Cloning, characterization and promoter analysis of common carp hairy/Enhancer-of-split-related gene, her6

Some members of hairy/Enhancer-of-split-related gene (HES) family have important effects on axial mesoderm segmentation and the establishment and maintenance of the somite fringe. In fishes. the her6 gene, a member of the HES family, is the homologue Of heS1 in mammals and chicken. In this study, the her6 gene and its full-length cDNA from the common carp (Cyprinus carpio) were isolated and characterized. The genomic sequence of common carp her6 is approximately 1.7 kb. with four exons and three introns, and the full-length cDNA of 1314 bp encodes a Putative polypeptide of 271 amino acids. To analyse the promoter sequence of common carp her6. sequences of various lengths upstream from the transcription initiation site of her6 were fused to enhanced green fluorescent. protein gene (eGFP) and introduced into zebrafish embryos by microinjection to generate transgenic embryos. Our results show that the upstream sequence of 500 bp can direct highly efficient and tissue-specific expression of eGFP in zebrafish embryos. whereas a fragment of 200 bp containing the TATA box and a partial suppressor of hairless paired site sequence (SPS) is not sufficient to drive eGFP expression in zebrafish embryos.

The innate immune response to grass carp hemorrhagic virus (GCHV) in cultured Carassius auratus blastulae (CAB) cells

Virus infection of mammalian cells activates an innate antiviral immune response characterized by production of interferon (IFN) and the subsequent transcriptional upregulation of IFN-stimulated genes (ISGs) by the JAK-STAT signaling pathway. Here, we report that a fish cell line, crucian carp (Carassius auratus L.) blastulae embryonic (CAB) cells, can produce IFN activity and then form an antiviral state after infection with UV-inactivated grass carp hemorrhagic virus (GCHV), a double-stranded (ds) RNA virus. From UV-inactivated GCHV-infected CAB cells, 15 pivotal genes were cloned and sequenced, and all of them were shown to be involved in IFN antiviral innate immune response. These IFN system genes include the dsRNA signal sensing factor TLR3, IFN, IFN signal transduction factor STAT1, IFN regulatory factor IRF7, putative IFN antiviral effectors Mx1, Mx2, PKR-like, Viperin, IFI56, and other IFN stimulated genes (ISGs) IFI58, ISG15-1, ISG15-2, USP18, Gig1 and Gig2. The identified fish IFN system genes were highly induced by active GCHV, UV-inactivated GCHV, CAB IFN or poly(I).poly(C), and showed similar expression patterns to mammals. The data indicate that an IFN antiviral innate immune response similar to that in mammals exists in the UV-inactivated GCHV-infected CAB cells, and the IFN response contributes to the formation of an antiviral state probably through JAK-STAT signaling pathway. This study provides strong evidence for existence of IFN antiviral innate immune response in fish, and will assist in elucidating the origin and evolution of vertebrate IFN system. (c) 2006 Elsevier Ltd. All rights reserved.

C-values of seven marine mammal species determined by flow cytometry

C-values, which estimate genome size, have puzzled geneticists for years because they bear no relationship to organismal complexity. Though C-values have been estimated for thousands of species, considerably more data are required in order to better understanding genome evolution. This is particularly true for mammals, in which C-values are known for less than 8% of the total number of mammalian species. Among marine mammals, a C-value has been estimated only for the bottlenose dolphin (Tursiops truncatus). Thus examination of additional species of marine mammals is necessary for comparative purposes. It will enable a better understanding of marine mammal genome evolution, and it is also relevant to conservation, because larger genome size has been linked to increased likelihood of extinction in some plant and animal groups. Our study presents C-values of seven marine mammal species, including five cetacean species that are endangered to varying degrees. Similarly to the results for other groups, our results suggest that larger genome size in cetaceans is related to an increased likelihood of extinction.

