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Cedrola F, Senra MVX, Morales MJA, Fregulia P, Canesin L, Dias RJP, Solferini VN. Giants' cooperation: a draft genome of the giant ciliate Muniziella cunhai suggests its ecological role in the capybara's digestive metabolism. Microb Genom 2024; 10. [PMID: 38953769 DOI: 10.1099/mgen.0.001263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024] Open
Abstract
Several hundred ciliate species live in animals' guts as a part of their microbiome. Among them, Muniziella cunhai (Trichostomatia, Pycnotrichidae), the largest described ciliate, is found exclusively associated with Hydrochoerus hydrochaeris (capybara), the largest known rodent reaching up to 90 kg. Here, we present the sequence, structural and functional annotation of this giant microeukaryote macronuclear genome and discuss its phylogenetic placement. The 85 Mb genome is highly AT rich (GC content 25.71 %) and encodes a total of 11 397 protein-coding genes, of which 2793 could have their functions predicted with automated functional assignments. Functional annotation showed that M. cunhai can digest recalcitrant structural carbohydrates, non-structural carbohydrates, and microbial cell walls, suggesting a role in diet metabolization and in microbial population control in the capybara's intestine. Moreover, the phylogenetic placement of M. cunhai provides insights on the origins of gigantism in the subclass Trichostomatia.
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Affiliation(s)
- Franciane Cedrola
- Laboratório de Diversidade Genética, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | | | - Millke Jasmine Arminini Morales
- Laboratório de Diversidade Genética, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Priscila Fregulia
- Laboratório de Protozoologia, Programa de Pós-Graduação em Biodiversidade e Conservação da Natureza, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | | | - Roberto Júnio Pedroso Dias
- Laboratório de Protozoologia, Programa de Pós-Graduação em Biodiversidade e Conservação da Natureza, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Vera Nisaka Solferini
- Laboratório de Diversidade Genética, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Center for Computational Engineering and Sciences, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
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2
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Lyu L, Zhang X, Gao Y, Zhang T, Fu J, Stover NA, Gao F. From germline genome to highly fragmented somatic genome: genome-wide DNA rearrangement during the sexual process in ciliated protists. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:31-49. [PMID: 38433968 PMCID: PMC10901763 DOI: 10.1007/s42995-023-00213-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 11/27/2023] [Indexed: 03/05/2024]
Abstract
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 during 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 processing are found throughout the core spirotrichs, offering unique opportunities to increase genetic diversity and regulation in this group. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00213-x.
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Affiliation(s)
- Liping Lyu
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Xue Zhang
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Yunyi Gao
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Tengteng Zhang
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Jinyu Fu
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Naomi A. Stover
- Department of Biology, Bradley University, Peoria, IL 61625 USA
| | - Feng Gao
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laoshan Laboratory, Qingdao, 266237 China
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3
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Zhuang W, Feng X, Li R, Al-Farraj SA, Hu X. Morphogenesis of an anaerobic ciliate Heterometopus palaeformis (Kahl, 1927) Foissner, 2016 (Ciliophora, Armophorea) with notes on its morphological and molecular characterization. Protist 2024; 175:126007. [PMID: 38141417 DOI: 10.1016/j.protis.2023.126007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 11/30/2023] [Accepted: 12/14/2023] [Indexed: 12/25/2023]
Abstract
The morphology, morphogenesis, and molecular phylogeny of Heterometopus palaeformis (Kahl, 1927) Foissner, 2016 were studied using microscopical observations on live and protargol-stained specimens as well SSU rRNA gene sequencing. The morphogenetic data for the genus are presented for the first time. Compared to other metopids, the morphogenesis of H. palaeformis is distinct since its (1) perizonal stripe rows 4 and 5 are involved in the formation of the opisthe's adoral polykinetids; (2) perizonal stripe rows 3-5 and two adjacent preoral dome kineties contribute to most of the opisthe's paroral membrane while perizonal stripe rows 1 and 2 contribute very little; (3) four kinety rows are formed to the left of the opisthe's adoral zone of polykinetids. The Chinese population resembles the original and neotype populations well in terms of general morphology - characterized by a life size of 55-120 × 10-20 μm, an elongate ellipsoidal body with a hardly spiralized flat preoral dome, about 18 somatic kineties and 20 adoral polykinetids. The SSU rDNA sequence of the present population exhibits a disparity of 1.33%-2.22% divergence from sequences of other populations. Nevertheless, phylogenetic analysis reveals that populations of H. palaeformis form a separate, stable cluster within the paraphyletic Metopidae clade.
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Affiliation(s)
- Wenbao Zhuang
- College of Fisheries, & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Xiaochen Feng
- College of Fisheries, & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Ran Li
- College of Fisheries, & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Xiaozhong Hu
- College of Fisheries, & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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4
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Bonacolta AM, Miravall J, Gómez-Gras D, Ledoux JB, López-Sendino P, Garrabou J, Massana R, Del Campo J. Differential apicomplexan presence predicts thermal stress mortality in the Mediterranean coral Paramuricea clavata. Environ Microbiol 2024; 26:e16548. [PMID: 38072822 DOI: 10.1111/1462-2920.16548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/21/2023] [Indexed: 01/30/2024]
Abstract
Paramuricea clavata is an ecosystem architect of the Mediterranean temperate reefs that is currently threatened by episodic mass mortality events related to global warming. The microbiome may play an active role in the thermal stress susceptibility of corals, potentially holding the answer as to why corals show differential sensitivity to heat stress. To investigate this, the prokaryotic and eukaryotic microbiome of P. clavata collected from around the Mediterranean was characterised before experimental heat stress to determine if its microbial composition influences the thermal response of the holobiont. We found that members of P. clavata's microeukaryotic community were significantly correlated with thermal stress sensitivity. Syndiniales from the Dino-Group I Clade 1 were significantly enriched in thermally resistant corals, while the apicomplexan corallicolids were significantly enriched in thermally susceptible corals. We hypothesise that P. clavata mortality following heat stress may be caused by a shift from apparent commensalism to parasitism in the corallicolid-coral host relationship driven by the added stress. Our results show the potential importance of corallicolids and the rest of the microeukaryotic community of corals to understanding thermal stress response in corals and provide a useful tool to guide conservation efforts and future research into coral-associated microeukaryotes.
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Affiliation(s)
- Anthony M Bonacolta
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, Florida, USA
- Programa de Biodiversiat, Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Jordi Miravall
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar-CSIC, Barcelona, Catalonia, Spain
| | - Daniel Gómez-Gras
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kaneohe, Hawaii, USA
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Institut de Recerca de la Biodiversitat (IRBIO), Universitat de Barcelona, Barcelona, Spain
| | - Jean-Baptiste Ledoux
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal
| | - Paula López-Sendino
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar-CSIC, Barcelona, Catalonia, Spain
| | - Joaquim Garrabou
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar-CSIC, Barcelona, Catalonia, Spain
| | - Ramon Massana
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar-CSIC, Barcelona, Catalonia, Spain
| | - Javier Del Campo
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, Florida, USA
- Programa de Biodiversiat, Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
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5
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Bétermier M, Klobutcher LA, Orias E. Programmed chromosome fragmentation in ciliated protozoa: multiple means to chromosome ends. Microbiol Mol Biol Rev 2023; 87:e0018422. [PMID: 38009915 PMCID: PMC10732028 DOI: 10.1128/mmbr.00184-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
SUMMARYCiliated protozoa undergo large-scale developmental rearrangement of their somatic genomes when forming a new transcriptionally active macronucleus during conjugation. This process includes the fragmentation of chromosomes derived from the germline, coupled with the efficient healing of the broken ends by de novo telomere addition. Here, we review what is known of developmental chromosome fragmentation in ciliates that have been well-studied at the molecular level (Tetrahymena, Paramecium, Euplotes, Stylonychia, and Oxytricha). These organisms differ substantially in the fidelity and precision of their fragmentation systems, as well as in the presence or absence of well-defined sequence elements that direct excision, suggesting that chromosome fragmentation systems have evolved multiple times and/or have been significantly altered during ciliate evolution. We propose a two-stage model for the evolution of the current ciliate systems, with both stages involving repetitive or transposable elements in the genome. The ancestral form of chromosome fragmentation is proposed to have been derived from the ciliate small RNA/chromatin modification process that removes transposons and other repetitive elements from the macronuclear genome during development. The evolution of this ancestral system is suggested to have potentiated its replacement in some ciliate lineages by subsequent fragmentation systems derived from mobile genetic elements.
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Affiliation(s)
- Mireille Bétermier
- Department of Genome Biology, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Lawrence A. Klobutcher
- Department of Molecular Biology and Biophysics, UCONN Health (University of Connecticut), Farmington, Connecticut, USA
| | - Eduardo Orias
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California, USA
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6
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Zhang X, Zhao Y, Zheng W, Nan B, Fu J, Qiao Y, Zufall RA, Gao F, Yan Y. Genome-wide identification of ATP-binding cassette transporter B subfamily, focusing on its structure, evolution and rearrangement in ciliates. Open Biol 2023; 13:230111. [PMID: 37788709 PMCID: PMC10547551 DOI: 10.1098/rsob.230111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 09/04/2023] [Indexed: 10/05/2023] Open
Abstract
ATP-binding cassette subfamily B (ABCB) has been implicated in various essential functions such as multidrug resistance, auxin transport and heavy metal tolerance in animals and plants. However, the functions, the genomic distribution and the evolutionary history have not been characterized systematically in lower eukaryotes. As a lineage of highly specialized unicellular eukaryotes, ciliates have extremely diverse genomic features including nuclear dimorphism. To further understand the genomic structure and evolutionary history of this gene family, we investigated the ABCB gene subfamily in 11 ciliates. The results demonstrate that there is evidence of substantial gene duplication, which has occurred by different mechanisms in different species. These gene duplicates show consistent purifying selection, suggesting functional constraint, in all but one species, where positive selection may be acting to generate novel function. We also compare the gene structures in the micronuclear and macronuclear genomes and find no gene scrambling during genome rearrangement, despite the abundance of such scrambling in two of our focal species. These results lay the foundation for future analyses of the function of these genes and the mechanisms responsible for their evolution across diverse eukaryotic lineages.
