99801
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Synergistic biodegradation of aromatic-aliphatic copolyester plastic by a marine microbial consortium. Nat Commun 2020; 11:5790. [PMID: 33188179 PMCID: PMC7666164 DOI: 10.1038/s41467-020-19583-2] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/13/2020] [Indexed: 12/12/2022] Open
Abstract
The degradation of synthetic polymers by marine microorganisms is not as well understood as the degradation of plastics in soil and compost. Here, we use metagenomics, metatranscriptomics and metaproteomics to study the biodegradation of an aromatic-aliphatic copolyester blend by a marine microbial enrichment culture. The culture can use the plastic film as the sole carbon source, reaching maximum conversion to CO2 and biomass in around 15 days. The consortium degrades the polymer synergistically, with different degradation steps being performed by different community members. We identify six putative PETase-like enzymes and four putative MHETase-like enzymes, with the potential to degrade aliphatic-aromatic polymers and their degradation products, respectively. Our results show that, although there are multiple genes and organisms with the potential to perform each degradation step, only a few are active during biodegradation. The degradation of plastics by marine microbes is not well understood. Here, Meyer-Cifuentes et al. use a meta-omics approach to study the biodegradation of an aromatic-aliphatic copolyester blend by a marine microbial enrichment culture, showing that different degradation steps are performed by different microorganisms.
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99802
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Pereira A, Teixeira J, Sousa S, Parreira R, Campino L, Meireles J, Maia C. Giardia duodenalis infection in dogs from the metropolitan area of Lisbon, Portugal: prevalence, genotyping and associated risk factors. J Parasit Dis 2020; 45:372-379. [PMID: 34295036 DOI: 10.1007/s12639-020-01307-4] [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: 07/13/2020] [Accepted: 11/02/2020] [Indexed: 11/28/2022] Open
Abstract
Abstract Giardia duodenalis is a cosmopolitan enteric protozoan that affects a wide range of vertebrates, including humans and dogs. Genetic characterisation reveals eight different assemblages, with A and B having been found mainly in humans and several other animals, and thus considered potentially zoonotic, while C and D are adapted to infect dogs. This study aimed to determine the prevalence of G. duodenalis, their distribution into assemblages, and risk factors associated with their infection of dogs from the metropolitan area of Lisbon. Giardia duodenalis cysts were microscopically identified in 33.8% (27/80) of the faecal samples analysed. Multivariate logistic regression analysis revealed that dogs under 6 months of age and from both breeders and shelters, had a significantly higher risk of being infected with G. duodenalis. Based on phylogenetic analysis of the partial coding sequences for β-giardin, glutamate dehydrogenase, and triosephosphate isomerase, the parasites found in three dog isolates were typed as G. duodenalis assemblage C, 11 were typed as D, and four were typed as C or D, depending on the targeted genes. The risk to public health seems to be reduced, as no genotypes with zoonotic potential have been detected. Nevertheless, better health management towards a minimisation of the environmental faecal pollution, as well as an increase in the awareness of health professionals, dog owners, dog breeders and caregivers regarding the risks posed by this protozoan to the health of animals and humans, are recommended. Graphic abstract
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Affiliation(s)
- André Pereira
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (NOVA), Lisboa, Portugal.,Medical Parasitology Unit, IHMT-NOVA, Lisboa, Portugal
| | - Joana Teixeira
- Faculdade de Medicina Veterinária, CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal, Universidade de Lisboa, Lisboa, Portugal
| | - Sofia Sousa
- Medical Parasitology Unit, IHMT-NOVA, Lisboa, Portugal.,Faculdade de Medicina Veterinária, Universidade Lusófona de Humanidades e Tecnologias, Lisboa, Portugal
| | - Ricardo Parreira
