata)海南群体(HN)和菲律宾群体(PH)共19尾个体的线粒体D-loop基因的核苷酸序列(约1017 bp),分析了花鳗鲡的种群遗传结构。结果表明:A、T、G、C 4种核苷酸的平均含量分别为39.8%、28.3%、12.4%、19.4%,A+T含量(68.1%)明显高于G+C含量(31.8%)。所测序列中存在73个变异位点,共有18个单倍型。其中海南群体的单倍型多样度(Hd)、核苷酸多态性(Pi)、平均核苷酸差异数(k)分别为0.982、0.21577和219.655,而菲律宾群体的单倍型多样度、核苷酸多态性、平均核苷酸差异数分别为1.000、0.26728和271.821,两个群体之间平均遗传距离(P)为0.3203。结果表明2个群体遗传变异较大,菲律宾群体的遗传多样性较海南群体更加丰富。通过构建NJ分子系统树表明2个群体的亲缘关系较近。利用中性检验Tajima’s D(海南群体D=1.35345,P>0.01;菲律宾群体D=0.79220,P>0.01)和Fs(海南群体Fs=3.759;菲律宾群体Fs=2.231)探讨其种群历史,表明花鳗鲡群体进化过程种群数量较为稳定。     

水产养殖环境常见四环素类抗生素抗性基因tet（M）的演化及传播的初步分析

利用分子系统学方法分析了20 条水产养殖环境中常见的四环素抗性tet（M）基因的序列特点、多态性及系统发育, 并对其细菌寄主分类、环境介质来源作相关性分析。结果表明, 20 条基因序列有4种单倍型, 其中tet（M）-b 和d 是两种远缘基因型, 而a 和c 则是二者之间的序列变异。系统发育树分成三大分支, tet（M...     

瘦尾胸刺水蚤适应近岸多变环境的灵活摄食策略

Centropages tenuiremis is a species with a wide distribution range in disturbed coastal waters.However,due to a lack of dietary information,it remains unclear as to how they maintain such dominance in fluctuating conditions.In this study,C.tenuiremis was collected from the Daya Bay Nuclear Power Plant both in inlet and outfall regions at 06:00,12:00 and 18:00 on April 27,2011 and their in situ diet was analyzed using a PCR protocol targeting 18S ribosomal genes.Thirty-four species of prey organisms were identified totally,including Dinophyta,Baciliariophyta,Viridiplantae,Rhizaria,Apicomplexa,Chordata,Mollusca,Arthropoda and Fungi,indicating an obvious omnivorous feeding habit of C.tenuiremis.Centropages tenuiremis obviously exhibited spatial and temporal variations in diet composition.More plant prey(land plants and phytoplankton)were consumed in the morning(~50%),while more animal prey(metazoans and protozoans)were ingested at midday and night(60%–70%).Furthermore,a more diverse diet was detected in the outfall region(10–11 taxa),where the temperatures were relatively higher and more fluctuating,than in the control region(5–10 taxa).This finding indicated that C.tenuiremis could potentially expand its food spectrum under stressful condition.Specifically,C.tenuiremis exhibited phytoplankton preference(58.62%–67.64%)in the outfall region with a lower omnivory index(0.27–0.35)than in the control region(0.51–0.95).However,phytoplankton density was lower than that in the control region,suggesting a possible herbivorous tendency of C.tenuiremis under elevated temperatures to balance the energy acquirement and feeding effort.The flexible food choices of C.tenuiremis observed here could effectively buffer environmental fluctuations and might be an important survival strategy in coastal ecosystems.     

Molecular analysis of complete ssu to lsu rdna sequence in the harmful dinoflagellatealexandrium tamarense (korean isolate, HY970328M)

New PCR primers (N=18) were designed for the isolation of complete SSU to LSU rDNA sequences from the dinoflagellateAlexandrium tamarense. Standard PCR, employing each primer set selected for amplifications of less than 1.5 kb, successfully amplified the expected rDNA regions of A. tamarense (Korean isolate, HY970328M). Complete SSU, LSU rDNAs and ITS sequences, including 5.8S rDNA, were recorded at 1,800 bp, 520 bp and 3,393 bp, respectively. The LSU rDNA sequence was the first report inAlexandrium genus. No intron was found in the LSU rRNA coding region. Twelve D-domains within the LSU rDNA were put together into 1,879 bp (44.4% G+C), and cores into 1514 bp (42.8% G+C). The core sequence was significantly different (0.0867 of genetic distance, 91% sequence similarity) in comparison withProrocentrum micans (GenBank access. no. X16108). The D2 region was the longest in length (300 bp) and highly variable among the 12 D-domains. In a phylogenetic analysis using complete LSU rDNA sequences of a variety of phytoplankton,A tamarense was clearly separated with high resolution against other species. The result suggests that the sequence may resolve the taxonomic ambiguities ofAlexandrium genus, particularly of the tamarensis complex.     

