低拷贝核基因在异源多倍体植物中的进化与表达

异源多倍体植物在自然界中广泛分布。在这类植物谱系中, 低拷贝核基因具有特殊的进化特点和丰富的植物系统发生信息, 在转录水平存在基因沉默、基因激活和不均等表达等特点。以低拷贝核基因为主线, 概述了其在多倍体植物系统发生中的应用和相关注意事项, 并对其在多倍体植物中的表达变化及其分子机制进行了探讨, 系统地介绍了国际上相关领域的研究成果和最新动向。     

基于线粒体COⅠ基因的凤蝶亚科部分物种系统发育关系

通过对凤蝶亚科Papilioninae11属27种的线粒体细胞色素c氧化酶Ⅰ基因(COⅠ)序列测定,以阿波罗绢蝶Parnassius apollo为外群,分别采用邻接法(NJ)、最大简约法(MP)和最大似然法(ML)构建凤蝶亚科的系统发育树,初步探讨了其系统发育关系。结果显示,凤蝶亚科11属27个物种分为4个主要的分支,分别是裳凤蝶族Troidini、凤蝶族Papilionini、燕凤蝶族Lampropterini和喙凤蝶族Teinopalpini,与传统分类学观点一致。其中,燕凤蝶族构成凤蝶亚科系统发育树基部的一个独立分支,且为单系发生。凤蝶属Papilio中美凤蝶亚属Menelaides和翠凤蝶亚属Princeps首先相聚,华凤蝶亚属Sinoprinceps和凤蝶亚属Papilio亲缘关系较近,随后两分支再聚为一支,构成凤蝶属。本研究结果从分子水平验证了凤蝶亚科传统的形态分类地位,并为澄清凤蝶亚科物种间系统发育关系提供了基础资料。     

初探低拷贝核基因在低等分类阶元系统发育重建中的适用性——以十字花科为例

分子系统学已被广泛用于解决物种之间的亲缘关系。迄今为止,被子植物分子系统学大都采用叶绿体和线粒体基因。但叶绿体和线粒体多数采用单亲遗传方式,不能完全记录物种的进化历史。而且叶绿体和线粒体基因相对保守,可用于系统发育重建的信息有限,很难用来解决科以下类群之间的亲缘关系。相反,核基因遵守双亲遗传方式并能提供大量信息位点,但却没有得到广泛运用。本文以十字花科为例,从17种十字花科植物中得到了5个编码蛋白的单拷贝核基因序列,采用最大简约法、最大似然法和贝叶斯法重建它们之间的亲缘关系。结果表明,和目前常用的基因相比,这些基因能提供更多的信息位点,由此得到的系统发育树具有很高的支持,利用最大简约法得到的5个核基因的系统树中各分支均得到了100%的自展支持率。结果表明,我们选取的核基因可以用来进行科、属及种间的系统发育重建。因此,这5个基因可以用来解决被子植物其它科内的亲缘关系,而且也可以作为DNA条形码研究的有效分子标记。     

初探低拷贝核基因在低等分类阶元系统发育重建中的适用性——以十字花科为例

分子系统学已被广泛用于解决物种之间的亲缘关系.迄今为止,被子植物分子系统学大都采用叶绿体和线粒体基因.但叶绿体和线粒体多数采用单亲遗传方式,不能完全记录物种的进化历史.而且叶绿体和线粒体基因相对保守,可用于系统发育重建的信息有限,很难用来解决科以下类群之间的亲缘关系.相反,核基因遵守双亲遗传方式并能提供大量信息位点,但却没有得到广泛运用.本文以十字花科为例,从17种十字花科植物中得到了5个编码蛋白的单拷贝核基因序列,采用最大简约法、最大似然法和贝叶斯法重建它们之间的亲缘关系.结果表明,和目前常用的基因相比,这些基因能提供更多的信息位点,由此得到的系统发育树具有很高的支持,利用最大简约法得到的5个核基因的系统树中各分支均得到了100％的自展支持率.结果表明,我们选取的核基因可以用来进行科、属及种间的系统发育重建.因此,这5个基因可以用来解决被子植物其它科内的亲缘关系,而且也可以作为DNA条形码研究的有效分子标记.     