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (NOVA), Lisboa, Portugal.,Medical Microbiology Unit, IHMT-NOVA, Lisboa, Portugal
| | - Lenea Campino
- Medical Parasitology Unit, IHMT-NOVA, Lisboa, Portugal
| | - José Meireles
- Faculdade de Medicina Veterinária, CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal, Universidade de Lisboa, Lisboa, Portugal
| | - Carla Maia
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (NOVA), Lisboa, Portugal.,Medical Parasitology Unit, IHMT-NOVA, Lisboa, Portugal
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99803
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Morán F, Canales C, Olmos A, Ruiz-García AB. Loquat ( Eriobotrya japonica) is a New Natural Host of Apple Stem Pitting Virus. PLANTS 2020; 9:plants9111560. [PMID: 33202713 PMCID: PMC7696262 DOI: 10.3390/plants9111560] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 01/09/2023]
Abstract
Loquat (Eriobotrya japonica) is a minor but important woody crop cultivated in Asia and Europe. High-throughput sequencing (HTS) analysis of an asymptomatic loquat plant using RNAseq Illumina technology has allowed the detection for the first time of apple stem pitting virus (ASPV), the type species of the genus Foveavirus in the family Betaflexiviridae, infecting this crop. A nearly complete genome of 9303 nts (ASPV-SL61) reconstructed bioinformatically shows the typical genomic structure of this viral species and a highest nucleotide identity (85.9%) with the Chinese ASPV isolate YLX from pear. A close phylogenetic relationship between ASPV-SL61 and ASPV-YLX has been confirmed by the sequence analysis of full-length ASPV genomic sequences available in the databases. In fact, a phylogenetic study based on a partial CP N-terminal sequence previously proposed to be involved in host adaptation has shown that ASPV-SL61 loquat isolate is more closely related to ASPV pear isolates. The presence of ASPV in loquat has been further confirmed by RT-PCR and Sanger sequencing and DAS-ELISA. An incidence of 15% was determined in one of the loquat Spanish growing areas. The sequence analysis of the partial CP sequences amplified by RT-PCR has shown a high level of variability between loquat isolates. To our knowledge, this is the first record of loquat as a natural host of ASPV.
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99804
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Gaafar YZA, Herz K, Hartrick J, Fletcher J, Blouin AG, MacDiarmid R, Ziebell H. Investigating the Pea Virome in Germany-Old Friends and New Players in the Field(s). Front Microbiol 2020; 11:583242. [PMID: 33281777 PMCID: PMC7691430 DOI: 10.3389/fmicb.2020.583242] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/28/2020] [Indexed: 12/21/2022] Open
Abstract
Peas are an important legume for human and animal consumption and are also being used as green manure or intermediate crops to sustain and improve soil condition. Pea production faces constraints from fungal, bacterial, and viral diseases. We investigated the virome of German pea crops over the course of three successive seasons in different regions of pea production to gain an overview of the existing viruses. Pools from 540 plants, randomly selected from symptomatic and asymptomatic peas, and non-crop plants surrounding the pea fields were used for ribosomal RNA-depleted total RNA extraction followed by high-throughput sequencing (HTS) and RT-PCR confirmation. Thirty-five different viruses were detected in addition to nine associated nucleic acids. From these viruses, 25 are classified as either new viruses, novel strains or viruses that have not been reported previously from Germany. Pea enation mosaic virus 1 and 2 were the most prevalent viruses detected in the pea crops, followed by pea necrotic yellow dwarf virus (PNYDV) and turnip yellows virus which was also found also in the surrounding non-legume weeds. Moreover, a new emaravirus was detected in symptomatic peas in one region for two successive seasons. Most of the identified viruses are known to be aphid transmissible. The results revealed a high virodiversity in the German pea fields that poses new challenges to diagnosticians, researchers, risk assessors and policy makers, as the impact of the new findings are currently unknown.
