The complete mitochondrial genome of the hybrid grouper Epinephelus moara (♀)×Epinephelus tukula (♂), and phylogenetic analysis in subfamily Epinephelinae

The mitochondrial genome (mitogenome) of hybrid grouper Epinephelus moara (♀)×Epinephelus tukula (♂), a new hybrid progeny, can provide valuable information for analyzing phylogeny and molecular evolution. In this study, the mitogenome was analyzed using PCR amplification and sequenced, then the phylogenetic relationship of E. moara (♀)×E. tukula (♂) and 35 other species were constructed using Maximum Likelihood and Neighbor-Joining methods with the nucleotide sequences of 13 conserved protein-coding genes (PCGs). The complete mitogenome of E. moara (♀)×E. tukula (♂) was 16 695 bp in length, which contained 13 PCGs, 2 rRNA genes, 22 tRNA genes, a replication origin and a control region. The composition and order of these genes were consistent with most other vertebrates. Of the 13 PCGs, 12 PCGs were encoded on the heavy strand, and ND6 was encoded on the light strand. The mitogenome of the E. moara (♀)×E. tukula (♂) had a higher AT nucleotide content, a positive AT-skew and a negative GC-skew. All protein initiation codons were ATG, except for COX and ND4 (GTG), ATP6 (CTG), and ND3 (ATA). ND2, COXII, ND3, ND4 and Cytb had T as the terminating codon, COXIII’s termination codon was TA, and the remaining PCGs of that were TAA. All tRNA genes, except for the lacking DHU-arm of tRNASer (AGN), were predicted to form a typical cloverleaf secondary structure. In addition, sequence similarity analysis (99% identity) and phylogenetic analysis (100% bootstrap value) indicated that the mitochondrial genome was maternally inherited. This study provides mitogenome data for studying genetic, phylogenetic relationships and breeding of grouper.     

Comparative mitochondrial genome analysis of Varunidae and its phylogenetic implications

Complete mitochondrial genomes(mitogenomes) can indicate phylogenetic relationships, as well as useful information for gene rearrangement mechanisms and molecular evolution. Currently, the phylogenetic location of the genus Varuna(Brachyura: Varunidae) has not been well resolved mainly because of limited representatives(only two extant species). Here, we determined a new mitogenome of this genus(Varuna litterata) and added the published mitogenomes to reconstruct the phylogeny of Varunidae. The ...     

基于线粒体COI和16S rRNA基因的中国沿海相手蟹系统发育研究

相手蟹科的诸多种类因其形态极其相似成为方蟹总科分类中疑问较多的一个类群。通过对中国沿海相手蟹线粒体COI和16S rRNA基因序列进行分子系统发育分析,结果表明14种相手蟹COI和16S rRNA基因序列之间差异分别为5.7%～14.5%和1.5%～12.1%,均达到了种间差异水平。构建的系统发育树显示,14种相手蟹分别为独立有效物种,但分属于拟相手蟹属和近相手蟹属的4种拟相手蟹和3种近相手蟹,没有分别形成2个独立的支系,而是混合聚成一大支系。而属于螳臂相手蟹属的无齿螳臂相手蟹则首先与属于中相手蟹属的中华中相手蟹聚成一支,再与红螯螳臂相手蟹聚为一大支,表现出与形态分类的不一致。错综复杂的分子系统关系预示着相手蟹类为多系起源,也表明它们之间的种间关系乃至于属间关系尚有诸多问题有待进一步厘定。     

新疆一种琥珀螺线粒体基因组测序分析

本研究利用高通量测序技术获得采自新疆昭苏琥珀螺科一未知种的线粒体全基因组序列。该种琥珀螺线粒体基因组全长14219bp,由13个蛋白质编码基因,22个tRNA基因,2个rRNA基因及1个控制区组成。基因组中AT含量为76.43%,GC含量为23.57%,表现出明显的AT偏好性。13个PCGs多使用ATG为起始密码子,TAA为终止密码子。tRNA基因中tRNA-Ser1和tRNA-Ser2缺少DHU臂,其中tRNA-Ser1在缺失的DHU臂处有一个小的茎环结构。非编码区位于COX3与tRNA-Ile之间,长度为58bp。琥珀螺科中现有腐败琥珀螺Succineaputris、五家渠尖缘螺Oxylomawujiaquensis和Omalonyxunguis的线粒体基因组被报道。三者的基因排列顺序和结构基本相似。昭苏琥珀螺未知种的基因排列顺序与它们有所不同。昭苏琥珀螺未知种的tRNA-Tyr和tRNA-Trp基因位于COX2和tRNA-Gly之间,上述三种tRNA-Tyr和tRNA-Trp基因位于tRNA-Ser2和tRNA-Ser1之间。系统发育树结果显示,琥珀螺科的四种聚为一支,为单系群,其中腐败琥珀螺和Omalonyxunguis亲缘关系更近。本研究结果支持昭苏琥珀螺未知种为中国一未报道的属种,但要确定其是否为一新属新种尚需更多的分子和形态数据。     

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...     

