猕猴桃属植物叶绿体基因PCR-RFLP分析

分别用2个不同限制性内切酶对猕猴桃属27个种和15个栽培品种的叶绿体基因(rbcL基因和psbA基因)的PCR扩增产物进行酶切分析,共得到25个限制性位点,其中24个具有多态性。确立了该属植物的单元型分布,对该属植物的系统发育方式和部分重要种类的亲缘关系进行了探讨,拓展了可用于该属植物分子系统学研究的遗传信息。     

基于线粒体和核基因序列的蜜蜂属系统发育分析

文章测定了中国分布的蜜蜂属(Apis)5种蜜蜂22个样本的线粒体基因ND2、CO2、16S rRNA以及核基因ITPR的序列,对序列的碱基组成和蜜蜂种间的遗传距离进行了分析。结合下载的蜜蜂属其他4个种的相关序列,采用最大简约法、邻接法和最大似然法重建了蜜蜂属系统发育关系。系统发育分析结果支持蜜蜂属划分为3个类群,即小蜜蜂类群(包括小蜜蜂和黑小蜜蜂)、大蜜蜂类群(包括大蜜蜂和黑大蜜蜂)和穴居蜜蜂类群(西方蜜蜂、东方蜜蜂、沙巴蜂、苏拉威西蜂、绿努蜂),且小蜜蜂类群较早分化。结果还显示,我国海南岛的大蜜蜂和大陆的大蜜蜂之间可能存在较大的遗传分歧。     

木兰族和含笑族的系统学关系——基于叶绿体matK基因序列分析

采用PCR直接测序法,对木兰属国产组(各1种)和含笑属各组(各1种)的叶绿体DNA,matK基因序列进行测定分析,结果表明：木兰属和含笑属不能明显区分开,故不支持以顶生花和腋生花来划分木兰族和含笑族。     

编码叶绿体蛋白质的某些核基因

高等植物叶绿体的一些重要蛋白质基因位于细胞核的基因组内。这些基因的细微结构已研究得较为清楚,并对不同植物的编码叶绿体蛋白质的核基因进行了比较研究。     

楤木属及其近缘类群叶绿体基因组比较与系统发育分析

分别对楤木属（Aralia）和羽叶参属（Pentapanax）各两个物种进行叶绿体基因组测序、组装和注释,并进行结构分析;结合NCBI下载的近缘类群叶绿体组序列,进行系统发育分析。结果显示,4个物种的叶绿体基因组均为环状四分体结构,长度为155 744～156 201 bp,GC含量为38.1%,均包含132个基因,其中蛋白质编码基因87个,rRNA基因8个,t RNA基因37个。边界分析发现IR(Inverted repeat)区均未发生收缩和扩张。SSR(Simple sequence repeat)序列数量在39～43个,多为单核苷酸和二核苷酸重复,位置多在非编码区。序列差异多出现在LSC(Large single copy)和SSC(Small single copy)区的非编码区。最大似然树揭示出两个高度支持的单系分支：第1分支包括羽叶参属、浓紫龙眼独活（Aralia atropurpurea Franch.）、食用土当归（Aralia cordata Thunb.）和东北土当归（Aralia continentalis Kitagawa）;第2分支则均由楤木属物种组成。总体...     

基于叶绿体psaA和psbA基因的中国熊野藻属植物系统发育分析

以中国产熊野藻属Kumanoa的两个种, 绞扭熊野藻K. intorta (=绞扭串珠藻Batrachospermum intortum), 弯形熊野藻K. curvata (=弯形串珠藻B. curvatum)和其他6种淡水红藻为实验材料, 对其psaA和psbA基因进行扩增和测序, 并与GenBank中相近序列进行比对分析, 以贝叶斯法、最大似然法和邻接法分别构建了单基因和联合基因系统发育树. 结果表明, 3种方法构建的系统树具有相似的拓扑结构, 反映的系统发育关系基本一致, 熊野藻属中的两个种聚为一支, 与串珠藻属相分离, 支持该属的建立; 中国产的熊野藻属分子学研究结果与来自南美洲及澳洲的该属植物结果一致, 说明该属的建立具有广泛的地理适用性. 系统发育树聚类结果也明确反映了熊野藻属与串珠藻属较近的亲缘关系, 根据果胞枝形态特点, 推测熊野藻属进化地位晚于串珠藻属植物, 而早于顶丝藻目和红索藻目. 此外, 胶串珠藻与其他串珠藻组植物分离, 支持将其单独分组, 红索藻目植物与串珠藻目植物分离, 支持红索藻目的建立. 同时也表明psaA和psbA基因用于淡水红藻分析, 能够较好地反映其系统发育关系.       

