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From germline genome to highly fragmented somatic genome:genome-wide DNA rearrangement during the sexual process in ciliated protists

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Marine Life Science & Technology 2024年第1期6卷 31-49页

作者： Liping Lyu Xue Zhang Yunyi Gao Tengteng Zhang Jinyu Fu Naomi A.Stover Feng Gao Key Laboratory of Evolution&Marine Biodiversity(Ministry of Education) and Institute of Evolution&Marine BiodiversityOcean University of ChinaQingdao 266003China Department of Biology Bradley UniversityPeoriaIL 61625USA Laoshan Laboratory Qingdao 266237China

Genomes are incredibly dynamic within diverse eukaryotes and programmed genome rearrangements(PGR)play important roles in generating genomic diversity.However,genomes and chromosomes in metazoans are usually large in size which prevents our understanding of the origin and evolution of PGR.To expand our knowledge of genomic diversity and the evolutionary origin of complex genome rearrangements,we focus on ciliated protists(ciliates).ciliates are single-celled eukaryotes with highly fragmented somatic chromosomes and massively scrambled germline genomes.PGR in ciliates occurs extensively by removing massive amounts of repetitive and selfish DNA elements found in the silent germline genome dur-ing development of the somatic genome.We report the partial germline genomes of two spirotrich ciliate species,namely Strombidium cf.sulcatum and Halteria grandinella,along with the most compact and highly fragmented somatic genome for S.cf.sulcatum.We provide the first insights into the genome rearrangements of these two species and compare these features with those of other ciliates.Our analyses reveal:(1)DNA sequence loss through evolution and during PGR in S.cf.sulcatum has combined to produce the most compact and efficient nanochromosomes observed to date;(2)the compact,transcriptome-like somatic genome in both species results from extensive removal of a relatively large number of shorter germline-specific DNA sequences;(3)long chromosome breakage site motifs are duplicated and retained in the somatic genome,revealing a complex model of chromosome fragmentation in spirotrichs;(4)gene scrambling and alternative pro-cessing are found throughout the core spirotrichs,offering unique opportunities to increase genetic diversity and regulation in this group.

关键词： Alternative processing ciliates Gene scrambling Genome rearrangement Germline genome Somatic genome

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Findings on three endocommensal scuticociliates(Protista,Ciliophora)from freshwater mollusks,including their morphology and molecular phylogeny with descriptions of two new species

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Marine Life Science & Technology 2024年第2期6卷 212-235页

作者： Tao Li Tengyue Zhang Mingjian Liu Zhe Zhang Jiachen Zhang Junhua Niu Xiangrui Chen Saleh A.Al‑Farraj Weibo Song Institute of Evolution and Marine Biodiversity Ocean University of China and Key Laboratory of Evolution and Marine Biodiversity(Ministry of Education)Qingdao 266003China The Key Laboratory of Zoological Systematics and Application College of Life SciencesHebei UniversityBaoding 071002China College of Marine Life Sciences Ocean University of ChinaQingdao 266003China School of Marine Sciences Ningbo UniversityNingbo 315800China Zoology Department College of ScienceKing Saud University11451 RiyadhSaudi Arabia Laboratory for Marine Biology and Biotechnology Laoshan LaboratoryQingdao 266237China

Species of the ciliate genera Myxophyllum and Conchophthirus are found as endocommensals of terrestrial and freshwater mollusks,respectively.So far,there have been few studies of these genera and morphological data for most members are often incomplete.In the present work,two new species,Myxophyllum weishanense sp.***.and Conchophthirus paracurtus sp.nov.,and a known species,Conchophthirus lamellidens,were isolated from hosts in Lake Weishan Wetland,China.Taxonomic studies indicate that M.weishanense sp.***.can be recognized mainly by the combination of about 60 somatic kineties on both ventral and dorsal sides and the presence of caudal cilia.Conchophthirus paracurtus sp.***.differs from congeners in its body shape and size,having a glabrous area on the posterior right side,and having fewer somatic kineties.In addition,differences in their ITS2(Internally Transcribed Spacer 2)secondary structures support the discrimination of the two new species from their highly similar congeners.An improved diagnosis for the poorly known species,C.lamel-lidens is also provided.Phylogenetic analyses reveal that members of the genus Myxophyllum belong to a fully supported clade that is sister to a large,poorly supported clade consisting of Hemispeiridae,Ancistridae,and several lineages of the nonmonophyletic Cyclidiidae.The Myxophyllum clade also includes Protophyra ovicola JQ956552,a possible misidenti-fication.Sequences of the two new Conchophthirus species cluster with other congeners in a fully supported clade that is unrelated to either the‘typical’thigmotrichs or to pleuronematids,thus conflicting with the traditional classification,and may represent an orphan scuticociliate lineage.

