Comparative DNA sequence analyses of Pyramimonas parkeae (Prasinophyceae) chloroplast genomes.

Abstract:

:Prasinophytes form a paraphyletic assemblage of early diverging green algae, which have the potential to reveal the traits of the last common ancestor of the main two green lineages: (i) chlorophyte algae and (ii) streptophyte algae. Understanding the genetic composition of prasinophyte algae is fundamental to understanding the diversification and evolutionary processes that may have occurred in both green lineages. In this study, we sequenced the chloroplast genome of Pyramimonas parkeae NIES254 and compared it with that of P. parkeae CCMP726, the only other fully sequenced P. parkeae chloroplast genome. The results revealed that P. parkeae chloroplast genomes are surprisingly variable. The chloroplast genome of NIES254 was larger than that of CCMP726 by 3,204 bp, the NIES254 large single copy was 288 bp longer, the small single copy was 5,088 bp longer, and the IR was 1,086 bp shorter than that of CCMP726. Similarity values of the two strains were almost zero in four large hot spot regions. Finally, the strains differed in copy number for three protein-coding genes: ycf20, psaC, and ndhE. Phylogenetic analyses using 16S and 18S rDNA and rbcL sequences resolved a clade consisting of these two P. parkeae strains and a clade consisting of these plus other Pyramimonas isolates. These results are consistent with past studies indicating that prasinophyte chloroplast genomes display a higher level of variation than is commonly found among land plants. Consequently, prasinophyte chloroplast genomes may be less useful for inferring the early history of Viridiplantae than has been the case for land plant diversification.

journal_name

J Phycol

journal_title

Journal of phycology

authors

Satjarak A,Graham LE

doi

10.1111/jpy.12515

subject

Has Abstract

pub_date

2017-04-01 00:00:00

pages

415-424

issue

2

eissn

0022-3646

issn

1529-8817

journal_volume

53

pub_type

杂志文章
  • BLOOM OF THE GIANT ANADYOMENE GIGANTODICTYON SP. NOV. (ANADYOMENACEAE, CLADOPHORALES) FROM THE OUTER SLOPE (25-50 m) OF THE BELIZE BARRIER REEF(1).

    abstract::A giant form of Anadyomene, most similar to Anadyomene pavonina (J. Agardh) Wille, a rare and diminutive alga endemic to Florida, appeared as up to 10 m long net-like strands covering 10%-80% of a 0.5 km region of the 25-50 m deep Belizean outer reef slope where none had been present up to 12 months earlier. This new ...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/j.1529-8817.2011.01108.x

    authors: Littler MM,Littler DS

    更新日期:2012-02-01 00:00:00

  • Functional group richness: implications of biodiversity for light use and lipid yield in microalgae.

    abstract::Currently, very few studies address the relationship between diversity and biomass/lipid production in primary producer communities for biofuel production. Basic studies on the growth of microalgal communities, however, provide evidence of a positive relationship between diversity and biomass production. Recent studie...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/jpy.12092

    authors: Stockenreiter M,Haupt F,Graber AK,Seppälä J,Spilling K,Tamminen T,Stibor H

    更新日期:2013-10-01 00:00:00

  • Genome size-dependent pcna gene copy number in dinoflagellates and molecular evidence of retroposition as a major evolutionary mechanism.

    abstract::Proliferating cell nuclear antigen (PCNA) plays critical roles in eukaryotic DNA replication and replication-associated processes. It is typically encoded by one or two gene copies (pcna) in eukaryotic genomes. Recently reported higher copy numbers of pcna in some dinoflagellates raised a question of how this gene has...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/jpy.12815

    authors: Hou Y,Ji N,Zhang H,Shi X,Han H,Lin S

    更新日期:2019-02-01 00:00:00

  • PHYLOGENETIC DIVERSITY OF TRENTEPOHLIALEAN ALGAE ASSOCIATED WITH LICHEN-FORMING FUNGI(1).