里白科植物的系统发育和分歧时间估计——基于叶绿体三个基因序列的证据

里白科(Gleicheniaceae)是古老的真蕨类植物,最早的化石记录可追溯到石炭纪。现存类群的属级分类和系统演化关系一直存在很大的分歧,为了进一步探讨该类群的起源演化,文中运用最大简约法和贝叶斯演绎方法对18种代表现存里白科植物全部6属(包括新测的12种)的叶绿体3个编码基因序列(atpB,rbcL和rps4)进行分析,探讨其主要分类群(属级)的系统演化关系。结果显示,里白科植物为一个单系群,由3个分支构成:里白属(Diplopterygium Nakai)和Gleichenia japonica构成一个分支;芒萁属(Dicranopteris Bernh.)和Gleichenella pec-tinata构成另一个分支;假芒萁属(Sticherus C.Presl)与单种属Stromatopteris Mettenius及Gleichenia dicarpa构成第三个分支。用宽松分子钟方法推测里白科主要类群的起源时间为:现代里白科植物起源于早白垩世(111—140Ma),其主要分支类群随后发生多样性分化,里白属和芒萁属的快速辐射演化均发生在古近纪(40—64Ma,36—50Ma)。起源时间的估算结果暗示化石种三叠里白Diplopterygium triassica不应归入现代里白属,其归属需要重新考虑。     

基于叶绿体DNA atpB-rbcL区序列探讨石蒜属种间系统发育关系

摘要：为了探讨石蒜属（Lycoris Herb.）的种间系统发育关系,对石蒜属95个材料包括15种、4变种及2个人工杂种的叶绿体 DNA atpB-rbcL间隔区进行了测序,结合花部形态和核型特征,探讨了石蒜属种间系统关系及其可能的杂交起源,结果表明：在系统发育树上亲缘关系近的材料聚在一起,其中矮小石蒜（L. radiata var. pumila）和换锦花（L. sprengeri）与2个人工杂交种（Hybrid 1、Hybrid 2）、麦秆石蒜（L. straminea）、江苏石蒜（L. houdyshelii）、短蕊石蒜（L. caldwellii）和乳白石蒜（L. albiflora）具有密切的亲缘关系。atpB-rbcL序列揭示的石蒜属种间关系与染色体核型的分类结果部分一致,主要表现在具有近端部着丝粒(A)染色体的种与具有中部(M)和端部(T)着丝粒染色体的种各成一支,与形态和染色体分类结果一致;不同之处在于具有中部、端部和近端部着丝粒染色体的种分散在两个主要分支内,进一步验证了具有中部、端部和近端部3种着丝粒类型染色体组的石蒜如麦秆石蒜、江苏石蒜、短蕊石蒜和乳白石蒜等是杂交起源的假设,结合2个人工杂交种分析,揭示了短蕊石蒜和乳白石蒜的近端部着丝粒染色体来源于换锦花;麦秆石蒜和江苏石蒜近端部着丝粒染色体来源于矮小石蒜。     

