系统发育基因组学——重建生命之树的一条迷人途径

生物基因组计划的相继启动对系统发育学研究的发展产生了深远影响。将基因组学和系统发育学结合起来的“系统发育基因组学”在这一背景下应运而生, 这门崭新交叉学科的出现成为重建“生命之树”的一条迷人途径。文章重点围绕系统发育基因组学的概念以及分析方法进行扼要介绍, 并探讨了它目前潜在的问题以及将来有待发展和完善的地方。     

基因树冲突与系统发育基因组学研究

随着越来越多的基因序列被运用于系统发育重建中,随之产生的基因树冲突已成为分子系统发育研究中日益突出的问题.因此,在分子系统发育研究中,应正确理解基因树和物种树之间的差异,充分注意和分析基因树冲突的原因,正确解释分子系统发育的结果.本文通过一些典型实例分析了在多基因系统发育研究中引发基因树冲突的三类主要原因:随机误差、系统误差和生物学因素.在此基础上,对近年来兴起的系统发育基因组学进行了介绍,并以稻属Oryza研究为例,阐述了系统发育基因组学方法在解决基因树冲突以及系统发育研究中的优势和应用价值,并进一步探讨了解决基因树冲突的策略和方法,以期为分子系统发育研究提供一些肩示和帮助.     

哺乳动物系统发育基因组学研究进展

哺乳动物是一类最进化并在地球上占主导地位的动物类群,重建其系统发育关系一直是分子系统学的研究热点。随着越来越多物种全基因组测序的完成,在基因组水平上探讨该类动物的系统发育关系与进化成为研究的热点。本文从全基因组序列,稀有基因组变异及染色体涂染等几个方面简要介绍了当前系统发育基因组学在现生哺乳动物分子系统学中的应用,综合已有的研究归纳整理了胎盘亚纲的总目及目间的系统发育关系,给出了胎盘动物19 个目的系统发育树。本文还分析了哺乳动物系统发育基因组学目前所面临的主要问题及未来的发展前景。     

基因组时代的放线菌系统分类学及其研究进展

由于放线菌在生物技术、医药卫生和环境治理等领域中的实际重要性,已经成为人们研究得最为深入的微生物类群之一。现代放线菌分类学是建立在对16S rRNA基因保守分子序列的系统发育学分析基础上、综合利用多种微生物信息的多相分类学(polyphasic taxonomy)。随着大规模基因测序技术的飞速发展,已经完成了超过100株放线菌的全基因组序列。近年来发展起来的"基因组系统发育学"有助让人们更加系统地理解放线菌类群的发生、演化,以及不同生境类群之间的相互关系。随着越来越多的以系统发育学为指导的基因组测序研究项目,例如"细菌和古菌基因组百科全书(Genomic Encyclopedia of Bacteria andArchaea,GEBA)计划"的出现,标志着放线菌系统学进入了基因组学研究时代。本文对基因组时代的放线菌系统学方法,以及国内外的相关研究成果进行综述。     

叶绿体系统发育基因组学的研究进展

系统发育基因组学是由系统发育研究和基因组学相结合产生的一门崭新的交叉学科。近年来,在植物系统发育研究中,基于叶绿体基因组的系统发育基因组学研究优势渐显端倪,为一些分类困难类群的系统学问题提出了解决方案,但同时也存在某些问题。本文结合近年来叶绿体系统发育基因组学研究中的一些典型实例,讨论了叶绿体系统发育基因组学在植物系统关系重建中的价值和应用前景,并针对其存在问题进行了探讨,其中也涉及了新一代测序技术对叶绿体系统发育基因组学的影响。     

基于叶绿体rps16基因和核基因ITS片段研究肉苁蓉属系统位置

在前人对列当科系统发育研究的基础上,追加了肉苁蓉属(Cistanche)的基因序列数据,运用最大简约法、最大似然法和贝叶斯推断方法探讨了其在列当科中的系统位置及列当科中属间关系.基于rps16基因序列及rps16+ ITS联合序列建立了列当科系统发育树,结果显示,肉苁蓉属、列当属(Orobanche)以及草苁蓉属(Boschniakia)聚在同一进化枝内,肉苁蓉属和列当属表现出最近亲缘关系;列当科中的全寄生类群、半寄生类群和非寄生类群分属在3个不同分支中.     