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Affiliation(s)
- Xue Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, People's Republic of China
- Key Laboratory of Evolution & Marine Biodiversity (OUC), Ministry of Education, Qingdao 266003, People's Republic of China
| | - Yan Zhao
- College of Life Sciences, Capital Normal University, Beijing 100048, People's Republic of China
| | - Weibo Zheng
- School of Life Sciences, Ludong University, Yantai, Shandong 264025, People's Republic of China
| | - Bei Nan
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, People's Republic of China
- Key Laboratory of Evolution & Marine Biodiversity (OUC), Ministry of Education, Qingdao 266003, People's Republic of China
| | - Jinyu Fu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, People's Republic of China
- Key Laboratory of Evolution & Marine Biodiversity (OUC), Ministry of Education, Qingdao 266003, People's Republic of China
| | - Yu Qiao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, People's Republic of China
- Key Laboratory of Evolution & Marine Biodiversity (OUC), Ministry of Education, Qingdao 266003, People's Republic of China
| | - Rebecca A. Zufall
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - Feng Gao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, People's Republic of China
- Key Laboratory of Evolution & Marine Biodiversity (OUC), Ministry of Education, Qingdao 266003, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, People's Republic of China
| | - Ying Yan
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, People's Republic of China
- Key Laboratory of Evolution & Marine Biodiversity (OUC), Ministry of Education, Qingdao 266003, People's Republic of China
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7
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Lyu L, Asghar U, Fu J, Gao Y, Zhang X, Al-Farraj SA, Chen Z, Gao F. Comparative analysis of single-cell genome sequencing techniques toward the characterization of germline and somatic genomes in ciliated protists. Eur J Protistol 2023; 88:125969. [PMID: 36822126 DOI: 10.1016/j.ejop.2023.125969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/31/2023] [Accepted: 02/05/2023] [Indexed: 02/12/2023]
Abstract
Ciliated protists contain both germline micronucleus (MIC) and somatic macronucleus (MAC) in a single cytoplasm. Programmed genome rearrangements occur in ciliates during sexual processes, and the extent of rearrangements varies dramatically among species, which lead to significant differences in genomic architectures. However, genomic sequences remain largely unknown for most ciliates due to the difficulty in culturing and in separating the germline from the somatic genome in a single cell. Single-cell whole genome amplification (WGA) has emerged as a powerful technology to characterize the genomic heterogeneity at the single-cell level. In this study, we compared two single-cell WGA, multiple displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC) in characterizing the germline and somatic genomes in ciliates with different genomic architectures. Our results showed that: 1) MALBAC exhibits strong amplification bias towards MAC genome while MDA shows bias towards MIC genome of ciliates with extensively fragmented MAC genome; 2) both MDA and MALBAC could amplify MAC genome more efficiently in ciliates with moderately fragmented MAC genome. Moreover, we found that more sample replicates could help to obtain more genomic data. Our work provides a reference for selecting the appropriate method to characterize germline and somatic genomes of ciliates.
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Affiliation(s)
- Liping Lyu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture (OUC), Ministry of Education, Qingdao 266003, China
| | - Usman Asghar
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture (OUC), Ministry of Education, Qingdao 266003, China
| | - Jinyu Fu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture (OUC), Ministry of Education, Qingdao 266003, China
| | - Yunyi Gao
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture (OUC), Ministry of Education, Qingdao 266003, China
| | - Xue Zhang
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture (OUC), Ministry of Education, Qingdao 266003, China
| | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Zigui Chen
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
| | - Feng Gao
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture (OUC), Ministry of Education, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China.
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8
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Smith SA, Santoferrara LF, Katz LA, McManus GB. Genome architecture used to supplement species delineation in two cryptic marine ciliates. Mol Ecol Resour 2022; 22:2880-2896. [PMID: 35675173 DOI: 10.1111/1755-0998.13664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/06/2022] [Accepted: 05/26/2022] [Indexed: 11/30/2022]
Abstract
The purpose of this study is to determine which taxonomic methods can elucidate clear and quantifiable differences between two cryptic ciliate species, and to test the utility of genome architecture as a new diagnostic character in the discrimination of otherwise indistinguishable taxa. Two cryptic tintinnid ciliates, Schmidingerella arcuata and Schmidingerella meunieri, are compared via traditional taxonomic characters including lorica morphometrics, ribosomal RNA (rRNA) gene barcodes and ecophysiological traits. In addition, single-cell 'omics analyses (single-cell transcriptomics and genomics) are used to elucidate and compare patterns of micronuclear genome architecture between the congeners. The results include a highly similar lorica that is larger in S. meunieri, a 0%-0.5% difference in rRNA gene barcodes, two different and nine indistinguishable growth responses among 11 prey treatments, and distinct patterns of micronuclear genomic architecture for genes detected in both ciliates. Together, these results indicate that while minor differences exist between S. arcuata and S. meunieri in common indices of taxonomic identification (i.e., lorica morphology, DNA barcode sequences and ecophysiology), differences exist in their genomic architecture, which suggests potential genetic incompatibility. Different patterns of micronuclear architecture in genes shared by both isolates also enable the design of species-specific primers, which are used in this study as unique "architectural barcodes" to demonstrate the co-occurrence of both ciliates in samples collected from a NW Atlantic estuary. These results support the utility of genomic architecture as a tool in species delineation, especially in ciliates that are cryptic or otherwise difficult to differentiate using traditional methods of identification.
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9
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Zheng W, Dou H, Li C, Al-Farraj SA, Byerly A, Stover NA, Song W, Chen X, Li L. Comparative Genome Analysis Reveals Cis-Regulatory Elements on Gene-Sized Chromosomes of Ciliated Protists. Front Microbiol 2022; 13:775646. [PMID: 35265055 PMCID: PMC8899921 DOI: 10.3389/fmicb.2022.775646] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
Gene-sized chromosomes are a distinct feature of the macronuclear genome in ciliated protists known as spirotrichs. These nanochromosomes are often only several kilobase pairs long and contain a coding region for a single gene. However, the ways in which transcription is regulated on nanochromosomes is still largely unknown. Here, we generated macronuclear genome assemblies for two species of Pseudokeronopsis ciliates to better understand transcription regulation on gene-sized chromosomes. We searched within the short subtelomeric regions for potential cis-regulatory elements and identified distinct AT-rich sequences conserved in both species, at both the 5’ and 3’ end of each gene. We further acquired transcriptomic data for these species, which showed the 5’ cis-regulatory element is associated with active gene expression. Gene family evolution analysis suggests nanochromosomes in spirotrichs may originated approximately 900 million years ago. Together our comparative genomic analyses reveal novel insights into the biological roles of cis-regulatory elements on gene-sized chromosomes.
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Affiliation(s)
- Weibo Zheng
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, China.,School of Life Sciences, Ludong University, Yantai, China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Huan Dou
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, China
| | - Chao Li
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Adam Byerly
- Department of Computer Science, Bradley University, Peoria, IL, United States
| | - Naomi A Stover
- Department of Biology, Bradley University, Peoria, IL, United States
| | - Weibo Song
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiao Chen
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, China
| | - Lifang Li
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, China
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10
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Ahsan R, Blanche W, Katz LA. Macronuclear development in ciliates, with a focus on nuclear architecture. J Eukaryot Microbiol 2022; 69:e12898. [PMID: 35178799 DOI: 10.1111/jeu.12898] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/20/2022] [Accepted: 02/14/2022] [Indexed: 11/30/2022]
Abstract
Ciliates are defined by the presence of dimorphic nuclei as they have both a somatic macronucleus and germline micronucleus within each individual cell. The size and structure of both germline micronuclei and somatic macronuclei varies tremendously among ciliates. Except just after conjugation (i.e. the nuclear exchange in sexual cycle), the germline micronucleus is transcriptionally-inactive and contains canonical chromosomes that will be inherited between generations. In contrast, the transcriptionally-active macronucleus contains chromosomes that vary in size in different classes of ciliates, with some lineages having extensively-fragmented gene-sized somatic chromosomes while others contain longer multigene chromosomes. Here, we describe the variation in somatic macronuclear architecture in lineages sampled across the ciliate tree of life, specifically focusing on lineages with extensively fragmented chromosomes (e.g. the classes Phyllopharyngea and Spirotrichea). Further, we synthesize information from the literature on the development of ciliate macronuclei, focusing on changes in nuclear architecture throughout life cycles. These data highlight the tremendous diversity among ciliate nuclear cycles, extend our understanding of patterns of genome evolution, and provide insight into different germline and somatic nuclear features (e.g. nuclear structure and development) among eukaryotes.
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Affiliation(s)
- Ragib Ahsan
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA.,University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, 01003, USA
| | - Wumei Blanche
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA.,University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, 01003, USA
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11
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Feng Y, Neme R, Beh LY, Chen X, Braun J, Lu MW, Landweber LF. Comparative genomics reveals insight into the evolutionary origin of massively scrambled genomes. eLife 2022; 11:82979. [PMID: 36421078 PMCID: PMC9797194 DOI: 10.7554/elife.82979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/03/2022] [Indexed: 11/25/2022] Open
Abstract
Ciliates are microbial eukaryotes that undergo extensive programmed genome rearrangement, a natural genome editing process that converts long germline chromosomes into smaller gene-rich somatic chromosomes. Three well-studied ciliates include Oxytricha trifallax, Tetrahymena thermophila, and Paramecium tetraurelia, but only the Oxytricha lineage has a massively scrambled genome, whose assembly during development requires hundreds of thousands of precisely programmed DNA joining events, representing the most complex genome dynamics of any known organism. Here we study the emergence of such complex genomes by examining the origin and evolution of discontinuous and scrambled genes in the Oxytricha lineage. This study compares six genomes from three species, the germline and somatic genomes for Euplotes woodruffi, Tetmemena sp., and the model ciliate O. trifallax. We sequenced, assembled, and annotated the germline and somatic genomes of E. woodruffi, which provides an outgroup, and the germline genome of Tetmemena sp. We find that the germline genome of Tetmemena is as massively scrambled and interrupted as Oxytricha's: 13.6% of its gene loci require programmed translocations and/or inversions, with some genes requiring hundreds of precise gene editing events during development. This study revealed that the earlier diverged spirotrich, E. woodruffi, also has a scrambled genome, but only roughly half as many loci (7.3%) are scrambled. Furthermore, its scrambled genes are less complex, together supporting the position of Euplotes as a possible evolutionary intermediate in this lineage, in the process of accumulating complex evolutionary genome rearrangements, all of which require extensive repair to assemble functional coding regions. Comparative analysis also reveals that scrambled loci are often associated with local duplications, supporting a gradual model for the origin of complex, scrambled genomes via many small events of DNA duplication and decay.