关键词： ciliates Endocommensal ITS2 secondary structure Mollusks New taxa Wetland

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Further analyses of variation of ribosome DNA copy number and polymorphism in ciliates provide insights relevant to studies of both molecular ecology and phylogeny

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Science China(Life Sciences) 2019年第2期62卷 203-214页

作者： Yurui Wang Chundi Wang Yaohan Jiang Laura A.Katz Feng Gao Ying Yan Institute of Evolution & Marine Biodiversity Ocean University of China Key Laboratory of Mariculture Ocean University of China Ministry of Education Department of Biological Sciences Smith College

Sequence-based approaches, such as analyses of ribosome DNA(rDNA) clone libraries and high-throughput amplicon sequencing, have been used extensively to infer evolutionary relationships and elucidate the biodiversity in microbial communities.However, recent studies demonstrate both r DNA copy number variation and intra-individual(intra-genomic) sequence variation in many organisms, which challenges the application of the rDNA-based surveys. In ciliates, an ecologically important clade of microbial eukaryotes, rDNA copy number and sequence variation are rarely studied. In the present study, we estimate the intraindividual small subunit rDNA(SSU r DNA) copy number and sequence variation in a wide range of taxa covering nine classes and 18 orders of the phylum Ciliophora. Our studies reveal that:(i) intra-individual sequence variation of SSU rDNA is ubiquitous in all groups of ciliates detected and the polymorphic level varies among taxa;(ii) there is a most common version of SSU rDNA sequence in each cell that is highly predominant and may represent the germline micronuclear template;(iii)compared with the most common version, other variant sequences differ in only 1–3 nucleotides, likely generated during macronuclear(somatic) amplification;(iv) the intra-cell sequence variation is unlikely to impact phylogenetic analyses;(v) the rDNA copy number in ciliates is highly variable, ranging from 103 to 106, with the highest record in Stentor roeselii. Overall,these analyses indicate the need for careful consideration of SSU r DNAvariation in analyses of the role of ciliates in ecosystems.

关键词： ciliates SSU rDNA sequence variation phylogenetic analyses rDNA copy number ecological significance

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Diversity of oligotrich ciliates(Ciliophora, Spirotrichea) in the northern coast of South China Sea as revealed in LSU rDNA sequences

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Journal of Oceanology and Limnology 2020年第1期38卷 156-167,I0001-I0011页

作者： LU Kaihui LIU Weiwei Alan WARREN XU Yusen ZHU Changyu ZHAO Yan YI Zhenzhen Laboratory of Protozoology Guangzhou Key Laboratory of Subtropical Biodiversity and BiomonitoringSchool of Life ScienceSouth China Normal UniversityGuangzhou 510631China Key Laboratory of Tropical Marine Bio-resources and Ecology South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou 510301China Department of Life Sciences Natural History MuseumLondon SW75BDUnited K ingdom College of Life Sciences Capital Normal UniversityBeijing 100048China

Although the taxonomy of oligotrich ciliates has been widely investigated,yet the species diversity remains poorly known.We newly designed a pair of oligotrich-specific LSU rDNA primers covering the 600-bp D1/D2 region,and it was effective for detecting oligotrich species.Using the primers,we constructed the cloning libraries to investigate the species diversity of oligotrichs in the northern coastal waters of the South China Sea.In total,165 oligotrich sequences were obtained from five widely separated sampling sites.Sixty operational taxonomic units(OTUs)were obtained at 99%similarity threshold,and low-abundance OTUs with no more than two sequences contributed most of these(about 78%).Our findings are consistent with previous morphological studies,Strombidium was found the most abundant and widely distributed genus in this area.In addition,the BLAST search in the NCBI database resulted in 95%OTUs matching with named oligotrich species in similarity below 99%.Therefore,oligotrich morphospecies diversity has been underestimated as low-abundance species,and the LSU rDNA oligotrich sequence database needs to be better promoted.

