Elongation of palindromic repetitive DNA by DNA polymerase from hyperthermophilic archaea: a mechanism of DNA elongation and diversification

DNA polymerase from hyperthermophilic bacteria can elongate tandem repetitive oligoDNA with a complete or incomplete palindromic sequence under isothermal conditions by "hairpin elongation". However, the product of the reaction has not yet been sufficiently characterized. Here, I demonstrate that when palindromic repetitive oligoDNA, e.g., (5'AGATATCT3')(6), was added as a "seed" to the DNA synthesis reaction catalyzed by DNA polymerase from the archaea Thermococcus litoralis (Vent polymerase) at 74 degrees C, the product was (5'AGATATCT3')(n). The product itself was palindromic and repetitive, and its motif (unit) sequence was exactly the same as that of the seed oligoDNA. On the other hand, when a pseudopalindrome, which contains a palindrome-breaking nucleotide (underlined), was present in seed oligoDNA, e.g., (5'GATTC3')(6), the product was (5'GATATC3')(n), which had a different motif sequence from that of the seed oligoDNA. When a pseudopalindrome (5'AGATATCA3')(6) was added to the reaction, the products were 5'TATCA . (AGATATCA)(3) . AGATATCT . (TGATATCT)(5) . TGATA3', etc. When 5'AGATATCA . (AGATATCT3')(5) was added, products were 5'TATCT . (AGATATCT)(2).TGATATCT . AGATATCT . AGATATCA . AGATATCT . AGA3', etc., demonstrating the generation of many "mutations" in the product DNA. I conclude that a tandem repetitive sequence is faithfully elongated (amplified) by hyperthermophilic DNA polymerase if it is completely palindromic, but is elongated with many errors if it is incompletely palindromic (pseudopalindromic) or mixed with a pseudopalindrome. The results suggest a protein-catalyzed elongation/diversification mechanism of short repetitive DNAs on the early earth.     

新疆塔里木拜城地区早白垩世舒善河组孢粉组合

基于新疆塔里木盆地北部拜城卡普沙良河剖面下白垩统舒善河组发现的29属48种孢子花粉的研究,建立舒善河组自下而上的4个孢粉亚组合,分别为Classopollis-Cycadopites-Lygodioisporites-Biretisporites(CCLB)亚组合,Classopollis-Dicheiropollis-Schizaeoisporites-Klukisporites(CDSK)亚组合,Classopollis-Dicheiropollis-Par-visaccites-Lygodiumsporites(CDPL)亚组合和Classopollis-Dicheiropollis-Pinuspollenites-Impardecispora(CDPI)亚组合。舒善河组孢粉植物群以松柏类掌鳞杉科植物占优势以及真蕨类海金沙科的繁盛为主要特征。该孢粉植物群与欧洲、亚洲、美洲和澳大利亚早白垩世尼欧克姆期孢粉植物群可以对比。根据孢粉学证据,舒善河组的时代属于尼欧克姆期或欧特里夫期至巴列姆期。     

新疆准噶尔盆地芳3井晚白垩世孢粉组合的发现及其地质意义

准噶尔盆地腹部芳3井紫泥泉子组所夹灰色泥岩中产丰富的盘星藻、葡萄藻等藻类、疑源类化石及一定数量的孢粉化石。孢粉化石计75属160种,并首次在新疆地区发现了可靠的鹰粉型化石Aquilapollenites以及在我国主要产于松辽盆地和广东三水盆地上白垩统的“大孢子”化石Balmeisporites,建立Schizaeoisporites grandus-Parcisporites parvisaccus-Liliacidites creticus(GPC)组合。通过对部分孢粉属种已知地质分布的分析以及与国内外部分地区晚白垩世孢粉组合的对比,将GPC组合的时代确定为晚白垩世坎潘期至马斯特里赫特期。根据紫泥泉子组的沉积特点及孢粉组合特征,认为晚白垩世准噶尔盆地应归属西北-东南孢粉植物区,局部层段沉积时期气候比较湿润,孢粉组合具有我国东北孢粉植物区与西北-东南孢粉植物区的过渡特点。     

白垩纪放射虫"Turbocapsula costata"带和藏南雅鲁藏布缝合带硅质岩系的时代问题

西地中海地区早白垩世阿普特期"costata亚带"(O’Dogherty,1994)的带化石"Turbocapsula costata( Wu)",源自藏南赛诺曼期冲堆组的Tricapsula costata Wu。2002年,Matsuoka等把藏南下鲁硅岩层位最高的放射虫带与"costata亚带"对比,称为"Turbocapsulacostata"带,并认为冲堆组时代也应为阿普特期。但西地中海区的"Turbocapsula costata( Wu)"和冲堆组的Tricapsula costata Wu,虽然壳体外形相似,但壳体结构却有重要差别,不是相同属种。前者种名和相应的化石带名都需重新命名。下鲁硅岩的"Turbocapsula costata(Wu)",据图版所示特征,应为Tricapsula costata。下鲁硅岩顶部的时代为晚白垩世赛诺曼期。     

Map and analysis of microsatellites in the genome of <Emphasis Type="Italic">Populus</Emphasis>: The first sequenced perennial plant