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Affiliation(s)
- Yahya Z A Gaafar
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Kerstin Herz
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Jonas Hartrick
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - John Fletcher
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Arnaud G Blouin
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand.,School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Robin MacDiarmid
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand.,School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Heiko Ziebell
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
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99805
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Springstein BL, Weissenbach J, Koch R, Stücker F, Stucken K. The role of the cytoskeletal proteins MreB and FtsZ in multicellular cyanobacteria. FEBS Open Bio 2020; 10:2510-2531. [PMID: 33112491 PMCID: PMC7714070 DOI: 10.1002/2211-5463.13016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/17/2020] [Accepted: 10/26/2020] [Indexed: 01/28/2023] Open
Abstract
Multiseriate and true‐branching cyanobacteria are at the peak of prokaryotic morphological complexity. However, little is known about the mechanisms governing multiplanar cell division and morphogenesis. Here, we study the function of the prokaryotic cytoskeletal proteins, MreB and FtsZ in Fischerella muscicola PCC 7414 and Chlorogloeopsis fritschii PCC 6912. Vancomycin and HADA labeling revealed a mixed apical, septal, and lateral trichome growth mode in F. muscicola, whereas C. fritschii exhibits septal growth. In all morphotypes from both species, MreB forms either linear filaments or filamentous strings and can interact with FtsZ. Furthermore, multiplanar cell division in F. muscicola likely depends on FtsZ dosage. Our results lay the groundwork for future studies on cytoskeletal proteins in morphologically complex cyanobacteria.
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Affiliation(s)
| | - Julia Weissenbach
- Institute of General Microbiology, Christian-Albrechts University of Kiel, Germany
| | - Robin Koch
- Institute of General Microbiology, Christian-Albrechts University of Kiel, Germany
| | - Fenna Stücker
- Institute of General Microbiology, Christian-Albrechts University of Kiel, Germany
| | - Karina Stucken
- Institute of General Microbiology, Christian-Albrechts University of Kiel, Germany
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99806
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An MF, Wang MY, Shen C, Sun ZR, Zhao YL, Wang XJ, Sheng J. Isoorientin exerts a urate-lowering effect through inhibition of xanthine oxidase and regulation of the TLR4-NLRP3 inflammasome signaling pathway. J Nat Med 2020; 75:129-141. [PMID: 33188510 DOI: 10.1007/s11418-020-01464-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022]
Abstract
Isoorientin (ISO), a natural flavonoid compound, has been identified in several plants and its biological activity is determined and the study on lowering uric acid has not been reported. In view of the current status of treatment of hyperuricemia, we evaluated the hypouricemic effects of ISO in vivo and in vitro, and explored the underlying mechanisms. Yeast extract-induced hyperuricemia animal model as well as hypoxanthine and xanthine oxidase (XOD) co-induced high uric acid L-O2 cell model and enzymatic experiments in vitro were selected. The XOD activity and uric acid (UA) level were inhibited after the treatment of ISO in vitro and in vivo. Furthermore, serum creatinine (CRE) and blood urea nitrogen (BUN) levels were also significantly reduced and liver damage was recovered in pathological histology after the ISO administration in hyperuricemia animal model. The results of mechanism illustrated that protein expressions such as XOD, toll-like receptor 4 (TLR4), cathepsin B (CTSB), NLRP3, and its downstream caspase-1 as well as interleukin-18 (IL-18) were markedly downregulated by ISO intervention in vitro and in vivo. Our results suggest that ISO exerts a urate-lowering effect through inhibiting XOD activity and regulating TLR4-NLRP3 inflammasome signal pathway, thus representing a promising candidate therapeutic agent for hyperuricemia. Both animal models and in vitro experiments suggested that ISO may effectively lower uric acid produce. The mechanism might be the inhibition of XOD activity and NLRP3 inflammasome of upregulation.