中国熊野藻属植物系统发育分析——基于叶绿体UPA序列

以中国产的6种熊野藻属(Kumanoa)和串珠藻属(Batrachospermum)植物为材料,测定其UPA序列,并在GenBank中下载相关基因序列,通过贝叶斯法、最大似然法和邻接法构建系统发育树,分析其系统发育。结果显示,UPA序列核苷酸变异位点占序列长度的43.1%,其中简约信息位点占序列长度的31.1%,种间差异度为0~1.81%,属间差异度大于4.19%,可以作为分子标记用于系统发育分析。中国产熊野藻属的两个种和来自世界范围内的多数该属种类聚为一大支,支持该属的建立。基于UPA序列的地理起源分析显示,两属的祖先分布区节点主要在北美洲和大洋洲,然后向其它地区扩散,熊野藻属向外扩散后,在南美洲分布较为集中。     

基于4个叶绿体基因识别蓑藓属(Macromitrium)植物的可行性研究

我国的蓑藓属植物形态变异式样复杂,分类问题多.DNA条形码技术是一种新的物种鉴定技术.本研究以采自浙江、福建、云南、广西、四川等省的蓑藓属(Macromitrium)7个物种及其外类群直叶藓Macrocoma tenue subsp. sullivantii和火藓Schlotheimia grevilleana的38份标本为对象,获得了它们的叶绿体基因trnL、trnG、psbT和rps4序列,基于这些基因的不同组合构建了15棵贝叶斯系统发育树,获得了相应的蓑藓属植物的物种识别率、种内和种间的遗传距离.发现基于trnL-rps4、trnL-trnG-rps4、trnL-psbT-rps4、trnG-psbT-rps4和trnL-trnG-rps4-psbT等5个组合能够较好地识别本研究中蓑藓属植物,均得到了100%的物种识别率.考虑到扩增和测序的成功率和得到的7种蓑藓属植物的系统发育关系,建议将trnL-trnG-psbT组合用于蓑藓属植物的系统发育分析和物种识别的DNA条形码.     

Phylogenetic relationships and natural hybridization in Triadica inferred from nuclear and chloroplast DNA analyses

Triadica (Euphorbiaceae) is a small genus endemic to East Asia and Southeast Asia, consisting of three species differentially adapted to heterogeneous habitats. To date, the phylogenetic relationships of this genus have not been resolved, and there has been no evidence for interspecific hybridization in Triadica. In this study, we sequenced the nrITS regions, two nuclear genes and a chloroplast gene to reconstruct the molecular phylogeny of Triadica and to test the hypothesis of natural hybridization between Triadica sebifera and Triadica cochinchinensis, and between T. sebifera and Tridica rotundifolia. Phylogenetic analysis showed that T. sebifera diverged first within this genus, and T. cochinchinensis and T. rotundifolia were sister species. Both of the two putative hybrids show chromatogram additivity at each of the two nuclear genes, providing convincing evidence for natural hybridization between T. sebifera and T. cochinchinensis, and between T. sebifera and T. rotundifolia. The chloroplast gene sequences of both hybrids were identical with that of T. sebifera, suggesting that T. sebifera was the maternal parent of the two hybrids. This is the first report of natural hybridization in Triadica, and the hybrids identified in this study should be a good starting point for further hybridization-based breeding in T. sebifera.     

Molecular phylogeny of the Chinese ranids inferred from nuclear and mitochondrial DNA sequences

The phylogeny of representative species of Chinese ranids was reconstructed using two nuclear (tyrosinase and rhodopsin) and two mitochondrial (12S rRNA, 16S rRNA) DNA fragments. Maximum parsimony, Bayesian, and maximum likelihood analyses were employed. In comparison with the results from nuclear and mitochondrial data, we used nuclear gene data as our preferred phylogenetic hypothesis. We proposed two families (Ranidae, Dicroglossidae) for Chinese ranids, with the exception of genus Ingerana. Within Dicroglossidae, four tribes were supported including Dicroglossini, Paini, Limnonectini, and Occidozygini. A broader sampling strategy and evidence from additional molecular markers are required to decisively evaluate the evolutionary history of Chinese ranids.     