单拷贝核基因在昆虫分子系统学中的应用

单拷贝核基因(single-copy nuclear gene,scnDNA)是指基因组中拷贝数目少,只有1个或几个拷贝的核基因,大多数是属于生物体内组成型表达的持家基因。单拷贝核基因是分子系统学中的一种极有价值的分子标记,在构建生命树的主干及主干和末梢之间的中间分枝中将起极其重要的作用。文章主要介绍了单拷贝核基因在昆虫分子系统学中的应用情况、一些单拷贝核基因的特点以及应用单拷贝核基因研究昆虫分子系统学时存在的问题及注意事项。     

基于5993个核基因的被子植物系统发育关系研究

系统发育关系的构建对被子植物分类及进化研究非常重要。长期以来,被子植物系统发育的研究,大多使用质体基因、线粒体基因或少数保守的单拷贝核基因。该研究从已注释基因组或转录组中搜集88种被子植物(包含58目)的核基因集;通过对其进行同源基因聚类及去旁系同源基因,获得了5 993个一对一的直系同源基因家族(即对于每个基因家族,每种植物最多一条序列,最少包含50个物种);使用截取各种不同数目基因集的DNA或氨基酸序列,采用串联法(concatenation)和溯祖法(coalescence),共构建了20棵进化树。比较这些进化树,虽然大部分结果支持APG IV中描述的被子植物主要支系之间的关系[(真双子叶植物,单子叶植物),木兰类植物],但真双子叶植物内部各目分支的演化关系与APG IV有一个很大的不同,即认为檀香目和石竹目是蔷薇类植物的姊妹群。基于这些进化树,估算了被子植物各目分支的分化时间,结果表明被子植物的起源时间为237.78百万年前(95%置信区间为202.6～278.08),与主流观点认为的225百万年至240百万年前一致。以上结果为构建进化树提供了一种可行性策略,这种方法允许使用基...     

核基因在鸟类分子系统发育学研究中的应用

核基因作为一种新的遗传标记,近年来被广泛应用于鸟类分子系统发育研究中.核基因与线粒体基因位于不同的遗传载体上,因此被引入到系统发育学研究中为物种树的重建提供独立的证据.常用的外显子标记为重组激活基因1(RAG-1),重组激活基因2(RAG-2),癌基因c-myc,原癌基因c-mos,它们由于缓慢的进化速率而被用于鸟类高级分类阶元的系统学研究中.常用的内含子标记是β纤维蛋白原基因内含子7(β-fibrinogen intron7,β-fibint7),肌红蛋白基因内含子Ⅱ(myoglobin intionⅡ).内含子标记通常与线粒体序列联合使用,形成具有互补系统发育信号的数据集,应用于各种分类阶元的系统学研究中.     

中国黄粉蝶亚科六属间基于COⅡ和EF-1α基因部分序列的系统发育关系（鳞翅目：粉蝶科）

为了探讨中国黄粉蝶亚科属间的系统发育关系,我们对其中6属9种的细胞色素氧化酶Ⅱ（COⅡ）的部分序列和延伸因子基因（EF-1α）部分序列进行了分析。分别采用最大简约法（maximum parsimony, MP）、最大似然法（maximum likelihood, ML）和贝叶斯推论法（bayesian inference, BI）构建黄粉蝶亚科分子系统树。结果表明：在测得的COⅡ基因的648 bp序列和EF-1α基因的504 bp序列中,有261个变异位点,151个简约信息位点,黄粉蝶亚科内各属COⅡ基因A+T含量（77.3%）均明显偏高。系统发育分析显示黄粉蝶属为亚科中较为原始的类群,分化较早,豆粉蝶属和迁粉蝶属亲缘关系较近,但钩粉蝶属与豆粉蝶属、迁粉蝶属之间的亲缘关系还不能确定。本研究结果和传统的基于形态学的黄粉蝶亚科的分类体系有所不同,最显著的分歧是本研究支持内群中分化最早的属应为黄粉蝶属,而不是豆粉蝶属和迁粉蝶属。     