海南万泉河口尖鳍鲤线粒体基因组测序与结构特征分析

为了解海南尖鳍鲤(Cyprinus acutidorsalis)线粒体基因组结构特征及其与鲤科(Cyprinidae)鱼类的进化关系,本文通过二代测序获得海南万泉河口尖鳍鲤线粒体基因组全序列,并对结构特征进行分析,结果显示具有典型的环状闭环双链分子,全长16581bp,碱基组成为A(31.96%)、G(15.69%)、C(27.53%)和T(24.82%),包含13个蛋白质编码基因(protein-codinggenes,PCGs)、2个r RNA基因、22个tRNA基因和1个可变控制区D环。对碱基含量分析发现尖鳍鲤的碱基组成中具有较高AT含量的偏向性,13个PCGs中有不少的偏好性密码子,如CGA(RSCU>3.506)、CCA(RSCU>2.208)等。除tRNA^Gln、tRNA^Ala、tRNA^Asn、tRNA^Cys、tRNA^Leu(CUN)、tRNA^Tyr、tRNA^Ser(UCN)、tRNA^Pro     

糖原含量与糖原磷酸化酶基因(GPH)和己糖激酶基因(HK)的表达在福建牡蛎生殖周期中的相关性分析

Glycogen, a polymer of glucose, is an important means of storing energy. It is degraded by glycogen phosphorylase (GPH) and hexokinase (HK), glycogen phosphorylase, and hexokinase cDNAs (Ca-GPH andCa-H...     

褐藻纲海带目Laminaria属和Saccharina属基于三个分子标记的系统发育分析

In the past two decades, many studies have focused on the classification within genus Laminaria, ultimately trying to divide it into two subgroups or genera: Laminaria and Saccharina. A significant debate still surrounds the question of its division, as the conflicting phylogenetic hypotheses that have resulted from the classification studies are based on different taxon sampling, molecular markers, or analysis methods. It is aimed at elucidate the molecular phylogeny within Laminaria and Saccharina. The nine species of Laminariales are sampled from northern Asia and Europe, and 23 new sequences in the nuclear, plastid, and mitochondrial genomes are determined to identify their taxonomic status. The phylogenetic analyses of 71 species are performed, including representatives from six of the seven families of the order Laminariales, based on three separate data sets. An evidence is provided to strongly support a clear split that maintains the two recognized genera, Laminaria and Saccharina, with Laminaria appearing to be the ancestor group. Further, analyses indicate that all taxa in Saccharina and Laminaria did not form a monophyletic lineage, instead Laminariaceae and Lessoniaceae grouped together interlacedly, and Costariaceae appeared as the sister taxon of the Lessoniaceae–Laminariaceae clade. In the phylogenetic analysis, mitochondrial c oxidase I(COI) sequences appeared to be the most credible molecular marker which was more befitting than nuclear encoded internal transcribed spacer(ITS) and plastid encoded rbcL for establishment of Laminariales systematics. It is the most comprehensive phylogeny of the order Laminariales, and contributes to an enhanced understanding and estimation of the phylogenetic relationships for the economically important seaweeds, Laminaria and Saccharina.     

长江中下游地区湖北钉螺线粒体CO I基因遗传变异研究

从长江中、下游的江苏省丹徒区和邗江区、浙江省平湖市、湖北省武昌区、江西省余干县和彭泽县、安徽省安庆市和贵池区等5个血吸虫病流行省8个点现场采集湖北钉螺样本,提取基因组DNA、PCR特异性扩增线粒体DNA细胞色素c氧化酶亚单位1（COI）基因,用ClustalX 1．81软件进行多序列比对,MEGA4．0软件中的Kimu...     