白额纵沟纽虫(Lineus alborostratus Takakura)的线粒体基因组

通过PCR扩增、测序获得白额纵沟纽虫线粒体基因组全序列并进行了生物信息学分析.白额纵沟纽虫线粒体基因组全长15 476bp,包含后生动物线粒体基因组典型的13个蛋白质编码基因、22个转运RNA基因、2个核糖体RNA基因和1个747bp的非编码区.除tRNA-Thr和tRNA-Pro基因外,其他基因均编码在重链上.基因组碱基组成具有AT偏向性,蛋白质编码基因偏好使用富含T的密码子.蛋白质编码基因的起始密码子均为ATG,终止密码子多为TAA或TAG,nad1、nad2、cytb基因具有不完全终止密码子T.预测的22个tRNA均具有典型三叶草结构.非编码区未发现在其他纽虫所报道的特殊茎环结构,但在nad4基因上发现有37 bp的发卡结构.白额纵沟纽虫的基因排列、起始密码子、tRNA反密码子与Lineus viridis完全一致,两者rrnL和非编码区长度差别较大,前者具有较少核苷酸插入.     

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     

文昌鱼线粒体基因组特征分析及分子标记探讨

线粒体基因组已被广泛应用于后生动物分子系统发育和群体遗传的研究。文昌鱼（Amphioxus）作为研究脊椎动物起源和进化的模式动物,在脊椎动物起源和进化研究中占据极为重要的位置。作者综合分析文昌鱼2科7个种的51条线粒体基因组全序列,全面揭示了文昌鱼线粒体基因组的基本特征。文昌鱼线粒体基因组均编码后生动物标准的37个基因...     

Complete nuclear ribosomal DNA sequence analyses of the black-footed abalone Haliotis iris

The black-footed abalone Haliotis iris is an economically important shellfish species in New Zealand. We successfully amplified, sequenced and analysed the complete nuclear ribosomal DNA (nrDNA) of H. iris. The length of the nrDNA was determined to be around 9.6?kb and included, in order, small subunit ribosomal RNA (nrSSU, 1858bp), internal transcribed spacer (ITS, 749?bp), large subunit ribosomal RNA (nrLSU, 3412bp) and an intergenic spacer (IGS, 3560–3662?bp). The nrLSU genes were identical in two individuals, whereas the nrSSU and ITS regions existed at three and four base differences, respectively. The IGS was more variable than the other nrDNA regions. A phylogenetic tree was constructed based on the ITS sequence datasets, which revealed that Haliotidae has two major subclades, mainly distributed in the North Pacific, Europe and Australia. The complete nrDNA sequence will be useful for the classification, phylogeny and breeding of this shellfish.     

尾索动物线粒体基因组特征比较及分子系统发育

为全面揭示尾索动物线粒体基因组的基本特征,作者系统分析了12种尾索动物的线粒体基因组全序列,尾索动物线粒体基因组所有的基因均在同一链上编码,这与脊椎动物、头索动物线粒体基因组的基因分布特征显著不同.与后生动物线粒体基因组标准的基因组成相比,尾索动物线粒体基因组存在转运 RNA基因的增加以及部分物种 atp8基因的缺失.在尾索动物线粒体基因组中发生了大规模的基因重排,即使在同属物种的线粒体基因组中,也存在主编码基因的基因重排及基因缺失.尾索动物线粒体基因组蛋白质编码基因的起始密码子、终止密码子及氨基酸长度存在明显差异.2个玻璃海鞘(Ciona intestinalis 和 C. savignyi)线粒体基因组12个蛋白质编码基因的 Ka/Ks 比值都低于1(0.0927~0.6752),显示出一定的负选择.在所有的主编码基因中, nad5基因和nad4基因的变异位点最多,可以作为备选的分子标记,用于分析尾索动物不同物种之间的生物多样性.基于线粒体基因组的系统发育分析,支持尾索动物在科级的亲缘关系为:(((柄海鞘科 Pyuridae+芋海鞘科 Styelidae)+(((三段海鞘科Polyclinidae+星骨海鞘科Didemnidae)+簇海鞘科Clavelinidae)+玻璃海鞘科Cionidae))+长纹海鞘科Ascidiidae)+海樽科Doliolidae.     