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Affiliation(s)
- Meng-Fei An
- Key Laboratory of Pu-erh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming, 650224, People's Republic of China
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650224, People's Republic of China
| | - Ming-Yue Wang
- Key Laboratory of Pu-erh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming, 650224, People's Republic of China
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650224, People's Republic of China
| | - Chang Shen
- Key Laboratory of Pu-erh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming, 650224, People's Republic of China
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650224, People's Republic of China
| | - Ze-Rui Sun
- Key Laboratory of Pu-erh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming, 650224, People's Republic of China
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650224, People's Republic of China
| | - Yun-Li Zhao
- Key Laboratory of Pu-erh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming, 650224, People's Republic of China.
- College of Science, Yunnan Agricultural University, Kunming, 650224, People's Republic of China.
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, People's Republic of China.
| | - Xuan-Jun Wang
- Key Laboratory of Pu-erh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming, 650224, People's Republic of China.
- College of Science, Yunnan Agricultural University, Kunming, 650224, People's Republic of China.
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming, 650224, People's Republic of China.
| | - Jun Sheng
- Key Laboratory of Pu-erh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming, 650224, People's Republic of China.
- College of Science, Yunnan Agricultural University, Kunming, 650224, People's Republic of China.
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming, 650224, People's Republic of China.
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99807
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De Santis V, Delmastro GB, Vanetti I, Britton JR, Zaccara S. Species composition of introduced and natural minnow populations of the Phoxinus cryptic complex in the westernmost part of the Po River Basin (north Italy). Biol Invasions 2020. [DOI: 10.1007/s10530-020-02406-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractInvasive alien species are a major driver of biodiversity loss, with their impacts potentially more intense when complexes of cryptic species are involved. In freshwaters, the anthropogenic manipulation of fish communities has resulted in altered fish communities, and in Europe has increased the complexity of Phoxinus species assemblages. Here, we investigated the Phoxinus communities of the westernmost part of the Po river basin, where adjacent freshwater ecosystems (Alpine high-altitude lakes and lowland streams) are representative of different management strategies (i.e. manipulated fish communities via stocking in Alpine lakes vs. natural populations in streams). We tested the genetic composition of the cryptic Phoxinus populations inhabiting these waters, as the species are morphologically indistinct. Sequences of the mitochondrial cytochrome oxidase I (COI) were obtained from 239 specimens, with the results indicating that 17 Alpine high-altitude lakes are now populated by a complex of Phoxinus species, comprising P. septimaniae (native to the Mediterranean area of France), P. csikii (native to the Central Balkans) and P. lumaireul (native to the North Adriatic Sea basins). Their introduction resulted from their use as angling live baits. Minnow populations in lowland streams were primarily comprised of native P. lumaireul, with only a single P. csikii specimen detected. While nuclear sequences of the recombination activating gene 1 (RAG1) marker were not useful for tracking the presence of alien alleles in these stream populations, the COI data emphasised the importance of using molecular tools to investigate cryptic species complexes that have been modified by anthropogenic activities.
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99808
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Comparative Genomics Reveals Novel Target Genes towards Specific Control of Plant-Parasitic Nematodes. Genes (Basel) 2020; 11:genes11111347. [PMID: 33202889 PMCID: PMC7696266 DOI: 10.3390/genes11111347] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 11/17/2022] Open
Abstract
Plant-parasitic nematodes cause extensive annual yield losses to worldwide agricultural production. Most cultivated plants have no known resistance against nematodes and the few bearing a resistance gene can be overcome by certain species. Chemical methods that have been deployed to control nematodes have largely been banned from use due to their poor specificity and high toxicity. Hence, there is an urgent need for the development of cleaner and more specific control methods. Recent advances in nematode genomics, including in phytoparasitic species, provide an unprecedented opportunity to identify genes and functions specific to these pests. Using phylogenomics, we compared 61 nematode genomes, including 16 for plant-parasitic species and identified more than 24,000 protein families specific to these parasites. In the genome of Meloidogyne incognita, one of the most devastating plant parasites, we found ca. 10,000 proteins with orthologs restricted only to phytoparasitic species and no further homology in protein databases. Among these phytoparasite-specific proteins, ca. 1000 shared the same properties as known secreted effectors involved in essential parasitic functions. Of these, 68 were novel and showed strong expression during the endophytic phase of the nematode life cycle, based on both RNA-seq and RT-qPCR analyses. Besides effector candidates, transcription-related and neuro-perception functions were enriched in phytoparasite-specific proteins, revealing interesting targets for nematode control methods. This phylogenomics analysis constitutes a unique resource for the further understanding of the genetic basis of nematode adaptation to phytoparasitism and for the development of more efficient control methods.
