Tempo and Mode of Spliceosomal Intron Evolution in Actin of Foraminifera

Spliceosomal introns are present in almost all eukaryotic genes, yet little is known about their origin and turnover in the majority of eukaryotic phyla. There is no agreement whether most introns are ancestral and have been lost in some lineage or have been gained recently. We addressed this question by analyzing the spatial and temporal distribution of introns in actins of foraminifera, a group of testate protists whose exceptionally rich fossil record permits the calibration of molecular phylogenies to date intron origins. We identified 24 introns dispersed along the sequence of two foraminiferan actin paralogues and actin deviating proteins, an unconventional type of fast-evolving actin found in some foraminifera. Comparison of intron positions indicates that 20 of 24 introns are specific to foraminifera. Four introns shared between foraminifera and other eukaryotes were interpreted as parallel gains because they have been found only in single species belonging to phylogenetically distinctive lineages. Moreover, additional recent intron gain due to the transfer between the actin paralogues was observed in two cultured species. Based on a relaxed molecular clock timescale, we conclude that intron gains in actin took place throughout the evolution of foraminifera, with the oldest introns inserted between 550 and 500 million years ago and the youngest ones acquired less than 100 million years ago. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Debashish Bhattacharya]     

Evidence for Gene Conversion Between Tandemly Duplicated Cytoplasmic Actin Genes of Helicoverpa armigera (Lepidoptera:Noctuidae)

Tandemly duplicated actin genes have been isolated from a Helicoverpa armigera genomic library. Sequence comparisons with actin genes from other species suggest they encode cytoplasmic actins, being most closely related to the Bombyx mori A3 actin gene. The duplicated H. armigera actin genes, termed A3a and A3b, share 98.3% nucleotide sequence identity over their entire putative coding region. Analysis of the distribution of nucleotide differences shows the first 763 bp are identical between the two coding regions, with the 18 nucleotide changes occurring in the remaining 366 bp. This observation suggests a gene conversion event has taken place between the duplicated H. armigera A3a and A3b actin genes. Translation of the open-reading frames indicates the products of these genes are identical, apart from a single amino acid difference at codon 273. Polymerase chain reaction and northern blot analysis have shown both H. armigera A3a and A3b genes are expressed during pupal development and in the brain of newly eclosed adults. A region 5′ of the H. armigera A3a actin gene start codon has been identified which contains regulatory sequences commonly found in the promoter region of actin genes, including TATA, CAAT, and CArG motifs. Received: 10 January 1996 / Accepted: 12 March 1996     

Actin Gene Family Dynamics in Cryptomonads and Red Algae

Here we present evidence for a complex evolutionary history of actin genes in red algae and cryptomonads, a group that acquired photosynthesis secondarily through the engulfment of a red algal endosymbiont. Four actin genes were found in the nuclear genome of the cryptomonad, Guillardia theta, and in the genome of the red alga, Galdieria sulphuraria, a member of the Cyanidiophytina. Phylogenetic analyses reveal that the both organisms possess two distinct sequence types, designated “type-1” and “type-2.” A weak but consistent phylogenetic affinity between the cryptomonad type-2 sequences and the type-2 sequences of G. sulphuraria and red algae belonging to the Rhodophytina was observed. This is consistent with the possibility that the cryptomonad type-2 sequences are derived from the red algal endosymbiont that gave rise to the cryptomonad nucleomorph and plastid. Red algae as a whole possess two very different actin sequence types, with G. sulphuraria being the only organism thus far known to possess both. The common ancestor of Rhodophytina and Cyanidiophytina may have had two actin genes, with differential loss explaining the distribution of these genes in modern-day groups. Our study provides new insight into the evolution and divergence of actin genes in cryptomonads and red algae, and in doing so underscores the challenges associated with heterogeneity in actin sequence evolution and ortholog/paralog detection.     

