European journal of protistology最新文献_第7页

Single-cell transcriptomic analysis reveals genome evolution in predatory litostomatean ciliates 单细胞转录组分析揭示了掠食性纤毛虫的基因组进化过程

IF 2.9 2区生物学

European journal of protistology Pub Date : 2024-02-05 DOI: 10.1016/j.ejop.2024.126062

Zhaorui Zhou , Chao Li , Qingxiang Yuan , Yong Chi , Yuqing Li , Ying Yan , Saleh A. Al-Farraj , Naomi A. Stover , Zigui Chen , Xiao Chen

{"title":"Single-cell transcriptomic analysis reveals genome evolution in predatory litostomatean ciliates","authors":"Zhaorui Zhou , Chao Li , Qingxiang Yuan , Yong Chi , Yuqing Li , Ying Yan , Saleh A. Al-Farraj , Naomi A. Stover , Zigui Chen , Xiao Chen","doi":"10.1016/j.ejop.2024.126062","DOIUrl":"https://doi.org/10.1016/j.ejop.2024.126062","url":null,"abstract":"<div>Many ciliated protists prey on other large microbial organisms, including other protists and microscopic metazoans. The ciliate class Litostomatea unites both predatory and endosymbiotic species. The evolution of predation ability in ciliates remains poorly understood, in part, due to a lack of genomic data. To fill this gap, we acquired the transcriptome profiles of six predatory litostomateans using single-cell sequencing technology and investigated their transcriptomic features. Our results show that: (1) in contrast to non-predatory ciliates, the predatory litostomateans have expanded gene families associated with transmembrane activity and reactive oxidative stress response pathways, potentially as a result of cellular behaviors such as fast contraction and extension; (2) the expansion of the calcium-activated BK potassium channel gene family, which hypothetically regulates cell contractility, is an ancient evolutionary event for the class Litostomatea, suggesting a rewired metabolism associated with the hunting behavior of predatory ciliates; and (3) three whole genome duplication (WGD) events have been detected in litostomateans, with genes associated with biosynthetic processes, transmembrane activity, and calcium-activated potassium channel activity being retained during the WGD events. In addition, we explored the evolutionary relationships among 17 ciliate species, including eight litostomateans, and provided a rich foundational dataset for future in-depth phylogenomic studies of Litostomatea. Our comprehensive analyses suggest that the rewired cellular metabolism via expanded gene families and WGD events might be the potential genetic basis for the predation ability of raptorial ciliates.</div>","PeriodicalId":12042,"journal":{"name":"European journal of protistology","volume":"93 ","pages":"Article 126062"},"PeriodicalIF":2.9,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139748116","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Nuclear genome of dinoflagellates: Size variation and insights into evolutionary mechanisms 甲藻的核基因组：尺寸变化和对进化机制的见解

IF 2.9 2区生物学

European journal of protistology Pub Date : 2024-02-03 DOI: 10.1016/j.ejop.2024.126061

Hui Wang , Peiling Wu , Lu Xiong , Han-Sol Kim , Jin Ho Kim , Jang-Seu Ki

{"title":"Nuclear genome of dinoflagellates: Size variation and insights into evolutionary mechanisms","authors":"Hui Wang , Peiling Wu , Lu Xiong , Han-Sol Kim , Jin Ho Kim , Jang-Seu Ki","doi":"10.1016/j.ejop.2024.126061","DOIUrl":"10.1016/j.ejop.2024.126061","url":null,"abstract":"<div>Recent progress in high-throughput sequencing technologies has dramatically increased availability of genome data for prokaryotes and eukaryotes. Dinoflagellates have distinct chromosomes and a huge genome size, which make their genomic analysis complicated. Here, we reviewed the nuclear genomes of core dinoflagellates, focusing on the genome and cell size. Till now, the genome sizes of several dinoflagellates (more than 25) have been measured by certain methods (e.g., flow cytometry), showing a range of 3–250 pg of genomic DNA per cell. In contrast to their relatively small cell size, their genomes are huge (about 1–80 times the human haploid genome). In the present study, we collected the genome and cell size data of dinoflagellates and compared their relationships. We found that dinoflagellate genome size exhibits a positive correlation with cell size. On the other hand, we recognized that the genome size is not correlated with phylogenetic relatedness. These may be caused by genome duplication, increased gene copy number, repetitive non-coding DNA, transposon expansion, horizontal gene transfer, organelle-to-nucleus gene transfer, and/or mRNA reintegration into the genome. Ultimate verification of these factors as potential causative mechanisms would require sequencing of more dinoflagellate genomes in the future.</div>","PeriodicalId":12042,"journal":{"name":"European journal of protistology","volume":"93 ","pages":"Article 126061"},"PeriodicalIF":2.9,"publicationDate":"2024-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139680308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Newly identified diversity of Dinomycetaceae (Rhizophydiales, Chytridiomycota), a family of fungal parasites of marine dinoflagellates 新发现的海洋甲藻真菌寄生家族 Dinomycetaceae（Rhizophydiales, Chytridiomycota）的多样性