We mapped and analyzed the microsatellites throughout 284295605 base pairs of the unambiguously assembled sequence scaffolds along 19 chromosomes of the haploid poplar genome. Totally, we found 150985 SSRs with repeat unit lengths between 2 and 5 bp. The established microsatellite physical map demonstrated that SSRs were distributed relatively evenly across the genome of Populus. On average, These SSRs occurred every 1883 bp within the poplar genome and the SSR densities in intergenic regions, introns, exons and UTRs were 85.4%, 10.7%, 2.7% and 1.2%, respectively. We took di-, tri-, tetra-and pentamers as the four classes of repeat units and found that the density of each class of SSRs decreased with the repeat unit lengths except for the tetranucleotide repeats. It was noteworthy that the length diversification of microsatellite sequences was negatively correlated with their repeat unit length and the SSRs with shorter repeat units gained repeats faster than the SSRs with longer repeat units. We also found that the GC content of poplar sequence significantly correlated with densities of SSRs with uneven repeat unit lengths (tri-and penta-), but had no significant correlation with densities of SSRs with even repeat unit lengths (di-and tetra-). In poplar genome, there were evidences that the occurrence of different microsatellites was under selection and the GC content in SSR sequences was found to significantly relate to the functional importance of microsatellites.     

The fossil pollen record of Araceae

The fossil record of Araceae pollen beginning in the late Early Cretaceous and peaking in the Paleocene/Eocene is very sparse up to now, consisting of three highly distinctive types: zona-aperturate pollen of the Monstera or Gonatopus type (very similar to Proxapertites operculatus), an ulcerate-spiny type typical for Limnobiophyllum, and a polyplicate, omniaperturate pollen type (an ephedroid pollen with non-gnetalean affinities) which was recently reported from the late Early Cretaceous (Mayoa portugallica). An extensive literature search has shown that some distinctive Ephedripites forms (the Paleogene Ephedripites vanegensis, and the Late Cretaceous Ephedripites elsikii) are very similar to pollen of Spathiphyllum and both species are here transferred from Ephedripites to Spathiphyllum (as comb. nov.). We also add new fossil findings to the Araceae record. The new findings include a zona-aperturate, microperforate to microreticulate pollen type from the Palaeocene of Colombia, highly similar to extant Gonatopus or Zamioculcas or Monstera pollen (Araceae) and to fossil Proxapertites operculatus, which is currently seen as a fossil equivalent; and, an ulcerate, spiny pollen from the Eocene of Stolzenbach, Germany, extending the range of Limnobiophyllum (Pandaniidites), which is thought to be an extinct member of extant Araceae. The three pollen types add considerably to the reliable fossil record of the family that now contains more than 20 records of these three pollen types: with the zona-aperturate type recorded from the tropical or subtropical regions of Northern and Southern America, Central Africa, Southern and Central Europe, from the Indian subcontinent and the Malayan Archipelago; the ulcerate type occurring in North America and Europe; and the polyplicate type mainly occurring in South America and South-West Europe. Now we have good evidence that some of the aroid subfamilies were already in existence in the Cretaceous, increasing in diversity and worldwide distribution in the Paleogene. Dedicated to Prof. Dr. Stefan Vogel on the occasion of his 80th birthday.     

Rapid evolution of outer egg membrane proteins in the Drosophila melanogaster subgroup: a case of ecologically driven evolution of female reproductive traits

Although sexual selection has been predominantly used to explain the rapid evolution of sexual traits, eggs of oviparous organisms directly face both the challenges of sexual selection as well as natural selection (environmental challenges, survival in niches, etc.). Being the outermost membrane in most insect eggs, the chorion layer is the interface between the embryo and the environment, thereby serving to protect the egg. Adaptive ecological radiations such as divergence in ovipositional substrate usage and host-plant specializations can therefore influence the evolution of eggshell proteins. We can hypothesize that proteins localized on the outer eggshell may be affected to a greater degree by ecological challenges compared with inner eggshell proteins, and therefore, proteins localized in the outer eggshell (chorion membrane) may evolve differently (faster) than proteins localized in the inner egg membrane (vitelline membrane). We compared the evolutionary divergence of vitelline with chorion membrane proteins in species of the melanogaster subgroup and found that chorion proteins as a group are indeed evolving faster than vitelline membrane proteins. At least one vitelline membrane protein (Vm32E), specifically localized on the outer eggshell, is also evolving faster than other vitelline membrane proteins suggesting that all proteins localized on the outer eggshell may be evolving rapidly. We also found evidence that specific codons in chorion proteins cp15 and cp16 are evolving under positive selection. Polymorphism surveys of cp16 revealed inflated levels of divergence relative to polymorphism in specific regions of the gene, indicating that these regions are under strong selection. At the morphological level, we found notable difference in eggshell surface morphologies between specialist (Drosophila sechellia and Drosophila erecta) and generalist species of Drosophila. We do not know if any of the chorion proteins actually interact with spermatozoids, therefore leaving the possibility of rapid evolution through gametic interaction wide open. At this point, however, our results support previous suggestions that divergences in ecology, particularly, ovipositional substrate divergences may be a strong force driving the evolution of eggshell proteins.     

Fundamental and specialized questions on host race formation and speciation – an introduction

Host race formation and speciation are at the core of the enormous insect diversification. Insect–host relationships can take many forms, ranging from parasitic to mutualistic. Despite its long history of study, many questions remain about host race formation and speciation. They are addressed in eight original papers of this special issue, including two review-type articles. In line with the scope of Entomologia Experimentalis et Applicata, they include both fundamental and applied studies. They reveal that host race formation and speciation can take many forms and that they are still active topics of entomological research.