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Affiliation(s)
- Yi Feng
- Departments of Biochemistry and Molecular Biophysics and Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Rafik Neme
- Departments of Biochemistry and Molecular Biophysics and Biological Sciences, Columbia UniversityNew YorkUnited States,Department of Chemistry and Biology, Universidad del NorteBarranquillaColombia
| | - Leslie Y Beh
- Departments of Biochemistry and Molecular Biophysics and Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Xiao Chen
- Pacific BiosciencesMenlo ParkUnited States
| | - Jasper Braun
- Department of Mathematics and Statistics, University of South FloridaTampaUnited States
| | - Michael W Lu
- Departments of Biochemistry and Molecular Biophysics and Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Laura F Landweber
- Departments of Biochemistry and Molecular Biophysics and Biological Sciences, Columbia UniversityNew YorkUnited States
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12
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Biodiversity-based development and evolution: the emerging research systems in model and non-model organisms. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1236-1280. [PMID: 33893979 DOI: 10.1007/s11427-020-1915-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/16/2021] [Indexed: 02/07/2023]
Abstract
Evolutionary developmental biology, or Evo-Devo for short, has become an established field that, broadly speaking, seeks to understand how changes in development drive major transitions and innovation in organismal evolution. It does so via integrating the principles and methods of many subdisciplines of biology. Although we have gained unprecedented knowledge from the studies on model organisms in the past decades, many fundamental and crucially essential processes remain a mystery. Considering the tremendous biodiversity of our planet, the current model organisms seem insufficient for us to understand the evolutionary and physiological processes of life and its adaptation to exterior environments. The currently increasing genomic data and the recently available gene-editing tools make it possible to extend our studies to non-model organisms. In this review, we review the recent work on the regulatory signaling of developmental and regeneration processes, environmental adaptation, and evolutionary mechanisms using both the existing model animals such as zebrafish and Drosophila, and the emerging nonstandard model organisms including amphioxus, ascidian, ciliates, single-celled phytoplankton, and marine nematode. In addition, the challenging questions and new directions in these systems are outlined as well.
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13
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Irwin NAT, Pittis AA, Mathur V, Howe LJ, Keeling PJ, Lynn DH, Bourland WA. The Function and Evolution of Motile DNA Replication Systems in Ciliates. Curr Biol 2020; 31:66-76.e6. [PMID: 33125869 DOI: 10.1016/j.cub.2020.09.077] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/09/2020] [Accepted: 09/25/2020] [Indexed: 01/31/2023]
Abstract
DNA replication is a ubiquitous and conserved cellular process. However, regulation of DNA replication is only understood in a small fraction of organisms that poorly represent the diversity of genetic systems in nature. Here we used computational and experimental approaches to examine the function and evolution of one such system, the replication band (RB) in spirotrich ciliates, which is a localized, motile hub that traverses the macronucleus while replicating DNA. We show that the RB can take unique forms in different species, from polar bands to a "replication envelope," where replication initiates at the nuclear periphery before advancing inward. Furthermore, we identify genes involved in cellular transport, including calcium transporters and cytoskeletal regulators, that are associated with the RB and may be involved in its function and translocation. These findings highlight the evolution and diversity of DNA replication systems and provide insights into the regulation of nuclear organization and processes.
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Affiliation(s)
- Nicholas A T Irwin
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Alexandros A Pittis
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - LeAnn J Howe
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Denis H Lynn
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - William A Bourland
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA.
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14
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Smith SA, Maurer-Alcalá XX, Yan Y, Katz LA, Santoferrara LF, McManus GB. Combined Genome and Transcriptome Analyses of the Ciliate Schmidingerella arcuata (Spirotrichea) Reveal Patterns of DNA Elimination, Scrambling, and Inversion. Genome Biol Evol 2020; 12:1616-1622. [PMID: 32870974 PMCID: PMC7523726 DOI: 10.1093/gbe/evaa185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 12/04/2022] Open
Abstract
Schmidingerella arcuata is an ecologically important tintinnid ciliate that has long served as a model species in plankton trophic ecology. We present a partial micronuclear genome and macronuclear transcriptome resource for S. arcuata, acquired using single-cell techniques, and we report on pilot analyses including functional annotation and genome architecture. Our analysis shows major fragmentation, elimination, and scrambling in the micronuclear genome of S. arcuata. This work introduces a new nonmodel genome resource for the study of ciliate ecology and genomic biology and provides a detailed functional counterpart to ecological research on S. arcuata.
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Affiliation(s)
- Susan A Smith
- Department of Marine Sciences, University of Connecticut, Groton
| | | | - Ying Yan
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
| | - Luciana F Santoferrara
- Department of Marine Sciences, University of Connecticut, Groton.,Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs
| | - George B McManus
- Department of Marine Sciences, University of Connecticut, Groton
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15
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Pecina L, Vďačný P. Two New Endozoic Ciliates, Clevelandella lynni sp. n. and Nyctotherus galerus sp. n., Isolated from the Hindgut of the Wood-feeding Cockroach Panesthia angustipennis (Illiger, 1801). J Eukaryot Microbiol 2020; 67:436-449. [PMID: 32108982 DOI: 10.1111/jeu.12793] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/24/2020] [Accepted: 02/19/2020] [Indexed: 11/30/2022]
Abstract
Two new ciliate species, Clevelandella lynni sp. n. and Nyctotherus galerus sp. n., were discovered in the hindgut of wood-feeding panesthiine cockroaches. Their morphology was studied using standard methods, and their phylogenetic positions within the order Clevelandellida were determined using the 18S rRNA gene sequences. Clevelandella lynni is characterized by a prominent peristomial projection, a notched left body margin, a tear-shaped to broadly ovoidal macronucleus, a karyophore attached to the right body margin, and by an adoral zone composed of on average 48 membranelles and extending about 51% of body length. The diagnostic features of N. galerus include a short posterior body projection, a spherical to broadly ellipsoidal macronucleus, a karyophore attached to the right and left body margins, refractile bodies densely packed anterior to the macronucleus, and an adoral zone composed of on average 57 membranelles and extending about 70% body length. The order Clevelandellida was consistently depicted as monophyletic in 18S rRNA gene phylogenies. Nyctotherus galerus was placed in the paraphyletic family Nyctotheridae, as sister taxon to all other Nyctotherus and Clevelandella species isolated from cockroaches. Clevelandella lynni fell in the monophyletic family Clevelandellidae, as sister taxon to C. panesthiae KC139718 but with very poor statistical support.
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Affiliation(s)
- Lukáš Pecina
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Peter Vďačný
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovak Republic
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16
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Chen X, Jiang Y, Gao F, Zheng W, Krock TJ, Stover NA, Lu C, Katz LA, Song W. Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors. Mol Ecol Resour 2019; 19:1292-1308. [PMID: 30985983 DOI: 10.1111/1755-0998.13023] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/05/2019] [Accepted: 04/08/2019] [Indexed: 12/11/2022]
Abstract
As a model organism for studies of cell and environmental biology, the free-living and cosmopolitan ciliate Euplotes vannus shows intriguing features like dual genome architecture (i.e., separate germline and somatic nuclei in each cell/organism), "gene-sized" chromosomes, stop codon reassignment, programmed ribosomal frameshifting (PRF) and strong resistance to environmental stressors. However, the molecular mechanisms that account for these remarkable traits remain largely unknown. Here we report a combined analysis of de novo assembled high-quality macronuclear (MAC; i.e., somatic) and partial micronuclear (MIC; i.e., germline) genome sequences for E. vannus, and transcriptome profiling data under varying conditions. The results demonstrate that: (a) the MAC genome contains more than 25,000 complete "gene-sized" nanochromosomes (~85 Mb haploid genome size) with the N50 ~2.7 kb; (b) although there is a high frequency of frameshifting at stop codons UAA and UAG, we did not observe impaired transcript abundance as a result of PRF in this species as has been reported for other euplotids; (c) the sequence motif 5'-TA-3' is conserved at nearly all internally-eliminated sequence (IES) boundaries in the MIC genome, and chromosome breakage sites (CBSs) are duplicated and retained in the MAC genome; (d) by profiling the weighted correlation network of genes in the MAC under different environmental stressors, including nutrient scarcity, extreme temperature, salinity and the presence of ammonia, we identified gene clusters that respond to these external physical or chemical stimulations, and (e) we observed a dramatic increase in HSP70 gene transcription under salinity and chemical stresses but surprisingly, not under temperature changes; we link this temperature-resistance to the evolved loss of temperature stress-sensitive elements in regulatory regions. Together with the genome resources generated in this study, which are available online at Euplotes vannus Genome Database (http://evan.ciliate.org), these data provide molecular evidence for understanding the unique biology of highly adaptable microorganisms.
