基于DNA条形码对北京地区蔷薇科花卉上蚜虫的快速鉴定

蔷薇科花卉植物是北京城市绿化的主要观赏植物,也是多种蚜虫的寄主植物。由于蚜虫体型小,形态特征特化或退化,具有复杂的多型现象,依据传统的形态学特征往往无法实现对物种的准确而快速的鉴定,因此会影响对蚜虫的及时有效防治。本研究应用DNA条形码技术,基于COⅠ基因序列分析,对北京地区主要蔷薇科花卉上的蚜虫进行编码,试图在花卉种植和害虫防治时用于物种的快速、准确鉴定。实验得到9属12种蚜虫的65条COⅠ基因序列,种内平均差异为0.70%,种间平均差异为9.45%,最高可达12.59%。基于COⅠ序列构建了NJ树和MP树,绝大多数物种的样品有效地聚为一支,且支持率达到了90%以上,构建的系统发育树可以很好的显示相同物种样品的聚类。结合遗传距离和系统发育树分析表明,基于COⅠ序列的DNA条形码能有效区分83%的北京地区蔷薇科花卉蚜虫物种。     

植物DNA条形码技术的发展及应用

在对DNA条形码技术的发展过程进行归纳分析的基础上,对植物DNA条形码技术的研究进展、工作流程及分析方法、影响其鉴定准确性的因素及其在植物分类学研究中的应用现状及存在的争议进行了综合分析和阐述,并展望了植物DNA条形码技术的发展趋势及应用前景。通过具体实例说明将植物DNA条形码技术与传统植物学知识相结合可作为民族植物学的研究手段之一。认为:目前常用的植物DNA条形码主要有单一片段和多片段组合2种方式,这2种方式各有优缺点;常用的DNA序列有matK、trnH-psbA、rbcL和ITS等,但均有一定的局限性;针对不同的使用目的,应选择不同的植物DNA条形码标准;影响植物DNA条形码鉴定准确性的因素包括物种的类型和数量、系统树构建方法、杂交/基因渗入、物种起源时间的差异、分子进化速率差异等;当前植物DNA条形码研究工作的重点是选择合适的DNA片段并对其进行评价。     

Foraging interactions between native and exotic bumblebees: enclosure experiments using native flowering plants

To assess the impact of Bombus terrestris invasion on the foraging efficiency of native Japanese bumblebees, consumption and acquisition of floral resources during foraging on flowers of native Japanese plant species were investigated using enclosures with three treatments: one with only B. terrestris (exotic), one with both B. terrestris and native Japanese bumblebee species (mixed), and one with only Japanese species (native), but with the bumblebee density held constant. Changes in the body mass of queens and the nest mass of colonies for two days did not significantly differ among four combinations of the species and treatment, B. terrestris in the exotic and mixed treatments and Japanese species in the mixed and native treatments. Thus, it is not clear that B. terrestris has higher foraging efficiency than native species and that B. terrestris individuals more negatively affect the foraging efficiency of native species than individuals of the native species themselves. The nectar standing crop of Cirsium kamtschaticum was smaller in the exotic treatment than in the mixed and native treatments. However, this may have been an artifact of differences in the numbers of flowers in the various treatments. T. Nagamitsu and T. Kenta contributed equally to this work     

DNA条形码与动植物分类学的研究

DNA条形码在动植物分类学中的研究最近几年非常火热。这项技术在国外研究的比较多,国内的许多方面的研究还没达到国际水平。我国的动植物种类比较繁多,地区差异也较大,怎样能将这些物种准确,快速的进行分类,是众多动植物学家一直在研究的难题。针对DNA条形码研究的现状和他在动植物学中应用以及它存在的争议来进一步认识DNA条形码。     

Selfish DNA and breeding system in flowering plants

In many species, some individuals carry one or more B chromosomes: extra, or supernumerary chromosomes not part of the normal complement. In most well-studied cases, Bs lower the fitness of their carrier and persist in populations only because of accumulation mechanisms analogous to meiotic drive. It has been suggested that such genomic parasites are expected to persist only in outcrossed sexual species, in which uninfected lines of descent can be continuously reinfected; in inbred or asexual species, all selection is between lines of descent, and the genomic parasites are either lost or must evolve into commensals or mutualists. Here we present a simple population genetic model of the effect of outcrossing rate on the frequency of B chromosomes, and find that outcrossing facilitates the spread of parasitic Bs, but inhibits the spread of mutualists. Data compiled from the literature on breeding system and B chromosomes of British plants indicate that Bs are much more likely to be reported from obligately outcrossed species than inbred species. These results support the ideas that most B chromosomes are parasitic, and that breeding systems play a central role in the biology of selfish genes.     