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99809
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Ouarti B, Mediannikov O, Righi S, Benakhla A, Raoult D, Parola P. Molecular detection of microorganisms in lice collected from farm animals in Northeastern Algeria. Comp Immunol Microbiol Infect Dis 2020; 74:101569. [PMID: 33181468 DOI: 10.1016/j.cimid.2020.101569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 10/17/2020] [Accepted: 10/20/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Basma Ouarti
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France.
| | - Oleg Mediannikov
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France.
| | - Souad Righi
- Université Chadli Bendjdid, Département des sciences Vétérinaire, El Tarf, 36000, Algeria.
| | - Ahmed Benakhla
- Université Chadli Bendjdid, Département des sciences Vétérinaire, El Tarf, 36000, Algeria.
| | - Didier Raoult
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.
| | - Philippe Parola
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France.
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99810
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Chakrabarti S, Medda PK, Kanturski M. Conifer-feeding aphids (Insecta: Hemiptera: Aphididae) of India, Bhutan and Nepal with descriptions of three new species of the genus Cinara. THE EUROPEAN ZOOLOGICAL JOURNAL 2020. [DOI: 10.1080/24750263.2020.1831086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- S. Chakrabarti
- Department of Zoology, Vidyasagar College, Kolkata, India
| | - P. K. Medda
- Department of Zoology, RKM VC College, Kolkata, India
| | - M. Kanturski
- Zoology Research Team, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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99811
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Mustelin T, Ukadike KC. How Retroviruses and Retrotransposons in Our Genome May Contribute to Autoimmunity in Rheumatological Conditions. Front Immunol 2020; 11:593891. [PMID: 33281822 PMCID: PMC7691656 DOI: 10.3389/fimmu.2020.593891] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/19/2020] [Indexed: 12/14/2022] Open
Abstract
More than 200 human disorders include various manifestations of autoimmunity. The molecular events that lead to these diseases are still incompletely understood and their causes remain largely unknown. Numerous potential triggers of autoimmunity have been proposed over the years, but very few of them have been conclusively confirmed or firmly refuted. Viruses have topped the lists of suspects for decades, and it seems that many viruses, including those of the Herpesviridae family, indeed can influence disease initiation and/or promote exacerbations by a number of mechanisms that include prolonged anti-viral immunity, immune subverting factors, and mechanisms, and perhaps “molecular mimicry”. However, no specific virus has yet been established as being truly causative. Here, we discuss a different, but perhaps mechanistically related possibility, namely that retrotransposons or retroviruses that infected us in the past and left a lasting copy of themselves in our genome still can provoke an escalating immune response that leads to autoimmune disease. Many of these loci still encode for retroviral proteins that have retained some, or all, of their original functions. Importantly, these endogenous proviruses cannot be eliminated by the immune system the way it can eliminate exogenous viruses. Hence, if not properly controlled, they may drive a frustrated and escalating chronic, or episodic, immune response to the point of a frank autoimmune disorder. Here, we discuss the evidence and the proposed mechanisms, and assess the therapeutic options that emerge from the current understanding of this field.