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Affiliation(s)
- Xiao Chen
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China.,Department of Genetics and Development, Columbia University Medical Center, New York, New York
| | - Yaohan Jiang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Feng Gao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China.,Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, China
| | - Weibo Zheng
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Timothy J Krock
- Department of Computer Science and Information Systems, Bradley University, Peoria, Illinois
| | - Naomi A Stover
- Department of Biology, Bradley University, Peoria, Illinois
| | - Chao Lu
- Department of Genetics and Development, Columbia University Medical Center, New York, New York
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
| | - Weibo Song
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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17
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Vďačný P, Foissner W. A huge diversity of metopids (Ciliophora, Armophorea) in soil from the Murray River floodplain, Australia. III. Morphology, ontogenesis and conjugation of Metopus boletus nov. spec., with implications for the phylogeny of the SAL supercluster. Eur J Protistol 2019; 69:117-137. [DOI: 10.1016/j.ejop.2019.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/15/2019] [Accepted: 04/04/2019] [Indexed: 02/02/2023]
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18
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Li M, Wang R, Bastos Gomes G, Zou H, Li WX, Wu SG, Wang GT, Ponce-Gordo F. Epidemiology and identification of two species of Chilodonella affecting farmed fishes in China. Vet Parasitol 2018; 264:8-17. [PMID: 30503097 DOI: 10.1016/j.vetpar.2018.10.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 10/28/2022]
Abstract
The genus Chilodonella includes free-living ciliated protozoa as well as pathogenic species for freshwater fish, with Chilodonella hexasticha and Chilodonella piscicola being the most important ones. These parasites cause outbreaks with high mortalities among farmed freshwater fishes with great economic losses. There are few reports of these species in China, and their identification has been based mostly on their morphological characteristics. In the present work, the parasites causing five outbreaks occurring in China between 2014 and 2017 have been identified by morphological and genetic analysis. We provide the first records of Ctenopharingodon idella and Siniperca chuatsi as hosts of C. hexasticha, and of Procypris rabaudi and Schizothorax wangchiachii as hosts of C. piscicola. There are no differences in the gross pathological findings produced by C. hexasticha and C. piscicola, consisting in desquamation and necrosis of epithelial cells in the skin and gills and in severe fusion of gill lamellae. However, both species differ in their geographic distribution: C. piscicola was found in farms located at altitudes over 1500 m above sea level and with a water temperature ≤18 °C, while C. hexasticha was found in farms located at altitudes under 50 m above sea level and with a water temperature ≥21 °C. Present results confirm that C. hexasticha and C. piscicola are two different species that can be differenced by their morphology; however, their biological variability may lead to erroneous identifications and the diagnosis should be preferably based in genetic analysis including nuclear LSU rDNA and mitochondrial SSU rDNA sequences.
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Affiliation(s)
- Ming Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Runqiu Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Giana Bastos Gomes
- Tropical Research Institute, James Cook University Singapore, Singapore 387380, Singapore
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wen-Xiang Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Shan-Gong Wu
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| | - Francisco Ponce-Gordo
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain.
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19
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Zheng W, Wang C, Yan Y, Gao F, Doak TG, Song W. Insights into an Extensively Fragmented Eukaryotic Genome: De Novo Genome Sequencing of the Multinuclear Ciliate Uroleptopsis citrina. Genome Biol Evol 2018; 10:883-894. [PMID: 29608728 PMCID: PMC5863220 DOI: 10.1093/gbe/evy055] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2018] [Indexed: 02/04/2023] Open
Abstract
Ciliated protists are a large group of single-celled eukaryotes with separate germline and somatic nuclei in each cell. The somatic genome is developed from the zygotic nucleus through a series of chromosomal rearrangements, including fragmentation, DNA elimination, de novo telomere addition, and DNA amplification. This unique feature makes them perfect models for research in genome biology and evolution. However, genomic research of ciliates has been limited to a few species, owing to problems with DNA contamination and obstacles in cultivation. Here, we introduce a method combining telomere-primer PCR amplification and high-throughput sequencing, which can reduce DNA contamination and obtain genomic data efficiently. Based on this method, we report a draft somatic genome of a multimacronuclear ciliate, Uroleptopsis citrina. 1) The telomeric sequence in U. citrina is confirmed to be C4A4C4A4C4 by directly blunt-end cloning. 2) Genomic analysis of the resulting chromosomes shows a "one-gene one-chromosome" pattern, with a small number of multiple-gene chromosomes. 3) Amino acid usage is analyzed, and reassignment of stop codons is confirmed. 4) Chromosomal analysis shows an obvious asymmetrical GC skew and high bias between A and T in the subtelomeric regions of the sense-strand, with the detection of an 11-bp high AT motif region in the 3' subtelomeric region. 5) The subtelomeric sequence also has an obvious 40 nt strand oscillation of nucleotide ratio. 6) In the 5' subtelomeric region of the coding strand, the distribution of potential TATA-box regions is illustrated, which accumulate between 30 and 50 nt. This work provides a valuable reference for genomic research and furthers our understanding of the dynamic nature of unicellular eukaryotic genomes.
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Affiliation(s)
- Weibo Zheng
- Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China.,Center for Mechanisms of Evolution, Arizona State University, Tempe, USA
| | - Chundi Wang
- Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Ying Yan
- Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Feng Gao
- Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China.,Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Thomas G Doak
- Department of Biology, Indiana University, Bloomington.,National Center for Genome Analysis Support, Indiana University, Bloomington
| | - Weibo Song
- Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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20
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Maurer-Alcalá XX, Yan Y, Pilling OA, Knight R, Katz LA. Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell 'Omics. Genome Biol Evol 2018; 10:1927-1939. [PMID: 29945193 PMCID: PMC6101598 DOI: 10.1093/gbe/evy133] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2018] [Indexed: 12/30/2022] Open
Abstract
The emergence of robust single-cell 'omics techniques enables studies of uncultivable species, allowing for the (re)discovery of diverse genomic features. In this study, we combine single-cell genomics and transcriptomics to explore genome evolution in ciliates (a > 1 Gy old clade). Analysis of the data resulting from these single-cell 'omics approaches show: 1) the description of the ciliates in the class Karyorelictea as "primitive" is inaccurate because their somatic macronuclei contain loci of varying copy number (i.e., they have been processed by genome rearrangements from the zygotic nucleus); 2) gene-sized somatic chromosomes exist in the class Litostomatea, consistent with Balbiani's (1890) observation of giant chromosomes in this lineage; and 3) gene scrambling exists in the underexplored Postciliodesmatophora (the classes Heterotrichea and Karyorelictea, abbreviated here as the Po-clade), one of two major clades of ciliates. Together these data highlight the complex evolutionary patterns underlying germline genome architectures in ciliates and provide a basis for further exploration of principles of genome evolution in diverse microbial lineages.
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Affiliation(s)
- Xyrus X Maurer-Alcalá
- Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst.,Department of Biological Sciences, Smith College, Northampton, Massachusetts.,Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Ying Yan
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
| | - Olivia A Pilling
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego.,Department of Computer Science and Engineering, University of California San Diego, San Diego.,Center for Microbiome Innovation, University of California San Diego, San Diego
| | - Laura A Katz
- Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst.,Department of Biological Sciences, Smith College, Northampton, Massachusetts
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21
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Zhang T, Wang C, Katz LA, Gao F. A paradox: rapid evolution rates of germline-limited sequences are associated with conserved patterns of rearrangements in cryptic species of Chilodonella uncinata (Protista, Ciliophora). SCIENCE CHINA-LIFE SCIENCES 2018; 61:1071-1078. [DOI: 10.1007/s11427-018-9333-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/06/2018] [Indexed: 10/28/2022]
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22
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Rajter Ľ, Vďačný P. Selection and paucity of phylogenetic signal challenge the utility of alpha-tubulin in reconstruction of evolutionary history of free-living litostomateans (Protista, Ciliophora). Mol Phylogenet Evol 2018; 127:534-544. [PMID: 29763665 DOI: 10.1016/j.ympev.2018.05.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/25/2018] [Accepted: 05/11/2018] [Indexed: 11/26/2022]
Abstract
The class Litostomatea represents a highly diverse but monophyletic group, uniting both free-living and endosymbiotic ciliates. Ribosomal RNA genes and ITS-region sequences helped to recognize and define the main litostomatean lineages, but did not provide enough phylogenetic signal to unambiguously resolve their interrelationships. In this study, we attempted to improve the resolution among main free-living predatory lineages by adding the gene coding for alpha-tubulin. However, our phylogenetic analyses challenged the performance of alpha-tubulin in reconstruction of evolutionary history of free-living litostomateans. We identified several mutually interconnected problems associated with the ciliate alpha-tubulin gene: the paucity of phylogenetic signal, molecular homoplasies and non-neutral evolution. Positive selection may generate molecular homoplasies (parallel evolution), while negative selection may cause a small number of changes and hence little phylogenetic informativness. Both problems were encountered in nucleotide and amino acid alpha-tubulin alignments, indicating an action of various selective pressures. Taking into account the involvement of alpha-tubulin in many essential biological processes, this protein could be so strongly affected by purifying selection that it even might have become an inappropriate molecular marker for reconstruction of phylogenetic relationships. Therefore, a great caution should be paid when tubulin genes are included in phylogenetic and/or phylogenomic analyses.
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Affiliation(s)
- Ľubomír Rajter
- Department of Zoology, Comenius University in Bratislava, 842 15 Bratislava, Slovak Republic
| | - Peter Vďačný
- Department of Zoology, Comenius University in Bratislava, 842 15 Bratislava, Slovak Republic.
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23
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Marinov GK, Kundaje A. ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation. Brief Funct Genomics 2018; 17:116-137. [PMID: 29529131 PMCID: PMC5889016 DOI: 10.1093/bfgp/ely004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Advances in the methods for detecting protein-DNA interactions have played a key role in determining the directions of research into the mechanisms of transcriptional regulation. The most recent major technological transformation happened a decade ago, with the move from using tiling arrays [chromatin immunoprecipitation (ChIP)-on-Chip] to high-throughput sequencing (ChIP-seq) as a readout for ChIP assays. In addition to the numerous other ways in which it is superior to arrays, by eliminating the need to design and manufacture them, sequencing also opened the door to carrying out comparative analyses of genome-wide transcription factor occupancy across species and studying chromatin biology in previously less accessible model and nonmodel organisms, thus allowing us to understand the evolution and diversity of regulatory mechanisms in unprecedented detail. Here, we review the biological insights obtained from such studies in recent years and discuss anticipated future developments in the field.