关键词： diversity low-abundance species oligotrich ciliates operational taxonomic units (OTUs)

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Molecular diversity and biogeography of benthic ciliates in the Bohai Sea and Yellow Sea

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Acta Oceanologica Sinica 2019年第2期38卷 78-86页

作者： Guihao Li Lei Su Qianqian Zhang Xiaoli Zhang Jun Gong Key Laboratory of Coastal Environmental Processes and Ecological Remediation Yantai Institute of Coastal Zone ResearchChinese Academy of Sciences University of Chinese Academy of Sciences School of Marine Sciences Sun Yat-Sen University

This study explored the molecular diversity and biogeography of benthic ciliates in Chinese marginal seas, the Bohai Sea(BHS), North Yellow Sea(NYS) and South Yellow Sea(SYS). From a previous 18S rRNA gene pyrosequencing dataset of the benthic microeukaryotes, we retrieved the sequences affiliated with phylum Ciliophora and analyzed alpha and beta diversities of ciliate communities. We found that BHS had the highest ciliate operational taxonomic unit(OTU) richness than NYS and SYS, whereas the richness was not significantly different between summer and winter. Among all the measured environmental variables, water depth showed consistently the strongest correlations with alpha diversities. Overall, the class Spirotrichea(mostly Choreotrichia and unassigned lineages within the class) dominated the communities in terms of both relative proportion of sequences(77.0%) and OTU richness(66.5%). OTU-level ciliate community structure was significant different among the three basins, but not between the seasons. Structurally, significant differences in relative proportion among the basins were detected for the class Litostomatea, but not for other classes. Partial Mantel tests demonstrated that water depth difference was more important than geographic and environment distances in shaping the community structure of benthic ciliates in the studied area. About 60% OTUs were not assigned at a class or order level and at least 45% OTUs shared a sequence similarity no more than 97% with the described species, indicating a great potential for ciliate species discovery in the offshore sediments. Compared with previous morphology-based surveys, the spatial pattern of ciliate diversity(decreasing from NYS to SYS) is also identified in the present study. Nevertheless, structurally, the dominant class appeared to be Spirotrichea in the sequencing dataset, which differs from previous morphology-based results(dominance of classes Prostomatea and Karyorelictea in biomass). The potential causes for the discrepancies between molecular and

关键词： 18S rDNA benthic ciliates diversity biogeography depth decay relationship

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Morphological studies of six free-living spirotrichean ciliates (Protozoa： Ciliophora) with three new records from the coastal South China Sea

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Acta Oceanologica Sinica 2018年第10期37卷 86-90页

作者： CHEN Xumiao XU Kuidong Department of Marine Organism Taxonomy and Phylogeny Institute of Oceanology Chinese Academy of Sciences Qingdao 266071 China Laboratory for Marine Biology and Biotechnology Pilot National Laboratory for Marine Science and Technology (Qingdao) Qingdao 266237 China University of Chinese Academy of Sciences Beijing 100049 China

The living morphology and infraciliature of six spirotrichous ciliates collected from the coastal South China Sea were investigated using live observation and protargol impregnation. These are Euplotes woodruffi Gaw, 1939, Hemigastrostyla enigmatica （Dragesco and Dragesco-Kerneis, 1986） Song and Wilbert, 1997, Neourostylopsis flavicana （Wang et al., 2011） Chen et al., 2013, Protogastrostyla pulchra （Perejaslawzewa, 1886） Gong et al., 2007, Pseudoamphisiella alveolata （Kahl, 1932） Song and Warren, 2000, and PseudokahlieUa marina （Foissner et al., 1982） Berger et al., 1985. Among these, Protogastrostyla pulchra, Pseudoamphisiella alveolata and PseudokahlieUa marina are reported from the South China Sea for the first time, which manifest obvious differences apart from other Chinese populations. As new contribution, the detailed description of isolates from mangrove habitat of E. woodruffi and 1t. enigmatica, and aquaculture pond isolate of N.flavicana, are present.