日本鼓虾与鲜明鼓虾线粒体基因组全序列的分析比较

首先通过基因组DNA的提取、通用引物PCR扩增和长PCR扩增,从而获得日本鼓虾(Alpheus japonicus)的线粒体DNA;应用鸟枪法和引物步移法测序,获得了日本鼓虾的线粒体基因组全序列。结合GenBank线粒体基因组数据库中鲜明鼓虾(A.distinguendus)的线粒体基因组,比较分析了鼓虾线粒体基因组的基本特征、基因排列、蛋白质编码基因、选择压力和差异位点等。研究结果表明,在日本鼓虾线粒体基因组中共存在9对基因的重叠。日本鼓虾线粒体基因组全长16 487 bp,较鲜明鼓虾线粒体基因组(15 700 bp)长,主要是由于最大非编码区的长度存在差异。日本鼓虾与鲜明鼓虾线粒体基因组均编码37个基因,且37个基因的基因排列完全一致;与泛甲壳动物线粒体基因组的原始排列相比,仅出现1个转运RNA基因(trnE)的易位和倒位。2个鼓虾线粒体基因组蛋白质编码基因的起始密码子和终止密码子存在差异。除了cob基因外,其余12个蛋白质编码基因所编码氨基酸的数目均完全相同。鼓虾线粒体基因组13个线粒体蛋白质编码基因的Ka/Ks比值都远远低于1,显示出较强的负选择。在15个主编码基因中,nad5基因的变异位点数最多,其次是nad4基因和lrRNA基因。因此,nad5,nad4和lrRNA基因可以作为备选的分子标记,用于分析鼓虾不同物种和群体之间的生物多样性。     

花鲈Argonaute基因家族的快速进化与表达分析

RNA干扰(RNA interfering,RNAi)是广泛存在于动植物等生物中的一种高度保守、序列特异的RNA降解机制.Argonaute蛋白是RNAi途径的关键组成部分,其结构、功能和进化模式在无脊椎动物中已得到广泛研究,但在脊椎动物特别是硬骨鱼中的报道还十分有限.本研究从已测序物种的基因组中鉴定了12种哺乳动物和...     

棘皮动物线粒体基因组研究进展

线粒体基因组是存在于真核生物线粒体中的重要遗传物质,可独立进行复制、转录和蛋白质合成.与核基因组相比,线粒体基因组具有长度相对较短、点突变率高等特点,被认为是研究生物系统进化的重要对象之一.近年来,在海洋生物研究中,线粒体基因组已被广泛应用于遗传分析、种质鉴定、分子标记挖掘以及系统进化研究等领域并取得了丰富的成果.棘皮...     

褐斜鲽(Plagiopsetta glossa)线粒体基因组特征及重排机制研究

冠鲽科(Samaridae)隶属于鲽形目(Pleuronectiformes), 包含冠鲽属(Samaris)、沙鲽属(Samariscus)和斜鲽属(Plagiopsetta)。目前研究表明, 冠鲽(Samaris cristatus)和满月沙鲽(Samariscus latus)的线粒体基因组结构都有重排, 并且两者的基因数量也有差别。为检测斜鲽属鱼类中是否也有不同的特征结构, 我们选用褐斜鲽(Plagiopsetta glossa)作为代表种进行斜鲽属鱼类线粒体基因组特征分析, 同时与冠鲽属及沙鲽属鱼类的线粒体基因组特征进行对比。分析显示, 褐斜鲽的线粒体基因组全长为18723bp, 包括39个基因: 13个蛋白基因、24个tRNA基因、2个rRNA基因、2个控制区、1个轻链复制起点和比典型基因组多的13个间隔子。和经典鱼类的线粒体基因组相比, 褐斜鲽和满月沙鲽都多了tRNA-Cys和tRNA-Tyr两个tRNA, 冠鲽只多了tRNA-Cys, 且3个种类都多了一个控制区, 但褐斜鲽与满月沙鲽的基因排列顺序相同。褐斜鲽线粒体基因的重排导致不同位置的6个tRNA形成了六连体基因簇“tRNA-Cys₁-Tyr₁- Ser1-Lys-Arg-Ser2”, “ND5-ND6-Glu-Cytb-Thr”则位于六连体之后, 但这11个基因相对的排序没有发生变化。采用双复制随机丢失模型(double replications and random loss, DRRL)对褐斜鲽基因的重排现象进行分析, 认为该鱼类基因数量、排列顺序以及比典型基因组多13个间隔子等特征为该模型提供了新的依据。     