IF 2.9 2区生物学

European journal of protistology Pub Date : 2024-01-26 DOI: 10.1016/j.ejop.2024.126053

Alan Denis Fernández-Valero , Sergey A. Karpov , Nagore Sampedro , Jordina Gordi , Natàlia Timoneda , Esther Garcés , Albert Reñé

{"title":"Newly identified diversity of Dinomycetaceae (Rhizophydiales, Chytridiomycota), a family of fungal parasites of marine dinoflagellates","authors":"Alan Denis Fernández-Valero , Sergey A. Karpov , Nagore Sampedro , Jordina Gordi , Natàlia Timoneda , Esther Garcés , Albert Reñé","doi":"10.1016/j.ejop.2024.126053","DOIUrl":"10.1016/j.ejop.2024.126053","url":null,"abstract":"<div>We identified two new parasite species of Chytridiomycota isolated during blooms of the dinoflagellate Alexandrium minutum in the coastal Mediterranean Sea. Light and electron microscopy together with molecular characterization of the nuclear 18S, ITS, and 28S rDNA regions led to their identification as two new species, Dinomyces gilberthii and Paradinomyces evelyniae, both belonging to the family Dinomycetaceae, order Rhizophydiales. Dinomyces gilberthii differs from the previously described D. arenysensis by the presence of discharge papillae and the development of a drop-shaped sporangium. Paradinomyces evelyniae differs from the previously described P. triforaminorum by the prominent lipid globule present in early sporangia and by the pointed end producing a rhizoid. The two chytrids differed in their geographical distribution. Dinomyces gilberthii was detected in several Mediterranean habitats, including harbours and beaches, and was particularly prevalent during summer dinoflagellate blooms. Its widespread occurrence in coastal ecosystems suggested a high level of adaptability to this environment. Paradinomyces evelyniae had a more restricted distribution in the coastal-marine environment, occurring in harbour sediments and only occasionally in the water column during winter and early spring. Paradinomyces evelyniae has previously been detected in the Baltic Sea, suggesting that its distribution encompasses contrasting coastal environments, although its presence is rare.</div>","PeriodicalId":12042,"journal":{"name":"European journal of protistology","volume":"93 ","pages":"Article 126053"},"PeriodicalIF":2.9,"publicationDate":"2024-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0932473924000038/pdfft?md5=f398b8db6d22cba7e082c1c9eb490c2f&pid=1-s2.0-S0932473924000038-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139588786","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Lighting lantern above Psalteriomonadidae: Unveiling novel diversity within the genus Psalteriomonas (Discoba: Heterolobosea) 点亮灯笼上的紫檀单胞菌科：揭示紫檀单胞菌属（碟形目：异叶目）内的新多样性

IF 2.9 2区生物学

European journal of protistology Pub Date : 2024-01-10 DOI: 10.1016/j.ejop.2024.126052

Martina Foučková, Kristýna Uhrová, Aneta Kubánková, Tomáš Pánek, Ivan Čepička

引用次数: 0

It's time to consider the Arcellinida shell as a weapon 是时候将 Arcellinida 贝壳视为武器了

IF 2.9 2区生物学

European journal of protistology Pub Date : 2024-01-02 DOI: 10.1016/j.ejop.2024.126051

Kenneth Dumack , Enrique Lara , Clément Duckert , Elizaveta Ermolaeva , Ferry Siemensma , David Singer , Valentyna Krashevska , Mariusz Lamentowicz , Edward A.D. Mitchell

引用次数: 0

The first arctic strain of Rhizochromulina: Morphology, ultrastructure, and position in the evolutionary tree of the order Rhizochromulinales (Heterokontophyta, Dictyochophyceae) 第一株北极根瘤藻：形态、超微结构和在根瘤藻目（异藻纲，双子叶植物）进化树中的位置

IF 2.9 2区生物学

European journal of protistology Pub Date : 2023-12-17 DOI: 10.1016/j.ejop.2023.126050

Pavel Safonov , Mariia Berdieva , Elena Nassonova , Sergei Skarlato , Ilya Pozdnyakov

