蕨类植物psaA基因的分子进化研究

采用“放松分子钟”模型、氨基酸位点正选择模型和分子内共进化网络估算方法,对蕨类植物光合系统Ⅰ核心蛋白PSAA编码基因psaA的进化趋势进行了研究。结果显示,叶绿体基因psaA编码区全序列具备成为蕨类植物系统发育关系重建位点的潜力,与rbcL基因联合后能构建高后验概率的系统发育树;蕨类植物的PSAA蛋白中存在一些曾经历正选择的氨基酸位点,其中29个位点聚合成为16个共进化组,通过共进化网络的方式协同影响光合系统Ⅰ的内部调整,提升其在被子植物兴起后光合环境下的适应能力。本文对蕨类植物进化潜能与分子机理的研究结果为揭示蕨类植物适应新生境提供了科学依据,也为植物系统分类学研究提供了分子依据。     

裸子植物psbA基因分子进化式样的研究

为阐明裸子植物对陆生生境生态响应的分子机制,以新近的裸子植物分类系统为指导,基于psb A基因编码全序列对4亚纲53种代表植物进行分子进化分析。首先,依据"放松分子钟"模型重建裸子植物在时间尺度下系统发育关系;其次,采用6个模型(MEC/JTT、MEC/cp REV、M5、M7、M8、M8a)估测氨基酸位点ω值,并对各模型结果进行统计检测;随后,利用Bootstrap方法检PSBA蛋白内部氨基酸位点的共进化动态。结果表明,系统树提示的物种分化历程支持前期分类结果;光合系统反应中心核心PSBA蛋白有3个氨基酸位点(13、19和243)曾经受正选择压力;PSBA蛋白内部有多对氨基酸位点间构成了共进化网络。因此,psb A基因编码序列具有作为描绘裸子植物系统发育关系标记的潜力,PSBA蛋白部分位点经历了适应性进化,通过位点间共进化网络协同作用方式辅助裸子植物响应陆生生境。     

蕨类植物叶绿体rps12基因的分子进化研究

以68种蕨类植物和2种石松类植物的rps12基因为对象,在系统发育背景下,结合最大似然法,使用HyPhy和PAML软件对该基因进行进化速率和适应性进化研究。结果显示:位于IR区的外显子2~3,其替换率明显降低,rps12基因编码序列的替换率也随之降低,且rps12基因密码子第3位的GC含量明显升高;在蕨类植物的进化过程中,3′-rps12更倾向定位于IR区,以保持较低的替换率;rps12基因编码的123个氨基酸位点中,共检测到4个正选择位点和116个负选择位点。研究结果表明基因序列进入到IR区后,显示出降低的替换率;强烈的负选择压力表明RPS12蛋白的高度保守性以及rps12基因的功能和结构已经趋于稳定。     

蕨类植物psbD基因的适应性进化和共进化分析

D2蛋白是植物光系统Ⅱ复合体（PSⅡ）核心蛋白之一,由叶绿体psbD基因编码。为了深入理解核心薄囊蕨类植物在阴生环境下的“辐射”式演化,我们对12种蕨类植物的psbD基因进行了克隆和测序,然后联合已公布的其他8种蕨类植物的psbD序列,基于ω值（非同义替换率ds和同义替换率ds的比值）探讨了该基因经受的选择压力。发现D2蛋白在大多数分支和位点受到强烈的负选择,但是树蕨类分支的psbD进化速率低且ω值较高。借助多种模型进行的共进化分析显示,树蕨类D2蛋白的168R、245H和272M两两组成具有共进化关系的氨基酸位点对。     

蕨类植物叶绿体rps4基因的适应性进化分析

在原核生物和植物叶绿体中,RPS4(ribosomal protein small subunit4)在核糖体30S小亚基形成起始过程中发挥重要作用;该蛋白在植物中由叶绿体rps4基因编码。为验证蕨类植物在白垩纪适应被子植物兴起而发生分化的观点,本文以23种蕨类植物为研究对象,利用分支模型、位点模型和分支位点模型对其叶绿体rps4基因进化适应性进行分析。分支模型检测到4个可能存在正选择的分支;位点模型和分支位点模型虽然没有检测出正选择位点,但是位点模型检测出了85个负选择位点。通过研究我们仅仅得出a、b两个代表水龙骨类的分支处于正选择压力下,这与水龙骨类在白垩纪发生辐射式演化的理论相一致。同时rps4基因处于强烈的负选择压力这一事实表明该基因的功能与结构已经趋于稳定。     