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Affiliation(s)
- Georgi K Marinov
- Corresponding author: Georgi K. Marinov, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. E-mail:
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24
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Chen X, Wang Y, Sheng Y, Warren A, Gao S. GPSit: An automated method for evolutionary analysis of nonculturable ciliated microeukaryotes. Mol Ecol Resour 2018; 18:700-713. [DOI: 10.1111/1755-0998.12750] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/25/2017] [Accepted: 12/26/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Xiao Chen
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao China
- Laboratory for Marine Biology and Biotechnology; Qingdao National Laboratory for Marine Science and Technology; Qingdao China
| | - Yurui Wang
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao China
- Laboratory for Marine Biology and Biotechnology; Qingdao National Laboratory for Marine Science and Technology; Qingdao China
| | - Yalan Sheng
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao China
- Laboratory for Marine Biology and Biotechnology; Qingdao National Laboratory for Marine Science and Technology; Qingdao China
| | - Alan Warren
- Department of Life Sciences; Natural History Museum; London UK
| | - Shan Gao
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao China
- Laboratory for Marine Biology and Biotechnology; Qingdao National Laboratory for Marine Science and Technology; Qingdao China
- College of Marine Life Sciences; Ocean University of China; Qingdao China
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25
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Exploration of the Germline Genome of the Ciliate Chilodonella uncinata through Single-Cell Omics (Transcriptomics and Genomics). mBio 2018; 9:mBio.01836-17. [PMID: 29317511 PMCID: PMC5760741 DOI: 10.1128/mbio.01836-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Separate germline and somatic genomes are found in numerous lineages across the eukaryotic tree of life, often separated into distinct tissues (e.g., in plants, animals, and fungi) or distinct nuclei sharing a common cytoplasm (e.g., in ciliates and some foraminifera). In ciliates, germline-limited (i.e., micronuclear-specific) DNA is eliminated during the development of a new somatic (i.e., macronuclear) genome in a process that is tightly linked to large-scale genome rearrangements, such as deletions and reordering of protein-coding sequences. Most studies of germline genome architecture in ciliates have focused on the model ciliates Oxytricha trifallax, Paramecium tetraurelia, and Tetrahymena thermophila, for which the complete germline genome sequences are known. Outside of these model taxa, only a few dozen germline loci have been characterized from a limited number of cultivable species, which is likely due to difficulties in obtaining sufficient quantities of “purified” germline DNA in these taxa. Combining single-cell transcriptomics and genomics, we have overcome these limitations and provide the first insights into the structure of the germline genome of the ciliate Chilodonella uncinata, a member of the understudied class Phyllopharyngea. Our analyses reveal the following: (i) large gene families contain a disproportionate number of genes from scrambled germline loci; (ii) germline-soma boundaries in the germline genome are demarcated by substantial shifts in GC content; (iii) single-cell omics techniques provide large-scale quality germline genome data with limited effort, at least for ciliates with extensively fragmented somatic genomes. Our approach provides an efficient means to understand better the evolution of genome rearrangements between germline and soma in ciliates. Our understanding of the distinctions between germline and somatic genomes in ciliates has largely relied on studies of a few model genera (e.g., Oxytricha, Paramecium, Tetrahymena). We have used single-cell omics to explore germline-soma distinctions in the ciliate Chilodonella uncinata, which likely diverged from the better-studied ciliates ~700 million years ago. The analyses presented here indicate that developmentally regulated genome rearrangements between germline and soma are demarcated by rapid transitions in local GC composition and lead to diversification of protein families. The approaches used here provide the basis for future work aimed at discerning the evolutionary impacts of germline-soma distinctions among diverse ciliates.
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Macronuclear Actin copy number variations in single cells of different Pseudokeronopsis (Alveolata, Ciliophora) populations. Eur J Protistol 2017; 59:75-81. [DOI: 10.1016/j.ejop.2017.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 02/01/2017] [Accepted: 02/08/2017] [Indexed: 10/20/2022]
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27
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Pilling OA, Rogers AJ, Gulla-Devaney B, Katz LA. Insights into transgenerational epigenetics from studies of ciliates. Eur J Protistol 2017; 61:366-375. [PMID: 28689743 DOI: 10.1016/j.ejop.2017.05.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 05/06/2017] [Accepted: 05/09/2017] [Indexed: 12/23/2022]
Abstract
Epigenetics, a term with many meanings, can be broadly defined as the study of dynamic states of the genome. Ciliates, a clade of unicellular eukaryotes, can teach us about the intersection of epigenetics and evolution due to the advantages of working with cultivable ciliate lineages, plus their tendency to express extreme phenotypes such as heritable doublet morphology. Moreover, ciliates provide a powerful model for studying epigenetics given the presence of dimorphic nuclei - a somatic macronucleus and germline micronucleus - within each cell. Here, we exemplify the power of studying ciliates to learn about epigenetic phenomena. We highlight "classical" examples from morphology and physiology including cortical inheritance, mating type determination, and serotype expression. In addition, we detail molecular studies of epigenetic phenomena, including: DNA elimination; alternative processing and unscrambling; and copy number determination. Based on the implications of these studies, we discuss epigenetics as a possible functional mechanism for rapid speciation in ciliates.
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Affiliation(s)
- Olivia A Pilling
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
| | - Anna J Rogers
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
| | | | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA; Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA.
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28
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Boscaro V, Rossi A, Vannini C, Verni F, Fokin SI, Petroni G. Strengths and Biases of High-Throughput Sequencing Data in the Characterization of Freshwater Ciliate Microbiomes. MICROBIAL ECOLOGY 2017; 73:865-875. [PMID: 28032127 DOI: 10.1007/s00248-016-0912-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 12/05/2016] [Indexed: 06/06/2023]
Abstract
Molecular surveys of eukaryotic microbial communities employing high-throughput sequencing (HTS) techniques are rapidly supplanting traditional morphological approaches due to their larger data output and reduced bench work time. Here, we directly compare morphological and Illumina data obtained from the same samples, in an effort to characterize ciliate faunas from sediments in freshwater environments. We show how in silico processing affects the final outcome of our HTS analysis, providing evidence that quality filtering protocols strongly impact the number of predicted taxa, but not downstream conclusions such as biogeography patterns. We determine the abundance distribution of ciliates, showing that a small fraction of abundant taxa dominates read counts. At the same time, we advance reasons to believe that biases affecting HTS abundances may be significant enough to blur part of the underlying biological picture. We confirmed that the HTS approach detects many more taxa than morphological inspections, and highlight how the difference varies among taxonomic groups. Finally, we hypothesize that the two datasets actually correspond to different conceptions of "diversity," and consequently that neither is entirely superior to the other when investigating environmental protists.
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Affiliation(s)
- Vittorio Boscaro
- Dipartimento di Biologia, Unità di Zoologia-Antropologia, Università di Pisa, 56126, Pisa, Italy.
- Department of Botany, University of British Columbia, Vancouver, BC, V6T1Z4, Canada.
| | - Alessia Rossi
- Dipartimento di Biologia, Unità di Zoologia-Antropologia, Università di Pisa, 56126, Pisa, Italy
| | - Claudia Vannini
- Dipartimento di Biologia, Unità di Zoologia-Antropologia, Università di Pisa, 56126, Pisa, Italy
| | - Franco Verni
- Dipartimento di Biologia, Unità di Zoologia-Antropologia, Università di Pisa, 56126, Pisa, Italy
| | - Sergei I Fokin
- Dipartimento di Biologia, Unità di Zoologia-Antropologia, Università di Pisa, 56126, Pisa, Italy
- Department of Invertebrate Zoology, St.-Petersburg State University, St.-Petersburg, 199034, Russia
| | - Giulio Petroni
- Dipartimento di Biologia, Unità di Zoologia-Antropologia, Università di Pisa, 56126, Pisa, Italy
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29
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Bastos Gomes G, Jerry DR, Miller TL, Hutson KS. Current status of parasitic ciliates Chilodonella spp. (Phyllopharyngea: Chilodonellidae) in freshwater fish aquaculture. JOURNAL OF FISH DISEASES 2017; 40:703-715. [PMID: 27474174 DOI: 10.1111/jfd.12523] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 06/02/2016] [Accepted: 06/02/2016] [Indexed: 06/06/2023]
Abstract
Freshwater fish farming contributes to more than two-thirds of global aquaculture production. Parasitic ciliates are one of the largest causes of production loss in freshwater farmed fishes, with species from the genus Chilodonella being particularly problematic. While Chilodonella spp. include 'free-living' fauna, some species are involved in mortality events of fish, particularly in high-density aquaculture. Indeed, chilodonellosis causes major productivity losses in over 16 species of farmed freshwater fishes in more than 14 countries. Traditionally, Chilodonella species are identified based on morphological features; however, the genus comprises yet uncharacterized cryptic species, which indicates the necessity for molecular diagnostic methods. This review synthesizes current knowledge on the biology, ecology and geographic distribution of harmful Chilodonella spp. and examines pathological signs, diagnostic methods and treatments. Recent advances in molecular diagnostics and the ability to culture Chilodonella spp. in vitro will enable the development of preventative management practices and sustained freshwater fish aquaculture production.
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Affiliation(s)
- G Bastos Gomes
- Marine Biology and Aquaculture Sciences, College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - D R Jerry
- Marine Biology and Aquaculture Sciences, College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - T L Miller
- Marine Biology and Aquaculture Sciences, College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
- Fish Health Laboratory, Department of Fisheries Western Australia, South Perth, WA, Australia
| | - K S Hutson
- Marine Biology and Aquaculture Sciences, College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
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30
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Bastos Gomes G, Miller TL, Vaughan DB, Jerry DR, McCowan C, Bradley TL, Hutson KS. Evidence of multiple species of Chilodonella (Protozoa, Ciliophora) infecting Australian farmed freshwater fishes. Vet Parasitol 2017; 237:8-16. [DOI: 10.1016/j.vetpar.2017.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/16/2017] [Accepted: 03/03/2017] [Indexed: 01/20/2023]
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31
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Maurer-Alcalá XX, Katz LA. Nuclear Architecture and Patterns of Molecular Evolution Are Correlated in the Ciliate Chilodonella uncinata. Genome Biol Evol 2016; 8:1634-42. [PMID: 27189988 PMCID: PMC4943175 DOI: 10.1093/gbe/evw099] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The relationship between nuclear architecture and patterns of molecular evolution in lineages across the eukaryotic tree of life is not well understood, partly because molecular evolution is traditionally explored as changes in base pairs along a linear sequence without considering the context of nuclear position of chromosomes. The ciliate Chilodonella uncinata is an ideal system to address the relationship between nuclear architecture and patterns of molecular evolution as the somatic macronucleus of this ciliate is composed of a peripheral DNA-rich area (orthomere) and a DNA-poor central region (paramere) to form a “heteromeric” macronucleus. Moreover, because the somatic chromosomes of C. uncinata are highly processed into “gene-sized” chromosomes (i.e., nanochromosomes), we can assess fine-scale relationships between location and sequence evolution. By combining fluorescence microscopy and analyses of transcriptome data from C. uncinata, we find that highly expressed genes have the greatest codon usage bias and are enriched in DNA-poor regions. In contrast, genes with less biased sequences tend to be concentrated in DNA abundant areas, at least during vegetative growth. Our analyses are consistent with recent work in plants and animals where nuclear architecture plays a role in gene expression. At the same time, the unusual localization of nanochromosomes suggests that the highly structured nucleus in C. uncinata may create a “gene bank” that facilitates rapid changes in expression of genes required only in specific life history stages. By using “nonmodel” organisms like C. uncinata, we can explore the universality of eukaryotic features while also providing examples of novel properties (i.e., the presence of a gene bank) that build from these features.