Phylogenetic analysis of aerobic anoxygenic phototrophic bacteria and their relatives based on farnesyl pyrophosphate synthase gene

The study aims to reveal phylogenetic and evolutionary relationship between aerobic anoxygenic phototrophic bacteria (AAnPB) and their relatives, anaerobic anoxygenic phototrophic bacteria (AnAnPB) and nonphototrophic bacteria (NPB, which had high homology of 16S rDNA gene with AAnPB and fell into the same genus), and validate reliability and usefulness of farnesyl pyrophosphate synthase (FPPS) gene for the phylogenetic determination. FPPS genes with our modified primers and 16S rDNA genes with general primers, were amplified and sequenced or retrieved from GenBank database. In contrast to 16S rDNA gene phylogenetic tree, AAnPB were grouped into two clusters and one branch alone with no intermingling with NPB and AnAnPB in the tree constructed on FPPS. One branch of AAnPB, in both trees, was located closer to outgroup species than AnAnPB, which implicated that some AAnPB would be diverged earlier in FPPS evolutionary history than AnAnPB and NPB. Some AAnPB and NPB were closer located in both trees and this suggested that they were the closer relatives than AnAnPB. Combination codon usage in FPPS with phylogenetic analysis, the results indicates that FPPS gene and 16S rRNA gene have similar evolutionary pattern but the former seems to be more reliable and useful in determining the phylogenic and evolutionary relationship between AAnPB and their relatives. This is the first attempt to use a molecular marker beside 16S rRNA gene for studying the phylogeny of AAnPB, and the study may also be helpful in understanding the evolutionary relationship among phototrophic microbes and the trends of photosynthetic genes transfer.     

高体(鱼狮)(Seriola dumerili)线粒体全基因组测定及结构特征分析

为快速有效鉴别(鱼师)属鱼类物种、加强(鱼师)鱼遗传多样性管理与种质资源保护,通过Illumina测序技术,获得了东海海域养殖高体(鱼师)(Seriola dumerili)线粒体基因组全序列(16 530bp),碱基组成为A (26.83%)、G (17.6%)、C (30.04%)和T (25.53%), A+T含量为52.36%,且非编码控制区(D-loop)A+T富含61.64%,表现明显的AT偏好性。与其他硬骨鱼一样,高体(鱼师)线粒体基因组包含13条蛋白编码基因, 22个tRNA基因, 2个rRNA基因,除ND6、tRNA^Gln、tRNA^Ala、tRNA^Asn、tRNA^Cys、tRNA^Tyr、tRNA^Ser、tRNA^Glu、tRNA^Pro基因外,其余均位于H链编码;蛋白编码基因中,除COⅠ、COⅡ和ND5的起始密码子分别为ATC、ATA和ATA外,其余10个蛋白编码基因的起始密码子均为ATG,以典型的TAA和TAG为终止密码子,在ND4和Cytb中存在不完全密码子T;除tRNA^Ser-GCT外,其余21个tRNA均为典型三叶草二级结构。比较中国和日本海域高体(鱼师)线粒体基因组发现, CO Ⅰ、CO Ⅱ和ND5蛋白编码基因在起止位置、片段长度及起止密码子上存在显著差异。此外,与同属的黄条(Seriola aureovittata)和五条(鱼师)(Seriola quinqueradiata)的线粒体基因组13个蛋白编码基因进行两两对比分析,结果表明3种(鱼师)属鱼类的蛋白编码基因的相似性在85%~100%之间。基于线粒体基因组全序列构建的系统发育树,成功将高体(鱼师)与其他(鱼师)属鱼类有效区分,高体(鱼师)与长鳍(鱼师)同属一支,亲缘关系最近;黄条(鱼师)和五条(鱼师)聚为一支,亲缘关系最近。     

