IF 1.9 3区生物学

Protist Pub Date : 2024-12-01 DOI: 10.1016/j.protis.2024.126073

Yan Xu , Xiayi Chen , Michael Melkonian , Sibo Wang , Sunil Kumar Sahu

{"title":"Comparative chloroplast genome analysis of two Desmodesmus species reveals genome diversity within Scenedesmaceae (Sphaeropleales, Chlorophyceae)","authors":"Yan Xu , Xiayi Chen , Michael Melkonian , Sibo Wang , Sunil Kumar Sahu","doi":"10.1016/j.protis.2024.126073","DOIUrl":"10.1016/j.protis.2024.126073","url":null,"abstract":"<div><div><em>Desmodesmus</em> (Sphaeropleales, Chlorophyceae) is a genus of freshwater green algae widely distributed in aquatic ecosystems and known for its potential in biotechnology and bioremediation. We present the complete chloroplast genome sequences of two <em>Desmodesmus</em> species, <em>D. hystrix</em> and <em>D. perforatus</em>. Comparative analysis revealed significant differences in their quadripartite structures, particularly in the lengths of the small single copy regions. We observed variations in G + C content across genomic regions, with inverted repeat regions showing a higher G + C content. Microsatellite analysis revealed that A/T mononucleotides were the most abundant type, while dispersed repeat analysis suggested a potential link to expansion of the single-copy region in <em>D. perforatus</em>. Gene annotation, codon usage analysis, and comparison of genome rearrangement highlighted both similarities and differences between the species. Nucleotide diversity analysis revealed higher variability in intergenic regions than in coding regions, with IR regions displaying relative conservation. Comparative analyses of genomes and IR border arrangements demonstrated that the <em>Desmodesmus</em> species exhibit substantial differences in genome structure and gene arrangement among Scenedesmaceae. Phylogenetic analysis, based on 51 single-copy genes from 34 species of Sphaeropleales provided additional information about phylogenetic relationships within Sphaeropleales. These findings contribute to our understanding of comparative plastid genomics in green algae.</div></div>","PeriodicalId":20781,"journal":{"name":"Protist","volume":"175 6","pages":"Article 126073"},"PeriodicalIF":1.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142747697","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

New and noteworthy chrysophycean stomatocysts from the Steppe zone of South Urals (Russia) with comments on the morphological variability 南乌拉尔（俄罗斯）草原带新发现的值得注意的chrysophysp口囊及其形态学变异。

IF 1.9 3区生物学

Protist Pub Date : 2024-11-28 DOI: 10.1016/j.protis.2024.126075

Marina Ignatenko , Tatyana Yatsenko-Stepanova , Dmitry Kapustin

引用次数: 0

Protists and Society: A report on the 2024 autumn meeting of Protistology-UK, at the natural history museum, London 原生生物与社会：英国原生生物学2024年秋季会议报告，伦敦自然历史博物馆

IF 1.9 3区生物学

Protist Pub Date : 2024-11-27 DOI: 10.1016/j.protis.2024.126072

David J.S. Montagnes

引用次数: 0

Integrative studies shed light on the pseudocryptic genus Crassohymena n. gen. (Protozoa, Ciliophora) 综合研究揭示了假隐属（原生动物，纤毛虫目）。

IF 1.9 3区生物学

Protist Pub Date : 2024-11-27 DOI: 10.1016/j.protis.2024.126074

Atef Omar , Jiwon Jung , Gaeul Lee , Jae-Ho Jung

{"title":"Integrative studies shed light on the pseudocryptic genus Crassohymena n. gen. (Protozoa, Ciliophora)","authors":"Atef Omar , Jiwon Jung , Gaeul Lee , Jae-Ho Jung","doi":"10.1016/j.protis.2024.126074","DOIUrl":"10.1016/j.protis.2024.126074","url":null,"abstract":"<div><div>The morphology, morphogenesis, molecular phylogeny, and the resting cyst morphology of the freshwater ciliate, <em>Crassohymena primicirrata</em> (<span><span>Berger and Foissner, 1987</span></span>) n. gen., n. comb., found in samples collected from South Korea, were investigated. The Korean two populations observed are identical to each other and are highly similar to the type population showing only few and minor differences in the size and arrangement of cortical granules and the length of dorsal kinety 4. The new genus <em>Crassohymena</em> n. gen. is established and characterized by a number of morphological and ontogenetic features: the thick undulating membranes comprising three or four rows of kinetosomes and in <em>Cyrtohymena</em> pattern; the anteriorly distinctly displaced transverse cirri; the posteriorly set-off cirrus V/3; the opisthe's anlagen IV–VI originate from cirri IV/2, V/4, and V/3, respectively; the proter's anlagen IV–VI originate from cirrus IV/3; and the enormous anlage I in each daughter cell. Phylogenetic analyses based on 18S rRNA gene sequences show that <em>Crassohymena primicirrata</em> n. gen., n. comb. is separated from all other morphologically most similar taxa and forms an adelphotaxon to the clade containing sequences of the families Neokeronopsidae and Spirofilidae, and the two oxytrichid genera <em>Australocirrus</em> and <em>Notohymena</em>.</div></div>","PeriodicalId":20781,"journal":{"name":"Protist","volume":"176 ","pages":"Article 126074"},"PeriodicalIF":1.9,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142780703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Long-read DNA sequencing reveals the organization of the mitochondrial genome in the early-branching dinoflagellate Oxyrrhis marina. 长读DNA测序揭示了早期分支甲藻Oxyrrhis marina线粒体基因组的组织结构。