酿酒酵母中亚硫酸盐转运基因SSU1的分子进化分析

SSU1基因是涉及亚硫酸外排及SO₂耐受性的重要因素之一。为了研究酿酒酵母(Saccharomyce cerevisiae)中SSU1对SO₂耐受性及其分化机制, 文章探讨了SSU1基因在酿酒酵母中的遗传特征及进化规律。基于SSU1基因序列的聚类分析表明, 酿酒酵母群体可通过该基因分为3个亚群, 且与其分离的地理位置无关; 基于群体数据的McDonald-Kreitman 检验表明, SSU1基因在酿酒酵母中受到适应性选择的作用; Ka/Ks检验表明, 在酿酒酵母中, 不同的亚群间有Ka/Ks显著大于1 的值, 且PAML的支系模型检验到正选择作用在群体中特定的支系上; PAML的支系-位点模型检验获得9个潜在正选择作用位点, 其中有4个发生在受正选择作用的特定支系中; 基于ssu1p蛋白结构的分析表明, 在特定支系存在的正选择作用位点中, 除345(R/K)位点上两氨基酸替换均为碱性氨基酸外, 其他3个位点均是极性氨基酸/疏水性氨基酸之间替换, 考虑不同区域的氨基酸pKa值对其维持正常的功能有着重要的作用, 在该类位点的替换可能影响到ssu1p蛋白对SO₂的转运作用。     

阴地蕨属药用植物matK基因编码区全序列测定及编码产物研究

以阴地蕨属(Botrychium)5种药用植物的matK基因为对象,分析matK基因编码区全序列和其编码产物MATK蛋白的氨基酸序列特征,并比较他们在用于阴地蕨属药用植物系统发育关系研究中的差异。结果显示,阴地蕨属5种植物matK基因全长为1500~1503 bp,共有153个变异位点,其编码产物均为不稳定的亲水性蛋白,无跨膜结构,二级结构以α-螺旋和无规则卷曲为主。系统发育分析结果表明,基于matK基因序列的系统发育分析更适合于阴地蕨属种间亲缘关系的鉴定,说明matK基因在阴地蕨属植物的鉴定中具有一定的应用价值。     

凤尾蕨科旱生蕨类rbcL基因的适应性进化和共进化分析

核酮糖-1,5-二磷酸羧化酶/加氧酶（Rubisco,EC 4.1.1.39）是植物参与光合作用的关键酶,其大亚基由叶绿体rbcL基因编码。为深入理解凤尾蕨科植物对干旱生境的分子适应机制,本研究以53种凤尾蕨科旱生植物的rbcL基因为对象,展开适应性进化和共进化研究。采用位点间可变ω比值模型以及SLAC、REL和FEL等方法进行的适应性进化分析显示：在氨基酸水平上共有15个正选择位点（66S、84E、139L、235G、245I、252A、273Y、295K、296N、299M、307G、330E、349S、365F、404A）,其中位点245I、252A和273Y对维持Rubisco功能起重要作用。共进化分析共鉴定出2组共进化位点,分别由139L、273Y、295K和273Y、295K、349S组成,这些氨基酸位点间的共进化方式与蛋白质的疏水性和分子量都显著相关。以上结果一方面支持基于ω比值检验DNA编码序列发生适应性进化的有效性,另一方面也提示凤尾蕨科植物对干旱生境的适应可能与rbcL基因的适应性进化有关。     