    abstract::Nearly one-fourth of the lichen-forming fungi associate with trentepohlialean algae, yet their genetic diversity remains unknown. Recent work focusing on free-living trentepohlialean algae has provided a phylogenetic context within which questions regarding the lichenization of these algae can be asked. Here, we conce...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/j.1529-8817.2011.00962.x

    authors: Nelsen MP,Plata ER,Andrew CJ,Lücking R,Lumbsch HT

    更新日期:2011-04-01 00:00:00

  • Identification of a new-to-science cyanobacterium, Toxifilum mysidocida gen. nov. & sp. nov. (Cyanobacteria, Cyanophyceae).

    abstract::Cyanobacteria occupy many niches within terrestrial, planktonic, and benthic habitats. The diversity of habitats colonized, similarity of morphology, and phenotypic plasticity all contribute to the difficulty of cyanobacterial identification. An unknown marine filamentous cyanobacterium was isolated from an aquatic an...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/jpy.12490

    authors: Zimba PV,Huang IS,Foley JE,Linton EW

    更新日期:2017-02-01 00:00:00

  • NOVEL PELLICLE SURFACE PATTERNS ON EUGLENA OBTUSA (EUGLENOPHYTA) FROM THE MARINE BENTHIC ENVIRONMENT: IMPLICATIONS FOR PELLICLE DEVELOPMENT AND EVOLUTION(1).

    abstract::Euglena obtusa F. Schmitz possesses novel pellicle surface patterns, including the greatest number of strips (120) and the most posterior subwhorls of strip reduction in any euglenid described so far. Although the subwhorls form a mathematically linear pattern of strip reduction, the pattern observed here differs from...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/j.1529-8817.2007.00447.x

    authors: Esson HJ,Leander BS

    更新日期:2008-02-01 00:00:00

  • Tackling Harmful Cyanobacterial Blooms with Chinese Colleagues: We're All in the Same Boat.

    abstract::Harmful cyanobacterial blooms (CyanoHABs) are a rapidly proliferating global problem, threatening the use and sustainability of our freshwater resources. In recent decades, the United States, China, and other developed and developing countries threatened by CyanoHAB expansion have established collaborative efforts aim...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/jpy.13058

    authors: Paerl HW

    更新日期:2020-12-01 00:00:00

  • Monitoring cellular C:N ratio in phytoplankton by means of FTIR-spectroscopy.

    abstract::Statistical growth rate modelling can be applied in a variety of ecological and biotechnological applications. Such models are frequently based on Monod or Droop equations and, especially for the latter, require reliable determination of model input parameters such as C:N quotas. Besides growth rate modelling, a C:N q...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/jpy.12858

    authors: Wagner H,Jebsen C,Wilhelm C

    更新日期:2019-06-01 00:00:00

  • Seasonal variation of Sargassum ilicifolium (Phaeophyceae) growth on equatorial coral reefs.

    abstract::Temporal and spatial variations in Sargassum ilicifolium thallus density and length were investigated on equatorial coral reefs in Singapore from November 2011 to October 2012. Thalli density varied little throughout the year, however, we found strong seasonal patterns in thallus length and identified temperature as t...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/jpy.12818

    authors: Low JKY,Fong J,Todd PA,Chou LM,Bauman AG

    更新日期:2019-04-01 00:00:00

  • A method to establish an "immortalized F2 " sporophyte population in the economic brown alga Undaria pinnatifida (Laminariales: Alariaceae).

    abstract::Studies of quantitative trait loci based on genetic linkage maps require the establishment of a mapping population. Permanent mapping populations are more ideal than temporary ones because they can be used repeatedly. However, there has been no reported permanent sporophyte population of economically important kelp sp...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/jpy.13066

    authors: Shan T,Pang S,Wang X,Li J,Li Q,Su L,Li X

    更新日期:2020-09-04 00:00:00

  • Symbiochlorum hainanensis gen. et sp. nov. (Ulvophyceae, Chlorophyta) isolated from bleached corals living in the South China Sea.