Molecular Phylogeny of Conjugating Green Algae (Zygnemophyceae, Streptophyta) Inferred from SSU rDNA Sequence Comparisons

Abstract Nuclear-encoded SSU rDNA sequences have been obtained from 64 strains of conjugating green algae (Zygnemophyceae, Streptophyta, Viridiplantae). Molecular phylogenetic analyses of 90 SSU rDNA sequences of Viridiplantae (inciuding 78 from the Zygnemophyceae) were performed using complex evolutionary models and maximum likelihood, distance, and maximum parsimony methods. The significance of the results was tested by bootstrap analyses, deletion of long-branch taxa, relative rate tests, and Kishino–Hasegawa tests with user-defined trees. All results support the monophyly of the class Zygnemophyceae and of the order Desmidiales. The second order, Zygnematales, forms a series of early-branching clades in paraphyletic succession, with the two traditional families Mesotaeniaceae and Zygnemataceae not recovered as lineages. Instead, a long-branch Spirogyra/Sirogonium clade and the later-diverging Netrium and Roya clades represent independent clades. Within the order Desmidiales, the families Gonatozygaceae and Closteriaceae are monophyletic, whereas the Peniaceae (represented only by Penium margaritaceum) and the Desmidiaceae represent a single weakly supported lineage. Within the Desmidiaceae short internal branches and varying rates of sequence evolution among taxa reduce the phylogenetic resolution significantly. The SSU rDNA-based phylogeny is largely congruent with a published analysis of the rbcL phylogeny of the Zygnemophyceae (McCourt et al. 2000) and is also in general agreement with classification schemes based on cell wall ultrastructure. The extended taxon sampling at the subgenus level provides solid evidence that many genera in the Zygnemophyceae are not monophyletic and that the genus concept in the group needs to be revised.     

Phylogeny and Molecular Evolution of the Green Algae

The green lineage (Viridiplantae) comprises the green algae and their descendants the land plants, and is one of the major groups of oxygenic photosynthetic eukaryotes. Current hypotheses posit the early divergence of two discrete clades from an ancestral green flagellate. One clade, the Chlorophyta, comprises the early diverging prasinophytes, which gave rise to the core chlorophytes. The other clade, the Streptophyta, includes the charophyte green algae from which the land plants evolved. Multi-marker and genome scale phylogenetic studies have greatly improved our understanding of broad-scale relationships of the green lineage, yet many questions persist, including the branching orders of the prasinophyte lineages, the relationships among core chlorophyte clades (Chlorodendrophyceae, Ulvophyceae, Trebouxiophyceae and Chlorophyceae), and the relationships among the streptophytes. Current phylogenetic hypotheses provide an evolutionary framework for molecular evolutionary studies and comparative genomics. This review summarizes our current understanding of organelle genome evolution in the green algae, genomic insights into the ecology of oceanic picoplanktonic prasinophytes, molecular mechanisms underlying the evolution of complexity in volvocine green algae, and the evolution of genetic codes and the translational apparatus in green seaweeds. Finally, we discuss molecular evolution in the streptophyte lineage, emphasizing the genetic facilitation of land plant origins.     

Phylogeny of phagotrophic euglenids (Euglenozoa) as inferred from hsp90 gene sequences

Molecular phylogenies of euglenids are usually based on ribosomal RNA genes that do not resolve the branching order among the deeper lineages. We addressed deep euglenid phylogeny using the cytosolic form of the heat-shock protein 90 gene (hsp90), which has already been employed with some success in other groups of euglenozoans and eukaryotes in general. Hsp90 sequences were generated from three taxa of euglenids representing different degrees of ultrastructural complexity, namely Petalomonas cantuscygni and wild isolates of Entosiphon sulcatum, and Peranema trichophorum. The hsp90 gene sequence of P. trichophorum contained three short introns (ranging from 27 to 31 bp), two of which had non-canonical borders GG-GG and GG-TG and two 10-bp inverted repeats, suggesting a structure similar to that of the non-canonical introns described in Euglena gracilis. Phylogenetic analyses confirmed a closer relationship between kinetoplastids and diplonemids than to euglenids, and supported previous views regarding the branching order among primarily bacteriovorous, primarily eukaryovorous, and photosynthetic euglenids. The position of P. cantuscygni within Euglenozoa, as well as the relative support for the nodes including it were strongly dependent on outgroup selection. The results were most consistent when the jakobid Reclinomonas americana was used as the outgroup. The most robust phylogenies place P. cantuscygni as the most basal branch within the euglenid clade. However, the presence of a kinetoplast-like mitochondrial inclusion in P. cantuscygni deviates from the currently accepted apomorphy-based definition of the kinetoplastid clade and highlights the necessity of detailed studies addressing the molecular nature of the euglenid and diplonemid mitochondrial genome.     