基于核基因c-mos的鸫亚科部分鸟类系统发生关系

采用分子系统学方法对鸫亚科Turdinae 11属21种鸟类的核基因c-mos进行了系统发生分析.所测序列经对位排列后共572个位点,其中核苷酸变异位点111个,简约信息位点71个.以太平鸟Bombycilla garrulus作外群,采用邻接法、最大简约法和最大似然法分别构建其系统发生树.重建的系统发生树显示:所研究鸫亚科21种鸟类分成2个支系,第1个支系包括鸫属Turdus和地鸫属Zoothera.第2个支系包括红尾鸲属Phoenicurus、矶鸫属Monticola、水鸲属Rhyacornis、鸲属Tarsiger、溪鸲属Chainarrornis、石即鸟属Saxicola、燕尾属Enivurus、歌鸲属Luscinia和鹊鸲属Copsychus.红尾鸲属为并系类群,水鸲属和溪鸲属聚到这一支系;歌鸲属与燕尾属互为姐妹群,再与鸲属聚合构成另一支系;宝兴歌鸫Turdus mupinensis独立于鸫属及地鸫属之外,形成单独一个分支.     

直突摇蚊亚科部分属基于线粒体COⅡ基因部分序列的系统发育关系(双翅目:摇蚊科)

利用线粒体CO Ⅱ部分基因序列对直突摇蚊亚科代表性属级阶元进行分子系统学研究.共测定24属30种基因序列,利用Clustal X软件对比并用MEGA 4.1软件分析其碱基组成,以Chironomus samoensis Edwards作为外群构建分子系统树.结果表明:拟开氏摇蚊属Parakiefferiella和克莱施...     

Selecting Single-Copy Nuclear Genes for Plant Phylogenetics: A Preliminary Analysis for the Senecioneae (Asteraceae)

Compared to organelle genomes, the nuclear genome comprises a vast reservoir of genes that potentially harbor phylogenetic signal. Despite the valuable data that sequencing projects of model systems offer, relatively few single-copy nuclear genes are being used in systematics. In part this is due to the challenges inherent in generating orthologous sequences, a problem that is ameliorated when the gene family in question has been characterized in related organisms. Here we illustrate the utility of diverse sequence databases within the Asteraceae as a framework for developing single-copy nuclear genes useful for inferring phylogenies in the tribe Senecioneae. We highlight the process of searching for informative genes by using data from Helianthus annuus, Lactuca sativa, Stevia rebaudiana, Zinnia elegans, and Gerbera cultivar. Emerging from this process were several candidate genes; two of these were used for a phylogenetic assessment of the Senecioneae and were compared to other genes previously used in Asteraceae phylogenies. Based on the preliminary sampling used, one of the genes selected during the searching process was more useful than the two previously used in Asteraceae. The search strategy described is valid for any group of plants but its efficiency is dependent on the phylogenetic proximity of the study group to the species represented in sequence databases. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Development of novel low-copy nuclear markers for Hieraciinae (Asteraceae) and their perspective for other tribes

? Premise of the study: The development of three low-copy nuclear markers for low taxonomic level phylogenies in Asteraceae with emphasis on the subtribe Hieraciinae is reported. ? Methods and Results: Marker candidates were selected by comparing a Lactuca complementary DNA (cDNA) library with public DNA sequence databases. Interspecific variation and phylogenetic signal of the selected genes were investigated for diploid taxa from the subtribe Hieraciinae and compared to a reference phylogeny. Their ability to cross-amplify was assessed for other Asteraceae tribes. All three markers had higher variation (2.1-4.5 times) than the internal transcribed spacer (ITS) in Hieraciinae. Cross-amplification was successful in at least seven other tribes of the Asteraceae. Only three cases indicating the presence of paralogs or pseudogenes were detected. ? Conclusions: The results demonstrate the potential of these markers for phylogeny reconstruction in the Hieraciinae as well as in other Asteraceae tribes, especially for very closely related species.     