    abstract::Light/scanning electron/transmission microscopy-based morphological analyses and multiple nucleotide sequences-based molecular phylogenetic analyses are used to identify and assess the phylogenetic position of a new unidentified green alga isolated from bleached corals living in the South China Sea. This new unidentif...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/jpy.12779

    authors: Gong S,Li Z,Zhang F,Xiao Y,Cheng H

    更新日期:2018-12-01 00:00:00

  • CARBON/NUTRIENT BALANCE IN RELATION TO BIOMASS PRODUCTION AND HALOGENATED COMPOUND CONTENT IN THE RED ALGA ASPARAGOPSIS TAXIFORMIS (BONNEMAISONIACEAE)(1).

    abstract::We tested how the availability of carbon and nitrogen determines both the production of Asparagopsis taxiformis (Delile) V. Trevis. and content of the two major halocarbons, bromoform and dibromoacetic acid. The halogenated secondary metabolites of Asparagopsis species are particularly interesting from an applied pers...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/j.1529-8817.2011.01083.x

    authors: Mata L,Gaspar H,Santos R

    更新日期:2012-02-01 00:00:00

  • Glycerol Utilization By Phytoplankton1.

    abstract::Dissolved organic carbon (DOC) is an important source of carbon and energy for microbes, but whether it can be used by phytoplankton has not been systematically studied, and the underlying molecular metabolism remains poorly understood. Here, we investigated the ability of phytoplankton to utilize glycerol as a repres...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/jpy.13031

    authors: Wang C,Baseler S,Lin S

    更新日期:2020-10-01 00:00:00

  • TWO NEW VARIETIES OF STAURASTRUM (DESMIDIACEAE) FROM SÃO PAULO, BRAZIL.

    abstract::Two new varieties of Staurastrum (Desmidiaceae) are described from Sao Paulo, southern Brazil: St. polymorphum Bréb. var. itirapinense and St. quadrangulare Bréb. var. sanctipaulense. ...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/j.1529-8817.1967.tb04630.x

    authors: de Mattos Bicudo CE

    更新日期:1967-03-01 00:00:00

  • Reevaluation and discovery of new species of the rare genus Watanabea and establishment of Massjukichlorella gen. nov. (Trebouxiophyceae, Chlorophyta) using an integrative approach.

    abstract::Chlorella-like coccoid green algae are widely distributed in almost all terrestrial habitats and belong to different lineages of the Chlorophyceae and Trebouxiophyceae. The Watanabea clade of the Trebouxiophyceae shows a high genetic biodiversity. Re-investigation of the authentic strain of the rarely found W. renifor...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/jpy.12830

    authors: Darienko T,Pröschold T

    更新日期:2019-04-01 00:00:00

  • High Nitrogen and Phosphorous Acquisition by Belowground Parts of Caulerpa prolifera (Chlorophyta) Contribute to the Species' Rapid Spread in Ria Formosa Lagoon, Southern Portugal.

    abstract::Despite worldwide proliferation of the genus Caulerpa and subsequent effects on benthic communities, little is known about the nutritional physiology of the Caulerpales. Here, we investigated the uptake rates of ammonium, nitrate, amino acids, and phosphate through the fronds and rhizoids + stolon, the internal transl...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/jpy.12988

    authors: Alexandre A,Santos R

    更新日期:2020-06-01 00:00:00

  • STUDIES IN SOME FOLIOSE RED ALGAE OF THE PACIFIC COAST. I. CRYPTONEMIACEXE(1).

    abstract::Pacific coast species of the red algae Halymenia and Cryptonemia are described Of the 8 previously reported species of Halymenia 3 (H. abyssicola Dawson, H. megaspore Dawson, H refugiensis Dawson) hive been placed in synonymy with other species. Halymenia hollenbergii from southern California is described as new; H co...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/j.1529-8817.1967.tb04648.x

    authors: Abbott IA

    更新日期:1967-09-01 00:00:00

  • Role of riboswitches in gene regulation and their potential for algal biotechnology.

    abstract::Riboswitches are regulatory elements in messenger RNA to which specific ligands can bind directly in the absence of proteins. Ligand binding alters the mRNA secondary structure, thereby affecting expression of the encoded protein. Riboswitches are widespread in prokaryotes, with over 20 different effector ligands know...