{"title":"The first arctic strain of Rhizochromulina: Morphology, ultrastructure, and position in the evolutionary tree of the order Rhizochromulinales (Heterokontophyta, Dictyochophyceae)","authors":"Pavel Safonov , Mariia Berdieva , Elena Nassonova , Sergei Skarlato , Ilya Pozdnyakov","doi":"10.1016/j.ejop.2023.126050","DOIUrl":"10.1016/j.ejop.2023.126050","url":null,"abstract":"<div>Rhizochromulina marina is a unicellular amoeboid alga capable of forming flagellate cells; it is a single validly named species in the genus. Besides, there are numerous environmental sequences and undescribed strains designated as Rhizochromulina sp. or R. marina. The biogeography of the genus is understudied: rhizochromulines from the Indian, Southern, and Arctic Oceans are unknown. Here, we present the description of Rhizochromulina sp. B44, which was for the first time isolated from an arctic habitat. Biofilms of this microalga grow at the bottom of a culture vessel, where neighbouring amoeboid cells form associations through a common network of pseudopodia, i.e. meroplasmodia. Pseudopodia branch, anastomose mainly during meroplasmodia formation, and are supported by microtubules that arise from the perinuclear zone. Actin filaments are localized in the cytoplasm and can be revealed only near the bases of pseudopodia. We succeeded in inducing the transformation of amoeboid cells into flagellates using a prolonged agitation of cultures. Morphological and molecular analyses revealed that the studied strain is most closely related to the type strain of R. marina. At the same time, 18S rDNA sequences of early branching-off rhizochromulinids differ significantly from Rhizochromulina sp. B44, suggesting a high divergence at the genus level.</div>","PeriodicalId":12042,"journal":{"name":"European journal of protistology","volume":"92 ","pages":"Article 126050"},"PeriodicalIF":2.9,"publicationDate":"2023-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138690117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Testate amoebae (Arcellinida, Amoebozoa) community diversity in New England bogs and fens assessed through lineage-specific amplicon sequencing 通过品系特异性扩增子测序评估新英格兰沼泽和沼泽中睾丸变形虫（Arcellinida，变形虫）群落多样性

IF 2.9 2区生物学

European journal of protistology Pub Date : 2023-12-15 DOI: 10.1016/j.ejop.2023.126049

Olivia K. Dufour , Evie Hoffman , Robin S. Sleith , Laura A. Katz , Agnes K.M. Weiner , Taylor R. Sehein

{"title":"Testate amoebae (Arcellinida, Amoebozoa) community diversity in New England bogs and fens assessed through lineage-specific amplicon sequencing","authors":"Olivia K. Dufour , Evie Hoffman , Robin S. Sleith , Laura A. Katz , Agnes K.M. Weiner , Taylor R. Sehein","doi":"10.1016/j.ejop.2023.126049","DOIUrl":"10.1016/j.ejop.2023.126049","url":null,"abstract":"<div>Testate amoebae (order Arcellinida) are abundant in freshwater ecosystems, including low pH bogs and fens. Within these environments, Arcellinida are considered top predators in microbial food webs and their tests are useful bioindicators of paleoclimatic changes and anthropogenic pollutants. Accurate species identifications and characterizations of diversity are important for studies of paleoclimate, microbial ecology, and environmental change; however, morphological species definitions mask cryptic diversity, which is a common phenomenon among microbial eukaryotes. Lineage-specific primers recently designed to target Arcellinida for amplicon sequencing successfully captured a poorly-described yet diverse fraction of the microbial eukaryotic community. Here, we leveraged the application of these newly-designed primers to survey the diversity of Arcellinida in four low-pH New England bogs and fens, investigating variation among bogs (2018) and then across seasons and habitats within two bogs (2019). Three OTUs represented 66% of Arcellinida reads obtained across all habitats surveyed. 103 additional OTUs were present in lower abundance with some OTUs detected in only one sampling location, suggesting habitat specificity. By establishing a baseline for Arcellinida diversity, we provide a foundation to monitor key taxa in habitats that are predicted to change with increasing anthropogenic pressure and rapid climate change.</div>","PeriodicalId":12042,"journal":{"name":"European journal of protistology","volume":"92 ","pages":"Article 126049"},"PeriodicalIF":2.9,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138689985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Description of Holostichides (Extraholostichides) eastensis tianjinensis subgen. nov. subspec. nov. (Ciliophora, Hypotricha) from northern China 描述来自中国北方的 Holostichides (Extraholostichides) eastensis tianjinensis subgen.