鼠疫耶尔森氏菌的进化研究:从系统发育学到系统发育基因组学

20世纪90年代末起,基因组学在细菌研究中应用越来越广泛,尤其在进化领域,取得了一系列革命性的发现.本文以鼠疫耶尔森氏菌进化研究为例,介绍了从利用基因组中少数特定片段(等位基因)多态性进行分析的传统系统发育学,到基于大量菌株全基因组序列进行系统发育基因组学的研究发展历程,回顾讨论了基因组学技术的进步为鼠疫菌进化研究领域带来的成果.     

绣球属(Hydrangea L.)植物分子系统学及系统发育分析

该研究基于对绣球属(Hydrangea L.)的大尺度取样,选取国内外61种绣球属和近缘属植物,分别基于核基因片段(ITS)和叶绿体基因片段(rbcL,trnL-F,atpB)重建了绣球属及其近缘种属的系统发育关系。结果表明:(1)核基因与叶绿体基因树之间在树形上没有明显的冲突,进而基于核基因和叶绿体基因联合数据重建了绣球属及其近缘种属的系统发育关系。(2)基于联合数据构建的系统树确认了2个大分支,并得到了果实顶端截平与否这一形态学证据的强力支持;每个大分枝又分为4个类群,共确定了8个类群。部分类群也得到了广义宏观形态性状的支持,如第1类群得到了叶形、花粉以及种子形态的支持。因此,该系统发育关系的重建对于全面理解绣球属及其近缘种属的演化关系具有重要的启发。     

胡颓子科叶绿体基因组系统发育分析与演化趋势推断

【目的】为探索胡颓子科叶绿体基因组演化趋势,从而为胡颓子科植物物种鉴定以及资源开发利用提供理论依据。【方法】研究从头组装并注释了沙棘属（Hippophae）和野牛果属（Shepherdia）共4个类群的叶绿体基因组,结合已发表的叶绿体基因组序列,比较了胡颓子科各类群叶绿体基因组的基因构成、重复序列和结构特征,建立了系统发育树,并通过高分化区定位了该科叶绿体基因组的潜在DNA条形码区域。【结果】胡颓子科各属叶绿体基因组在四分体结构、基因数量和排列上高度相似;沙棘属和野牛果属的反向重复区（IR）和整个基因组重复序列数目较胡颓子属有扩张和增加的趋势。基于胡颓子科18个类群的叶绿体全基因组序列的系统发育树中,胡颓子属、沙棘属和野牛果属各自聚为一支,前者先分化出来,沙棘属和野牛果属有最近共同祖先;从长单拷贝区（LSC）和短单拷贝区（SSC）筛选出3个DNA条形码候选区,其中ycf1基因的鉴定效果最佳,基于此构建的各类群系统发育关系与基于全基因组序列的结果一致。【结论】胡颓子科的叶绿体基因组结构保守,但其非编码区序列在各属间存在明显差异,且IR区序列与重复序列在演化过程中分别有扩张和增多的趋势。研究选定的DNA条形码序列能很好区分胡颓子科各属之间以及胡颓子属内物种间关系。     

Use of whole genome sequence data to infer baculovirus phylogeny

Several phylogenetic methods based on whole genome sequence data were evaluated using data from nine complete baculovirus genomes. The utility of three independent character sets was assessed. The first data set comprised the sequences of the 63 genes common to these viruses. The second set of characters was based on gene order, and phylogenies were inferred using both breakpoint distance analysis and a novel method developed here, termed neighbor pair analysis. The third set recorded gene content by scoring gene presence or absence in each genome. All three data sets yielded phylogenies supporting the separation of the Nucleopolyhedrovirus (NPV) and Granulovirus (GV) genera, the division of the NPVs into groups I and II, and species relationships within group I NPVs. Generation of phylogenies based on the combined sequences of all 63 shared genes proved to be the most effective approach to resolving the relationships among the group II NPVs and the GVs. The history of gene acquisitions and losses that have accompanied baculovirus diversification was visualized by mapping the gene content data onto the phylogenetic tree. This analysis highlighted the fluid nature of baculovirus genomes, with evidence of frequent genome rearrangements and multiple gene content changes during their evolution. Of more than 416 genes identified in the genomes analyzed, only 63 are present in all nine genomes, and 200 genes are found only in a single genome. Despite this fluidity, the whole genome-based methods we describe are sufficiently powerful to recover the underlying phylogeny of the viruses.     