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Affiliation(s)
- Tomas Mustelin
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Kennedy C Ukadike
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, United States
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99812
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Fan C, Tie D, Sun Y, Jiang J, Huang H, Gong Y, Zhao C. Characterization and Genomic Analysis of Escherichia coli O157:H7 Bacteriophage FEC14, a New Member of Genus Kuttervirus. Curr Microbiol 2020; 78:159-166. [PMID: 33185717 DOI: 10.1007/s00284-020-02283-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 11/02/2020] [Indexed: 12/20/2022]
Abstract
Escherichia coli O157:H7 is an important foodborne pathogen that has become a major worldwide factor affecting the public safety of food. Bacteriophage has gradually attracted attention because of its ability to kill specific pathogens. In this study, a lytic phage of E. coli O157:H7, named FEC14, was isolated from hospital sewage. Transmission electron microscopy analysis showed that phage FEC14 had an isometric head 80 ± 5 nm in diameter and a contractile tail whose terminal spikes present an umbrella-like structure. Phage FEC14 revealed 158,639 bp double-stranded DNA, with the G+C content of 44.6%, 209 ORFs and four tRNAs. Genome DNA of FEC14 could not be digested by some endonucleases. Many of the features of phage FEC14 are very similar to those of the newly classified genus "Kuttervirus", including morphology, genome size and organization, etc. Phage FEC14 is proposed to be a new isolate of genus "Kuttervirus" within the family Ackermannviridae, moreover, the endonuclease resistance of phage FEC14, has priority over other genera of bacteriophages for its use in biocontrol of foodborne pathogens.
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Affiliation(s)
- Congcong Fan
- Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, People's Republic of China
| | - Dandan Tie
- Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, People's Republic of China
| | - Yanbo Sun
- Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, People's Republic of China
| | - Jie Jiang
- Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, People's Republic of China
| | - Honglan Huang
- Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, People's Republic of China
| | - Yunwei Gong
- Changchun Center for Disease Control and Prevention Department of Microbiology, Changchun, Jilin, People's Republic of China
| | - Chunyan Zhao
- Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, People's Republic of China.
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99813
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Plant Growth-Promoting Rhizobacteria Isolated from Degraded Habitat Enhance Drought Tolerance of Acacia ( Acacia abyssinica Hochst. ex Benth.) Seedlings. Int J Microbiol 2020; 2020:8897998. [PMID: 33178283 PMCID: PMC7646561 DOI: 10.1155/2020/8897998] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/01/2020] [Indexed: 11/25/2022] Open
Abstract
Drought stress (DS) is the most impacting global phenomenon affecting the ecological balance of a particular habitat. The search for potential plant growth-promoting rhizobacteria (PGPR) capable of enhancing plant tolerance to drought stress is needed. Thus, this study was initiated to evaluate the effect of inoculating Acacia abyssinica seedlings with PGPR isolated from rhizosphere soil of Ethiopia to enhance DS tolerance. The strains were selected based on in vitro assays associated with tolerance to drought and other beneficial traits such as salinity, acidity, temperature, heavy metal tolerances, biofilm formation, and exopolysaccharide (EPS) production. The strains with the best DS tolerance ability were selected for the greenhouse trials with acacia plants. The results indicate that out of 73 strains, 10 (14%) were completely tolerant to 40% polyethylene glycol. Moreover, 37% of the strains were strong biofilm producers, while 66 (90.41%) were EPS producers with a better production in the medium containing sucrose at 28 ± 2°C and pH 7 ± 0.2. Strains PS-16 and RS-79 showed tolerance to 11% NaCl. All the strains were able to grow in wider ranges of pH (4–10) and temperature (15–45°C) and had high tolerance to heavy metals. The inoculated bacterial strains significantly (p ≤ 0.05) increased root and shoot length and dry biomass of acacia plants. One of the strains identified as P. fluorescens strain FB-49 was outstanding in enhancing DS tolerance compared to the single inoculants and comparable to consortia. Stress-tolerant PGPR could be used to enhance acacia DS tolerance after testing other phytobeneficial traits.