The distribution and economic losses of alien species invasion to China

Invasive alien species have become one of the most serious environmental issues in the world. Data of taxon, origin, pathway, and environmental impacts of invasive alien microorganisms, invertebrates, amphibians and reptiles, fish, birds, mammals, herbs, trees, and, marine organisms in terrestrial, aquatic, and marine ecosystems of China were analyzed during 2001 and 2003, based on literature retrieval and field survey. There were 283 invasive alien species in China, and the number of species of invasive alien microorganisms, aquatic plants, terrestrial plants, aquatic invertebrates, terrestrial invertebrates, amphibians and reptiles, fish, and mammals were 19, 18, 170, 25, 33, 3, 10, and 5, respectively. The proportion of invasive alien species originated from America, Europe, Asia, Africa, and Oceania were 55.1, 21.7, 9.9, 8.1, and 0.6%, respectively. Methods for estimation of direct economic losses to agriculture, forestry, stockbreeding, fishery, road and water transportation, storage, water conservancy, environment and public facilities, and human health were established. Methods for estimation of indirect economic losses caused by invasive alien species to service functions of forest ecosystems, agricultural ecosystems, grassland ecosystems, and wetland ecosystems were also established. The total economic losses caused by invasive alien species to China were to the time of USD 14.45 billion, with direct and indirect economic losses accounting for 16.59% and 83.41% of total economic losses, respectively.

The status and causes of alien species invasion in China

Data of classification, origin, pathway and environmental impacts of invasive alien micro-organisms, invertebrates, amphibians and reptiles, fish, birds, mammals, weeds, trees, and marine organisms in terrestrial, aquatic and marine ecosystems of China, were analyzed, based on literature retrieval, field survey and consultation. Some 283 invasive alien species were recorded in China, including 19 invasive alien micro-organisms, 18 aquatic plants, 170 terrestrial plants, 25 aquatic invertebrates, 33 terrestrial invertebrates, 3 amphibians and reptiles, 10 fish, and 5 mammals. Of the invasive alien species, 55.1% originated from North and South America, 21.7% from Europe, 9.9% from Asia, 8.1% from Africa and 0.6% from Oceania. Many institutions and individuals in China lack adequate knowledge of ecological and environmental consequences caused by invasive alien species, with some ignorance of the dangerous invasion in the introduction of alien species. For instance, 50.0% of invasive alien plants were intentionally introduced as pasture, feedingstuff, ornamental plants, textile plants, medicinal plants, vegetables, or lawn plants, 25% of alien invasive animals were intentionally introduced for cultivation, ornament, or biological control, In addition, more efforts are being made in the introduction of alien species, and little attention is paid on the management of introduced alien species, which may cause their escape into natural environment and potential threats to the environment. There were also gaps in quarantine system in China. All microorganisms were unintentionally introduced, through timber, seedling, flowerpot, or soil; 76.3% of alien invasive animals invaded through commodity or transportation facility because of the failure of quarantine. Therefore, quarantine measures should be strictly implemented; and meanwhile the intentional introduction of alien species should be strictly managed and a system of risk assessment should be implemented.

Diurnal changes of behavior and respiration of Yangtze finless porpoises (Neophocaena phocaenoides asiaeorientalis) in captivity

A preliminary study was carried out to investigate diurnal changes of behavior of three, one adult mate, one adult female, and one juvenile female, Yangtze finless porpoises (Neophocaena phocaenoides asiaeorientalis) in captivity. The respiration and behavior of the porpoises were recorded for 222 hr across 42 days. Behavioral data were recorded for eight general categories: aerial display and fast swimming, begging for fish, playing, nonsexual socializing, sexual behavior, resting, rubbing, and miscellaneous (i.e., other behaviors not included in the above categories). Each behavioral category was scored using one-zero sampling with 10-min intervals. The adult male showed shorter mean respiratory intervals at night (19:00-7:00 h), whereas the mean respiratory intervals of the females were shorter during the day (7:00-19:00 h). Begging for fish of all individuals, playing of the juvenile female, nonsexual socializing, and miscellaneous behavior of the adult female and resting of the male were observed more easily in the day, and aerial display and fast swimming of the adults and resting of the females were observed more easily at night. No significant diurnal difference was found, however, in the remaining categories of each individual. Each of the three porpoises therefore showed a distinct diurnal pattern, but none was obviously more active in the daytime than during the nighttime. Results suggest that daytime-only feeding schedules may be insufficient to meet the energetic needs of marine mammals that show a 24-hr activity cycle, and that nighttime feeding may be a worthwhile addition to husbandry routines.