SsC1qDC基因在毛蚶免疫防御中的作用

含C1q结构域蛋白(C1qDCs)在无脊椎动物免疫应答中发挥重要作用,但目前有关毛蚶(Scapharca subcrenata)C1qDCs免疫功能的研究鲜有报道。本研究从毛蚶中鉴定出一个含有典型C1q结构域的基因(命名为SsC1qDC),并分析了其对主要病原感染的响应特征。SsC1qDC的cDNA全长序列为711bp,编码含有N端信号肽和199个氨基酸的蛋白,系统进化分析显示SsC1qDC与双壳贝类的C1qDCs聚在一起。SsC1qDC在毛蚶卵细胞到眼点幼虫时期的表达量随发育阶段显著增加,且该基因在成体毛蚶各组织中均有表达,其中在肝胰腺和闭壳肌中表达水平较高。副溶血弧菌刺激可显著诱导SsC1qDC基因高表达,敲降SsC1qDC基因表达后毛蚶死亡率和血细胞凋亡水平显著升高,且导致毛蚶血细胞总数和吞噬活力显著下降。同时,敲降SsC1qDC基因的表达可显著抑制母源免疫相关基因Vg、LSZ、Dscam、TEP和SsC1qDC-3的表达,而C3、PAF3、SsC1qDC-1和SsC1qDC-2等基因的表达显著上调。本研究结果表明, SsC1qDC在毛蚶抗弧菌响应中发挥重要作用,对贝类免疫学和抗...     

大菱鲆家系选育二代7种免疫因子的分析

为选育高成活率的大菱鲆(Scophthalmus maximus)抗鳗弧菌(Vibrio anguillarum)群体,对30个大菱鲆选育二代家系(F2)和1个普通养殖群体进行鳗弧菌攻毒实验(周期为14 d),统计分析死亡率。选取死亡率不同的6个选育家系和普通养殖群体构成7个实验组,采用半定量-聚合酶链反应(semi-quantitative polymerase Chain reaction,RT-PCR)技术对它们肝脏、脾脏、头肾的相关免疫因子——溶菌酶(Lysozyme)、抗菌肽(Hepcidin)、热激蛋白70(HSP70)、热激蛋白90(HSP90)、免疫球蛋白(Ig M)、C-型凝集素(C-type lectin)、Lily-型凝集素(Lily-type lectin)的表达量开展研究,并应用SPSS 16.0软件对攻毒前后各免疫因子的表达量与攻毒后存活率之间的相关性进行分析。研究结果表明:攻毒前后选育家系幼鱼肝脏、脾脏、头肾中7个免疫因子的表达量普遍高于普通养殖幼鱼,且在7个实验组中,攻毒后的表达量相较攻毒前均呈现下降趋势;攻毒前,肝脏中lysozyme、Ig M的表达量与存活率为极显著性正相关(P0.01),HSP70、HSP90、C-type lectin、Lily-type lectin的表达量与存活率为显著性正相关(P0.05);脾脏中,Hepcidin、HSP70和HSP90的表达量与存活率为极显著性正相关(P0.01);头肾中,HSP70的表达量与存活率为显著正相关(P0.05)。综上,可以推断选育家系相对于普通养殖群体大菱鲆抗鳗弧菌性能更强,且7种免疫因子在鳗弧菌感染鱼体的过程中发挥重要的抗感染作用;从F2中获得一个抗鳗弧菌性能较强的家系(23号),可用于今后大菱鲆抗鳗弧菌品系的选育指导工作,为大菱鲆高成活率群体的选育提供参考资料和理论依据。     

厚壳贻贝(Mytilus coruscus)Hox基因家族的鉴定、进化与表达分析

为探究厚壳贻贝Hox基因家族的定位、进化以及在不同成体组织中的表达模式,基于厚壳贻贝全基因组数据,结合生物信息学方法,鉴定分析厚壳贻贝Hox基因家族成员的理化性质、染色体分布、系统进化关系、基因结构以及表达分析。结果显示,从厚壳贻贝全基因组数据中鉴定出11条Hox基因序列,并分别命名为Hox1-5、Antp、Lox2、Lox4、Lox5、Post1、Post2。对11条Hox序列的基本特征分析发现最长的是编码703个氨基酸的Hox2,最短的是编码190个氨基酸Post2,等电点5.11～10.22,且不均等分布于同一条染色体上。亚细胞定位预测结果显示,除Post1基因在细胞质和细胞核中均有发现,其余10个基因亚细胞均定位在细胞核内。系统进化分析发现,使用厚壳贻贝中鉴定出的101条氨基酸序列进行建树,聚类的结果倾向于四类,而从已鉴定的厚壳贻贝11个基因结合软体动物Hox建树结果分析, Post1和Post2聚为一支, Hox4、Antp、Lox5、Lox2和Lox4聚为一个大类,Hox1、Hox2和Hox3各自聚为一类Hox,此外,Hox5单独聚为一类。厚壳贻贝不同组织的qRT-PCR结...     