Molecular phylogeny of Dipterocarpaceae in Southeast Asia using RFLP of PCR-amplified chloroplast genes

Dipterocarpaceae is the dominant family of Southeast Asia's climax tropical rain forest region, and it contains the region's most important commercial timber species. A molecular phylogeny of the Dipterocarpaceae subfamily Dipterocapoideae was constructed using restriction fragment length polymorphisms of polymerase chain reaction-amplified specific genes in chloroplast DNA. A total of 141 site changes were detected among ten genera and 30 species in 11 different genes: rbcL, psbA, psbD, rpoB, rpoC, petB, atpH, 16S, psaA, petA and trnK. Phylogenetic trees constructed by Wanger parsimony and neighbor-joining methods, using Upuna as the outgroup, displayed five monophytelic groups that included Upuna: HopeaShorea-Parashorea-Neobalanocarpus; Dryobalanops; Dipterocarpus; Anisoptera-Vatica-Cotylelobium; and Upuna. The phylogenetic trees clearly separate species with two different base chromosome numbers: the first group is x=7, and the other is x=11. The x=7 group is thought to be in a synapomorphic character state. Parashorea lucida is a sister to most Shorea species. Neobalanocarpus heimii and Hopea from a clade of a sister to two Shorea species, and Cotylelobium and Vatica are closely related species. Our conclusions agree with a phylogeny derived from wood anatomy data analysis, and with Symington's and Ashton's taxonomic classifications.The raw data of the PCR-RFLP analysis can be obtained from the authors     

A molecular phylogeny of the Canidae based on six nuclear loci

We have reconstructed the phylogenetic relationships of 23 species in the dog family, Canidae, using DNA sequence data from six nuclear loci. Individual gene trees were generated with maximum parsimony (MP) and maximum likelihood (ML) analysis. In general, these individual gene trees were not well resolved, but several identical groupings were supported by more than one locus. Phylogenetic analysis with a data set combining the six nuclear loci using MP, ML, and Bayesian approaches produced a more resolved tree that agreed with previously published mitochondrial trees in finding three well-defined clades, including the red fox-like canids, the South American foxes, and the wolf-like canids. In addition, the nuclear data set provides novel indel support for several previously inferred clades. Differences between trees derived from the nuclear data and those from the mitochondrial data include the grouping of the bush dog and maned wolf into a clade with the South American foxes, the grouping of the side-striped jackal (Canis adustus) and black-backed jackal (Canis mesomelas) and the grouping of the bat-eared fox (Otocyon megalotis) with the raccoon dog (Nycteruetes procyonoides). We also analyzed the combined nuclear + mitochondrial tree. Many nodes that were strongly supported in the nuclear tree or the mitochondrial tree remained strongly supported in the nuclear + mitochondrial tree. Relationships within the clades containing the red fox-like canids and South American canids are well resolved, whereas the relationships among the wolf-like canids remain largely undetermined. The lack of resolution within the wolf-like canids may be due to their recent divergence and insufficient time for the accumulation of phylogenetically informative signal.     

Molecular phylogeny of Drosophila based on ribosomal RNA sequences

Nucleotide sequences of 72 species of Drosophilidae were determined for divergent D1 and D2 domains (representing 200 and 341 nucleotides respectively in D. melanogaster) of large ribosomal RNA, using the rRNA direct sequencing method. Molecular phylogenetic trees were reconstructed using both distance and parsimony methods and the robustness of the nodes was evaluated by the bootstrap procedure. The trees obtained by these methods revealed four main lineages or clades which do not correspond to the taxonomical hierarchy. In our results, the genus Chymomyza is associated with the subgenus Scaptodrosophila of the genus Drosophila and their cluster constitutes the most ancient clade. The two other clades are constituted of groups belonging to the subgenus Sophophora of the genus Drosophila: the so-called Neotropical clade including the willistoni and saltans groups and the obscura-melanogaster clade itself split into three lineages: (1) obscura group + ananassae subgroup, (2) montium subgroup, and (3) melanogaster + Oriental subgroups. The fourth clade, the Drosophila one, contains three lineages. D. polychaeta, D. iri, and D. fraburu are branched together and constitute the most ancient lineage; the second lineage includes the annulimana, bromeliae, dreyfusi, melanica, mesophragmatica, repleta, robusta, and virilis groups. The third lineage is composed of the immigrans and the cardini, funebris, guaramunu, guarani, histrio, pallidipennis, quinaria, and tripunctata groups. The genera Samoaia, Scaptomyza, and Zaprionus are branched within the Drosophila clade. Although these four clades appear regularly in almost all tree calculations, additional sequencing will be necessary to determine their precise relationships.Correspondence to: M. Pelandakis     

