食肉目哺乳动物（Carnivora）的分子进化研究

追溯生物界不同生物类型的起源及进化关系，即重建生物类群的系统发育树是进化生物学领域中一个十分重要的内容，并日益受到广泛的关注。美国和一些欧洲国家已率先启动了类似人类基因组计划的"生命之树，，计划（TreeofLife，TOL），将对生物学研究的发展产生深远影响。本研究瞄准了"生命之树"这一国际关注的焦点问题，选择具有重要进化理论意义和保护生物学价值的食肉目进行研究，除采用流行的多个线粒体基因外，还筛选多个有效的核基因标记，通过多基因序列数据的整合分析，构建可靠的食肉目分子系统树。此外，我们在食肉目部分物种的一个内含子区域发现了SINE家族的插入，考虑到这个内含子区域可能是SINE家族序列的一个插入热点，我们还增加了一些胎盘类哺乳动物目对这个内含子区域发生的多次SINE家族插入进行了详尽的进化研究。世界现生食肉目动物共计有11科280种，一般将它们归为两大超科，犬型超科（熊科，犬科，洗熊科，锄科，海狮科，海象科和海豹科）和猫型超科（灵猫科、猫科、鼠狗科和獴科）。犬型超科由于包含的物种种类繁多而且形态差异极"大，因此物种之间的系统发育关系方面争论颇多，难以解决。我们选用四个核基因序列片段和一个线粒体蛋白编码基因（共4417个碱基）对16个大型超科食肉目代表物种进行研究，探讨这一超科中科间的系统发育关系以及两个熊猫（大，小熊猫）的位置。结果表明不同基因在各分枝上表现出不同的解决能力，核基因和线粒体基因不含有冲突的，而是含有互补的系统发育信号，因而当把它们合并在一起进行系统发育分析时得到了一个大部分分枝都有很高支持程度的系统树拓扑结构。系统发育重建支持犬科是犬型超科中最早分歧的谱系，洗熊科和勃科的关系最近。小熊猫是洗熊科和触科的姐妹群，大熊猫是熊科中最早分歧的成员。鳍脚类（海狮科，海象科和海豹科）和熊科依次是由洗熊科，融科和小熊猫组成的进化枝最近的姐妹群。其中，鳍脚类和熊科的系统发育学位置在合并所有基因片段进行的ML和贝叶斯分析方法中都有较高的支持率和后验概率，但是在孵分析中的支持率却很低。因此，鳍脚类，熊科和由洗熊科，融科，小熊猫组成的进化枝三者之间的系统发育关系的解决将是以后食肉目犬型超科科水平系统发育学研究的趋势和重点。食肉目中不仅各科之间的进化关系扑朔迷离，科内的系统发育关系也很不清楚，尤其是熊科和猫科。因为这两个科都是在非常近期才发生物种分化的类群，代表了快速的进化辐射和间隔时间非常短的物种形成事件，因而重建科内各物种之间的系统发育关系对于系统学家来说是一项艰巨，极富挑战性的任务，也是造成熊科和猫科物种系统发育关系一直无法得到完全解决的重要原因。我们首次从两个核基因的角度，并与以前发表的五个线粒体基因数据进行单独和合并分析来探讨所有熊科物种（8个）的系统发育关系（约4kb）。结果不仅证实了目前普遍接受的观点，包括眼镜熊是除大熊猫以外最早分歧的熊科物种，以及棕熊和北极熊的姐妹群关系，而且进一步支持了亚洲黑熊和美洲黑熊之间的紧密关系，但是就在大多数以前的线粒体基因研究暗示懒熊极有可能是Ursus属中分歧最早的熊科物种时，我们的核基因分析提出新的假说，强烈支持懒熊和马来熊之间的姐妹群关系，使得懒熊和马来熊的系统发育位置又要成为将来熊科系统发育学研究中讨论的热点。另外，我们也探讨了核基因和线粒体基因表现出不一致系统发育信号的可能原因。猫科物种一般分成三大谱系：家猫谱系，豹谱系和虎猫谱系。其中由Panthera属和一些中等体型大小的猫类组成的豹谱系分化时间最近而且包含的物种最多，因此围绕它的系统发育学未解决的问题也最多。我们首次使用三个核基因对猫科中豹谱系部分物种系统发育关系进行探讨，同时还测定了两个完整线粒体编码基因，并结合以前发表的其它四个线粒体基因片段进行单独和结合分析，了解猫科豹谱系物种的进化历史。另外，我们还比较了这9个基因序列片段在进化特征和猫科系统发育关系应用价值方面的异同点。通过对14个猫科部分物种，主要为豹谱系物种的多个线粒体和核基因序列片段的综合分析，得到了一些非常有价值的重要结论，包括Panthera属的单源性以及Panthera属内部物种之间新的系统发育关系，云豹与Panthera属关系最近，美洲狮和猎豹是姐妹群，兔孙仍然属于家猫谱系等等。本研究中的核基因DNA在追溯如此近期才分化的猫科类群过程中积累的序列差异较少，因而贡献非常有限，它们可能会更适合用来解决食肉目中更高水平的物种之间系统发育关系。此外，当我们使用FGB基因第七内含子进行食肉目犬型超科各科和猫科部分物种的系统发育关系研究时，发现犬科代表物种和两个猫科物种中的不同位置上都发现了SINE片段的插入。我们又增加了除食肉目以外的部分哺乳动物目代表物种（共30个分类群）来进一步分析FGB基因第七内含子发生的多次SINEs家族插入事件。我们的结果表明：在所有哺乳动物内含子中的直源位置都发现了起源于tRNA的M琅元件，除了啮齿目。研究发现啮齿目小鼠中较高的序列变异速率以及大鼠中随着寄主DNA的大段丢失而发生了罕有的遗失是造成啮齿目中MIR缺失的原因。此外，在我们分析的12个哺乳动物目中，食肉目，偶蹄目和兔形目的FGB基因第七内含子不同位置还发现了至少五次谱系特异性SINE家族的独立插入事件。在食肉目中，三个独立的CANSINEs插入支持了这个SINE家族在食肉目所有类群中都有分布的假说（即"pan-camivores"假说）。研究中最重要的发现就是那些谱系特异的sINE家族有插入到己存在的MIRs内部或MIRs附近的强烈倾向，表明MIR很有可能是其它SINEs连续插入的"热点"区域，因而使这个内含子区域有如此多的逆转座子插入。我们认为SINEs要比以前所意识到的具有更大的插入"灵活性"和区域"特异性"。另外，本论文还重点介绍了现代系统发育学中常用的系统发育重建方法和策．略以及随着基因组时代的到来，"系统发育基因组学（P坤logenomics））'这门崭新的交叉学科在"重建生命之树"方面所具有的巨大优势和潜力。