Phylogenetic inferences in Antennaria (Asteraceae: Gnaphalieae: Cassiniinae) based on sequences from Nuclear Ribosomal DNA internal transcribed spacers (ITS)

The phylogenetic relationships among sexually reproducing species of Antennaria (Asteraceae) are poorly understood. An earlier cladistic analysis based on morphology did not fully resolve the phylogeny of these taxa and therefore a different approach using molecular data was explored. The internal transcribed spacer regions (ITS-1 and ITS-2) of nuclear ribosomal DNA were sequenced for 30 species of Antennaria and one species from each of the outgroup genera Anaphalis, Ewartia, Leontopodium, and Pseudognaphalium. The ITS-1 sequence in Antennaria ranged from 253 to 260 base pairs (bp) in length, and the proportion of nucleotide differences between pairs of species of Antennaria ranged from 1 to 14%. For ITS-2, the divergence between pairs of species of Antennaria ranged from 0 to 8%. ITS-2 is shorter than ITS-1, ranging from 213 to 219 bp. Phylogenetic analysis indicates that, relative to the outgroups included, Antennaria is a well-supported monophyletic group. Based on the genera surveyed, Leontopodium appears to be the sister genus of Antennaria. The general topology of the molecular trees agrees with that based on previous morphological analyses and indicates that Antennaria is composed of six clades of equal rank, corresponding to the traditionally recognized informal groups, the Geyeriae, Argenteae, Arcuatae, Dimorphae, Pulcherrimae, and Catipes. Sequence and morphological data indicate that the Alpinae and Dioicae are unnatural, polyphyletic units that should be abandoned and redefined as the monophyletic Catipes group. Phylogenetic analysis of ITS sequences also suggests the dissociation of A. stenophylla from the Dimorphae, where it is traditionally placed, and its affiliation with the Argenteae, as well as the placement of A. arcuata in its own group.     

Allopolyploidy in the Wintergreen Group of tribe Gaultherieae (Ericaceae) inferred from low‐copy nuclear genes

DNA sequence data from the low‐copy nuclear genes waxy (GBSSI) and leafy were compared with plastid and ITS sequence data from prior studies to reconstruct phylogenetic relationships in the Wintergreen Group of tribe Gaultherieae (Ericaceae). We conducted phylogenetic analysis with 102 species that includes representatives of all 15 major clades previously identified within the Wintergreen Group and that together span its circum‐Pacific distribution. Results yielded two distinct homeologous copies of waxy for two of the clades, each in widely separated parts of the tree. It also yielded two copies of leafy for one of the clades; only one copy of leafy was found for the other clade, but it was placed in the same major clade as its waxy counterpart and well away from its placement in a prior plastid analysis. A combined four‐locus (waxy, leafy, ITS and plastid data) phylogenetic analysis of all available relevant data placed the copies of each of the clades in two distinct positions in the phylogeny with strong overall statistical support. In combination with evidence from morphology, reproductive biology and cytology, the results suggest that these clades arose through allopolyploid hybridization between lineages deep in the phylogeny but relatively close geographically. This finding confirms previous assumptions that hybridization has played an important role in the evolution of the Gaultherieae.     

Nuclear DNA Polymorphisms Among Strains of Microseris bigelovii (Asteraceae: Lactuceae) Amplified from Arbitrary Primers

The autogamous annual Microseris bigelovii occurs in isolated populations along a narrow strip of land along the Pacific Coast from Southern California to Victoria, B. C. — Thirteen inbred strains were derived from 11 representative populations. Nuclear DNA from these strains was amplified using single arbitrary 10-base-pair primers. 194 amplification products were obtained with 22 primers. Of these, 44 were shared by all strains, 32 were present or absent in only one of the strains. The remaining 118 amplification products were shared by 2 to 11 strains. Attempts to construct a cladogram of the 13 inbred genotypes revealed 5 monophyletic groups. Two of these consist of duplicate isolates from two populations each, two comprise two strains each derived from neighboring populations, and one comprises the three populations from Victoria, B. C., which are postulated to be the result of local differentiation after a single founder event. The Victoria populations share the only known chloroplast mutation in M. bigelovii with a strain from the San Mateo County south of San Francisco. Beyond the local groups of strains we found more or less random allele associations rather than cladistic groupings, with overall genetic distances (UPGMA) more or less related to geographic distance. Achene transport, too rare for direct observationmust be effective to allow gene flow among populationsin M. bigelovii.     