比较基因组学分析弧菌属群体感应通路的分布与进化

群体感应是一种细菌细胞间的通讯过程, 细菌通过测量细胞外自诱导剂浓度从而感知群体细胞密度变化。群体感应使细菌能够在两种基因表达模式下转换: 在低细胞密度时有利于个体发展, 而在高细胞密度时则有利于群体发展。目前主要有7种群体感应通路, 分别以oligopeptides、AHL(Acylated Homoserine Lactones)、AI-2(Autoinducer-2)、CAI-1(Cholera Autoinducer-1)、PQS(Pseudomonas Quinolone Signal)、AI-3(Autoinducer-3)以及DSF(Diffusible Signal Factor)作为各群体感应通路的信号分子; 其中oligopeptides存在于革兰氏阳性细菌中, 其余6种信号分子存在于革兰氏阴性细菌中。弧菌是导致人类感染和水产品污染的主要病原菌, 传统的抗生素治疗弧菌感染具有很强的选择压力, 导致越来越多耐药弧菌出现。面对愈发严峻的弧菌耐药性问题, 目前群体感应淬灭被认为是治疗弧菌感染的重要替代手段之一, 因而有必要调查弧菌属细菌不同群体感应通路的分布情况, 为针对弧菌的群体感应淬灭剂研发提供重要参考信息。通过比较基因组学分析, 发现全基因组测序的46株弧菌存在AHL、AI-2以及CAI-1这3种信号分子通路, 其中5株弧菌均含有上述3种信号分子通路, 共有30株弧菌只含有AI-2和CAI-1两种信号分子通路; 而46株弧菌都不存在PQS、AI-3以及DSF群体感应通路。此外, 弧菌群体感应通路的分布与物种进化有关, 含有同种群体感应信号分子通路的弧菌, 其亲缘关系较近, 说明该通路的基因进化自它们的共同祖先。本研究表明开发针对弧菌的群体感应淬灭剂应以AI-2和CAI-1两种信号分子介导的通路作为靶点。     

耳鲍(Haliotis asinina)核糖体小亚基(18S rRNA)编码基因的克隆与序列分析

采用分子生物学的方法,对南海不同海区的两个地理群体耳鲍(Haliotis asinina)18S rRNA基因全长进行了克隆和序列分析,并将耳鲍18S rRNA基因的序列与NCBI数据库中已收录鲍的18SrRNA基因进行了比较。结果发现,南海耳鲍核糖体18S rRNA基因与耳鲍H.asinina isolate H11核糖体18S rRNA基因序列的相同率高达98%;同一地理群体内耳鲍核糖体18S rRNA基因序列完全一致;不同地理群体间耳鲍核糖体18S rRNA基因在碱基组成上的相似率为99%,仅在某些位点处发生了碱基替换,即腺嘌呤(T)被鸟嘌呤(G)替换;同时,将这两个不同群体中耳鲍的18S rRNA基因与泰国耳鲍18S rRNA基因序列进行比较分析发现,它们之间也只是发生了碱基替换。     

长菱形藻(Nitzschia longissima)和新月细柱藻(Cylindrotheca closterium)分子分类研究

本研究自胶州湾分离了两种底栖硅藻,形态学初步鉴定为长菱形藻和新月细柱藻。对其18S rDNA和rbcL基因进行了测序并用邻接法构建了系统树。结果表明,两藻在18S rD-NA和rbcL基因序列上均存在较大的差异,基于DNA序列的分类结果与形态学分类结果一致。在依据形态指标难以确定藻类分类地位的情况下,18S rDNA和rbcL基因序列是有用的鉴定工具。     

软甲纲(节肢动物门:甲壳动物亚门)系统发育线粒体基因组研究

Along with the sequencing technology development and continual enthusiasm of researchers on the mitochondrial genomes, the number of metazoan mitochondrial genomes reported has a tremendous growth in the past decades. Phylomitogenomics—reconstruction of phylogenetic relationships based on mitochondrial genomic data—is now possible across large animal groups. Crustaceans in the class Malacostraca display a high diversity of body forms and include large number of ecologically and commercially important species. In this study, comprehensive and systematic analyses of the phylogenetic relationships within Malacostraca were conducted based on 86 mitochondrial genomes available from Gen Bank. Among 86 malacostracan mitochondrial genomes, 54 species have identical major gene arrangement(excluding t RNAs) to pancrustacean ground pattern,including six species from Stomatopoda, three species from Amphipoda, two krill, seven species from Dendrobranchiata(Decapoda), and 36 species from Pleocyemata(Decapoda). However, the other 32 mitochondrial genomes reported exhibit major gene rearrangements. Phylogenies based on Bayesian analyses of nucleotide sequences of the protein-coding genes produced a robust tree with 100% posterior probability at almost all nodes. The results indicate that Amphipoda and Isopoda cluster together(Edriophthalma)(BPP=100).Phylomitogenomic analyses strong support that Euphausiacea is nested within Decapoda, and closely related to Dendrobranchiata, which is also consistent with the evidence from developmental biology. Yet the taxonomic sampling of mitochondrial genome from Malacostraca is very biased to the order Decapoda, with no complete mitochondrial genomes reported from 11 of the 16 orders. Future researches on sequencing the mitochondrial genomes from a wide variety of malacostracans are necessary to further elucidate the phylogeny of this important group of animals. With the increase in mitochondrial genomes available, phylomitogenomics will emerge as an important component in the Tree of Life researches.