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。

TRIM5α基因的分子进化及AIDS 免疫治疗相关腺病毒载体的构建

本文包括两方面的研究工作。第一部分对TRIM5α基因在灵长类动物中的分 子进化进行了详尽的研究，希望能从分子进化的角度认识该基因在灵长类动物抵 抗病毒感染尤其是在限制HIV-1 感染过程中所起的作用，并希望能够从中寻找适 合用于AIDS 基因治疗的基因。第二部分构建了艾滋病治疗性DC 疫苗相关的腺 病毒载体，包括表达HIV-1 gp120 基因、表达HIV-1 gp41 基因、表达HSP70 基 因以及仅表达绿色荧光蛋白基因的重组腺病毒，为利用HIV-1 抗原刺激的DC 免 疫治疗AIDS 的研究奠定了基础。 在长期的HIV-1 和AIDS 研究中，人们发现很多种旧大陆猴不能被HIV-1 感 染，而旧大陆猴中的平顶猴却对HIV-1 有易感性，并且对SIV 的感染也表现出较 其它旧大陆猴更为严重的症状，TRIM5α基因的发现解释了这一“历史之谜”。人 们发现旧大陆猴的TRIM5α基因具有很强的抗HIV-1 的功能，是旧大陆猴抵抗 HIV-1 感染必须的免疫因子；并且进一步证明TRIM5α是灵长类动物中普遍存在 的、具有抗多种逆转录病毒功能的天然免疫因子。我们通过对TRIM5α基因在灵 长类动物中的分子进化研究发现，证明该基因在进化过程中表现出很强的达尔文 正向选择作用，尤其是其负责识别逆转录病毒衣壳蛋白的SPRY 结构域。TRIM5 α基因表现出的正向选择很可能是灵长类动物在长期的进化过程中反复被病毒 感染的选择压力造成的，这也从另一个方面证明TRIM5α基因是一个普遍存在的、 具有抗病毒功能的天然免疫因子。对不同灵长类动物的TRIM5α基因序列分析发 现，该基因的序列变化很大，这可能是不同灵长类动物被HIV-1 感染后表现不同 症状的原因；基于密码子的中性检测证明，TRIM5α基因SPRY 结构域上第347、 354、552 位氨基酸表现出很强的正向选择，说明这些位点可能与其抗病毒功能 关系紧密。另外，我们发现平顶猴的TRIM5α基因与CypA 基因以一种新的方式 融合，这种融合方式不同于鹰猴中该基因与CypA 基因的融合，而且与具有较强抗HIV-1 功能的恒河猴的TRIM5α基因比较，平顶猴的TRIM5α基因在几个与其 抗病毒功能紧密相关的位点上的氨基酸也发生了变化，这可能是其被HIV-1 和 SIV 感染后表现出较其它旧大陆猴更为严重症状的原因。 将经过HIV-1 抗原刺激的DC 回输到HIV-1 感染者体内可以诱导产生较强的 抗HIV-1 细胞免疫反应，这种免疫反应理论上可以治疗AIDS，而且对HARRT 治 疗能够产生很好的协同作用；HSP70 蛋白可以提高DC 对抗原的加工和呈递。为 了检测经HIV-1 抗原刺激的DC 免疫治疗AIDS 的实际效果，同时检验通过HSP70 增强DC 对HIV-1 抗原的加工和呈递功能，发现并解决这一治疗方案存在的问题， 我们首先从HIV-1 的基因组及带有HSP70 基因的质粒上克隆了gp120、gp41 和 HSP70 基因，测序及序列分析证明所克隆的基因没有发生影响表达的突变。然后 我们分别构建了表达有关基因的重组腺病毒载体。在荧光显微镜下可以观察到感 染后的细胞内绿色荧光蛋白报告基因的表达，证明成功构建了四种重组腺病毒， 而PCR 扩增也证明在其中三种重组腺病毒的基因组上确实分别带有gp120、gp41、 HSP70 基因。同时我们还构建了不表达外源基因的重组腺病毒，作为未来实验中 的对照载体。未来的研究工作包括目的基因表达检测，重组腺病毒感染DC 及腺 病毒感染DC 功能分析等。