Phylogenetic implications of corolla morphology in subfamily Barnadesioideae (Asteraceae)

The previously insignificant and small South American subtribe Barnadesiinae of tribe Mutisieae has been shown recently to be ancient within Asteraceae. Due to absence of a 22 kb diagnostic chloroplast inversion, plus other features, this subtribe has been elevated to subfamilial status as Barnadesioideae, now containing 90 species in nine genera. Recent cladistic analyses at the generic and specific levels based on morphology and DNA sequences (ITS and trnL intron) have revealed different relationships among taxa of the subfamily. To better understand these conflicts, we analyze specific morphological features of corollas (shape and vascularization) to develop trends (trees) in these features based on minimal structural change (i.e., morphological parsimony), and to compare these with relationships among genera derived from the two recent cladistic analyses. We define six principal types of corollas in Barnadesioideae (tubular, split, double split, ligulate, subbilabiate and bilabiate) and six principal types of corolla vascularization patterns (combinations of presence or absence of central bundles, fusion of adjacent bundles and fusion of bundles at the apex of corolla lobes). In all features we assume character states in Calyceraceae to be ancestral. In corolla shape, from tubular ancestry, we hypothesize two general evolutionary trends within the subfamily: (1) splitting of the tube, and (2) flattening of the tube. In vascularization of corollas, from an ancestral condition of one central and one lateral bundle in each corolla lobe and all traces fused at the apex, we hypothesize four basic trends: (1) gain or (2) loss of lateral vascular traces in each lobe, (3) loss of the central vein, and (4) loss of fusion of traces in lobe apices. These morphological trends allow tests of the two previous phylogenetic hypotheses by (1) counting step changes (following steps in the morphological network) in the two characters on the two competing phylogenetic trees and (2) constructing an index of morphological advancement for each genus (based on morphological trees of the two characters) and correlating these with cladistic distances within the two phylogenies. Results of both tests reveal the molecular phylogeny to be more compatible with evolutionary inferences from the two morphological features. With Fulcaldea excluded, a highly significant correlation is seen between morphological advancement and cladistic distance in the molecular phylogeny.     

DNA序列在悬钩子属植物分子系统学研究中的应用进展

悬钩子属植物种类繁多,类群复杂,而且多为多倍体和杂种。该文就近年来国内外有关DNA序列在悬钩子属植物分子系统学研究中的应用现状和进展进行了综述,并对中国悬钩子属植物系统发育研究进行了展望。研究认为:叶绿体DNA序列多应用非编码区,且多与ITS序列联合分析;核基因组中ITS序列应用最为广泛,主要用于研究悬钩子属空心莓组与木莓组的进化关系、栽培品种间亲缘关系及部分杂种和多倍体的起源等;在该属植物中发现了ITS个体内多态性,但未进行ITS假基因检测,其系统学应用价值需重新评价;低拷贝核基因只有GBSSI和LEAFY有相关应用。同时认为,悬钩子属植物系统学研究中应用的DNA序列及研究类群均较少,缺乏对整个悬钩子属全面而系统的研究。指出应进一步选择具有代表性的样本、筛选合适的DNA片段,并结合形态学、孢粉学和细胞学等手段对中国悬钩子属植物系统关系进行深入研究。     

Phylogenetic relationships of the enigmatic species Serratula chinensis and Serratula forrestii (Asteraceae - Cardueae)

The phylogenetic relationships of the Chinese species Serratula forrestii and S. chinensis within the subtribe Centaureinae (Asteraceae – Cardueae) were investigated based on nuclear ribosomal DNA external and internal transcribed spacer sequences. Results indicated that Serratula s. l. is clearly polyphyletic, none of the two species showing close affinities to either Serratula s. str. or Klasea, a genus traditionally included in Serratula. Serratula forrestii has a basal position within the subtribe and has retained most plesiomorphic character states. Serratula chinensis is related to the genera of the Rhaponticum group. Its chromosome number was determined as 2n = 26, and the relationship between this species and the Rhapon-ticum group is discussed from a morphological and karyological point of view.