文昌鱼肌动蛋白基因家族的扩增(英文)

肌动蛋白是一种分布广泛而且在进化上十分保守的蛋白,是构成细胞骨架的关键组分.肌动蛋白通常被分成肌肉型和胞质型两种类型,各自行使着不同的功能.在此,作者对弗罗里达文昌鱼基因组中的肌动蛋白基因家族进行了系统分析,发现文昌鱼中该基因家族成员多达30多个,其中很多都是连锁分布的.基因结构趋于多样,分别包含2～7个外显子.进化分析的结果显示,文昌鱼的肌动蛋白基因家族可能通过串联重复而发生了扩增.作者还克隆了厦门文昌鱼两个不同的肌肉犁肌动蛋白基因,并比较了它们在文昌鱼早期胚胎中的表达图式.结果显示,这两个基因在表达上有着细微的差别,提示文昌鱼肌动蛋白基因家族成员在功能上的分化.上述结果将有助于阐明肌动蛋白基因家族及其功能在脊索动物中的演化.     

Nucleus-encoded, plastid-targeted acetolactate synthase genes in two closely related chlorophytes, Chlamydomonas reinhardtii and Volvox carteri : phylogenetic origins and recent insertion of introns

Acetolactate synthase (ALS) catalyzes the first committed step in the synthesis of branched-chain amino acids. In green plants and fungi, ALS is encoded by a nuclear gene whose product is targeted to plastids (in plants) or to mitochondria (in fungi). In red algae, the gene is plastid-encoded. We have determined the complete sequence of nucleus-encoded ALS genes from the green algae Chlamydomonas reinhardtii and Volvox carteri. Phylogenetic analyses of the ALS gene family indicate that the ALS genes of green algae and plants are closely related, sharing a recent common ancestor. Furthermore, although these genes are clearly of eubacterial origin, a relationship to the ALS genes of red algae and cyanobacteria (endosymbiotic precursors of plastids) is only weakly indicated. The algal ALS genes are distinguished from their homologs in higher plants by the fact that they are interrupted by numerous spliceosomal introns; plant ALS genes completely lack introns. The restricted phylogenetic distribution of these introns suggests that they were inserted recently, after the divergence of these green algae from plants. Two introns in the Volvox ALS gene, not found in the Chlamydomonas gene, are positioned precisely at sites which resemble “proto-splice” sequences in the Chlamydomonas gene. Received: 27 November 1998 / Accepted: 21 April 1999     

Expression of Actin Gene During Development of Snake Gourd (Luffa cylindrica) and Cucumber (Cucumis sativum)

Results of Northern blot and Dot blot analysis indicated that actin genes exhibit organ-specific expression in snake gourd (Luffa cylindrica L. ) and cucumber (Cucumis sativum L. ). Actin genes showed obvious developmental specificity during'the development of snake gourd seedlings, mRNA levels in stems of 30-day old seedlings were 4 ～ 6 times higher than that of roots and cotyledons of 8-day old seedlings and roots and hypocotyls of 15-day old seedlings, and were even 10～12 times higher than that of stems and leaves of flowering plants. Actin genes also showed organ-specific expression in young fruits (15 days after flowering) of cucumber.     