圆斑蝰蛇毒磷脂酶A_2蛋白活性表现和分子进化探讨及菜花烙铁头、烙铁头蛇毒中Jerdonase、TmF的研究

磷脂酶AZ（PLA2）是蛇毒中含量较为丰富的一类作用于梭酷键的酶。迄今为止，己有多种形式的PLA2从不同地域、不同种属的蛇毒中得以纯化并进行了较为系统的研究。其中，以VipoXin为代表的异二聚体形式PLA2较为引人注目，原因在于这种形式不同于此类蛋白家族中的诸多其它个体。目前，己经有许多关于此异二聚体PL凡生物学特性的报道，包括对此类形式存在原因、活性变化、结构表现、系统进化等方面的讨论。然而至今，这种以异二聚体形式存在的PLA2仅发现于几种蛙亚科（ViperinaeSubfamily）蛇种的蛇毒中，其中就包括我国台湾岛的圆斑蜂蛇台湾亚种（Doboiarusselliiformosensis），而蝮亚科（CrotaiinaeSubfamil）蛇种的蛇毒至今却没有此类报道。我国大陆西南端接壤东南亚，存在于云南、福建一带的圆斑蛙蛇隶属圆斑蛙蛇泰国亚种（Daboiarusselliisiamensis），那么这种蛇毒中是否也含有异二聚体形式的PLA2呢？本工作就此疑问对云南产圆斑蛙蛇泰国亚种（D.r.siamensis）蛇毒中的PLA2进行了研究，结果得到三个新的PLAZ，分别命名为DRS-PLA2-I、DRS-PLA2-II和DRS-PLA2-III。其中，DRS-PLA2-I的分子量为13864.06Da，理论pI为4.56，PLA2活性为12.35μmol/mg/min；DRS-PLA2-II的分子量为13635.99Da，理论pI为8.74，PLA2活性为8.76μmol／mg/min；DRS-PLA2-III的分子量为13619.80Da，理论厂为4.61，无PLA2活性。这三个蛋白酶N端的30个氨基酸残基恰好和三个阳性克隆的cDNA序列推导的蛋白序列吻合，结合已经报道的PLA2蛋白家族蛋白序列的保守性表现，我们可以断定它们之间存在对应关系。分子系统学分析表明DRS-PLA2-II和DRS-PLA2-III在进化关系上和蛙亚科的异二聚体PLA2关系较近，并且二者酶活性分别与异二聚体PLA2的Normalchain和Inhibitorchain相一致，只是没有发现类似Vipoxin形式的异二聚体结合蛋白。这些分析表明DRS-PLA2-nORS-PLA2-III类似圆斑蛙蛇台湾亚种（D.r.forlnos翻s沽）中的PV-4/RV-7，是PLA2异二聚体的一种特殊形式，在进化上滞后于VinOXin。另夕卜本工作还相继从云南产菜花烙铁头（Trimeresrusjerdonii）蛇毒和湖南产烙铁头（Trimeresurusmucrosquamatus）蛇毒中分离得到Jerdonase和TmF。前者为一个丝氨酸蛋白酶性质的、具有纤维蛋白原水解作用和激肤释放酶原水解作用双重活性表现的、高分子量的份五brinogenase，其活性表现可以被PMSF彻底抑制，而EDTA对此却没有影响。其它的几种抑制剂如大豆胰蛋白酶抑制剂、l-cysteine、DTT对Jerdonase的活性表现也有不同程度的影响。在Jerdonase的这些生化特性上中，分子量的大小和对纤维蛋白酶水解的特性这两方面有别于蛇毒中诸多其它来源的同类蛋白；后者T淤为一个舒缓激肚增强肤（BradykninPQtentiatingPePtide，BPP），电离质谱分析表明其分子量为1110.7Da。此小肚氨基酸序列为促进舒缓激肚（Bradki垃n，BK）诱导的豚鼠回肠纵行肌收缩的活力单位为（1.13±0.3）（m留L），T妊抑制血管紧张素转化酶（ACE）对BK水解的半数抑制剂量IC50为2μg。比较已报道的从Agkistrodon属和Bothrops属中纯化得到的BPP氨基酸序列发现：BPP的N端都是特征性的pGlu，C端为IIe-Pro-Pro，有高度的保守性。另外，TmF是Trimeresurus属中此类小肤的首次纯化。总之，本研究对国产的几种常见蛇毒中的几种常见蛋白多肤进行了一定程度的探讨和分析，和相同类别的其它蛋白、多肤比较可以看到，有许多相同的地方，也有许多不同的表现，研究结果为相应领域的深入研究提供资料和思路。