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99814
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Brown BRP, Nunez JCB, Rand DM. Characterizing the cirri and gut microbiomes of the intertidal barnacle Semibalanus balanoides. Anim Microbiome 2020; 2:41. [PMID: 33499976 PMCID: PMC7807441 DOI: 10.1186/s42523-020-00058-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 10/16/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Natural populations inhabiting the rocky intertidal experience multiple ecological stressors and provide an opportunity to investigate how environmental differences influence microbiomes over small geographical scales. However, very few microbiome studies focus on animals that inhabit the intertidal. In this study, we investigate the microbiome of the intertidal barnacle Semibalanus balanoides. We first describe the microbiome of two body tissues: the feeding appendages, or cirri, and the gut. Next, we examine whether there are differences between the microbiome of each body tissue of barnacles collected from the thermally extreme microhabitats of the rocky shores' upper and lower tidal zones. RESULTS Overall, the microbiome of S. balanoides consisted of 18 phyla from 408 genera. Our results showed that although cirri and gut microbiomes shared a portion of their amplicon sequence variants (ASVs), the microbiome of each body tissue was distinct. Over 80% of the ASVs found in the cirri were also found in the gut, and 44% of the ASVs found in the gut were also found in the cirri. Notably, the gut microbiome was not a subset of the cirri microbiome. Additionally, we identified that the cirri microbiome was responsive to microhabitat differences. CONCLUSION Results from this study indicate that S. balanoides maintains distinct microbiomes in its cirri and gut tissues, and that the gut microbiome is more stable than the cirri microbiome between the extremes of the intertidal.
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Affiliation(s)
- Bianca R P Brown
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St., Providence, RI, 02912, USA.
- Institute at Brown for Environment and Society, Brown University, 85 Waterman St., Providence, RI, 02912, USA.
| | - Joaquin C B Nunez
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St., Providence, RI, 02912, USA
- Department of Biology, University of Virginia, 485 McCormick Road, Charlottesville, VA, 22904, USA
| | - David M Rand
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St., Providence, RI, 02912, USA.
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99815
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Kliot A, Johnson RS, MacCoss MJ, Kontsedalov S, Lebedev G, Czosnek H, Heck M, Ghanim M. A proteomic approach reveals possible molecular mechanisms and roles for endosymbiotic bacteria in begomovirus transmission by whiteflies. Gigascience 2020; 9:giaa124. [PMID: 33185242 PMCID: PMC7662926 DOI: 10.1093/gigascience/giaa124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/21/2020] [Accepted: 10/08/2020] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Many plant viruses are vector-borne and depend on arthropods for transmission between host plants. Begomoviruses, the largest, most damaging and emerging group of plant viruses, infect hundreds of plant species, and new virus species of the group are discovered each year. Begomoviruses are transmitted by members of the whitefly Bemisia tabaci species complex in a persistent-circulative manner. Tomato yellow leaf curl virus (TYLCV) is one of the most devastating begomoviruses worldwide and causes major losses in tomato crops, as well as in many agriculturally important plant species. Different B. tabaci populations vary in their virus transmission abilities; however, the causes for these variations are attributed among others to genetic differences among vector populations, as well as to differences in the bacterial symbionts housed within B. tabaci. RESULTS Here, we performed discovery proteomic analyses in 9 whitefly populations from both Middle East Asia Minor I (MEAM1, formerly known as B biotype) and Mediterranean (MED, formerly known as Q biotype) species. We analysed our proteomic results on the basis of the different TYLCV transmission abilities of the various populations included in the study. The results provide the first comprehensive list of candidate insect and bacterial symbiont (mainly Rickettsia) proteins associated with virus transmission. CONCLUSIONS Our data demonstrate that the proteomic signatures of better vector populations differ considerably when compared with less efficient vector populations in the 2 whitefly species tested in this study. While MEAM1 efficient vector populations have a more lenient immune system, the Q efficient vector populations have higher abundance of proteins possibly implicated in virus passage through cells. Both species show a strong link of the facultative symbiont Rickettsia to virus transmission.