IF 1.9 3区生物学

Protist Pub Date : 2024-11-22 DOI: 10.1016/j.protis.2024.126071

Ronie Haro , Nikita Walunjkar , Soham Jorapur , Claudio H. Slamovits

{"title":"Long-read DNA sequencing reveals the organization of the mitochondrial genome in the early-branching dinoflagellate Oxyrrhis marina.","authors":"Ronie Haro , Nikita Walunjkar , Soham Jorapur , Claudio H. Slamovits","doi":"10.1016/j.protis.2024.126071","DOIUrl":"10.1016/j.protis.2024.126071","url":null,"abstract":"<div><div>The mitochondrial genomes of dinoflagellate protists are remarkable for their highly fragmented and heterogeneous organization. Early attempts to determine their structure without ‘next-generation’ DNA sequencing failed to recover a defined genome. Still, it coincided in showing that the proteins coding genes, three in total, and parts of the ribosomal RNA genes were spread across a diffuse assortment of small linear fragments. In contrast, a recent study employed Illumina sequencing to assemble a 326 kbp long single-molecule, circular mitochondrial genome in the symbiotic dinoflagellate <em>Breviolum minutum</em>. Here, we used a combination of short- and long-read massively-parallel DNA sequencing to analyze further the mitochondrial DNA of the early-branching dinoflagellate <em>Oxyrrhis marina</em>. We found that the mitochondrial genome of <em>O. marina</em> consists of 3 linear chromosomes sized 15.9, 33.8 and 40.6 kbp for a total of 90.3 kbp. It contains the <em>cox</em>1, <em>cox</em>3 and <em>cob</em> genes, the same three proteins encoded in the mitochondrion of all myzozoans (Apicomplexa and Dinophyceae), some fragments of ribosomal RNA genes as well as many non-functional gene fragments and extensive noncoding DNA. Our analysis unveiled segments syntenic patterns and rearrangements encompassing coding and non-coding regions, suggesting that recombination is a pervasive process driving the evolution of these genomes.</div></div>","PeriodicalId":20781,"journal":{"name":"Protist","volume":"175 6","pages":"Article 126071"},"PeriodicalIF":1.9,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142720748","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Flagellar proteomic analysis of the brown alga Mutimo cylindricus revealed a novel calcium-binding protein abundantly localized in the anterior flagellum 褐藻 Mutimo cylindricus 的鞭毛蛋白质组分析发现了一种新型钙结合蛋白，该蛋白大量定位于前鞭毛中

IF 1.9 3区生物学

Protist Pub Date : 2024-10-26 DOI: 10.1016/j.protis.2024.126070

Nana Kinoshita-Terauchi , Kogiku Shiba , Makoto Terauchi , Hideki Noguchi , Kazuo Inaba

引用次数: 0

The protists of Ernst Haeckel’s Kunstformen der Natur 恩斯特-海克尔《自然形态学》中的原生生物

IF 1.9 3区生物学

Protist Pub Date : 2024-10-05 DOI: 10.1016/j.protis.2024.126069

John R. Dolan

{"title":"The protists of Ernst Haeckel’s Kunstformen der Natur","authors":"John R. Dolan","doi":"10.1016/j.protis.2024.126069","DOIUrl":"10.1016/j.protis.2024.126069","url":null,"abstract":"<div><div>Haeckel’s ’art book’, <em>Kunstformen der Natur</em>, is likely familiar to most protistologists as it is probably Haeckel’s best known work, and it prominently featured protists. No doubt many of us have used some of the images from it in our lectures. Most familiar are perhaps the often-reproduced images of nassularian radiolaria, but plates were also devoted to phaeodarians, acantharia, foraminifera, ciliates, diatoms, dinoflagellates and desmids. Despite the fame of <em>Kunstformen der Natur</em>, there are aspects of the work that have received little attention, and are of potential interest to protistologists. These include the overall importance of protists in the work, compared to other taxa, the surprisingly under appreciated role of Haeckel’s collaborator, Adolph Giltsch in creating the figures, the disputed fidelity of the illustrations of protists, and Haeckel’s discrete inclusion of many descriptions of new species of protists, forcing us to consider <em>Kunstformen</em> a scientific publication. Here these aspects, and the 20 plates featuring protists will be reviewed. The goal of this review is to familiarize protistologists with the most famous work featuring protists, and point out the many particular figures of protists we may wish to avoid showcasing, as the illustrations are questionable. A supplemental file is provided listing the currently accepted names of the protist taxa (for names found in a database), and the reasons for considering some illustrations as questionable.</div></div>","PeriodicalId":20781,"journal":{"name":"Protist","volume":"175 6","pages":"Article 126069"},"PeriodicalIF":1.9,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142418976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Dead reckoning of protist viability with propidium monoazide (PMA)-quantitative PCR; a case study using Neoparamoeba perurans 利用单氮化丙啶（PMA）-定量 PCR 对原生生物的存活率进行死算；以周龄新巴拉米阿米巴为例进行研究