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Affiliation(s)
- Xyrus X Maurer-Alcalá
- Department of Biological Sciences, Smith College, Northampton, MA Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst
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32
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Dimond KL, Zufall RA. Hidden genetic variation in the germline genome of Tetrahymena thermophila. J Evol Biol 2016; 29:1284-92. [PMID: 26998689 DOI: 10.1111/jeb.12868] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 02/29/2016] [Accepted: 03/13/2016] [Indexed: 11/28/2022]
Abstract
Genome architecture varies greatly among eukaryotes. This diversity may profoundly affect the origin and maintenance of genetic variation within a population. Ciliates are microbial eukaryotes with unusual genome features, such as the separation of germline and somatic genomes within a single cell and amitotic division. These features have previously been proposed to increase the rate of molecular evolution in these species. Here, we assessed the fitness effects of genetic variation in the two genomes of natural isolates of the ciliate Tetrahymena thermophila. We find more extensive genetic variation in fitness in the transcriptionally silent germline genome than in the expressed somatic genome. Surprisingly, this variation is not primarily deleterious, but has both beneficial and deleterious effects. We conclude that Tetrahymena genome architecture allows for the maintenance of genetic variation that would otherwise be eliminated by selection. We consider the effect of selection on the two genomes and the impacts of reproductive strategies and the mechanism of sex determination on the structure of this variation.
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Affiliation(s)
- K L Dimond
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - R A Zufall
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
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33
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Fernandes NM, Paiva TDS, da Silva-Neto ID, Schlegel M, Schrago CG. Expanded phylogenetic analyses of the class Heterotrichea (Ciliophora, Postciliodesmatophora) using five molecular markers and morphological data. Mol Phylogenet Evol 2015; 95:229-46. [PMID: 26549427 DOI: 10.1016/j.ympev.2015.10.030] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/30/2015] [Accepted: 10/31/2015] [Indexed: 11/25/2022]
Abstract
Most studies of the molecular evolution of Heterotrichea have been based solely on the 18S-rDNA gene, which were inconsistent with morphological classification. Because of the limitations of single locus phylogenies and the recurring problem of lack of resolution of deeper nodes found in previous studies, we present hypotheses of the evolution of internal groups of the class Heterotrichea based on multi-loci analyses (18S-rDNA, 28S-rDNA, ITS1-5.8S-ITS2 region, COI and alpha-tubulin) and morphological data. Phylogenetic trees from protein coding gene data are presented for Heterotrichea for the first time. Phylogenetic analyses included Bayesian inference, maximum likelihood, maximum parsimony methods, and optimal trees were statistically compared to alternative topologies from the literature. Additionally, the Bayesian concordance approach (BCA algorithm) was used to assess the concordance factor between topologies obtained from isolated analyses. Because different loci may evolve at different rates, resulting in different gene topologies, we also estimated a species tree for Heterotrichea using the STAR coalescence-based method. The results show that: (1) single gene trees are inconsistent regarding the position of some heterotrichean families; (2) the concatenation of all data in a total-evidence tree improved the resolution of deep nodes among the heterotrichean families and genera; (3) the coalescent-based species tree is consistent with phylogenies based on the 18S-rDNA gene and shows Spirostomidae as the stem group of Heterotrichea; (4) however, the total-evidence tree suggests that the large Heterotrichea cluster is divided into nine lineages in which Peritromidae diverges at the base of the Heterotrichea tree.
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Affiliation(s)
- Noemi M Fernandes
- Laboratório de Biologia Evolutiva Teórica e Aplicada, Departamento de Genética, Universidade Federal do Rio de Janeiro, Brazil.
| | - Thiago da Silva Paiva
- Laboratório de Protistologia, Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Brazil; Laboratório de Biologia Molecular "Francisco Mauro Salzano", Instituto de Ciências Biológicas, Universidade Federal do Pará, Brazil
| | - Inácio D da Silva-Neto
- Laboratório de Protistologia, Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Brazil
| | - Martin Schlegel
- Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Germany
| | - Carlos G Schrago
- Laboratório de Biologia Evolutiva Teórica e Aplicada, Departamento de Genética, Universidade Federal do Rio de Janeiro, Brazil.
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34
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Morgens DW, Cavalcanti ARO. Amitotic chromosome loss predicts distinct patterns of senescence and non-senescence in ciliates. Protist 2015; 166:224-33. [PMID: 25840368 DOI: 10.1016/j.protis.2015.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 02/24/2015] [Accepted: 03/02/2015] [Indexed: 11/26/2022]
Abstract
Over time and repeated asexual divisions, many ciliate species display the characteristics of senescence, reduced fecundity and increased mortality. Their only path to recovery is sexual conjugation or autogamy. While more traditional models of cellular aging have been proposed, one of the most accepted explanations relies on the faulty mechanism by which ciliates duplicate their somatic nucleus, a process referred to as amitosis. Amitosis involves the random segregation of chromosomes with no consideration for homology. Over subsequent divisions, chromosome copy numbers will fluctuate until an entire chromosome is lost, resulting in death. Via simulations of this process, we find that senescence and death via chromosome loss is not the only possible result of amitosis. Random chromosome loss is less damaging to populations than previously thought, and strict adherence to the model predicts that Paramecium tetraurelia would not senesce. A combination of the reciprocal nature of amitosis and lethal selection against low-copy number chromosomes is responsible for this startling prediction. Additionally, our results provide an alternate explanation to recent evidence for selection on chromosome copy number in Tetrahymena thermophila and peculiar patterns of senescence in Tetrahymena pyriformis.
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Affiliation(s)
- David W Morgens
- Biology Department, Pomona College, 175W 6(th) Street, Claremont, CA 91711, USA
| | - Andre R O Cavalcanti
- Biology Department, Pomona College, 175W 6(th) Street, Claremont, CA 91711, USA.
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35
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Analyses of alternatively processed genes in ciliates provide insights into the origins of scrambled genomes and may provide a mechanism for speciation. mBio 2015; 6:mBio.01998-14. [PMID: 25650397 PMCID: PMC4324306 DOI: 10.1128/mbio.01998-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Chromosome rearrangements occur in a variety of eukaryotic life cycles, including during the development of the somatic macronuclear genome in ciliates. Previous work on the phyllopharyngean ciliate Chilodonella uncinata revealed that macronuclear β-tubulin and protein kinase gene families share alternatively processed germ line segments nested within divergent regions. To study genome evolution in this ciliate further, we characterized two additional alternatively processed gene families from two cryptic species of the ciliate morphospecies C. uncinata: those encoding histidine acid phosphatase protein (Hap) and leishmanolysin family protein (Lei). Analyses of the macronuclear Hap and Lei sequences reveal that each gene family consists of three members in the macronucleus that are marked by identical regions nested among highly divergent regions. Investigation of the micronuclear Hap sequences revealed a complex pattern in which the three macronuclear sequences are derived either from a single micronuclear region or from a combination of this shared region recombined with additional duplicate micronuclear copies of Hap. We propose a model whereby gene scrambling evolves by gene duplication followed by partial and reciprocal degradation of the duplicate sequences. In this model, alternative processing represents an intermediate step in the evolution of scrambled genes. Finally, we speculate on the possible role of genome architecture in speciation in ciliates by describing what might happen if changes in alternatively processed loci occur in subdivided populations. Genome rearrangements occur in a variety of eukaryotic cells and serve as an important mechanism for generating genomic diversity. The unusual genome architecture of ciliates with separate germline and somatic nuclei in each cell, provides an ideal system to study further principles of genome evolution. Previous analyses revealed complex forms of chromosome rearrangements, including gene scrambling and alternative processing of germ line chromosomes. Here we describe more complex rearrangements between germ line and somatic chromosomes than previously seen in alternatively processed gene families. Drawing on the present and previous findings, we propose a model in which alternative processing of duplicated micronuclear regions represents an intermediate stage in the evolution of scrambled genes. Under this model, alternative processing may provide insights into a mechanism for speciation in ciliates. Our data on gene scrambling and alternative processing also enhance views on the dynamic nature of genomes across the eukaryotic tree of life.