粗枝云杉( Picea asperata Mast.)天然群体的遗传变异

西南地区在我国的经济发展和生态环境建设中占重要地位，但也是我国生态环境最脆弱的地区之一，生态系统退化，生态功能减弱，严重制约着西南林业的可持续经营与发展。本项目采用DNA 分子标记SSR 研究不同生境条件下粗枝云杉群体的遗传变异及其时空分布格局，考察遗传变异与复杂的山地生态环境间的潜在联系，系统地揭示粗枝云杉天然群体与环境系统相互作用的生态适应与分子进化机制。粗枝云杉适应性强，生长迅速，在植树造林和工业用材方面占有重要地位，研究成果可为中国西南部亚高山天然林的可持续经营及退化生态系统的恢复与重建提供理论依据和科学指导。主要研究结果如下： 1. SSR 位点变异丰富，等位基因频率的分布格局多样。7 个SSR 标记全是多态位点，每位点的等位基因数变化范围为13~24，平均为19.9 个。SSR 位点的等位基因片段长度范围变化较大。73.1%的等位基因变异遵循逐步突变模型(SSM)而发生1 个重复基元的变化，22.3%和4.6%的变异分别按两阶段突变模型(TMP)发生1 个重复基元以上的变化和在SSR 位点侧翼区发生1 个碱基变化的插入-删除事件。 2. 粗枝云杉拥有中等偏高水平的遗传多样性和相对大的群体间遗传分化。通过分析代表10 个群体的250 个个体在7 个SSR位点的变化，调查了源自中国西南山区的粗枝云杉的微卫星变异。相当高的遗传多样性和强烈的群体分化发生在粗枝云杉中， 其群体平均Nei's 期望杂合度为0.707 ， 群体间遗传距离为0.121~0.224(FST)和0.100~0.537(RST)。然而，群体间遗传距离与地理距离之间无相关性，从而排除了简单的距离分离模式并暗示迁移不是影响粗枝云杉遗传变异格局的主要因素。事实上，使用私有等位基因估算的基因流数量非常低，仅等于0.753。等位基因置换检验(Allele permutation tests)揭示逐步突变及遗传漂变都对群体间分化有贡献。另外，在多数位点检测到显著的群体间遗传差异，这个结果说明自然选择，假设通过环境压力，是引起粗枝云杉微地理分化的主要因素之一。根据SSR基因型，250 个粗枝云杉个体的70%被正确地归类入其各自的来源群体，结果表明微卫星(SSR)对区分来自中国不同生态地理位点的粗枝云杉基因型是有效的。 3. 在SSR、RAPD 和AFLP 位点，显著的群体间遗传结构被发现的，但三种标记间遗传分化程度和群体遗传关系有差异。利用来自10 个群体的247 个个体，我们报告了关于样本粗枝云杉群体间遗传关系的总体看法。根据各自对评价遗传关系的信息能力和适用性，SSR、RAPD 和AFLP 标记被选用，三种技术非常有效地区别这些基因型。使用的SSR、RAPD 和AFLP 标记分别估计平均Dice 相似性系数。Mantel 检验产生显著但相对低的共表型适合度(RAPD = 0.63£AFLP = 0.60和SSR = 0.75)。比较三种标记系统，RAPD 和AFLP 共表型指数相对高地相关(r =0.59)，而RAPD 和SSR 及SSR 和AFLP 之间的相关系数分别是0.53 和0.35。所有系统树，包括不同标记资料结合获得的系统树，反映了多数群体依据它们的地理条件而成某种特定关系。结果暗示单个或结合标记系统能用来深入洞察粗枝云杉遗传研究，并且不同标记系统合并资料能提供更可靠的信息。 Southwestern region plays an important role in economic developmentand ecological construction in China. Yet, it is also one of the weak regionsof ecological environment in China with degraded ecosystem and imperfectfunction, which restricts the sustaining management and development ofsouthwestern forestry. The genetic variation and spatial distribution patternof P. asperata populations originating from different habitats wereinvestigated using SSR molecular markers in this study. The correlationsbetween genetic variation and ecological and environmental conditionswere detected, and the interaction between P. asperata populations andenvironmental system and the mechanism of ecological adaption -molecular evolution were revealed. Given the significant ecological andeconomic roles of the fast-growing and wide-adaptive species in reforestation and production of pulp wood and timber, the study couldprovide a strong theoretical evidence and scientific direction for thesustaining management of subalpine natural forest, and the afforestationand rehabilitation of degraded ecosystem. The results are as follows: 1. The genetic variation at SSR loci was abundant and the distributionof allelic frequencies was uneven. All seven loci were polymorphic, and thenumber of alleles per locus varied from 13 to 24 with a mean valueequaling 19.9. The allele sizes at SSR loci were found to vary widely.73.1% of allelic variation followed stepwise mutation model (SSM) whichresults increase or decrease by one repeat type, and 22.3% and 4.6% wereresulted from two-phase mutation model (TMP) with allele size varying bymore than one repeat type and from insertion-deletion events in theflanking regions at SSR loci with a single basepair changing, respectively. 2. P. asperata possessed a moderate to high level of genetic diversityand considerable genetic differentiation. Microsatellite variation of P.asperata. originating from the mountains of southwestern China wasinvestigated by analyzing variation at seven SSR loci in 250 individualsrepresenting ten populations. A fair degree of genetic diversity and strongpopulation subdivision occurred with the mean gene diversity (H) of 0.707,and genetic distances among populations varying between 0.121 and 0.224(FST) and between 0.100 and 0.537 (RST). However, inter-populationgenetic distances showed no correlation with geographic distances between the population sites. This ruled out a simple isolation by distance modeland suggested that migration does not have a great impact. In fact, theamount of gene flow, detected using private alleles, was very low, equalingonly 0.753. Allele permutation tests revealed that stepwise-like mutations,coupled with genetic drift, could contribute to population differentiation.Moreover, significant genetic differences between populations weredetected at most loci. The results indicate that natural selection, presumablythrough environmental stress, may be one of the main factors causingmicro-geographical differentiation in the genetic structure of P. asperata.Based on SSR genotypes, 70% of the 250 individuals were correctlyclassified into their sites of origin. This suggests that microsatellites (SSRs) are effective in distinguishing genotypes of P. asperata originating fromdiverse eco-geographical sites in China. 3. Using a set of 247 individuals from ten P. asperata populations wereport an overview on the genetic relationship among the sampled P.asperata populations. RAPD, AFLP and SSR were used in terms of theirinformativeness and applicability for evaluate relationship and all threetechniques discriminated the genotypes very effectively. Mean Dicesimilarities coefficient were estimated using RAPD, AFLP and SSR,respectively. The Mantel test resulted in a significant but relatively low fit(RAPD = 0.63, AFLP = 0.60 and SSR = 0.75) of cophenetic values.Comparing the three marker systems to each other, RAPD and AFLP cophenetic indices were highly correlated (r = 0.59), while correlationcoefficient between RAPD and SSR was r = 0.53 and between SSR andAFLP was r = 0.35. For all markers a relatively high similarity indendrogram topologies was obtained although some differences wereobserved. All the dendrograms, including that obtained by the combineduse of all the marker data, reflect some relationships for most of thepopulations according to their geographic conditions. The results indicatethat single or combined marker system could be used to insight into geneticstudy in P. asperata and the combined data of different marker systems canprovide more reliable information.

Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria

Cyanobacteria are an ancient group of gram-negative bacteria with strong genome size variation ranging from 1.6 to 9.1 Mb. Here, we first retrieved all the putative restriction-modification (RM) genes in the draft genome of Spirulina and then performed a range of comparative and bioinformatic analyses on RM genes from unicellular and filamentous cyanobacterial genomes. We have identified 6 gene clusters containing putative Type I RMs and 11 putative Type II RMs or the solitary methyltransferases (MTases). RT-PCR analysis reveals that 6 of 18 MTases are not expressed in Spirulina, whereas one hsdM gene, with a mutated cognate hsdS, was detected to be expressed. Our results indicate that the number of RM genes in filamentous cyanobacteria is significantly higher than in unicellular species, and this expansion of RM systems in filamentous cyanobacteria may be related to their wide range of ecological tolerance. Furthermore, a coevolutionary pattern is found between hsdM and hsdR, with a large number of site pairs positively or negatively correlated, indicating the functional importance of these pairing interactions between their tertiary structures. No evidence for positive selection is found for the majority of RMs, e. g., hsdM, hsdS, hsdR, and Type II restriction endonuclease gene families, while a group of MTases exhibit a remarkable signature of adaptive evolution. Sites and genes identified here to have been under positive selection would provide targets for further research on their structural and functional evaluations.