蕨类植物叶绿体rps12基因的分子进化研究

以68种蕨类植物和2种石松类植物的rps12基因为对象,在系统发育背景下,结合最大似然法,使用Hy Phy和PAML软件对该基因进行进化速率和适应性进化研究。结果显示:位于IR区的外显子2～3,其替换率明显降低,rps12基因编码序列的替换率也随之降低,且rps12基因密码子第3位的GC含量明显升高;在蕨类植物的进化过程中,3'-rps12更倾向定位于IR区,以保持较低的替换率; rps12基因编码的123个氨基酸位点中,共检测到4个正选择位点和116个负选择位点。研究结果表明基因序列进入到IR区后,显示出降低的替换率;强烈的负选择压力表明RPS12蛋白的高度保守性以及rps12基因的功能和结构已经趋于稳定。     

念珠藻属植物hetR基因的适应性进化分析

以念珠藻属(Nostoc)及其近缘类群hetR基因的51条序列为研究对象,对hetR基因的编码蛋白进行生物信息学分析和系统发育分析,并使用分支模型、位点模型和分支-位点模型进行该基因位点的适应性进化研究。系统发育分析结果显示,51条hetR基因蛋白序列可分为4个大分支。适应性进化分析结果表明,在3种进化模型中,大多数分支及藻株都没有检测到统计学上具有显著性的正选择位点,说明检测的位点大多处于负选择压力下。但在普通念珠藻(Nostoc commune,CHAB2802)中检测到正选择位点(126T),提示念珠藻属植物hetR基因发生了适应性改变。     

First insights into fern matK phylogeny

MatK, the only maturase gene in the land plant plastid genome, is a very popular phylogenetic marker that has been extensively applied in reconstructing angiosperm phylogeny. However, the use of matK in fern phylogeny is largely unknown, due to difficulties with amplification: ferns have lost the flanking trnK exons, typically the region used for designing stable priming sites. We developed primers that are either universal or lineage-specific that successfully amplify matK across all fern families. To evaluate whether matK is as powerful a phylogenetic marker in ferns as in angiosperms, we compared its sequence characteristics and phylogenetic performance to those of rbcL and atpA. Among these three genes, matK has the highest variability and substitution evenness, yet shows the least homoplasy. Most importantly, applying matK in fern phylogenetics better resolved relationships among families, especially within eupolypods I and II. Here we demonstrate the power of matK for fern phylogenetic reconstruction, as well as provide primers and extensive sequence data that will greatly facilitate future evolutionary studies of ferns.     

Molecular evolution and positive Darwinian selection of the chloroplast maturase matK

It is not clear whether matK evolves under Darwinian selection. In this study, 70 plant groups, representing 2,279 species at various evolutionary levels, were used to illustrate the molecular adaptation and evolutionary dynamics of gene divergence in matKs. Selective influences were investigated using standard dN/dS ratio methods. Analyses revealed the presence of positive selection in matKs of 32 plant groups. More positively selected sites were detected in the N-terminal region than in the RT domain and domain X of matK. Moreover, removing amino acid sites that are under positive selection has a significant effect on the bootstrap values of phylogenetic reconstruction. Our results suggest that the rapidly evolving matK evolves under positive selection in some lineages of land plants. Several regions of matK have experienced molecular adaptation, which fine-tunes maturase performance.     

Physicochemical evolution and positive selection of the gymnosperm matK proteins

It is not clear whether matK evolves under Darwinian selection. In this study, the gymnosperm Taxaceae, Cephalotaxaceae and Pinaceae were used to illustrate the physicochemical evolution, molecular adaptation and evolutionary dynamics of gene divergence in matKs. matK sequences were amplified from 27 Taxaceae and 12 Cephalotaxaceae species. matK sequences of 19 Pinaceae species were retrieved from GenBank. The phylogenetic tree was generated using conceptual-translated amino acid sequences. Selective influences were investigated using standard d _N/d _S ratio methods and more sensitive techniques investigating the amino acid property changes resulting from nonsynonymous replacements in a phylogenetic context. Analyses revealed the presence of positive selection in matKs (N-terminal region, RT domain and domain X) of Taxaceae and Pinaceae, and found positive destabilizing selection in N-terminal region and RT domain of Cephalotaxaceae matK. Moreover, various amino acid properties were found to be influenced by destabilizing positive selection. Amino acid sites relating to these properties and to different secondary structures were found and have the potential to affect group II intron maturase function. Despite the evolutionary constraint on the rapidly evolving matK, this protein evolves under positive selection in gymnosperm. Several regions of matK have experienced molecular adaptation which fine-tunes maturase performance.     