Alignments of mitochondrial genome arrangements: applications to metazoan phylogeny

Mitochondrial genomes provide a valuable dataset for phylogenetic studies, in particular of metazoan phylogeny because of the extensive taxon sample that is available. Beyond the traditional sequence-based analysis it is possible to extract phylogenetic information from the gene order. Here we present a novel approach utilizing these data based on cyclic list alignments of the gene orders. A progressive alignment approach is used to combine pairwise list alignments into a multiple alignment of gene orders. Parsimony methods are used to reconstruct phylogenetic trees, ancestral gene orders, and consensus patterns in a straightforward approach. We apply this method to study the phylogeny of protostomes based exclusively on mitochondrial genome arrangements. We, furthermore, demonstrate that our approach is also applicable to the much larger genomes of chloroplasts.     

Using whole genome presence/absence data to untangle function in 12 Drosophila genomes

The Drosophila 12 genome data set was used to construct whole genome, gene family presence/absence matrices using a broad range of E value cutoffs as criteria for gene family inclusion. The various matrices generated behave differently in phylogenetic analyses as a function of the e-value employed. Based on an optimality criterion that maximizes internal corroboration of information, we show that values of e-105 to e-125 extract the most internally consistent phylogenetic signal. Functional class of most genes and gene families can be accurately determined based on the D. melanogaster genome annotation. We used the gene ontology (GO) system to create partitions based on gene function. Several measures of phylogenetic congruence (diagnosis, consistency, partitioned support , hidden support) for different higher and lower level GO categories, were used to mine the data set for genes and gene families that show strong agreement or disagreement with the overall combined phylogenetic hypothesis. We propose that measures of phylogenetic congruence can be used as criteria to identify loci with related GO terms that have a significant impact on cladogenesis.     

Among-site rate variation and phylogenetic analysis of 12S rRNA in sigmodontine rodents

We analyze sequences from two mitochondrial genes, cytochrome b (cyt b) and 12S rRNA (12S), for a group of sigmodontine rodents among which phylogenetic relationships are well understood based on concordance of morphological, chromosomal, allozyme, and other DNA data sets. Because these two genes are physically linked on the nonrecombining mitochondrial genome, they necessarily share the same history. Phylogenetic analysis of the cyt b gene recovers the well-corroborated relationships, generally with strong support. None of the methods that we employed, including variously weighted parsimony, neighbor joining on both single-rate and gamma-corrected distances, and maximum likelihood, were able to recover these relationships for the 12S gene. Parsimony analyses of the 12S data resulted in a relatively strongly supported placement of Peromyscus eremicus that conflicts with that suggested by cyt b and all other data. There is extreme among-site rate variation in the 12S sequences and moderate levels in the cyt b sequences. This highly skewed distribution of rates in the 12S gene makes phylogenetic analyses of these sequences particularly susceptible to the misleading effects of nonindependence and other nonrandom noise, suggesting that phylogenetic analyses of data sets that contain a great deal of among-site rate variation be interpreted with caution.      