葡萄Actin基因家族的鉴定及进化和表达分析

采用生物信息学方法从葡萄(Vitis vinifera Linn.)全基因组中鉴定Actin基因家族,并对各基因的染色体定位和结构特征,编码蛋白质的理化性质、亚细胞定位、二级结构、三级结构和系统进化,以及不同组织的基因表达进行研究.结果表明:葡萄Actin基因家族16个基因分布在12条染色体上.16个基因的结构特征及其编码蛋白质的理化性质差异较大.16个基因的长度及其内含子总长度的变化范围较大,编码序列(CDS)和外显子总长度的变化范围较小.除登录号GSVIVG01008254001和GSVIVG01014035001的基因外,其他14个基因的GC含量均低于其CDS的GC含量.除登录号GSVIVG01008254001的基因外,其他15个基因编码的蛋白质的理论相对分子质量为12534.54~82612.33,理论等电点为pI 4.92~pI 9.13.16个基因编码蛋白质的消光系数为14105~73645,脂肪族氨基酸指数为65.54~92.06,其中9个为稳定蛋白,7个为不稳定蛋白.除登录号GSVIVG01014035001的基因外,其他15个基因编码的蛋白质均为亲水性蛋白.登录号GSVIVG01016517001的基因编码的蛋白质定位于细胞质和细胞核,其他15个基因编码的蛋白质定位于细胞质.二级结构和三级结构显示:葡萄Actin基因家族16个基因编码的蛋白质均由α螺旋、无规则卷曲和延伸链构成,且总体以无规则卷曲为主.系统进化分析和不同组织的基因表达分析结果显示:与拟南芥〔Arabidopsis thaliana(Linn.)Heynh.〕相似,葡萄Actin基因家族16个基因编码的蛋白质分为3个亚家族,ClassⅡ亚家族(营养型)包括登录号GSVIVG01003099001和GSVIVG01026580001的基因编码的蛋白质,这2个基因在所有组织中的表达均较高;ClassⅢ亚家族(生殖型)包括登录号GSVIVG01033494001、GSVIVG01024980001和GSVIVG01016550001的基因编码的蛋白质,这3个基因在花粉、雄蕊和花中的表达均较高;ClassⅠ亚家族包括其他11个基因编码的蛋白质,这11个基因在各组织中的表达总体上较低.研究结果显示:葡萄Actin基因家族的表达具有组织特异性.     

miR156靶基因SPL在植物中的系统分布和进化模式分析

Squamosa promoterbinding proteinlike genes （SPLs）在植物发育过程中具有重要作用。很多SPLs被miR156调节,然而,对于它们在植物中的系统分布和进化模式还知之甚少。本文对9个测序物种（藻类,苔藓,石松,单子叶和双子叶植物）的183个SPLs进行了生物信息学分析。结果表明miR156应答元件（MREs）仅在陆生植物SPLs中发现,藻类中不存在。系统进化分析显示陆生植物SPLs分为两大分支：group I和group II。 MiR156靶基因仅分布于group II,表明它们有着共同的祖先。Group II进一步分为7个亚支（IIaIIg）,miR156靶基因分布在除IId外的其余6个亚支的特定SPLs。系统分类与基因结构的相关性反映了SPL靶基因结构上的变化。在进化过程中,它们可能发生外显子的丢失且伴随MRE的丢失。另外,基因重复对SPL靶基因的丰度变化影响很大,尤其是被子植物与低等植物分歧后它们数量明显增加。以拟南芥为模式植物分析发现串联重复和片段重复是SPL靶基因扩张的主要机制。     

Confocal Microscopic Observations on Actin Filament Distribution in Lily Pollen Protoplasts