    journal_title:Journal of phycology

    pub_type: 杂志文章,评审

    doi:10.1111/jpy.12416

    authors: Nguyen GT,Scaife MA,Helliwell KE,Smith AG

    更新日期:2016-06-01 00:00:00

  • Improvement of phytoplankton culture isolation using single cell sorting by flow cytometry.

    abstract::Flow cytometry provides a tool to physically sort single algal cells in order to obtain clonal cultures. During sorting, cells are submitted to physical stress factors such as high fluidic pressure, exposure to the laser beam, electrostatic charges, deflection through high voltage fields, and collisions with container...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/jpy.12495

    authors: Marie D,Le Gall F,Edern R,Gourvil P,Vaulot D

    更新日期:2017-04-01 00:00:00

  • FORECASTED CO2 MODIFIES THE INFLUENCE OF LIGHT IN SHAPING SUBTIDAL HABITAT(1).

    abstract::Some abiotic conditions are well known to play disproportionately large roles in shaping contemporary assemblages, yet their roles may not continue to have similar magnitudes of effect into the future. We tested whether forecasted levels of CO2 could alter the strength of influence of an abiotic factor (i.e., light in...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/j.1529-8817.2011.01002.x

    authors: Russell BD,Passarelli CA,Connell SD

    更新日期:2011-08-01 00:00:00

  • The immediate wound-induced oxidative burst of Saccharina latissima depends on light via photosynthetic electron transport.

    abstract::Reactive oxygen species (ROS) produced by an oxidative burst are an important component of the wound response in algae, vascular plants, and animals. In all taxa, ROS production is usually attributed solely to a defense-related enzyme like NADPH-oxidase (Nox). However, here we show that the initial, wound-induced oxid...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/jpy.12302

    authors: McDowell RE,Amsler MO,Li Q,Lancaster JR Jr,Amsler CD

    更新日期:2015-06-01 00:00:00

  • Whole genome comparison of six Crocosphaera watsonii strains with differing phenotypes.

    abstract::Crocosphaera watsonii, a unicellular nitrogen-fixing cyanobacterium found in oligotrophic oceans, is important in marine carbon and nitrogen cycles. Isolates of C. watsonii can be separated into at least two phenotypes with environmentally important differences, indicating possibly distinct ecological roles and niches...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/jpy.12090

    authors: Bench SR,Heller P,Frank I,Arciniega M,Shilova IN,Zehr JP

    更新日期:2013-08-01 00:00:00

  • ANALYSIS OF ALEXANDRIUM TAMARENSE (DINOPHYCEAE) GENES REVEALS THE COMPLEX EVOLUTIONARY HISTORY OF A MICROBIAL EUKARYOTE().

    abstract::Microbial eukaryotes may extinguish much of their nuclear phylogenetic history due to endosymbiotic/horizontal gene transfer (E/HGT). We studied E/HGT in 32,110 contigs of expressed sequence tags (ESTs) from the dinoflagellate Alexandrium tamarense (Dinophyceae) using a conservative phylogenomic approach. The vast maj...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/j.1529-8817.2012.01194.x

    authors: Chan CX,Soares MB,Bonaldo MF,Wisecaver JH,Hackett JD,Anderson DM,Erdner DL,Bhattacharya D

    更新日期:2012-10-01 00:00:00

  • COMPARISON OF RESISTANCE TO LIGHT STRESS IN TOXIC AND NON-TOXIC STRAINS OF MICROCYSTIS AERUGINOSA (CYANOPHYTA)(1).

    abstract::Blooms of Microcystis aeruginosa (Kützing) Kützing occur frequently in many freshwater ecosystems around the world, but the role of environmental factors in promoting the growth and determining the proportion of toxic and non-toxic strains still requires more investigation. In this study, four strains (toxic CPCC299 &...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/j.1529-8817.2012.01191.x

    authors: Deblois CP,Juneau P

    更新日期:2012-08-01 00:00:00

  • LIGHT-INDUCED OIL GLOBULE MIGRATION IN HAEMATOCOCCUS PLUVIALIS (CHLOROPHYCEAE).