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36
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Gregori M, Fernández-Leborans G, Roura Á, González ÁF, Pascual S. Description of a new epibiotic relationship (Suctorian-Copepoda) in NE Atlantic waters: from morphological to phylogenetic analyses. ACTA ZOOL-STOCKHOLM 2015. [DOI: 10.1111/azo.12113] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maria Gregori
- Marine Ecology and Biodiversity Department; Instituto de Investigaciones Marinas (CSIC); Eduardo Cabello s/n Vigo 36208 Spain
| | | | - Álvaro Roura
- Department of Genetics; La Trobe Institute for Molecular Science; Kingsbury Drive, Bundoora 3086 Melbourne VIC Australia
| | - Ángel F. González
- Marine Ecology and Biodiversity Department; Instituto de Investigaciones Marinas (CSIC); Eduardo Cabello s/n Vigo 36208 Spain
| | - Santiago Pascual
- Marine Ecology and Biodiversity Department; Instituto de Investigaciones Marinas (CSIC); Eduardo Cabello s/n Vigo 36208 Spain
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37
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Popenko VI, Potekhin AA, Karajan BP, Skarlato SO, Leonova OG. The Size of DNA Molecules and Chromatin Organization in the Macronucleus of the Ciliate Didinium nasutum
(Ciliophora). J Eukaryot Microbiol 2014; 62:260-4. [DOI: 10.1111/jeu.12161] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 06/18/2014] [Accepted: 06/24/2014] [Indexed: 02/02/2023]
Affiliation(s)
- Vladimir I. Popenko
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; Moscow 119991 Russia
| | - Alexey A. Potekhin
- Faculty of Biology and Soil Science; St. Petersburg State University; St. Petersburg 199034 Russia
| | - Bella P. Karajan
- Institute of Cytology; Russian Academy of Sciences; St. Petersburg 194064 Russia
| | - Sergei O. Skarlato
- Institute of Cytology; Russian Academy of Sciences; St. Petersburg 194064 Russia
| | - Olga G. Leonova
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; Moscow 119991 Russia
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38
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Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages. Mol Phylogenet Evol 2014; 78:36-42. [DOI: 10.1016/j.ympev.2014.04.020] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 03/18/2014] [Accepted: 04/18/2014] [Indexed: 11/19/2022]
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39
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Špaková T, Pristaš P, Javorský P. Telomere repeats and macronuclear DNA organization in the soil ciliate Kahliella matisi (Ciliophora, Hypotricha). Eur J Protistol 2014; 50:231-5. [PMID: 24882684 DOI: 10.1016/j.ejop.2014.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 02/27/2014] [Accepted: 03/01/2014] [Indexed: 11/29/2022]
Abstract
To better understand the structure of macronuclear chromosomes in ciliates, the organization of macronuclear DNA was investigated in the hypotrich Kahliella matisi. Total DNA of K. matisi separated by agarose gel electrophoresis showed continuous smear ranging in size from ∼500bp to ∼15kb. This fragmentation was found to be due to the presence of gene-sized macronuclear chromosomes. The sequence analysis of four randomly cloned macronuclear chromosomes showed that K. matisi telomeres consist of 5'-dC4A4-3' repeats and carry one or two open reading frames. The transcription unit was found to be flanked with non-coding AT rich 5' leader and 3' trailer. No consensus transcription-regulatory sequences were identified in 5' leader and only one of analyzed gene-sized chromosomes showed the presence of conserved poly(A) addition signal sequence in 3' trailer. All ORFs showed highest relatedness to Oxytricha trifallax macronuclear chromosomes with conserved exon/intron structure. Sequence comparisons indicate that macronuclear chromosome organization is at least partially conserved in ciliates.
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Affiliation(s)
- Tímea Špaková
- Associated Tissue Bank of Faculty of Medicine of P. J. Šafárik University and L. Pasteur University Hospital, Trieda SNP 1, 041 66 Košice, Slovakia.
| | - Peter Pristaš
- Institute of Animal Physiology, Slovak Academy of Sciences, Šoltésovej 4-6, 040 01 Košice, Slovakia
| | - Peter Javorský
- Institute of Animal Physiology, Slovak Academy of Sciences, Šoltésovej 4-6, 040 01 Košice, Slovakia
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40
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Dunthorn M, Stoeck T, Clamp J, Warren A, Mahé F. Ciliates and the Rare Biosphere: A Review. J Eukaryot Microbiol 2014; 61:404-9. [DOI: 10.1111/jeu.12121] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 03/14/2014] [Accepted: 03/14/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Micah Dunthorn
- Department of Ecology; University of Kaiserslautern; D-67663 Kaiserslautern Germany
| | - Thorsten Stoeck
- Department of Ecology; University of Kaiserslautern; D-67663 Kaiserslautern Germany
| | - John Clamp
- Department of Biology; North Carolina Central University; Durham North Carolina 27707 USA
| | - Alan Warren
- Department of Life Sciences Department; Natural History Museum; London SW7 5BD United Kingdom
| | - Frédéric Mahé
- Department of Ecology; University of Kaiserslautern; D-67663 Kaiserslautern Germany
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41
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Gao F, Song W, Katz LA. Genome structure drives patterns of gene family evolution in ciliates, a case study using Chilodonella uncinata (Protista, Ciliophora, Phyllopharyngea). Evolution 2014; 68:2287-95. [PMID: 24749903 DOI: 10.1111/evo.12430] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 04/06/2014] [Indexed: 01/02/2023]
Abstract
In most lineages, diversity among gene family members results from gene duplication followed by sequence divergence. Because of the genome rearrangements during the development of somatic nuclei, gene family evolution in ciliates involves more complex processes. Previous work on the ciliate Chilodonella uncinata revealed that macronuclear β-tubulin gene family members are generated by alternative processing, in which germline regions are alternatively used in multiple macronuclear chromosomes. To further study genome evolution in this ciliate, we analyzed its transcriptome and found that (1) alternative processing is extensive among gene families; and (2) such gene families are likely to be C. uncinata specific. We characterized additional macronuclear and micronuclear copies of one candidate alternatively processed gene family-a protein kinase domain containing protein (PKc)-from two C. uncinata strains. Analysis of the PKc sequences reveals that (1) multiple PKc gene family members in the macronucleus share some identical regions flanked by divergent regions; and (2) the shared identical regions are processed from a single micronuclear chromosome. We discuss analogous processes in lineages across the eukaryotic tree of life to provide further insights on the impact of genome structure on gene family evolution in eukaryotes.
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Affiliation(s)
- Feng Gao
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063; Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
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Huang J, Katz LA. Nanochromosome copy number does not correlate with RNA levels though patterns are conserved between strains of the ciliate morphospecies Chilodonella uncinata. Protist 2014; 165:445-51. [PMID: 24907652 DOI: 10.1016/j.protis.2014.04.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 04/14/2014] [Accepted: 04/16/2014] [Indexed: 11/29/2022]
Abstract
In some ciliates, extensive genome fragmentation leads to a macronucleus (i.e. somatic nucleus) containing gene-sized chromosomes that vary in copy number. Yet the relationship between copy number and expression level is not well understood as previous work has shown a variety of patterns. For example, nanochromosome copy numbers are positively correlated to mRNA levels in spirotrichous ciliates, while one study of Chilodonella uncinata suggested that they were inversely correlated. To study further copy number and expression levels in C. uncinata, we analyzed 11 members in five gene families (SSU-rDNA, actin, alpha-tubulin, histidine acid phosphatase family protein and a protein kinase domain containing protein) from one strain. We find that macronuclear copy numbers of these genes range from hundreds to thousands per cell, and that copy number does not correlate with expression level as measured by steady-state RNA in predominantly-vegetative cultures. We also compared six of these genes to their orthologs in a second genetically-isolated strain of C. uncinata to reveal that patterns of nanochromosome and transcript copy numbers are conserved between strains. Our data suggest that nanochromosome copy number may be related to a feature like nuclear architecture.
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Affiliation(s)
- Jie Huang
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA; Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA; Program in Organismic and Evolutionary Biology, UMass-Amherst, Amherst, MA 01003, USA.
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Dunthorn M, Otto J, Berger SA, Stamatakis A, Mahé F, Romac S, de Vargas C, Audic S, Stock A, Kauff F, Stoeck T. Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context. Mol Biol Evol 2014; 31:993-1009. [PMID: 24473288 DOI: 10.1093/molbev/msu055] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Nucleotide positions in the hypervariable V4 and V9 regions of the small subunit (SSU)-rDNA locus are normally difficult to align and are usually removed before standard phylogenetic analyses. Yet, with next-generation sequencing data, amplicons of these regions are all that are available to answer ecological and evolutionary questions that rely on phylogenetic inferences. With ciliates, we asked how inclusion of the V4 or V9 regions, regardless of alignment quality, affects tree topologies using distinct phylogenetic methods (including PairDist that is introduced here). Results show that the best approach is to place V4 amplicons into an alignment of full-length Sanger SSU-rDNA sequences and to infer the phylogenetic tree with RAxML. A sliding window algorithm as implemented in RAxML shows, though, that not all nucleotide positions in the V4 region are better than V9 at inferring the ciliate tree. With this approach and an ancestral-state reconstruction, we use V4 amplicons from European nearshore sampling sites to infer that rather than being primarily terrestrial and freshwater, colpodean ciliates may have repeatedly transitioned from terrestrial/freshwater to marine environments.
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Affiliation(s)
- Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
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da Silva Paiva T, do Nascimento Borges B, da Silva-Neto ID. Phylogenetic study of Class Armophorea (Alveolata, Ciliophora) based on 18S-rDNA data. Genet Mol Biol 2013; 36:571-85. [PMID: 24385862 PMCID: PMC3873190 DOI: 10.1590/s1415-47572013000400017] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 07/18/2013] [Indexed: 11/25/2022] Open
Abstract
The 18S rDNA phylogeny of Class Armophorea, a group of anaerobic ciliates, is proposed based on an analysis of 44 sequences (out of 195) retrieved from the NCBI/GenBank database. Emphasis was placed on the use of two nucleotide alignment criteria that involved variation in the gap-opening and gap-extension parameters and the use of rRNA secondary structure to orientate multiple-alignment. A sensitivity analysis of 76 data sets was run to assess the effect of variations in indel parameters on tree topologies. Bayesian inference, maximum likelihood and maximum parsimony phylogenetic analyses were used to explore how different analytic frameworks influenced the resulting hypotheses. A sensitivity analysis revealed that the relationships among higher taxa of the Intramacronucleata were dependent upon how indels were determined during multiple-alignment of nucleotides. The phylogenetic analyses rejected the monophyly of the Armophorea most of the time and consistently indicated that the Metopidae and Nyctotheridae were related to the Litostomatea. There was no consensus on the placement of the Caenomorphidae, which could be a sister group of the Metopidae + Nyctorheridae, or could have diverged at the base of the Spirotrichea branch or the Intramacronucleata tree.