Molecular phylogeny of Plumbaginaceae with emphasis on Acantholimon Boiss. based on nuclear and plastid DNA sequences in Iran

The present study represents phylogenetic analyses of Plumbaginaceae with emphasis on Acantholimon from Iran using nrDNA ITS and plastid trnY-T sequences. The analyses support the monophyly and the close relationship of Limonium, Armeria and Psylliostachys. This is the first report of the close relationship between Acantholimon and Cephalorhizum. The data for the position of Cephalorhizum is unclear. The Shimodaira–Hasegawa test of nrDNA ITS and the combined datasets indicated that Acantholimon and Cephalorhizum are distinct genera. The molecular data revealed that the traditionally recognized multi-specific Acantholimon sections (Acantholimon, Acmostegia, Glumaria, Microstegia, Staticopsis and Tragacanthina) are not monophyletic. Their members are intermixed with each other and scattered across the Acantholimon clade, but the smaller sections including Platystegia and Pterostegia, each comprising two species, are monophyletic.     

Molecular phylogeny of Lysimachia (Myrsinaceae) based on chloroplast trnL-F and nuclear ribosomal ITS sequences

Both nuclear ribosomal ITS and chloroplast trnL-F sequences were acquired for 57 species (accessions) of Lysimachia and its close relatives, and were analyzed together with sequences retrieved from databases. The results of phylogenetic analyses based on these data (separately or combined) show that Lysimachia is paraphyletic, with the monotypic genus Glaux nested deeply inside. Previous suggestions that Anagallis and Trientalis could be ingroups of Lysimachia were not corroborated by our results. The molecular phylogenies do not support the current infrageneric divisions of Lysimachia. Subgenus Lysimachia contains at least five independent lineages. The Hawaii endemic subgenus Lysimachiopsis was shown to group with subgenera Palladia and Heterostylandra, instead of subgenus Idiophyton as previously suggested. The two North American representatives of Lysimachia, subgenus Seleucia and section Verticillatae of subgenus Lysimachia are group together as the most basal clade of the genus. Parallel and independent evolutions were inferred for morphological characters that were previously used as diagnostic criteria. Molecular phylogenies do not offer clear inferences on the overall historical biogeography of Lysimachia, but Southeast Asia origins of several clades, including the Hawaiian endemic clade and the Iberian Lysimachia ephemerum are strongly supported.     

The phylogenetic position of red algae revealed by multiple nuclear genes from mitochondria-containing eukaryotes and an alternative hypothesis on the origin of plastids