Molecular cloning of the viperin gene and its promoter region from the mandarin fish Siniperca chuatsi

A viperin gene has been cloned from the mandarin fish (Siniperca chuatsi). From the first transcription initiation site, the mandarin fish viperin gene extends 3163 nucleotides to the end of the 3' untranslated region, and it contains six exons and five introns. The open reading frame of the viperin transcript has 1062 nucleotides which encode a 354 amino acid peptide. The amino acid sequence of mandarin fish viperin shows high identities with its homologues in teleosts and mammals except for the first 70 amino acids. A characteristic feature in the viperin promoter region was the presence of five putative ICSBP (IRF8) binding sites and one IRFI binding site. The viperin gene expressed mainly in lymphoid tissues before stimulation, but its expression can be examined in almost all the organs investigated after stimulation with virus or Poly I:C. The expression pattern and promoter sequence may be considered as the indirect evidence that the transcription of viperin is regulated by interferons or interferon induced genes. (C) 2004 Elsevier B.V. All rights reserved.

Characterization and phylogenetic analysis of the chitinase gene from the Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus

A putative chitinase gene was identified within the fragment EcoRI-K of the Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus (HearNPV, also called HaSNPIV) genome. The open reading frame (ORF) contains 1713 nucleotides (nt) and encodes a protein of 570 amino acids (aa) with a predicted molecular weight of 63.6 kDa. Transcription started at about 18 h post infection (p.i.) and the protein was first detected at 20 h p.i. The times of transcription and expression are characteristic of a late baculovirus gene. 5' and 3' RACE indicated that transcription was initiated from the adenine residue located at -246 nt upstream from the ATG start site and the poly (A) tail was added at 267 nt downstream from the stop codon. This is the first report on the molecular characterization of a chitinase from a single nucleocapsid NPV. The phylogeny of baculoviral chitinase genes were extensively examined in comparison with chitinases derived from bacteria, fungi, nematode, actinomycetes, viruses, insects and mammals. Neighbor-joining and most parsimony analyses showed that the baculoviral chitinases were clustered exclusively within gamma-proteobacteria. Our results strongly suggest that baculoviruses acquired their chitinase genes from bacteria. (C) 2004 Elsevier B.V. All rights reserved.

Identification and expression analysis of two IFN-inducible genes in crucian carp (Carassius auratus L.)

Interferon (IFN) exerts its antiviral effects mainly through activation of a subset of IFN-stimulated genes (ISG), but relatively few of fish ISGs have been isolated and characterized so far. Here, we report two fish ISGs, termed CaIF158 and CaIF156, cloned from a subtractive cDNA library constructed with mRNAs obtained from crucian carp (Carassius auratus L.) blastulae embryonic (CAB) cells infected by UV-inactivated GCHV and mock-infected cells. Database search revealed that both ISGs had a high-level homology with all members of a well conserved gene family with multiple tetratricopeptide repeat (TPR) motifs, including human IF160, IF158, IF156, IFI54 and their homologues in some other mammalian species. The transcripts of CaIF158 and CaIF156 were undetectable in CAB cells but could be induced by active GCHV, UV-inactivated GCHV or CAB IFN. Analysis of expression difference between them and IFN signal factors, CaSTAT1 and CaIRF7, indicated that their transcriptions were mediated possibly through JAK-STAT signal pathway, which was further supported by the induction analysis in UV-inactivated GCHV infected, IFN-treated and untreated cells in the presence or absence of cycloheximide (CHX), a potent inhibitor of protein synthesis. In addition, a pufferfish (Fugu rubrides) DNA sequence representing putative FrIFI56 was also revealed when CalF158 and CalF156 were used to search the pufferfish genome database. Phylogenetic analysis showed that these fish ISGs form a unique clad independent of mammalian homologues, reflecting a distant evolutionary relationship from mammals. These studies identified the first teleost IFI56 and IFI58 orthologues. (C) 2003 Elsevier B.V All rights reserved.

Molecular characterization and IFN signal pathway analysis of Carassius auratus CaSTAT1 identified from the cultured cells in response to virus infection