    abstract::Astaxanthin-rich oil globules in Haematococcus pluvialis display rapid light-induced peripheral migration that is unique to this organism and serves to protect the photosynthetic system from excessive light. We observed rapid light-induced peripheral migration that is associated with chlorophyll fluorescence quenching...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/j.1529-8817.2012.01210.x

    authors: Peled E,Pick U,Zarka A,Shimoni E,Leu S,Boussiba S

    更新日期:2012-10-01 00:00:00

  • SPECIFICITY AND FUNCTION OF GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE IN A FRESHWATER DIATOM, ASTERIONELLA FORMOSA (BACILLARIOPHYCEAE)(1).

    abstract::The plastidic glyceraldehyde-3-phosphate dehydrogenase (GAPDH) catalyzes the only reductive step in the Calvin cycle and exists as different forms of which GapC1 enzyme is present in chromalveolates, such as diatoms. Biochemical studies on diatoms are still fragmentary, and, thus, in this report, GAPDH from the freshw...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/j.1529-8817.2008.00600.x

    authors: Erales J,Gontero B,Maberly SC

    更新日期:2008-12-01 00:00:00

  • VARIATIONS IN THE CELL WALLS AND PHOTOSYNTHETIC PROPERTIES OF PORPHYRA YEZOENSIS (BANGIALES, RHODOPHYTA) DURING ARCHEOSPORE FORMATION(1).

    abstract::The formation of archeospores is characteristic of Porphyra yezoensis Ueda and is important for Porphyra aquaculture. Recently, it has been regarded as a valuable seed source for propagation of thalli in mariculture. Cell wall composition changes are associated with archeospore formation in P. yezoensis. Here, we repo...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/j.1529-8817.2011.01003.x

    authors: Gao S,Wang G,Yang R,Xie X,Pan G,Xu P,Zhu J

    更新日期:2011-08-01 00:00:00

  • CAROTENOID PIGMENTS OF THE DINOFLAGELLATE GLENODINIUM FOLIACEUM STEIN(1) (2).

    abstract::The marine dinoflagellate, Glenoclinium foliaceum Stein, has been shown to contain fucoxanthin, instead of peridinin, as the major xanthophyll. In addition, 2 carotenes-β-carotene and a compound with spectral properties reminiscent of isomerized y-carotene-and 2 xanthophylls-diadinoxanthin and an unidentified compound...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/j.1529-8817.1968.tb04706.x

    authors: Mandelli EF

    更新日期:1968-12-01 00:00:00

  • The diversity of algal phospholipase D homologs revealed by biocomputational analysis.

    abstract::Phospholipase D (PLD) participates in the formation of phosphatidic acid, a precursor in glycerolipid biosynthesis and a second messenger. PLDs are part of a superfamily of proteins that hydrolyze phosphodiesters and share a catalytic motif, HxKxxxxD, and hence a mechanism of action. Although HKD-PLDs have been thorou...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/jpy.12334

    authors: Beligni MV,Bagnato C,Prados MB,Bondino H,Laxalt AM,Munnik T,Ten Have A

    更新日期:2015-10-01 00:00:00

  • REGULATION OF BIOSYNTHESIS OF DIMETHYLSULFONIOPROPIONATE AND ITS UPTAKE IN STERILE MUTANT OF ULVA PERTUSA (CHLOROPHYTA)1.

    abstract::It has been shown that marine algae produce the compatible solute dimethylsulfoniopropionate (DMSP) from methionine (Met) via four enzymatic reactions in which the third step, synthesis of 4-dimethylsulfonio-2-hydroxy-butyrate (DMSHB) from 4-methylthio-2-hydroxybutyrate (MTHB), is the committing step. However, regulat...

    journal_title:Journal of phycology

    pub_type: 杂志文章

    doi:10.1111/j.1529-8817.2011.00977.x

    authors: Ito T,Asano Y,Tanaka Y,Takabe T

    更新日期:2011-06-01 00:00:00