The complete mitochondrial genome of the large yellow croaker, Larimichthys crocea (Perciformes, Sciaenidae): Unusual features of its control region and the phylogenetic position of the Sciaenidae

To understand the systematic status of Larimichthys crocea in the Percoidei, we determined the complete mitochondrial (mt) genome sequence using 454 sequencing-by-synthesis technology. The complete mt genome is 16,466 bp in length including the typical structure of 22 tRNAs, 2 rRNAs, 13 protein-coding genes and the noncoding control region (CR). Further sequencing for the complete CR was performed using the primers Cyt b-F and 12S-R on six L crocea individuals and two L polyactis individuals. Interestingly, all seven CR sequences from L crocea were identical while the three sequences from L polyactis were distinct (including one from GenBank). Although the conserved blocks such as TAS and CSB-1, -2, and -3 are readily identifiable in the control regions of the two species, the typical central conserved blocks CSB-D, -E, and -F could not be detected, while they are found in Cynoscion acoupa of Sciaenidae and other Percoidei species. Phylogenetic analysis shows that L crocea is a relatively recently emerged species in Sciaenidae and this family is closely related to family Pomacanthidae within the Percoidei. L crocea, as the first species of Sciaenidae with complete mitochondrial genome available, will provide important information on the molecular evolution of the group. Moreover, the genus-specific pair of primers designed in this study for amplifying the complete mt control region will be very useful in studies on the population genetics and conservation biology of Larimichthys. (c) 2008 Elsevier B.V. All rights reserved.

The complete mitochondrial genome sequence of the cutlassfish Trichiurus japonicus (Perciformes: Trichiuridae) : Genome characterization and phylogenetic considerations

Mitochondrial genome sequence and structure analysis has become a powerful tool for studying molecular evolution and phylogenetic relationships. To understand the systematic status of Trichiurus japonicus in suborder Scombroidei, we determined the complete mitochondrial genome (mitogenome) sequence using the long-polymerase chain reaction (long-PCR) and shotgun sequencing method. The entire mitogenome is 16,796 by in length and has three unusual features, including (1) the absence of tRNA(Pro) gene, (2) the possibly nonfunctional light-strand replication origin (O-L) showing a shorter loop in secondary structure and no conserved motif (5'-GCCGG-3'), (3) two sets of the tandem repeats at the 5' and 3' ends of the control region. The three features seem common for Trichiurus mitogenomes, as we have confirmed them in other three T. japonicus individuals and in T nanhaiensis. Phylogenetic analysis does not support the monophyly of Trichiuridae, which is against the morphological result. T. japonicus is most closely related to those species of family Scombridae; they in turn have a sister relationship with Perciformes members including suborders Acanthuroidei, Caproidei, Notothenioidei, Zoarcoidei, Trachinoidei, and some species of Labroidei, based on the current dataset of complete mitogenome. T japonicus together with T. brevis, T lepturus and Aphanopus carbo form a clade distinct from Lepidopus caudatus in terms of the complete Cyt b sequences. T. japonicus mitogenome, as the first discovered complete mitogenome of Trichiuridae, should provide important information on both genomics and phylogenetics of Trichiuridae. (C) 2009 Elsevier B.V. All rights reserved.

Evidence for positive selection in phycoerythrin genes of red algae and cyanobacteria Prochlorococcus and Synechococcus

Because of the shortage of phycoerythrin (PE) gene sequences from rhodophytes, peBA encoding beta- and alpha-subunits of PE from three species of red algae (Ceramium boydenn, Halymenia sinensis, and Plocamium telfariae) were cloned and sequenced. Different selection forces have affected the evolution of PE lineages. 8.9 % of the codons were subject to positive selection within the PE lineages (excluding high-irradiance adapted Prochlorococcus). More than 40 % of the sites may be under positive selection, and nearly 20 % sites are weakly constraint sites in high-irradiance adapted Prochlorococcus. Sites most likely undergoing positive selection were found in the chromophore binding domains, suggesting that these sites have played important roles in environmental adaptation during PE diversification. Moreover, the heterogeneous distribution of positively selected sites along the PE gene was revealed from the comparison of low-irradiance adapted Prochlorococcus and marine Synechococcus, which firmly suggests that evolutionary patterns of PEs in these two lineages are significantly different.