IF 1.9 3区生物学

Protist Pub Date : 2024-09-24 DOI: 10.1016/j.protis.2024.126068

James W. Wynne , Anca G. Rusu , Ben T. Maynard , Megan L. Rigby , Richard S. Taylor

{"title":"Dead reckoning of protist viability with propidium monoazide (PMA)-quantitative PCR; a case study using Neoparamoeba perurans","authors":"James W. Wynne , Anca G. Rusu , Ben T. Maynard , Megan L. Rigby , Richard S. Taylor","doi":"10.1016/j.protis.2024.126068","DOIUrl":"10.1016/j.protis.2024.126068","url":null,"abstract":"<div><div>The ability to distinguish between viable and non-viable protozoan parasites is central to improved human and animal health management. While conceptually simple, methods to differentiate cell viability in situ remain challenging. Amoebic gill disease, caused by <em>Neoparamoeba perurans</em> is a parasitic disease impacting Atlantic salmon aquaculture globally. Although commercial freshwater treatments alleviate AGD, viable amoebae remain on gills or in used treatment water. Existing PCR-based assays are able to quantify <em>N. perurans</em> abundance but cannot discriminate amoeba viability. We investigated the use of propidium monoazide (PMA) application, prior to real-time PCR, to distinguish between alive and dead cells. We demonstrate that 200 μM PMA can significantly reduce amplification from non-viable (isopropanol treated) cultured amoebae across at least three logs of cell concentrations. Using a serial dilution of viable and non-viable cells, we show that non-PMA PCR amplifies both viable and non-viable amoebae, while PMA exposure suppresses (but does not completely inhibit) amplification from non-viable amoebae. The effect of freshwater treatment on <em>N. perurans</em> viability was assessed using the PMA-PCR. Following PMA exposure, amplification from freshwater treated amoebae was reduced by approximately 94–97 %. Taken together this study demonstrates that PMA combined with traditional real-time PCR can estimate amoeba viability.</div></div>","PeriodicalId":20781,"journal":{"name":"Protist","volume":"175 6","pages":"Article 126068"},"PeriodicalIF":1.9,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142326407","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Dinotoms possess two evolutionary distinct autophagy-related ubiquitin-like conjugation systems 恐龙在进化过程中拥有两种不同的自噬相关泛素类连接系统

IF 1.9 3区生物学

Protist Pub Date : 2024-09-21 DOI: 10.1016/j.protis.2024.126067

Euki Yazaki , Tadaaki Uehara , Hirokazu Sakamoto , Yuji Inagaki

{"title":"Dinotoms possess two evolutionary distinct autophagy-related ubiquitin-like conjugation systems","authors":"Euki Yazaki , Tadaaki Uehara , Hirokazu Sakamoto , Yuji Inagaki","doi":"10.1016/j.protis.2024.126067","DOIUrl":"10.1016/j.protis.2024.126067","url":null,"abstract":"<div><div>Autophagy is an intracellular degradation mechanism by which cytoplasmic materials are delivered to and degraded in the lysosome-fused autophagosome (autolysosome) and proposed to have been established at an early stage of eukaryotic evolution. Dinoflagellates harboring endosymbiotic diatoms (so-called “dinotoms”), which retain their own nuclei and mitochondria in addition to plastids, have been investigated as an intermediate toward the full integration of a eukaryotic phototroph into the host-controlled organelle (i.e., plastid) through endosymbiosis. Pioneering studies systematically evaluated the degree of host governance on several metabolic pathways in the endosymbiotic diatoms (ESDs). However, little attention has been paid to the impact of the endosymbiotic lifestyle on the autophagy operated in the ESDs. In this study, we searched for ATG3, ATG4, ATG5, ATG7, ATG8, ATG10, and ATG12, which are required for autophagosome formation, in the RNA-seq data from dinotoms <em>Durinskia baltica</em> and <em>Kryptoperidinium foliaceum</em>. We detected two evolutionally distinct sets of the ATG proteins in the dinotom species, one affiliated with the dinoflagellate homologs and the other with the diatom homologs in phylogenetic analyses. The results suggest that the ATG proteins descended from the diatom taken up by the dinoflagellate host persist for autophagosome formation and, most likely, autophagy.</div></div>","PeriodicalId":20781,"journal":{"name":"Protist","volume":"175 6","pages":"Article 126067"},"PeriodicalIF":1.9,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142323616","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Basic biology, ecology, and biotechnology of euglenids 八目鳗的基础生物学、生态学和生物技术

IF 1.9 3区生物学

Protist Pub Date : 2024-09-12 DOI: 10.1016/j.protis.2024.126066

Michael L. Ginger Guest Editor, Anna Karnkowska Guest Editor, Vladimír Hampl Guest Editor, Scott C. Farrow Guest Editor

引用次数: 0

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