Type I interferon (IFN) exerts its pleiotropic effects mainly through the JAK-STAT signaling pathway, which is presently best described in mammals. By subtractive suppression hybridization, two fish signaling factors, JAK1 and STAT1, had been identified in the IFN-induced crucian carp Carassius auratus L. blastulae embryonic (CAB) cells after treatment with UV-inactivated grass carp hemorrhagic virus (GCHV). Further, the full-length cDNA of STAT1, termed CaSTAT1, was obtained. It contains 2926 bp and encodes a protein of 718 aa. CaSTAT1 is most similar to rat STAT1 with 59% identity overall and displays all highly conserved domains that the STAT family possesses. Like human STAT1beta, it lacks the C-terminus acting as transcriptional activation domain in mammals. By contrast, only a single transcript was detected in virus-induced CAB cells. Expression analysis showed that CaSTAT1 could be activated by stimulation of CAB cells with poly I:C, active GCHV, UV-inactivated GCHV or CAB IFN, and displayed diverse expression patterns similar to that of mammalian STATI. Additionally, the expression of an antiviral gene CaMx1 was also induced under the same conditions, and expression difference between CaSTAT1 and CaMx1 was revealed by induction of CAB IFN. These results provide molecular evidence supporting the notion that the fish IFN signaling transduction pathway is similar to that in mammals. Fish IFN exerts its multiple functions, at least antiviral action, through a JAK-STAT pathway. (C) 2004 Elsevier Ltd. All rights reserved.

Identification of antiviral-relevant genes in the cultured fish cells induced by UV-inactivated virus

UV-inactivated grass carp hemorrhage virus (GCHV) can induce high titer of interferon in cultured CAB (crucian carp (Carassius auratus L.) blastulae) cells, and thus defend host cells against the virus invasion. The mechanism is proposed that an antiviral state should be established in the host cells by activating expression of a set of antiviral-relevant genes. In this study, suppressive subtractive hybridization is applied to constructing a subtracted cDNA library with mRNAs isolated from UV-inactivated GCHV infected and mock-infected CAB cells. 272 differential cDNA fragments are identified by both PCR and dot blot from the subtractive cDNA library. Sequencing analysis reveals 69 genes, including 46 known gene homologues, and 23 unknown putative genes. The known genes include the genes involved in interferon signaling pathways, such as Stat1 and Jak1, the antiviral genes, such as Mx and Viperin, and a set of interferon-stimulated genes observed in mammalian cells. Most of the unknown putative genes contain AU-rich element in their sequences. Differential expressions of these genes are further confirmed by virtual Northern blot and RT-PCR. The data imply that UV-inactivated GCHV is not only able to induce production of interferon in the infected CAB cells, but also leads to the expression of a series of antiviral-relevant genes or immune-relevant genes, and therefore reveals that the signaling pathway of interferon system and antiviral mechanism in fish are similar to those in mammals.