An estimate of divergence time of parazoa and eumetazoa and that of cephalochordata and vertebrata by aldolase and triose phosphate isomerase clocks

Previously we suggested that four proteins including aldolase and triose phosphate isomerase (TPI) evolved with approximately constant rates over long periods covering the whole animal phyla. The constant rates of aldolase and TPI evolution were reexamined based on three different models for estimating evolutionary distances, It was shown that the evolutionary rates remain essentially unchanged in comparisons not only between different classes of vertebrates but also between vertebrates and arthropods and even between animals and plants, irrespective of the models used, Thus these enzymes might be useful molecular clocks for inferring divergence times of animal phyla, To know the divergence time of Parazoa and Eumetazoa and that of Cephalochordata and Vertebrata, the aldolase cDNAs from Ephydatia fluviatilis, a freshwater sponge, and the TPI cDNAs from Ephydatia fluviatilis and Branchiostoma belcheri an amphioxus, have been cloned and sequenced, Comparisons of the deduced amino acid sequences of aldolase and TPI from the freshwater sponge with known sequences revealed that the Parazoa-Eumetazoa split occurred about 940 million years ago (Ma) as determined by the average of two proteins and three models, Similarly, the aldolase and TPI clocks suggest that vertebrates and amphioxus last shared a common ancestor around 700 Ma and they possibly diverged shortly after the divergence of deuterostomes and protostomes.

Evolutionary analysis of phycobiliproteins: Implications for their structural and functional relationships

Phycobiliproteins, together with linker polypeptides and various chromophores, are basic building blocks of phycobilisomes, a supramolecular complex with a light-harvesting function in cyanobacteria and red algae. Previous studies suggest that the different types of phycobiliproteins and the linker polypeptides originated from the same ancestor. Here we retrieve the phycobilisome-related genes from the well-annotated and even unfinished cyanobacteria genomes and find that many sites with elevated d(N)/d(S) ratios in different phycobiliprotein lineages are located in the chromophore-binding domain and the helical hairpin domains (X and Y). Covariation analyses also reveal that these sites are significantly correlated, showing strong evidence of the functional-structural importance of interactions among these residues. The potential selective pressure driving the diversification of phycobiliproteins may be related to the phycobiliprotein-chromophore microenvironment formation and the subunits interaction. Sites and genes identified here would provide targets for further research on the structural-functional role of these residues and energy transfer through the chromophores.

Epidemiology and comparative analysis of Yersinia in Ireland

Yersiniosis is an acute or chronic enteric zoonosis caused by enteropathogenic Yersinia species. Although yersiniosis is predominantly associated with gastroenteric forms of infection, extraintestinal forms are often reported from the elderly or patients with predisposing factors. Yersiniosis is often reported in countries with cold and mild climates (Northern and Central Europe, New Zealand and North of Russian Federation). The Irish Health Protection Surveillance Centre (HPSC) currently records only 3-7 notified cases of yersiniosis per year. At the same time pathogenic Yersinia enterocolitica is recovered from pigs (main source of pathogenic Y. enterocolitica) at the levels similar to that observed in Yersinia endemic countries. Introduction of Yersinia selective culture procedures may increase Yersinia isolation rates. To establish whether the small number of notifications of human disease was an underestimate due to lack of specific selective culture for Yersinia we carried out a prospective culture study of faecal samples from outpatients with diarrhoea, with additional culture of appendix and throat swabs. Higher levels of anti-Yersinia seroprevalence than yersiniosis notification rates in endemic countries suggests that most yersiniosis cases are unrecognised by culture. Subsequently, in addition to a prospective culture study of clinical specimens, we carried out serological screening of Irish blood donors and environmental screening of human sewage. Pathogenic Yersinia strains were not isolated from 1,189 faeces samples, nor from 297 throat swabs, or 23 appendix swabs. This suggested that current low notification rates in Ireland are not due to the lack of specific Yersinia culture procedures. Molecular screening detected a wider variety of Y. enterocolitica-specific targets in pig slurry than in human sewage. A serological survey for antibodies against Yersinia YOP (Yersinia Outer Proteins) proteins in Irish blood donors found antibodies in 25%, with an age-related trend to increased seropositivity, compatible with the hypothesis that yersiniosis may have been more prevalent in Ireland in the recent past. Y. enterocolitica is a heterogeneous group of microorganisms that comprises strains with different degree of pathogenicity. Although non-pathogenic Y. enterocolitica lack conventional virulence factors, these strains can be isolated from patients with diarrhoea. Insecticidal Toxin Complex (ITC) and Cytolethal Distending Toxins can potentially contribute to the virulence of non-pathogenic Y. enterocolitica in the absence of other virulence factors. We compared distribution of ITC and CDT loci among pathogenic and non-pathogenic Y. enterocolitica. Additionally, to demonstrate potential pathogenicity of non-pathogenic Y. enterocolitica we compared their virulence towards Galleria mellonella larvae (a non-mammalian model of human bacterial infections) with the virulence of highly and mildly pathogenic Y. enterocolitica strains. Surprisingly, virulence of pathogenic and non-pathogenic Y. enterocolitica in Galleria mellonella larvae observed at 37°C did not correlate with their pathogenic potential towards humans. Comparative phylogenomic analysis detects predicted coding sequences (CDSs) that define host-pathogen interactions and hence providing insights into molecular evolution of bacterial virulence. Comparative phylogenomic analysis of microarray data generated in Y. enterocolitica strains isolated in the Great Britain from humans with diarrhoea and domestic animals revealed high genetic heterogeneity of these species. Because of the extensive human, animal and food exchanges between the UK and Ireland the objective of this study was to gain further insight into genetic heterogeneity and relationships among clinical and non-clinical Y. enterocolitica strains of various pathogenic potential isolated in Ireland and Great Britain. No evidence of direct transfer of strains between the two countries was found.