关键词： South China Sea new record ciliates Spirotrichea taxonomy

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Morphological Studies on Four Brackish Water ciliates of the Class Spirotrichea(Protista, Ciliophora)

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Journal of Ocean University of China 2019年第3期18卷 663-674页

作者： SONG Yuan LIU Yongqiang PAN Bo LUO Xiaotian SONG Wen WARREN Alan College of Marine Life Sciences Ocean University of China Qingdao 266003 China Institute of Evolution and Marine Biodiversity Ocean University of China Qingdao 266003 China Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan 430072 China Department of Life Sciences Natural History Museum Cromwell Road London SW7 5BD UK

We reinvestigate the morphology of two oligotrich and two hypotrich ciliates collected from the coasts of north and south China, viz., Parallelostrombidium obesum Liu et al., 2015, Spirostrombidium apourceolare Liu et al., 2013, Protogastrostyla pulchra(Pereyaslawzewa, 1886) Gong et al., 2007, and Uncinata bradburyae(Gong et al., 2001) Luo et al., 2015. All the populations match well with the original samples identified in previous studies. Supplemental taxonomic data were supplied for these four species of the new populations. The species Parallelostrombidium obesum is characterised by its dorsal-ventrally flattened body shape with anterior and posterior ends transversely truncating, as well as two thigmotactic membranelles and girdle kinety that spirals around the cell one and a half times. Spirostrombidium apourceolare is characterised by its elongate ellipsoidal and dorsal-ventrally flattened body shape, two thigmotactic membranelles, about 11-27 ovoid macronuclear nodules, and girdle kinety that spirals around the cell twice with two undulations. Protogastrostyla pulchra is characterised by its elongate body shape and unique, caudally located food vacuole. Based on the new populations, we described the smaller cortical granules, clustered around dorsal bristles for the first time. The new population of Uncinata bradburyae shares the diagnostic features with the type population, which include prominent beak-like projection in anterior region, the conspicuous gap of adoral zone, proximalmost adoral membranelles distinctly elongated, and infraciliature.

关键词： hypotrichs ciliates oligotrichs Parallelostrombidium Protogastrostyla Spirostrombidium taxonomy Uncinata

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New considerations on the phylogeny of Sessilida(Protista:Ciliophora:Peritrichia)based on multiple-gene information,with emphasis on colonial taxa

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Marine Life Science & Technology 2022年第4期4卷 569-583页

作者： Zhe Wang Xiaoting Feng Lifang Li Khaled A.S.Al-Rasheid Alan Warren Chundi Wang Zemao Gu Marine College Shandong UniversityWeihai264209China College of Fisheries/Shuangshui ShuanglüInstitute Huazhong Agricultural UniversityWuhan430070China Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention Wuhan430070China Department of Zoology College of ScienceKing Saud UniversityRiyadh11451Saudi Arabia Department of Life Sciences Natural History MuseumLondonSW75BDUK

The subclass Peritrichia,containing two orders Sessilida and Mobilida,is a major group of ciliates with worldwide distribution and high species diversity.Several studies have investigated the phylogeny of peritrichs;however,the evolutionary relationships and classification of some families and genera within the Sessilida remain unclear.In the present study,we isolated and identified 22 peritrich populations representing four families and six genera and obtained 64 rDNA sequences to perform phylogenetic analyses and assess their systematic relationships.Ancestral character reconstruction was also carried out to infer evolutionary routes within the Sessilida.The results indicate:(1)family Vaginicolidae is monophyletic and acquisition of the typical peritrich lorica represents a single evolutionary divergence;(2)core epistylidids evolved from a Zoothamnium-like ancestor and experienced spasmoneme loss during evolution;(3)Campanella clusters with species in the basal clade and shows stable morphological differences with other epistylidids,supporting its assignment to a separate family;(4)the structure of the peristomial lip may be a genus-level character rather than a diagnostic character for discriminating Epistylididae and Operculariidae,thus a redefinition of Operculariidae should be carried out when more species have been investigated;(5)some characters,such as lifestyle(solitary or colonial),spasmoneme and living habit(sessile or free-swimming),evolved repeatedly among sessilids indicating that species with non-contractile stalks or that are free-swimming have multiple evolutionary routes and might derive from any sessilid lineage without a lorica.The close phylogenetic relationships of some morphologically distinct sessilids imply that the diagnoses of some genera and families should be improved.