三叶因子在结直肠癌组织中的表达与临床关系及三叶因子-2在大肠杆菌中的重组表达和活性研究

癌症是世界发达国家和许多发展中国家人口的疾病主要死亡原因之一，其中，每年结直肠癌的新增病例和死亡病例排在癌症的第三位。在我国，北京、上海等地的统计资料显示，结直肠癌的发病上升很快 ，已排在癌症的第二位。结直肠癌的发生发展过程涉及一系列细胞和分子事件的改变，包括基因结构的异常和基因表达谱的异常。三叶因子（trefoil factor, TFF）是在上世纪80年代末到90初初由不同研究小组先后发现的含特殊的三叶因子结构域的蛋白多肽，其结构域的特征是含38-40个氨基酸残基的肽段中，有6保守的个半胱氨酸残基以1—5、2—4、3—6的方式形成二硫键，从而形成紧密的三叶结构域。在哺乳动物体内目前发现的三叶因子有三种，由粘膜组织内不同细胞合成并分泌到粘膜表面，对粘膜起保护作用。在粘膜损伤时，可通过多种途径促进上皮细胞迁移和抑制细胞凋亡，并促进血管形成，参与粘膜损伤的修复和重建。三叶因子在肿瘤组织中表达，则可能对癌症的发展起促进作用。研究资料显示，三叶因子在肿瘤中的表达异常与多种肿瘤的发生和发展过程有关。我们通过DNA测序检测结直肠癌组织中TFF1和TFF3基因各外显子的核苷酸序列，以确定是否存在基因突变。并用QRT-PCR和免疫组织化学的方法检测结直肠癌组织中TFF1和TFF3的mRNA和蛋白质的表达水平，分析其表达与结直肠癌的临床和病理特征之间的关系。同时，用ELISA方法检测结直肠癌患者血清中TFF1和TFF3的含量，以分析其与临床的关系，并逐步研究这两种三叶因子有否可能作为结直肠癌有用的血清分子标记。 目前得到以下研究结果：①在TFF1基因5`-端非翻译区位于起始密码上游—2bp处有一高频率的（C→T）突变位点,频率为40%，在其他非编码区也发现若干个较低频率的突变位点。未发现TFF3的基因突变；②TFF1和TFF3的mRNA水平在不同患者结直肠癌组织中的表达水平差异很大。与临床病理关系由于样品例数较少，未作统计学出理。结直肠癌组织中TFF1和TFF3蛋白表达检出阳性率分别为90%和94%。TFF1的表达与结直肠癌临床及病理类型未发现统计学意义，TFF3的表达上调与肿瘤淋巴结转移有关；③结直肠癌患者血清中TFF1的含量为（78.6575±53.300ng/ml），比健康人群血清TFF1含量（19.6457±5.3880ng/ml），增高约4倍，这一结果属首次报道。结直肠癌患者血清中TFF3的含量为（27.96±21.985ng/ml），比正常人群血清TFF3含量（9.0875±2.0315ng/ml）增高约3 1 倍。TFF1和TFF3能否作为结直肠癌的血清分子标志，尚需完善相关资料和作进一步研究。 TFF1和TFF3分别含一个三叶结构域，在靠近C-末端有一个游离的半胱氨酸巯基，TFF1和TFF3通过此二硫键形成同源二聚体，是其活性的主要形式。TFF2含两个三叶结构域，在三叶结构域外其靠近N-端和C-端各有一个半胱氨酸，两者以二硫键相连，形成紧密的结构。我们用pET系统克隆和表达人TFF2(hTFF2)，以及TFF2三叶结构域外二硫键解开的突变型TFF2(MhTFF2)，并测定细胞迁移活性。结果获得高效表达的hTFF2和MhTFF2，占细胞质总蛋白量的40%以上，经亲和层析后得到样品纯度在95%以上。对HCT116细胞株的划痕试验表明，hTFF2和MhTFF2对HCT116细胞具有迁移作用，细胞迁移数约为对照BSA的1.5倍。 结论:①结直肠癌组织中三叶因子-1和三叶因子-3基因突变不是三叶因子表达异常的主要原因；②TFF1和TFF3的转录水平在不同结直肠癌组织中有很多差异，TFF3蛋白的高表达与结直肠癌淋巴转移有关；③血清中TFF1和TFF3的含量检测可能会成为结直肠癌有用的血清分子标志；④pET质粒系统可高效表达可溶性三叶因子-2，并可表达获得有细胞迁移活性的重组融合蛋白TFF2；⑤TFF2的三叶结构域外的二硫键对TFF2的细胞迁移活性不是必须的。