Molecular epidemiology of clinically high-risk Pseudomonas aeruginosa strains: Practical overview

In recent years, numerous outbreaks of multidrug-resistant Pseudomonas aeruginosa have been reported across the world. Once an outbreak occurs, besides routinely testing isolates for susceptibility to antimicrobials, it is required to check their virulence genotypes and clonality profiles. Replacing pulsed-field gel electrophoresis DNA fingerprinting are faster, easier-to-use, and less expensive polymerase chain reaction (PCR)-based methods for characterizing hospital isolates. P. aeruginosa possesses a mosaic genome structure and a highly conserved core genome displaying low sequence diversity and a highly variable accessory genome that communicates with other Pseudomonas species via horizontal gene transfer. Multiple-locus variable-number tandem-repeat analysis and multilocus sequence typing methods allow for phylogenetic analysis of isolates by PCR amplification of target genes with the support of Internet-based services. The target genes located in the core genome regions usually contain low-frequency mutations, allowing the resulting phylogenetic trees to infer evolutionary processes. The multiplex PCR-based open reading frame typing (POT) method, integron PCR, and exoenzyme genotyping can determine a genotype by PCR amplifying a specific insertion gene in the accessory genome region using a single or a multiple primer set. Thus, analyzing P. aeruginosa isolates for their clonality, virulence factors, and resistance characteristics is achievable by combining the clonality evaluation of the core genome based on multiple-locus targeting methods with other methods that can identify specific virulence and antimicrobial genes. Software packages such as eBURST, R, and Dendroscope, which are powerful tools for phylogenetic analyses, enable researchers and clinicians to visualize clonality associations in clinical isolates.     

Reconciling gene and genome duplication events: using multiple nuclear gene families to infer the phylogeny of the aquatic plant family Pontederiaceae

Most plant phylogenetic inference has used DNA sequence data from the plastid genome. This genome represents a single genealogical sample with no recombination among genes, potentially limiting the resolution of evolutionary relationships in some contexts. In contrast, nuclear DNA is inherently more difficult to employ for phylogeny reconstruction because major mutational events in the genome, including polyploidization, gene duplication, and gene extinction can result in homologous gene copies that are difficult to identify as orthologs or paralogs. Gene tree parsimony (GTP) can be used to infer the rooted species tree by fitting gene genealogies to species trees while simultaneously minimizing the estimated number of duplications needed to reconcile conflicts among them. Here, we use GTP for five nuclear gene families and a previously published plastid data set to reconstruct the phylogenetic backbone of the aquatic plant family Pontederiaceae. Plastid-based phylogenetic studies strongly supported extensive paraphyly of Eichhornia (one of the four major genera) but also depicted considerable ambiguity concerning the true root placement for the family. Our results indicate that species trees inferred from the nuclear genes (alone and in combination with the plastid data) are highly congruent with gene trees inferred from plastid data alone. Consideration of optimal and suboptimal gene tree reconciliations place the root of the family at (or near) a branch leading to the rare and locally restricted E. meyeri. We also explore methods to incorporate uncertainty in individual gene trees during reconciliation by considering their individual bootstrap profiles and relate inferred excesses of gene duplication events on individual branches to whole-genome duplication events inferred for the same branches. Our study improves understanding of the phylogenetic history of Pontederiaceae and also demonstrates the utility of GTP for phylogenetic analysis.     

The complete mitochondrial genome of the nudibranch Roboastra europaea (Mollusca: Gastropoda) supports the monophyly of opisthobranchs

The complete nucleotide sequence (14,472 bp) of the mitochondrial genome of the nudibranch Roboastra europaea (Gastropoda: Opisthobranchia) was determined. This highly compact mitochondrial genome is nearly identical in gene organization to that found in opisthobranchs and pulmonates (Euthyneura) but not to that in prosobranchs (a paraphyletic group including the most basal lineages of gastropods). The newly determined mitochondrial genome differs only in the relative position of the trnC gene when compared with the mitochondrial genome of Pupa strigosa, the only opisthobranch mitochondrial genome sequenced so far. Pupa and Roboastra represent the most basal and derived lineages of opisthobranchs, respectively, and their mitochondrial genomes are more similar in sequence when compared with those of pulmonates. All phylogenetic analyses (maximum parsimony, minimum evolution, maximum likelihood, and Bayesian) based on the deduced amino acid sequences of all mitochondrial protein-coding genes supported the monophyly of opisthobranchs. These results are in agreement with the classical view that recognizes Opisthobranchia as a natural group and contradict recent phylogenetic studies of the group based on shorter sequence data sets. The monophyly of opisthobranchs was further confirmed when a fragment of 2,500 nucleotides including the mitochondrial cox1, rrnL, nad6, and nad5 genes was analyzed in several species representing five different orders of opisthobranchs with all common methods of phylogenetic inference. Within opisthobranchs, the polyphyly of cephalaspideans and the monophyly of nudibranchs were recovered. The evolution of mitochondrial tRNA rearrangements was analyzed using the cox1+rrnL+nad6+nad5 gene phylogeny. The relative position of the trnP gene between the trnA and nad6 genes was found to be a synapomorphy of opisthobranchs that supports their monophyly.     