Abstract Red algae are one of the main photosynthetic eukaryotic lineages and are characterized by primitive features, such as a lack of flagella and the presence of phycobiliproteins in the chloroplast. Recent molecular phylogenetic studies using nuclear gene sequences suggest two conflicting hypotheses (monophyly versus non-monophyly) regarding the relationships between red algae and green plants. Although kingdom-level phylogenetic analyses using multiple nuclear genes from a wide-range of eukaryotic lineages were very recently carried out, they used highly divergent gene sequences of the cryptomonad nucleomorph (as the red algal taxon) or incomplete red algal gene sequences. In addition, previous eukaryotic phylogenies based on nuclear genes generally included very distant archaebacterial sequences (designated as the outgroup) and/or amitochondrial organisms, which may carry unusual gene substitutions due to parasitism or the absence of mitochondria. Here, we carried out phylogenetic analyses of various lineages of mitochondria-containing eukaryotic organisms using nuclear multigene sequences, including the complete sequences from the primitive red alga Cyanidioschyzon merolae. Amino acid sequence data for two concatenated paralogous genes (α- and β-tubulin) from mitochondria-containing organisms robustly resolved the basal position of the cellular slime molds, which were designated as the outgroup in our phylogenetic analyses. Phylogenetic analyses of 53 operational taxonomic units (OTUs) based on a 1525-amino-acid sequence of four concatenated nuclear genes (actin, elongation factor-1α, α-tubulin, and β-tubulin) reliably resolved the phylogeny only in the maximum parsimonious (MP) analysis, which indicated the presence of two large robust monophyletic groups (Groups A and B) and the basal eukaryotic lineages (red algae, true slime molds, and amoebae). Group A corresponded to the Opisthokonta (Metazoa and Fungi), whereas Group B included various primary and secondary plastid-containing lineages (green plants, glaucophytes, euglenoids, heterokonts, and apicomplexans), Ciliophora, Kinetoplastida, and Heterolobosea. The red algae represented the sister lineage to Group B. Using 34 OTUs for which essentially the entire amino acid sequences of the four genes are known, MP, distance, quartet puzzling, and two types of maximum likelihood (ML) calculations all robustly resolved the monophyly of Group B, as well as the basal position of red algae within eukaryotic organisms. In addition, phylogenetic analyses of a concatenated 4639-amino-acid sequence for 12 nuclear genes (excluding the EF-2 gene) of 12 mitochondria-containing OTUs (including C. merolae) resolved a robust non-sister relationship between green plants and red algae within a robust monophyletic group composed of red algae and the eukaryotic organisms belonging to Group B. A new scenario for the origin and evolution of plastids is suggested, based on the basal phylogenetic position of the red algae within the large clade (Group B plus red algae). The primary plastid endosymbiosis likely occurred once in the common ancestor of this large clade, and the primary plastids were subsequently lost in the ancestor(s) of the Discicristata (euglenoids, Kinetoplastida, and Heterolobosea), Heterokontophyta, and Alveolata (apicomplexans and Ciliophora). In addition, a new concept of “Plantae” is proposed for phototrophic and nonphototrophic organisms belonging to Group B and red algae, on the basis of the common history of the primary plastid endosymbiosis. The Plantae include primary plastid-containing phototrophs and nonphototrophic eukaryotes that possibly contain genes of cyanobacterial origin acquired in the primary endosymbiosis.     

基于细胞色素b序列的鲹科分子系统发育

测定了中国鲹科8属9种鱼的细胞色素b基因的全序列(1141bp),结合来自GenBank中分布于美国、安哥拉、希腊以及巴拿马的鲹科4属14种鱼的相应同源序列生成供系统发育分析的序列矩阵,用最大简约法和邻接法构建分子系统树。结果显示:(1)支持科下设四个亚科(鲹亚科,亚科,鲳鲹亚科,鰆鲹科)阶元的分类系统;(2)亚科属下不宜设亚属分类阶元;(3)及达副叶鲹与丽叶鲹亲缘关系较近,应同属于副叶鲹属;(4)我国传统的鱼类检索系统将狮鼻鲳鲹误鉴定为卵形鲳鲹,建议予以修正。     

Molecular phylogeny of Allomyces macrogynus: Congruency between nuclear ribosomal RNA- and mitochondrial protein-based trees

We have sequenced the nuclear and mitochondrial small subunit rRNA genes (rns) and the mitochondrial genes coding for subunits 1 and 3 of the cytochrome oxidase (cox1 and cox3, respectively) of the chytridiomycete Allomyces macrogynus. Phylogenetic trees inferred from the derived COX1 and COX3 proteins and the nuclear rns sequences show with good bootstrap support that A. macrogynus is an early diverging fungus. The trees inferred from mitochondrial rns sequences do not yield a topology that is supported by bootstrap analysis. The similarity and the relative robustness of the nuclear rns and the mitochondrial protein-derived phylogenetic trees suggest that protein sequences are of higher value than rRNA sequences for reconstructing mitochondrial evolution. In addition, our trees support a monophyletic origin of mitochondria for the range of analyzed eukaryotes. Correspondence to: B. Franz Lang