哺乳动物生长激素/泌乳刺激素基因超家族的分子进化研究

生长激素（Growthhormone，GH）和泌乳刺激素（Prolactin，PRL）基因具有相似的结构和功能，它们和其他一些相关基因组成了GH/PRL基因超家族。在大部分哺乳动物基因组中，GH和PRL都是单拷贝基因。但在灵长目动物中，PRL是单拷贝基因，GH基因却发生了串联重复事件，形成一个基因家族。而在啮齿目中则相反，GH是单拷贝的，PRL却发生了串联重复事件形成一个基因家族。用PCR、克隆、测序的方法，我们从7种灵长目动物中得到了35条GH－类似基因。系统发育分析的结果显示所有旧大陆猴／人猿超科（OWM/H）的GH一类似基因和所有新大陆猴（NWM）的GH-类似基因分别形成两个单系，提示新大陆猴的GH基因家族和旧大陆猴／人猿超科GH基因家族起源于独立的基因重复事件。我们的分析结果还提示在。H基因家族的进化历程中发生了多次基因重复和基因转换事件。此外，不同GH基因家族成员的进化速率和所受到的选择压力存在显著差异。GHN基因在人猿超科和旧大陆猴中进化速率都比较慢，且受到了很强的纯化选择的作用；而CSH基因在两个世系中进化速率都比较快而且可能受到近中性选择的作用；GHV的进化速率和选择压力在旧大陆猴和人猿超科之间存在显著差异。对于新大陆猴GH基因家族，我们发现3个主要的功能基因簇，有趣的是这3个基因簇分别受到了纯化选择、近中性选择和正选择3种不同类型的选择压力。进一步分析的结果显示GH基因家族的进化符合所谓"生一和一灭（Birth-and-death）"的进化模式，该模式以频繁的基因重复和假基因化为主要特征。啮齿目泌乳刺激素基因家族由多个结构相似、在染色体上串联排列的基因组成，创门主要在生殖过程中协调作用。我们利用生物信息学手段在大鼠中得到了两个新的家族成员。结合系统发育、基因转换分析及染色体相对位置的比较，我们认为啮齿目PRL基因家族中的PL-I和PL-II基因亚家族是在大、小鼠分歧之后由物种特异的基因重复事件形成的。此外，啮齿目PRL基因家族的进化历程较复杂，因为除了通常的5-外显子结构的基因外，该家族还包含6-外显子结构的基因，后者在前者的第2和第3外显子之间获得了一个额外的外显子。本研究中我们意外地发现这个外显子在两个基因簇中的起源方式并不相同。在groupA中，它来源于一段外源DNA的插入，而在groupB中则来源于原先的非编码序列。对同义替换和异义替换速率比较的结果显示，在这些获得额外外显子的基－因中纯化选择压力得到了放松。激素蛋白必须与其受体结合经过信号传导才能发挥其生物学功能，因此，研究激素和受体的协同进化就显得尤为重要。我们对哺乳动物泌乳刺激素基因和其受体（PRLR）基因进行了协同进化分析，结果发现哺乳动物PRLR的膜外区和膜内区显示出和PRL一致的"插曲"式的进化模式。皮耳森相关系数计算的结果说明PRLR的膜外区和PRL基因发生了协同进化，同时PRLR的两个功能区域：膜外区和膜内区之间也发生了协同进化。此外，我们还发现灵长目PRL基因也发生了和GH基因类似的"插曲"式的进化，而且快速进化可能是选择压力放松的结果。

哺乳动物适应性进化的分子机制探讨——若味受体基因和犁鼻器受体1基因的研究

动物的适应进化是生物学研究的最基本的问题之一。虽然，人们早从形态学上研究了动物的适应现象，但是对适应的遗传学机制知之甚少。动物感觉系统对周围环境的适应是动物适应进化中的一个关键问题。因此，我们选取了动物感觉系统中苦味受体基因家族（T2R）和犁鼻器受体1基因家族（VIR）为研究对象，对哺乳动物适应性进化的分子机制进行探讨。通过生物信息学和分子生物学手段相结合，我们在哺乳动物6个目共16个物种中获得了157个的苦味味觉受体基因，并对这些TZR基因的系统发育关系进行分析，结果显示哺乳动物的TZR基因家族经历了"生一和一灭"的进化模式，即频繁的基因重复和假基因化。另外，结果还显示这些基因可以被分为3个主要类群，分别命名为A，B和C。有趣的是，B和C类群的基因在所研究的物种间普遍是一对一的直系同源的，而A类群基因则显示了种属或世系特异性。有可能B和C类群的基因是识别哺乳动物共同的苦味物质所必需的，而A类群基因则是用于识别具有种属特异性的苦味物质。这个分析还揭示了在系统发育关系上近相关的基因在它们的染色体位置上也是靠近的，这证明了串联重复是新的TZR基因产生的主要方式。此外，通过核昔酸的异义替换数和同义替换数的比较显示不同物种新近产生的基因所编码的受体蛋白在膜外区的异义替换数显著地大于同义替换数，提示着这些通过基因重复产生的新基因受到了正选择的作用。在自然界中，许多的天然有毒物质一般都是苦的，因此，我们推测哺乳动物TZR基因的分"化选择是为了使其在探索新的生活环境和寻找新食物时能够辨别出更多不同的有毒物质，更好地适应新环境。此外，我们还研究了苦味受体基因和甜味／鲜味受体基因的进化途径。结果显示苦味受体基因和甜味／鲜味受体基因在进化上具有远相关，并具有不同的进化途径，提示着这可能是导致了这些受体基因具有不同功能，传导不同味觉的原因。犁鼻受体噬因家族（VIR）是哺乳动物的信息素受体。应用生物信息学手，我们从大鼠和小鼠的基因组中分别得到了152和115个VIR基因。大鼠VIR基因家族包含11个亚家族，其中10个是与小鼠共享的，而M家族是大鼠特有的；另夕卜大鼠缺少了H和I亚家族，而这两个亚家族存在于小鼠的基因组中。系统发育关系分析发现，"生一和一灭"进化模式也在V1R基因的进化过程中占了主导地位。所有检测到的亚家族都出现于啮齿目和灵长目分歧之后，这说明V1R基因的多样性反映了这一基因家族在啮齿目内基因重复、丢失，基因漂变及自然选择等作用的动态过程。我们的分析还表明大部分不同亚家族下的基因簇爆发的时间接近于大、小鼠分歧的时间。此外，用最大似然法分析的结果表明在这些基因簇中异义替换和同义替换的比值远大于1，揭示了正选择在这些基因的分化过程的作用。一般认为V1R在动物识别信息素过程中起重要的作用，因此我们推测V1R基因的适应性进化是为了使不同的哺乳动物能够识别不同的、复杂的信息素。