蕨类植物rpoC1内含子缺失及其分子进化速率

rpoC1基因编码RNA聚合酶β°亚基蛋白, 在转录过程中与DNA模板结合, 与β亚基形成的β-β°亚基复合体构成RNA合成的催化中心。以rpoC1基因为研究对象, 在贝叶斯因子大于20的条件下, 用HyPhy软件位点模型检测到3个正选择位点和541个负选择位点; 用PAML软件位点模型检测到10个正选择位点, 其中3个位点的后验概率超过99%。此外, 基于最大似然法构建64种蕨类植物的系统发育树, 结合HyPhy软件分析rpoC1基因的转换率、颠换率、转换率/颠换率、同义替换率、非同义替换率以及同义替换率/非同义替换率, 探讨rpoC1基因内含子丢失与分子进化速率的关系。结果表明, rpoC1基因内含子缺失对转换率、颠换率以及非同义替换率有一定影响。     

Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level

Recent years have seen an explosion of interest in evidence for positive Darwinian selection at the molecular level. This quest has been hampered by the use of statistical methods that fail adequately to rule out alternative hypotheses, particularly the relaxation of purifying selection and the effects of population bottlenecks, during which the effectiveness of purifying selection is reduced. A further problem has been the assumption that positive selection will generally involve repeated amino-acid changes to a single protein. This model was derived from the case of the vertebrate major histocompatibility complex (MHC), but the MHC proteins are unusual in being involved in protein-protein recognition and in a co-evolutionary process of pathogens. There is no reason to suppose that repeated amino-acid changes to a single protein are involved in selectively advantageous phenotypes in general. Rather adaptive phenotypes are much more likely to result from other causes, including single amino-acid changes; deletion or silencing of genes or changes in the pattern of gene expression.     

Molecular systematics of Trilliaceae II. Phylogenetic analyses of Trillium and its allies using sequences of rbcL and matK genes of cpDNA and internal transcribed spacers of 18S–26S nrDNA

Coding regions of the rbcL and matK genes of cp DNA and internal transcribed spacers (ITS) of nuclear ribosomal DNA were sequenced to study phylogenetic relationships within and among all four genera of Trilliaceae: Trillium, Paris, Daiswa and Kinugasa . The rbcL gene has evolved much slower than matK and in particular ITS; hence the phylogenetic trees based on the rbcL gene show a much lower resolution than trees based on either matK or ITS. The general topology of phylogenetic trees resulting from separate parsimony analyses of the matK and ITS sequences are relatively congruent, with the exception of the placement of T. pusillum . Both matK and ITS phylogenies reveal that T. rivale diverges at the base of the trees. In both trees, Paris, Daiswa and Kinugasa form a relatively weakly supported group. Within this group, the allo-octaploid Kinugasa japonica is the sister group of Daiswa species. The Paris–Daiswa – Kinugasa group, the major Trillium group, and T. undulatum and T. govanianum showed a loosely related topology, but their affinities are not evident according to these two molecular markers. However, phylogenetic analysis of amino acid sequences derived from matK shows that T. rivale together with clades T. undulatum–T. govanianum, Daiswa–Kinugasa and Paris is basally diverged as a sister group to the remainder of Trillium .     

海鲈核糖体蛋白L8cDNA的克隆与进化分析

本文构建了海鲈(Lateolabrax japonicus)头肾全长eDNA文库.PCR方法扩增得到海鲈的核糖体蛋白L8基因,全长848bp,编码257个氨基酸,含有L2及L2-C两个保守区.进化分析结果表明,以L8为参照的进化鉴定结果同经典的分子生物学标准18s鉴定结果十分相似,因此核糖体蛋白L8基因L8可以作为鉴定物种进化程度的新标准.