Phylogeny and phylogeography of the land hermit crab Coenobita purpureus (Decapoda: Anomura: Coenobitidae) in the Northwestern Pacific Region

Hermit crabs of the family Coenobitidae comprise the land hermit crabs, with 16 Coenobita species, and the coconut crab Birgus latro. They are terrestrial but spend their marine life as planktonic larvae. Some coenobitid crabs are widely distributed in the Indo‐West Pacific region, and some species occupy narrower ranges. To improve our knowledge of coenobitid crab speciation and geographical distribution patterns, we examined the phylogenetic relationship between Coenobita purpureus, which has a narrow distribution in the Northwestern Pacific, and its more widely distributed coenobitids including B. latro, Coenobita brevimanus, Coenobita cavipes, Coenobita perlatus, Coenobita rugosus and Coenobita violascens based on the mtDNA cytochrome c oxidase subunit I (COI) and 16S rDNA genes. We also assessed the phylogeography of Co. purpureus populations based on the COI gene. Our phylogenetic and phylogeographical analyses revealed that (i) Co. purpureus clustered with Co. rugosus and (ii) the Co. purpureus population in the Ogasawara Islands was genetically distinct from those in other regions, which showed genetic panmixia. It has been hypothesized that Co. purpureus evolved in the isolated landmasses of the Ryukyu region during the Pliocene, and that its population expanded and colonized the Ogasawara Islands in the late Pleistocene. Further phylogeographical studies on Coenobita species with relatively narrow distributions coupled with characterization of their phylogenetic relationships with widely distributed congeners will advance our knowledge of the speciation and geographical distribution history of coenobitid crabs.     

狄氏斧蛤(Donax dysoni)线粒体全基因组测定及结构特征分析

为解析狄氏斧蛤(Donax dysoni)线粒体全基因组结构特征以及进化地位,采用二代高通量测序技术获得狄氏斧蛤线粒体基因组全序列,对线粒体基因进行注释并对其序列结构进行分析。结果表明,狄氏斧蛤的线粒体全基因组序列全长为16 908 bp,碱基组成为A (26.81%)、T (41.13%)、G(21.21%)和C (10.85%),A+T含量为67.94%,表现出明显的AT偏向。与其他双壳贝类相似,狄氏斧蛤共编码13个蛋白质编码基因,包含22个t RNA和2个r RNA,且所有基因均位于H链;蛋白质编码基因拥有3种起始密码子(ATG、ATT、ATA),而除了ND3、ND4以及ATP6使用TAG作为终止密码子外,其余所有蛋白质编码基因都使用TAA作为终止密码子。除t RNASer不能折叠成典型的三叶草结构,没有明显的DHU茎环,其余t RNA都能折叠成典型的三叶草结构。狄氏斧蛤与斧蛤科(Donacidae)其他物种具有相同的基因排列,未发现基因重排现象。基于线粒体12个蛋白质编码基因构建62种贝类的进化树,结果显示:Donax semiestriatus和Donax vittatus聚...     

Investigating the molecular systematic relationships amongst selected Plesionika (Decapoda: Pandalidae) from the Northeast Atlantic and Mediterranean Sea