Actin filaments (F-actin) were localized in the isolated pollen protoplasts of lily using TRITC-phalloidin probe and confocal microscopy. Two kinds of pollen protoplasts were examined: one from pollen grains of non-dehiscent anthers(referred to as ‘nearly mature’ pollen); and the other from pollen grains of just dehiscent anthers(referred to as ‘just mature’ pollen). In the cytoplasm of the pollen protoplasts of the ‘nearly mature’ pollen there was a very well organized actin network made up of thick actin bundles. Two types of bundle connections were seen in the network; namely ‘branch’ connections and 'junction' connections. The ‘branch’ connection (or branching points) was formed due to branching or merging of bundies. The ‘junction’ connection (or 'junction' point) had two or more bundles associated with it. Some of the ‘junction’ points might be actin filament organization: centres. The generative cell in iht pollen protoplasts of the ‘nearly mature’ pollen also contained an actin network. But this network was structurally quite loose and the pundles made up the network were short and thick. In the cytoplasm of the pollen protoplasts of the ‘just mature’ pollen the actin net work was more densely packed. The bundles made up the network were also thinner. The actin network in the generative cell was, however, less densely packed. If the pollen protoplasts from both the ‘nearly mature’ and the 'just mature' pollen grains were transferred from a B5 medium into a Brewbaker and Kwack medium supplemented with sucrose, protoplasts rapidly (i.e. within 2 to 3 hours) developed vacuoles and transvacuolar strand. In these va cuolated protoplasts the vegetative nucleus andthe generative cell became tightly surrounded by a new actin network. In the transvacuolar strands there were numerous actin bundles. The “ends” of some of these bundles appeared to be tightly attached to the protoplast membrane indicating that some kind of structures might be present in the protoplast membrane for actin filament attachment.     

Phylogeny and taxonomy of Cinnamomum (Lauraceae)

Taxonomy of Cinnamomum Schaeff. of Lauraceae remains problematic because recent phylogenetic studies have suggested that this genus is not monophyletic. In this study, we assembled three sequence matrices including plastomes (datamatrix I), nrITS sequences alone (datamatrix II), and nrITS plus plastid psbA‐trnH sequences (datamatrix III) of the Cinnamomum‐Ocotea complex of Lauraceae and conducted a new phylogenetic study with thusfar the most extensive species sampling of the Cinnamomum‐Ocotea group. We determined that the Old World Cinnamomum is diphyletic: sect. Camphora Meisn. is sister to Sassafras J.Presl and sect. Cinnamomum is sister to the African Kuloa Trofimov & Rohwer. A recent study indicated that characters of leaf micromorphological anatomy can define the two clades: one possessing reticulate periclinal and the other having non‐reticulate periclinal walls. As result, we divided the genus Cinnamomum of Lauraceae into two genera, i.e., Cinnamomum and Camphora Fabr. The generic name Cinnamomum is retained for those species mainly having reticulate periclinal epidermal cell walls, inconspicuous non‐perulate terminal buds and usually tripliveined leaves; the oldest generic name, Camphora, is applied to the second group which contains those species mainly possessing non‐reticulate periclinal epidermal cell walls, prominent perulate terminal buds and pinnately‐veined leaves. A census of the species and their type specimens listed under Cinnamomum in Asia resulted in the transfer of 18 species to Camphora, including 15 new combinations.     

Cloning and Sequencing of the cDNA Fragment Containing Sorghum Actin Gene（SoAcl）

ＣｌｏｎｉｎｇａｎｄＳｅｑｕｅｎｃｉｎｇｏｆｔｈｅｃＤＮＡＦｒａｇｍｅｎｔＣｏｎｔａｉｎｉｎｇＳｏｒｇｈｕｍＡｃｔｉｎＧｅｎｅ（ＳｏＡｃｌ）ＺＨＯＵＬｉ（周立）;ＺＨＡＮＧＸｉａｏ－ｌｉｎ（张筱林）;ＷＵＮａｉ－ｈｕ（吴乃虎）（Ｉｎｓｔｉｔｕｔｅｏｆ...     