Construction of a Phylogenetic Tree of Photosynthetic Prokaryotes Based on Average Similarities of Whole Genome Sequences

Phylogenetic trees have been constructed for a wide range of organisms using gene sequence information, especially through the identification of orthologous genes that have been vertically inherited. The number of available complete genome sequences is rapidly increasing, and many tools for construction of genome trees based on whole genome sequences have been proposed. However, development of a reasonable method of using complete genome sequences for construction of phylogenetic trees has not been established. We have developed a method for construction of phylogenetic trees based on the average sequence similarities of whole genome sequences. We used this method to examine the phylogeny of 115 photosynthetic prokaryotes, i.e., cyanobacteria, Chlorobi, proteobacteria, Chloroflexi, Firmicutes and nonphotosynthetic organisms including Archaea. Although the bootstrap values for the branching order of phyla were low, probably due to lateral gene transfer and saturated mutation, the obtained tree was largely consistent with the previously reported phylogenetic trees, indicating that this method is a robust alternative to traditional phylogenetic methods.     

Integrated gene and species phylogenies from unaligned whole genome protein sequences

MOTIVATION: Most molecular phylogenies are based on sequence alignments. Consequently, they fail to account for modes of sequence evolution that involve frequent insertions or deletions. Here we present a method for generating accurate gene and species phylogenies from whole genome sequence that makes use of short character string matches not placed within explicit alignments. In this work, the singular value decomposition of a sparse tetrapeptide frequency matrix is used to represent the proteins of organisms uniquely and precisely as vectors in a high-dimensional space. Vectors of this kind can be used to calculate pairwise distance values based on the angle separating the vectors, and the resulting distance values can be used to generate phylogenetic trees. Protein trees so derived can be examined directly for homologous sequences. Alternatively, vectors defining each of the proteins within an organism can be summed to provide a vector representation of the organism, which is then used to generate species trees. RESULTS: Using a large mitochondrial genome dataset, we have produced species trees that are largely in agreement with previously published trees based on the analysis of identical datasets using different methods. These trees also agree well with currently accepted phylogenetic theory. In principle, our method could be used to compare much larger bacterial or nuclear genomes in full molecular detail, ultimately allowing accurate gene and species relationships to be derived from a comprehensive comparison of complete genomes. In contrast to phylogenetic methods based on alignments, sequences that evolve by relative insertion or deletion would tend to remain recognizably similar.     

Conditioned genome reconstruction: how to avoid choosing the conditioning genome

Genome phylogenies can be inferred from data on the presence and absence of genes across taxa. Logdet distances may be a good method, because they allow expected genome size to vary across the tree. Recently, Lake and Rivera proposed conditioned genome reconstruction (calculation of logdet distances using only those genes present in a conditioning genome) to deal with unobservable genes that are absent from every taxon of interest. We prove that their method can consistently estimate the topology for almost any choice of conditioning genome. Nevertheless, the choice of conditioning genome is important for small samples. For real bacterial genome data, different choices of conditioning genome can result in strong bootstrap support for different tree topologies. To overcome this problem, we developed supertree methods that combine information from all choices of conditioning genome. One of these methods, based on the BIONJ algorithm, performs well on simulated data and may have applications to other supertree problems. However, an analysis of 40 bacterial genomes using this method supports an incorrect clade of parasites. This is a common feature of model-based gene content methods and is due to parallel gene loss.