线粒体基因组的变异与哺乳动物高原适应性

青藏高原是世界上最大、最年轻的高原。大气氧分压低、太阳辐射强烈和 气候寒冷等自然特点使得生活在青藏高原上的动物在形态、生态、行为以及生 理机能上都受到深刻的影响，并在进化过程中对高原环境产生了特殊的适应性。 生活在高原上的动物分为世居动物和移居动物，它们处于高原适应过程中的不 同阶段，并且有着不同的高原适应性的特点。为了研究高原哺乳动物所拥有的 特殊高原适应性的遗传基础和进化历史，以及探讨处于不同高原适应阶段的哺 乳动物对高原的适应性在遗传基础上的异同，本研究首次测定和分析了高原世 居动物中的藏羚羊（Pantholops hodgsonii）和高原鼠兔（Ochotona curzoniae） 以及高原移居动物中的藏马（Equns caballus）这三种具有代表性的高原动物的 线粒体全基因组。 1. 藏羚羊线粒体DNA 中的变异及其进化史 在对线粒体上13 个基因进行了进化分析后，我们发现细胞色素氧化酶1 （COX1）基因在藏羚羊和牦牛中都有高的非同义突变的现象。COX1 基因编码 的蛋白是线粒体氧化呼吸链上复合物Ⅳ的一部分，它将电子传递给氧，进行有 氧呼吸并产生能量。考虑到藏羚羊与牦牛都是生活在相同的气候环境中，我们 猜想线粒体基因组编码的COX1 基因的进化可能对青藏高原世居动物适应高原 环境起到作用。藏羚羊的线粒体DNA 数据表明，藏羚羊与绵羊、山羊的亲缘 关系较近，而与羚羊属家族的动物则相对较远，同时我们估算了藏羚羊与绵羊 山羊的分化时间大约为220 万年左右。这一时间与一些学者所估计的青藏高原 隆起时间大致吻合。 2. 高原鼠兔线粒体DNA 中的变异及其进化史 对高原鼠兔线粒体基因组上的基因进行进化分析后发现，对于高原鼠兔这一 分枝上，COX1 基因也有高的非同义突变速率。这表明COX1 基因在高原鼠兔 适应青藏高原高寒缺氧的环境过程中也可能受到选择压力的作用，结合我们在 藏羚羊和牦牛中的分析结果，我们推测高原世居动物在COX1 基因的进化过程 中很多都表现出类似的受选择现象。3. 藏马线粒体DNA 中的变异及其进化史 我们测定了西藏那曲(4500m)、云南中甸(3300m)、云南德钦(3300m)地区共 三匹藏马线粒体全基因组序列。通过对线粒体蛋白编码区的分析发现，与藏羚 羊、高原鼠兔等高原世居动物表现出的COX1 基因受选择不同，在三匹藏马中 NADH6 基因均表现高的非同义突变现象。NDAH6 基因编码的蛋白是线粒体氧 化呼吸链上复合物Ⅰ的一部分，它催化电子从NADH 传递给辅酶Q。不同地区 藏马中NADH6 基因类似的进化方式表明NADH6 基因的进化可能与藏马对高 原极端环境的适应有关。藏马在线粒体基因进化上所表现出的与其它高原世居 动物的不同究竟是由于动物在适应高原的不同阶段其遗传基础和策略的不同所 造成的，还是由于物种间的差异所造成的我们尚不能确定。还需要进一步对高 原动物线粒体基因进行研究。此外，我们对藏马进化史的研究表明藏马可能为 多地区起源