DNA barcoding of arid wild plants using rbcL gene sequences

DNA barcoding is currently gaining popularity due to its simplicity and high accuracy as compared to the complexity and subjective biases associated with morphology-based identification of taxa. The standard chloroplast DNA barcode for land plants recommended by the Consortium for the Barcode of Life (CBOL) plant working group needs to be evaluated for a wide range of plant species. We therefore tested the potential of the rbcL marker for the identification of wild plants belonging to diverse families of arid regions. Maximum likelihood tree analysis was performed to evaluate the discriminatory power of the rbcL gene. Our findings showed that using rbcL gene sequences enabled identification of the majority of the samples (92%) to genus level and only 17% to species level.     

基于DNA条形码对桃属植物上蚜虫的快速鉴定

桃属(Amygdalus)植物是我国重要的果树,有些种类是常见的城市绿化观赏树种,也是多种蚜虫的寄主。蚜虫的体型小,有复杂的多型现象,传统的形态学特征往往无法实现对物种的准确而快速的鉴定。本研究应用DNA条形码技术,基于COⅠ基因序列分析,对我国桃属植物上的蚜虫进行编码,为桃属植物上蚜虫的物种快速、准确鉴定提供有力的支持。本研究共编码桃属植物上蚜虫12种,其中蚜亚科Aphidinae 6属10种,毛管蚜亚科Greenideinae 1属1种,毛蚜亚科Chaitophorinae 1属1种。共获得COⅠ基因序列96条,种内平均差异为0.76%,种间为5.7%¹5.5%。基于COⅠ序列构建了NJ树,绝大多数物种的样品有效地聚为一支,且支持率达到了95%以上。结合遗传距离和系统发育树分析表明,基于COⅠ序列的DNA条形码能有效区分99%的桃属植物上的蚜虫物种。     

Ancient flowering plants: DNA sequences and angiosperm classification

Phylogenetic analyses of gene sequences provide a clear pattern of which extant flowering plant genera diversified earliest. Combined with complete genomic sequences, these data will vastly improve understanding of the genetic basis of plant diversity.     

DNA barcoding is a new approach in comparative genomics of plants

DNA barcoding was proposed as a method for recognition and identification of eukaryotic species through comparison of sequences of a standard short DNA fragment—DNA barcode—from an unknown specimen to a library of reference sequences from known species. This allows identifying an organism at any stage of development from a very small tissue sample, fresh or conserved many years ago. Molecular identification of plant samples can be used in various scientific and applied fields. It would also help to find new species, which is particularly important for cryptogamic plants. An optimal DNA barcode region is a small fragment presented in all species of a major taxonomic group, having invariable nucleotide sequence in all members of the same species, but with sufficient variation to discriminate among the species. This fragment should be flanked by low-variable regions for use of universal primers in PCR for amplification and sequencing. The DNA barcode that is well established in animals is a sequence of a fragment of the mitochondrial cytochrome c oxidase gene CO1. However, searching for DNA barcode in plants proved to be a more challenging task. No DNA region universally suitable for all plants and meeting all of the necessary criteria has been found. Apparently, a multilocus or two-stage approach should be applied for this purpose. Several fragments of the chloroplast genome (trnH-psbA, matK, rpoC, rpoB, rbcL) in combinations of two or three regions were suggested as candidate regions with highest potential, but more representative samples should be examined to choose the best candidate. The possibility is discussed to use as DNA barcode internal transcribed spacers (ITS) of nuclear rRNA genes, which are highly variable, widely employed in molecular phylogenetic studies at the species level, but also have some limitations.     

Variation in the phenology and abundance of flowering by native and exotic plants in subalpine meadows

The timing and abundance of flower production is important to the reproductive success of angiosperms as well as pollinators and floral and seed herbivores. Exotic plants often compete with native plants for space and limiting resources, potentially altering community floral dynamics. We used observations and a biomass-removal experiment to explore the effects of an invasive exotic flowering plant, Linaria vulgaris, on community and individual species flowering phenology and abundance in subalpine meadows in Colorado, USA. Invasion by L. vulgaris was associated with a shift in both the timing and abundance of community flowering. Invaded plant communities exhibited depressed flowering by 67% early in the season relative to uninvaded communities, but invaded sites produced 7.6 times more flowers than uninvaded sites once L. vulgaris began flowering. This increase in flowers at the end of the season was driven primarily by prolific flowering of L. vulgaris. We also found lower richness and evenness of resident flowering species in invaded plots during the period of L. vulgaris flowering. At the species level, a common native species (Potentilla pulcherrima) produced 71% fewer flowers in invaded relative to uninvaded plots, and the species had reduced duration of flowering in invaded relative to uninvaded sites. This result suggests that L. vulgaris does not simply alter the flowering of subordinate species but also the flowering of an individual common species in the plant community. We then used observational data to explore the relationship between L. vulgaris density and resident floral production but found only partial evidence that higher densities of L. vulgaris were associated with stronger effects on resident floral production. Taken together, results suggest that a dominant invasive plant can affect community and individual-species flowering.     