Despite the high number of species and ecological diversity of pandalid shrimps, there has been no previous attempt to resolve evolutionary relationships of several genera using molecular tools. Although mitochondrial DNA cytochrome oxidase I (COI) is widely used in barcoding studies to delimit species boundaries, additional insights into phylogenetic affinities can be obtained, especially when used in combination with data from additional genes. The knowledge of molecular diversity is essential to understand phylogenetic relationships and will help systematic clarifications. Based on partial fragments of the 16S and COI genes, we have focused specifically on addressing the systematic relationships of the economically and ecologically important shrimp genus Plesionika within a framework of five genera from within the Pandalidae. Our results showed that species within Plesionika are substantially divergent when compared with other genera, exhibiting the highest average nucleotide divergence, with 0.1123 and 0.0846 in COI and 16S genes, respectively. In addition, sequence divergence was found to vary greatly within the genus Plesionika (COI/16S): 0.0247/0.0016 between Plesionika antigai and Plesionika heterocarpus and 0.1616/0.098 between Plesionika heterocarpus and Plesionika edwardsii. We did not find amino acid sequence divergence between P. heterocarpus and P. antigai compared with P. heterocarpus and P. edwardsii (8.10%, K2P distance). Three species of Plesionika (P. antigai, P. heterocarpus and Plesionika scopifera) appear well separated from other Plesionika species in both maximum likelihood and Bayesian analyses. The present study confirms the utility of COI over 16S as a genetic marker to resolve relationships between different species of Plesionika from the Northeast Atlantic and Mediterranean Sea, in addition to species delimitation. The findings highlight the need to further review paraphyly within Plesionika in an attempt to recognize a concordance in the evolutionary history of Plesionika with major ecological and geological events.     

基于脂肪酸生物标记法探讨中国沿海六群体绒螯蟹(Eriocheir sensu stricto)的种群遗传

水产动物肌肉中的脂肪酸组成可用于评价其种群遗传。本研究通过测定和比较辽河(LH)、黄河(HH)、长江(YZ)、瓯江(OJ)、闽江(MJ)和南流江(NLJ)水系野生绒螯蟹(Eriocheir sensu stricto)肌肉中的脂肪酸组成,进一步分析了6群体间的遗传多样性和亲缘关系。结果显示:(1)在6水系群体中检测出26种脂肪酸,其中C20:5n3、C18:1n9、C22:6n3、C16:0、C20:4n6、C18:2n6和C18:0为主要种类,其总和占总脂肪酸的74%以上;(2)逐步判别分析法筛选出8种判别贡献较大的脂肪酸,分别是C17:0、C18:0、C20:0、C22:1n9、C18:3n3、C18:3n6、C20:2n6和C22:5n3,据此分别建立判别方程,综合判别准确率为98.33%;(3)聚类分析显示:OJ与MJ群体的欧氏距离最小, HH与YZ群体的欧氏距离比OJ与MJ群体的要大,NLJ群体与其他5个群体的欧氏距离相对最大;(4)6群体间脂肪酸含量的变异系数在2.99%—30.00%之间,遗传多样性指数变化幅度在3.2732—3.3204之间。综上,基于脂肪酸生物标记法表明6水系绒螯蟹群体遗传多样性指数均较高,脂肪酸可以有效鉴别6水系野生绒螯蟹种群,整体上南流江群体和其余5群体间相距最远;本研究结果可为绒螯蟹种质资源评价和开发利用等提供基础资料。     

漳州西施舌线粒体基因组全序列:腔蛤蜊属存在新种的证据

利用长PCR扩增漳州西施舌线粒体DNA(ZZ-mtDNA),用引物步移法测序,获得线粒体基因组DNA全序列,研究其基因组特点。结合双壳类49个物种线粒体全基因组,分析基因间核苷酸和蛋白质氨基酸序列的差异,构建系统进化树,探讨漳州西施舌系统演化地位。研究结果表明:漳州西施舌线粒体基因组DNA全长17 199 bp,A+T含量为64.2%,编码36个基因,其中12个蛋白质编码基因,22个转运RNA基因(tRNAs),2个核糖体RNA基因(lrRNA 和srRNA),全部基因均位于重链上,tRNASer为单拷贝,tRNAMet为双拷贝;非编码区占10.9%(1 882 bp/17 199 bp),其中,主非编码区为882 bp,与RZ-mtDNA主非编码区差异明显,另有一个较大(400 bp)的非编码区为漳州西施舌特异性非编码区;以双壳纲帘蛤目文蛤属3种贝类、贻贝目贻贝属4种贝类、珍珠贝目牡蛎科的6种贝类为参照,对编码基因的核苷酸序列和蛋白质氨基酸序列进行差异分析显示,漳州西施舌与日照西施舌达到了种间差异水平。线粒体基因组编码的基因、tRNA组成、非编码区均揭示漳州西施舌是腔蛤蜊属的一个新种。