IF 2.9 2区生物学

European journal of protistology Pub Date : 2023-12-12 DOI: 10.1016/j.ejop.2023.126048

Ziyan Liu, Ziyu Wang, Qi Zhang, Qiukun Wang, Fengchao Li

{"title":"Description of Holostichides (Extraholostichides) eastensis tianjinensis subgen. nov. subspec. nov. (Ciliophora, Hypotricha) from northern China","authors":"Ziyan Liu, Ziyu Wang, Qi Zhang, Qiukun Wang, Fengchao Li","doi":"10.1016/j.ejop.2023.126048","DOIUrl":"10.1016/j.ejop.2023.126048","url":null,"abstract":"<div>The morphology and morphogenesis of a new urostylid, Holostichides (Extraholostichides) eastensis tianjinensis subgen. nov. subspec. nov. were analyzed. The new subspecies differs from the nominotypical subspecies H. (Extraholostichides) eastensis eastensis Wang et al., 2022 by the relatively long frontoterminal row (about 60% vs. 30% of body length), colorless cortical granules (vs. dark brown), two (vs. one) parabuccal cirri, and usually an extra cirrus behind the first midventral pair (vs. lacking). Based on the difference in the frontal ciliature, we split Holostichides into two subgenera: H. (Extraholostichides) subgen. nov. (type species Holostichides eastensis Wang et al., 2022; with a short cirral row behind the middle frontal cirrus) and H. (Holostichides) Foissner, 1987 (type species Holostichides chardezi Foissner, 1987; lacking this short row). The main morphogenetic characters of the new subspecies are very similar to those of H. (Extraholostichides) eastensis eastensis except for some minor differences. Phylogenetic analyses based on SSU rDNA sequences indicate that H. (Extraholostichides) subgen. nov. is monophyletic and nested within the monophyletic genus Holostichides, which is sister to Eschaneustyla lugeri.</div>","PeriodicalId":12042,"journal":{"name":"European journal of protistology","volume":"92 ","pages":"Article 126048"},"PeriodicalIF":2.9,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138572377","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Morphology and molecular phylogeny of two hypotrichous ciliates (Ciliophora, Spirotrichea) from South Korea, including Hemiurosomoida koreana n. sp. 韩国两种次毛纤毛虫(纤毛虫、螺旋体纤毛虫)的形态和分子系统发育，包括朝鲜半毛纤毛虫

IF 2.9 2区生物学

European journal of protistology Pub Date : 2023-12-06 DOI: 10.1016/j.ejop.2023.126045

Atef Omar , Ji Hye Moon , Jae-Ho Jung

{"title":"Morphology and molecular phylogeny of two hypotrichous ciliates (Ciliophora, Spirotrichea) from South Korea, including Hemiurosomoida koreana n. sp.","authors":"Atef Omar , Ji Hye Moon , Jae-Ho Jung","doi":"10.1016/j.ejop.2023.126045","DOIUrl":"10.1016/j.ejop.2023.126045","url":null,"abstract":"<div>The living morphology, infraciliature, and molecular phylogeny of a new soil ciliate, Hemiurosomoida koreana n. sp., discovered in a sample collected from a mountain in the northeast of South Korea, were investigated. The new species possesses the characteristics of the genus Hemiurosomoida, i.e., a reduced number of frontal-ventral-transverse cirri, three dorsal kineties of which kineties 1 and 2 each bears a caudal cirrus, and a single dorsomarginal kinety. It is distinguishable from congeners and other similar species by at least one distinct qualitative or quantitative character including the body size, the presence and arrangement of cortical granules, the number of adoral membranelles, marginal cirri, and dorsal dikinetids, or by the arrangement of transverse cirri. Phylogenetic analyses based on 18S rRNA gene sequences also support the assignment of the new species to the non-monophyletic genus Hemiurosomoida. In addition, the living morphology, infraciliature, and the 18S rRNA gene sequence of a Korean population of Nothoholosticha flava were studied.</div>","PeriodicalId":12042,"journal":{"name":"European journal of protistology","volume":"92 ","pages":"Article 126045"},"PeriodicalIF":2.9,"publicationDate":"2023-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138534298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Morphology, morphogenesis, and molecular phylogeny of Aspidisca koreana n. sp. (Ciliophora, Euplotida) from South Korea 韩国朝鲜蛛的形态、形态发生和分子系统发育(纤毛蛛科，整虫目)

IF 2.9 2区生物学

European journal of protistology Pub Date : 2023-12-01 DOI: 10.1016/j.ejop.2023.126037

Ji Hye Choi , Atef Omar , Jae-Ho Jung

引用次数: 0