DNA barcoding of blastocystis

We have developed a simple method for subtyping the intestinal protistan parasite Blastocystis using an approach equivalent to DNA barcoding in animals. Amplification of a 600 bp region of the small subunit ribosomal RNA gene followed by single primer sequencing of the PCR product provides enough data to assign isolates to specific subtypes unambiguously. We believe that this approach will prove useful in future epidemiological studies.     

DNA barcoding of billfishes

DNA barcoding is a method promising fast and accurate identification of animal species based on the sequencing of the mitochondrial c oxidase subunit (COI) gene. In this study, we explore the prospects for DNA barcoding in one particular fish group, the billfishes (suborder Xiphioidei--swordfish, marlins, spearfishes, and sailfish). We sequenced the mitochondrial COI gene from 296 individuals from the 10 currently recognized species of billfishes, and combined these data with a further 57 sequences from previously published projects. We also sequenced the rhodopsin gene from a subset of 72 individuals to allow comparison of mitochondrial results against a nuclear marker. Five of the 10 species are readily distinguishable by COI barcodes. Of the rest, the striped marlin (Kajikia audax) and white marlin (K. albida) show highly similar sequences and are not unambiguously distinguishable by barcodes alone, likewise are the three spearfishes Tetrapturus angustirostris, T. belone, and T. pfluegeri. We discuss the taxonomic status of these species groups in light of our and other data, molecular and morphological.     

DNA barcoding of Dutch birds

The mitochondrial cytochrome c oxidase subunit I (COI) can serve as a fast and accurate marker for the identification of animal species, and has been applied in a number of studies on birds. We here sequenced the COI gene for 387 individuals of 147 species of birds from the Netherlands, with 83 species being represented by > 2 sequences. The Netherlands occupies a small geographic area and 95% of all samples were collected within a 50 km radius from one another. The intraspecific divergences averaged 0.29% among this assemblage, but most values were lower; the interspecific divergences averaged 9.54%. In all, 95% of species were represented by a unique barcode, with 6 species of gulls and skua (Larus and Stercorarius) having at least one shared barcode. This is best explained by these species representing recent radiations with ongoing hybridization. In contrast, one species, the Lesser Whitethroat Sylvia curruca showed deep divergences, averaging 5.76% and up to 8.68% between individuals. These possibly represent two distinct taxa, S. curruca and S. blythi, both clearly separated in a haplotype network analysis. Our study adds to a growing body of DNA barcodes that have become available for birds, and shows that a DNA barcoding approach enables to identify known Dutch bird species with a very high resolution. In addition some species were flagged up for further detailed taxonomic investigation, illustrating that even in ornithologically well-known areas such as the Netherlands, more is to be learned about the birds that are present.     

Apomixis and amphimixis in flowering plants

The objective of the present article is to compare apomictic and sexual reproduction (amphimixis) in flowering plants. Light-optical and ultrastructural aspects of the cytoembryological processes in apomicts, beginning with the early stages of development of the ovule and concluding with the newly formed seed, are considered. In the overwhelming majority of apomicts, an inability to develop an autonomous endosperm or to form viable seeds without the involvement of the process of fertilization of the nuclei of the central cell of the embryo sac is observed. Characteristic features of the ultrastructural differentiation of the megasporocytes in diplospory, of aposporous initial cells in apospory, of embryocytes in adventive embryony, and of ovicells in parthenogenesis and synergids in apogamety are identified and are compared to the generative structures of amphimicts. The hypothesis is made that the mechanisms of genetic regulation in the formation and development of the generative structures in apomixis and amphimixis are similar at the cellular level. The present study is not a survey of apomixis in general. Previously published original results that have been obtained by the present author as a result of many years of research in the area of apomixis have served as a basis for the preparation of the study.     

Polyploidy and self-fertilization in flowering plants

Mating systems directly control the transmission of genes across generations, and understanding the diversity and distribution of mating systems is central to understanding the evolution of any group of organisms. This basic idea has been the motivation for many studies that have explored the relationships between plant mating systems and other biological and/or ecological phenomena, including a variety of floral and environmental characteristics, conspecific and pollinator densities, growth form, parity, and genetic architecture. In addition to these examples, a potentially important but poorly understood association is the relationship between plant mating systems and genome duplication, i.e., polyploidy. It is widely held that polyploid plants self-fertilize more than their diploid relatives, yet a formal analysis of this pattern does not exist. Data from 235 species of flowering plants were used to analyze the association between self-fertilization and ploidy. Phylogenetically independent contrasts and cross-species analyses both lend support to the hypothesis that polyploids self-fertilize more than diploids. Because polyploidy and self-fertilization are so common among angiosperms, these results contribute not only to our understanding of the relationship between mating systems and polyploidy in particular, but more generally, to our understanding of the evolution of flowering plants.