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Affiliation(s)
- Thiago da Silva Paiva
- Laboratório de Protistologia, Departamento de Zoologia, Instituto de Biologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ,
Brazil
- Laboratório de Biologia Molecular “Francisco Mauro Salzano”, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA,
Brazil
| | | | - Inácio Domingos da Silva-Neto
- Laboratório de Protistologia, Departamento de Zoologia, Instituto de Biologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ,
Brazil
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Tazioli S, Di Camillo CG. Ecological and morphological characteristics of Ephelota gemmipara (Ciliophora, Suctoria), epibiontic on Eudendrium racemosum (Cnidaria, Hydrozoa) from the Adriatic Sea. Eur J Protistol 2013; 49:590-9. [DOI: 10.1016/j.ejop.2013.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 03/16/2013] [Accepted: 04/12/2013] [Indexed: 11/16/2022]
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Vogt A, Goldman AD, Mochizuki K, Landweber LF. Transposon domestication versus mutualism in ciliate genome rearrangements. PLoS Genet 2013; 9:e1003659. [PMID: 23935529 PMCID: PMC3731211 DOI: 10.1371/journal.pgen.1003659] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Ciliated protists rearrange their genomes dramatically during nuclear development via chromosome fragmentation and DNA deletion to produce a trimmer and highly reorganized somatic genome. The deleted portion of the genome includes potentially active transposons or transposon-like sequences that reside in the germline. Three independent studies recently showed that transposase proteins of the DDE/DDD superfamily are indispensible for DNA processing in three distantly related ciliates. In the spirotrich Oxytricha trifallax, high copy-number germline-limited transposons mediate their own excision from the somatic genome but also contribute to programmed genome rearrangement through a remarkable transposon mutualism with the host. By contrast, the genomes of two oligohymenophorean ciliates, Tetrahymena thermophila and Paramecium tetraurelia, encode homologous PiggyBac-like transposases as single-copy genes in both their germline and somatic genomes. These domesticated transposases are essential for deletion of thousands of different internal sequences in these species. This review contrasts the events underlying somatic genome reduction in three different ciliates and considers their evolutionary origins and the relationships among their distinct mechanisms for genome remodeling.
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Affiliation(s)
- Alexander Vogt
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Aaron David Goldman
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Kazufumi Mochizuki
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Laura F. Landweber
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- * E-mail:
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Morgens DW, Lindbergh KM, Adachi M, Radunskaya A, Cavalcanti ARO. A model for the evolution of extremely fragmented macronuclei in ciliates. PLoS One 2013; 8:e64997. [PMID: 23705024 PMCID: PMC3660376 DOI: 10.1371/journal.pone.0064997] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 04/22/2013] [Indexed: 11/19/2022] Open
Abstract
While all ciliates possess nuclear dimorphism, several ciliates - like those in the classes Phyllopharyngea, Spirotrichea, and Armophorea - have an extreme macronuclear organization. Their extensively fragmented macronuclei contain upwards of 20,000 chromosomes, each with upwards of thousands of copies. These features have evolved independently on multiple occasions throughout ciliate evolutionary history, and currently no models explain these structures in an evolutionary context. In this paper, we propose that competition between two forces - the limitation and avoidance of chromosomal imbalances as a ciliate undergoes successive asexual divisions, and the costs of replicating massive genomes - is sufficient to explain this particular nuclear structure. We present a simulation of ciliate cell evolution under control of these forces, allowing certain features of the population to change over time. Over a wide range of parameters, we observe the repeated emergence of this unusual genomic organization found in nature. Although much remains to be understood about the evolution of macronuclear genome organization, our results show that the proposed model is a plausible explanation for the emergence of these extremely fragmented, highly polyploid genomes.
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Affiliation(s)
- David W. Morgens
- Department of Biology, Pomona College, Claremont, California, United States of America
- Department of Mathematics, Pomona College, Claremont, California, United States of America
| | - Kristen M. Lindbergh
- Department of Biology, Pomona College, Claremont, California, United States of America
- Department of Mathematics, Pomona College, Claremont, California, United States of America
| | - Marie Adachi
- Department of Biology, Pomona College, Claremont, California, United States of America
- Department of Mathematics, Pomona College, Claremont, California, United States of America
| | - Ami Radunskaya
- Department of Mathematics, Pomona College, Claremont, California, United States of America
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Lynn DH, Wright ADG. Biodiversity and molecular phylogeny of Australian Clevelandella species (Class Armophorea, Order Clevelandellida, Family Clevelandellidae), intestinal endosymbiotic ciliates in the wood-feeding roach Panesthia cribrata Saussure, 1864. J Eukaryot Microbiol 2013; 60:335-41. [PMID: 23590673 DOI: 10.1111/jeu.12037] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 01/07/2013] [Accepted: 01/13/2013] [Indexed: 11/26/2022]
Abstract
There are over 100 species in the Order Clevelandellida distributed in many hosts. The majority is assigned to one of the five families, the Nyctotheridae. Our knowledge of clevelandellid genetic diversity is limited to species of Nyctotherus and Nyctotheroides. To increase our understanding of clevelandellid genetic diversity, species were isolated from intestines of the Australian wood-feeding roach Panesthia cribrata Saussure, 1864 from August to October, 2008. Four morphospecies, similar to those reported in Java and Japan by Kidder [Parasitologica, 29:163-205], were identified: Clevelandella constricta, Clevelandella nipponensis, Clevelandella parapanesthiae, and Clevelandella panesthiae. Small subunit rRNA gene sequences assigned all species to a "family" clade that was sister to the clade of species assigned to the Family Nyctotheridae in the Order Clevelandellida. Genetics and morphology were consistent for the first three Clevelandella species, but isolates assigned to C. panesthiae were assignable to three different genotypes, suggesting that this may be a cryptic species complex.
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Affiliation(s)
- Denis H Lynn
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada, N1G 2W1.
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Abstract
Ciliates are an ancient and diverse group of microbial eukaryotes that have emerged as powerful models for RNA-mediated epigenetic inheritance. They possess extensive sets of both tiny and long noncoding RNAs that, together with a suite of proteins that includes transposases, orchestrate a broad cascade of genome rearrangements during somatic nuclear development. This Review emphasizes three important themes: the remarkable role of RNA in shaping genome structure, recent discoveries that unify many deeply diverged ciliate genetic systems, and a surprising evolutionary "sign change" in the role of small RNAs between major species groups.
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Swart EC, Bracht JR, Magrini V, Minx P, Chen X, Zhou Y, Khurana JS, Goldman AD, Nowacki M, Schotanus K, Jung S, Fulton RS, Ly A, McGrath S, Haub K, Wiggins JL, Storton D, Matese JC, Parsons L, Chang WJ, Bowen MS, Stover NA, Jones TA, Eddy SR, Herrick GA, Doak TG, Wilson RK, Mardis ER, Landweber LF. The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. PLoS Biol 2013; 11:e1001473. [PMID: 23382650 PMCID: PMC3558436 DOI: 10.1371/journal.pbio.1001473] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 12/12/2012] [Indexed: 01/03/2023] Open
Abstract
With more chromosomes than any other sequenced genome, the macronuclear genome of Oxytricha trifallax has a unique and complex architecture, including alternative fragmentation and predominantly single-gene chromosomes. The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation. During sexual genome development, the expressed, somatic macronuclear genome is whittled down to the genic portion of a small fraction (∼5%) of its precursor “silent” germline micronuclear genome by a process of “unscrambling” and fragmentation. The tiny macronuclear “nanochromosomes” typically encode single, protein-coding genes (a small portion, 10%, encode 2–8 genes), have minimal noncoding regions, and are differentially amplified to an average of ∼2,000 copies. We report the high-quality genome assembly of ∼16,000 complete nanochromosomes (∼50 Mb haploid genome size) that vary from 469 bp to 66 kb long (mean ∼3.2 kb) and encode ∼18,500 genes. Alternative DNA fragmentation processes ∼10% of the nanochromosomes into multiple isoforms that usually encode complete genes. Nucleotide diversity in the macronucleus is very high (SNP heterozygosity is ∼4.0%), suggesting that Oxytricha trifallax may have one of the largest known effective population sizes of eukaryotes. Comparison to other ciliates with nonscrambled genomes and long macronuclear chromosomes (on the order of 100 kb) suggests several candidate proteins that could be involved in genome rearrangement, including domesticated MULE and IS1595-like DDE transposases. The assembly of the highly fragmented Oxytricha macronuclear genome is the first completed genome with such an unusual architecture. This genome sequence provides tantalizing glimpses into novel molecular biology and evolution. For example, Oxytricha maintains tens of millions of telomeres per cell and has also evolved an intriguing expansion of telomere end-binding proteins. In conjunction with the micronuclear genome in progress, the O. trifallax macronuclear genome will provide an invaluable resource for investigating programmed genome rearrangements, complementing studies of rearrangements arising during evolution and disease. The macronuclear genome of the ciliate Oxytricha trifallax, contained in its somatic nucleus, has a unique genome architecture. Unlike its diploid germline genome, which is transcriptionally inactive during normal cellular growth, the macronuclear genome is fragmented into at least 16,000 tiny (∼3.2 kb mean length) chromosomes, most of which encode single actively transcribed genes and are differentially amplified to a few thousand copies each. The smallest chromosome is just 469 bp, while the largest is 66 kb and encodes a single enormous protein. We found considerable variation in the genome, including frequent alternative fragmentation patterns, generating chromosome isoforms with shared sequence. We also found limited variation in chromosome amplification levels, though insufficient to explain mRNA transcript level variation. Another remarkable feature of Oxytricha's macronuclear genome is its inordinate fondness for telomeres. In conjunction with its possession of tens of millions of chromosome-ending telomeres per macronucleus, we show that Oxytricha has evolved multiple putative telomere-binding proteins. In addition, we identified two new domesticated transposase-like protein classes that we propose may participate in the process of genome rearrangement. The macronuclear genome now provides a crucial resource for ongoing studies of genome rearrangement processes that use Oxytricha as an experimental or comparative model.
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Affiliation(s)
- Estienne C. Swart
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - John R. Bracht
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Vincent Magrini
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Patrick Minx
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Xiao Chen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Yi Zhou
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Jaspreet S. Khurana
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Aaron D. Goldman
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Mariusz Nowacki
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Klaas Schotanus
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Seolkyoung Jung
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Robert S. Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Amy Ly
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sean McGrath
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kevin Haub
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jessica L. Wiggins
- Sequencing Core Facility, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Donna Storton
- Sequencing Core Facility, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - John C. Matese
- Sequencing Core Facility, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Lance Parsons
- Bioinformatics Group, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Wei-Jen Chang
- Department of Biology, Hamilton College, Clinton, New York, United States of America
| | - Michael S. Bowen
- Biology Department, Bradley University, Peoria, Illinois, United States of America
| | - Nicholas A. Stover
- Biology Department, Bradley University, Peoria, Illinois, United States of America
| | - Thomas A. Jones
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Sean R. Eddy
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Glenn A. Herrick
- Biology Department, University of Utah, Salt Lake City, Utah, United States of America
| | - Thomas G. Doak
- Department of Biology, University of Indiana, Bloomington, Indiana, United States of America
| | - Richard K. Wilson
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Elaine R. Mardis
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Laura F. Landweber
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- * E-mail:
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