关键词： Ancestral state reconstruction ciliates Morphology Peritrichs Phylogenetic analyses

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The widely reported but poorly studied ciliate family Folliculinidae(Protozoa,Ciliophora,Heterotrichea):a revision with notes on its taxonomy,morphology and phylogenetic relationships

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Marine Life Science & Technology 2022年第4期4卷 471-492页

作者： Tingting Ye Yaohan Jiang Shuchang Chen Yixiang Xu Lifang Li Mann Kyoon Shin Xiangrui Chen School of Marine Sciences Ningbo UniversityNingbo315800China Laboratory of Marine Protozoan Biodiversity and Evolution Marine CollegeShandong UniversityWeihai264209China Institute of Evolution and Marine Biodiversity and College of FisheriesOcean University of ChinaQingdao266003China Department of Biological Sciences University of UlsanUlsan44610South Korea

ciliates of the heterotrich family Folliculinidae are widespread in various habitats and are distinguished by their transparent loricae of various shapes,conspicuous peristomial lobes,and dimorphic life cycles.They usually attach firmly to the surface of substrates,feed on bacteria and microalgae,and play a significant role in energy flow and material cycling in the microbial food web.However,little is known regarding their biodiversity and systematics.In this work,we establish the terminology of the family Folliculinidae and select six crucial features for genus recognition.Based on previous studies,we revise the classification of Folliculinidae,supply improved diagnoses for each of the 33 folliculinid genera,and provide a key to their identification.Moreover,phylogenetic analyses based on small subunit ribosomal DNA(SSU rDNA)sequences revealed that the family is monophyletic and comprises two subclades(subclades I II)which can be identified by the flexibility of their peristomial lobes and the sculpturing of their necks.Furthermore,we investigate the evolutionary relationships of folliculinids using the six chosen generic features.

关键词： ciliates Evolutionary relationships Folliculinidae Heterotrichea Review

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Integrative studies on the taxonomy and molecular phylogeny of four new Pleuronema species(Protozoa,Ciliophora,Scuticociliatia)

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Marine Life Science & Technology 2022年第2期4卷 179-200页

作者： Mingjian Liu Yujie Liu Tengteng Zhang Borong Lu Feng Gao Jing Gu Saleh AAl-Farraj Xiaozhong Hu Weibo Song Institute of Evolution and Marine Biodiversity Ocean University of ChinaQingdao266003China College of Fisheries Ocean University of ChinaQingdao266003China Laboratory of Protozoological Biodiversity and Evolution in Wetland College of Life SciencesShaanxi Normal UniversityXi’an710119China Qingdao No.47 Middle School Qingdao266022China Zoology Department College of ScienceKing Saud UniversityRiyadh11451Saudi Arabia Laboratory for Marine Biology and Biotechnology Pilot National Laboratory for Marine Science and Technology(Qingdao)Qingdao266237China

The ciliate genus Pleuronema comprises approximately 30 nominal species and has been reported in freshwater,brackish water,and marine habitats.Nevertheless,recent studies have indicated that there might be a large undiscovered species diversity.In the present work,four new Pleuronema species,namely P.foissneri sp.nov.,P.parasmalli sp.nov.,P.parasalmastra sp.nov.,and P.paraorientale sp.nov.,collected from Shenzhen,southern China,was investigated using taxonomic methods.The diagnosis,description,comparisons with morphologically related species and detailed morphometric data are supplied for each.The small subunit ribosomal RNA(SSU rRNA)gene of the four new species is sequenced and their molecular phylogeny is analyzed.The SSU rRNA gene tree shows that Pleuronema is polyphyletic comprising several separate clades.All four new species cluster consistently with P.orientale KF206429,P.puytoraci KF840520 and P.setigerum FJ848874 within the core Pleuronematidae+Peniculistomatidae clade.Phylogenies of Pleuronematidae-related taxa are also discussed.

关键词： ciliates Ciliature Morphology New species Pleuronematids SSU rRNA gene

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