Phylogeny and Classification of Prunus sensu lato （Rosaceae）

The classification of the economically important genus Prunus L. sensu lato （s.L） is controversial due to the high levels of convergent or the parallel evolution of morphological characters. In the present study, phylogenetic analyses of fifteen main segregates of Prunus s.I. represented by eighty-four species were conducted with maximum parsimony and Bayesian approaches using twelve chloroplast regions （atpB- rbcL, matK, ndhF, psbA-trnH, rbcL, rpL 16, rpoC1, rps16, trnS-G, trnL, trnL-F and ycfl） and three nuclear genes （ITS, s6pdh and Sbel） to explore their infrageneric used to develop a new, phylogeny-based classification relationships. The results of these analyses were of Prunus s.I. Our phylogenetic reconstructions resolved three main clades of Prunus s.I. with strong supports. We adopted a broad-sensed genus, Prunus, and recognised three subgenera corresponding to the three main clades： subgenus Padus, subgenus Cerasus and subgenus Prunus. Seven sections of subgenus Prunus were recognised. The dwarf cherries, which were previously assigned to subgenus Cerasus, were included in this subgenus Prunus. One new section name, Prunus L. subgenus Prunus section Persicae （T. T. yu ＆ L. T. Lu） S. L. Zhou and one new species name, Prunus tianshanica （Pojarkov） S. Shi, were proposed.     

Phylogeny of the hermit hummingbirds (trochilidae: Phaethornithinae)

A phylogeny of the hummingbirds of the genera Ramphodon, Eutoxeres, Glaucis, Threnetes, and Phaethornis is presented on the basis of external morphological characters. All 34 species of hermit hummingbirds are included in this study. Differences in 96 characters were examined with regard to their apomorphic (derived) or plesiomor‐phic (primitive) states, resulting in evolutionary trees drawn on the basis of cladistic principles. The most important results are: (1) “Ramphodon “ dohrnii is closer to Glaucis than to Ramphodon; (2) “Phaethornis” gounellei is the sister species to all Phaethornis and merits reevaluation as a separate genus, Anopetia; (3) Phaethornis philippii and P. koepckeae are the sister group to P. syrmatophorus, their straight bill having evolved independently of P. bourcieri; (4) the Phaethornis superciliosus/malaris species group includes P. longirostris as a third species; (5) Phaethornis subochraceus, P. pretrei, and P. augusti share a common ancestor, and (6) Phaethornis longuemareus (sensu Peters 1945) is polyphyletic, being comprised of four seperate species. Due to the lack of synapomorphies, the relationships of some species cannot be reliably determined on the basis of external morphological characters alone.     

Phylogeny and classification of phylum Cercozoa (Protozoa)

The protozoan phylum Cercozoa embraces numerous ancestrally biciliate zooflagellates, euglyphid and other filose testate amoebae, chlorarachnean algae, phytomyxean plant parasites (e.g. Plasmodiophora, Phagomyxa), the animal-parasitic Ascetosporea, and Gromia. We report 18S rRNA sequences of 27 culturable zooflagellates, many previously of unknown taxonomic position. Phylogenetic analysis shows that all belong to Cercozoa. We revise cercozoan classification in the light of our analysis and ultrastructure, adopting two subphyla: Filosa subphyl. nov. a clade comprising Monadofilosa and Reticulofilosa, ranked as superclasses, ancestrally having the same very rare base-pair substitution as all opisthokonts; and subphylum Endomyxa emend. comprising classes Phytomyxea (Plasmodiophorida, Phagomyxida), Ascetosporea (Haplosporidia, Paramyxida, Claustrosporida ord. nov.) and Gromiidea cl. nov., which did not. Monadofilosa comprise Sarcomonadea, zooflagellates with a propensity to glide on their posterior cilium and/or generate filopodia (e.g. Metopion;Cercomonas; Heteromitidae – Heteromita, Bodomorpha, Proleptomonas and Allantion) and two new classes: Imbricatea (with silica scales: Euglyphida; Thaumatomonadida, including Allas, Thaumatomastix) and Thecofilosea (Cryomonadida; Tectofilosida ord. nov. – non-scaly filose amoebae, e.g. Pseudodifflugia). Reticulofilosa comprise classes Chlorarachnea, Spongomonadea and Proteomyxidea (e.g. Massisteria, Gymnophrys, a Dimorpha-like protozoan). Cercozoa, now with nine classes and 17 orders (four new), will probably include many, possibly most, other filose and reticulose amoebae and zooflagellates not yet assigned to phyla.