Identification of three novel Phyllomedusa sauvagei dermaseptins (sVI-sVIII) by cloning from a skin secretion-derived cDNA library

The defensive skin secretions of many amphibians contain a wide spectrum of biologically active compounds, particularly antimicrobial peptides that act as a first line of defence against bacterial infection. Here we describe for the first time the identification of three novel dermaseptin-related peptides (dermaseptins sVI–sVIII) whose primary structures were deduced from cDNAs cloned from a library constructed from lyophilised skin secretion of the South American hylid frog, Phyllomedusa sauvagei. The molecular masses of each were subsequently confirmed by interrogation of archived LC/MS files of fractionated skin secretion followed by automated Edman degradation sequencing. The heterogeneity of primary structures encountered in amphibian skin antimicrobial peptides may in part be explained by individual variation—a factor essential for selective functional molecular evolution and perhaps, ultimately in speciation.

High incidence of cryptic repeated elements in microsatellite flanking regions of galatheid genomes and its evolutionary implications

During the development of PCR primer sets for icrosatellite marker loci from enriched genomic libraries for three squat lobster species from Galatheidae (Decapoda: Anomura); Munida rugosa (Fabricius, 1775), M. sarsi (Huus, 1935), and Galathea strigosa (Linnaeus, 1761) (collectively known as squat lobsters), a number of unforeseen problems were encountered. These included PCR amplification failure, lack of amplification consistency, and the amplification of multiple fragments. Careful examination of microsatellite containing sequences revealed the existence of cryptic repeated elements on presumed unique flanking regions. BLAST analysis of these and other VNTR containing sequences (N 5 252) indicates that these cryptic elements can be grouped into families based upon sequence similarities. The unique features characterising these families suggest that different molecular mechanisms are involved. Of particular relevance is the association of microsatellites with mobile elements. This is the first reported observation of this phenomenon in crustaceans, and it also helps to explain why microsatellite primer development in galatheids has been relatively unsuccessful to date. We suggest a number of steps that can be used to identify similar problems in microsatellite marker development for other species, and also alternative approaches for both marker development and for the study of molecular evolution of species characterised by complex genome organisation. More specifically, we argue that new generation sequencing methodologies, which capitalise on parallel and multiplexed sequencing may pave the way forward for future crustacean research.

Functional and Structural Diversification of the Anguimorpha Lizard Venom System

Venom has only been recently discovered to be a basal trait of the Anguimorpha lizards. Consequently, very little is known about the timings of toxin recruitment events, venom protein molecular evolution, or even the relative physical diversifications of the venom system itself. A multidisciplinary approach was used to examine the evolution across the full taxonomical range of this similar to 130 million-year-old clade. Analysis of cDNA libraries revealed complex venom transcriptomes. Most notably, three new cardioactive peptide toxin types were discovered (celestoxin, cholecystokinin, and YY peptides). The latter two represent additional examples of convergent use of genes in toxic arsenals, both having previously been documented as components of frog skin defensive chemical secretions. Two other novel venom gland-overexpressed modified versions of other protein frameworks were also recovered from the libraries (epididymal secretory protein and ribonuclease). Lectin, hyaluronidase, and veficolin toxin types were sequenced for the first time from lizard venoms and shown to be homologous to the snake venom forms. In contrast, phylogenetic analyses demonstrated that the lizard natriuretic peptide toxins were recruited independently of the form in snake venoms. The de novo evolution of helokinestatin peptide toxin encoding do-mains within the lizard venom natriuretic gene was revealed to be exclusive to the helodermatid/anguid subclade. New isoforms were sequenced for cysteine-rich secretory protein, kallikrein, and phospholipase A 2 toxins. Venom gland morphological analysis revealed extensive evolutionary tinkering. Anguid glands are characterized by thin capsules and mixed glands, serous at the bottom of the lobule and mucous toward the apex. Twice, independently this arrangement was segregated into specialized serous protein-secreting glands with thick capsules with the mucous lobules now distinct (Heloderma and the Lanthanotus/Varanus clade). The results obtained highlight the importance of utilizing evolution-based search strategies for biodiscovery and emphasize the largely untapped drug design and development potential of lizard venoms. Molecular & Cellular Proteomics 9:2369-2390, 2010.