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Affiliation(s)
- Adi Kliot
- Department of Entomology, The Volcani Center, HaMacabim Rd., Rishon LeZion, 50250, Israel
- Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
- Genomic Pipelines, Earlham Institute, Colney lane, Norwich, NR7 4UH, UK
| | - Richard S Johnson
- Department of Genome Sciences, University of Washington, Foege Building, 98195-5065 Seattle, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Foege Building, 98195-5065 Seattle, USA
| | - Svetlana Kontsedalov
- Department of Entomology, The Volcani Center, HaMacabim Rd., Rishon LeZion, 50250, Israel
| | - Galina Lebedev
- Department of Entomology, The Volcani Center, HaMacabim Rd., Rishon LeZion, 50250, Israel
| | - Henryk Czosnek
- Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Michelle Heck
- USDA-Agricultural Research Service, Boyce Thompson Institute for Plant Research, Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, USA
| | - Murad Ghanim
- Department of Entomology, The Volcani Center, HaMacabim Rd., Rishon LeZion, 50250, Israel
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99816
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Styles MQ, Nesbitt EA, Hoffmann TD, Queen J, Ortenzi MV, Leak DJ. The heterologous production of terpenes by the thermophile Parageobacillus thermoglucosidasius in a consolidated bioprocess using waste bread. Metab Eng 2020; 65:146-155. [PMID: 33189879 DOI: 10.1016/j.ymben.2020.11.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/26/2020] [Accepted: 11/08/2020] [Indexed: 11/16/2022]
Abstract
Parageobacillus thermoglucosidasius is a genetically tractable thermophile that grows rapidly at elevated temperatures, with a doubling time at 65 °C comparable to the shortest doubling times of Escherichia coli. It is capable of using a wide variety of substrates, including carbohydrate oligomers, and has been developed for the industrial production of ethanol. In this study, P. thermoglucosidasius NCIMB11955 has been engineered to produce the sesquiterpene τ-muurolol by introduction of a heterologous mevalonate pathway constructed using genes from several thermophilic archaea together with a recently characterised thermostable τ-muurolol synthase. P. thermoglucosidasius naturally uses the methylerythritol phosphate pathway for production of the terpene precursor, isopentenyl pyrophosphate, while archaea use a version of the mevalonate pathway. By introducing the orthogonal archaeal pathway it was possible to increase the flux through to sesquiterpene biosynthesis. Construction of such a large metabolic pathway created problems with genetic vector introduction and stability, so recombinant plasmids were introduced by conjugation, and a thermostable serine integrase system was developed for integration of large pathways onto the chromosome. Finally, by making the heterologous pathway maltose-inducible we demonstrate that the new strain is capable of using waste bread directly as an autoinduction carbon source for the production of terpenes in a consolidated bioprocess.
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Affiliation(s)
- Matthew Q Styles
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Edward A Nesbitt
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Timothy D Hoffmann
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Junichi Queen
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Maria V Ortenzi
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - David J Leak
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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99817
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Yoshioka Y, Yamashita H, Suzuki G, Zayasu Y, Tada I, Kanda M, Satoh N, Shoguchi E, Shinzato C. Whole-Genome Transcriptome Analyses of Native Symbionts Reveal Host Coral Genomic Novelties for Establishing Coral-Algae Symbioses. Genome Biol Evol 2020; 13:5981117. [PMID: 33185681 PMCID: PMC7850063 DOI: 10.1093/gbe/evaa240] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2020] [Indexed: 01/14/2023] Open
Abstract
Reef-building corals and photosynthetic, endosymbiotic algae of the family Symbiodiniaceae establish mutualistic relationships that are fundamental to coral biology, enabling coral reefs to support a vast diversity of marine species. Although numerous types of Symbiodiniaceae occur in coral reef environments, Acropora corals select specific types in early life stages. In order to study molecular mechanisms of coral–algal symbioses occurring in nature, we performed whole-genome transcriptomic analyses of Acropora tenuis larvae inoculated with Symbiodinium microadriaticum strains isolated from an Acropora recruit. In order to identify genes specifically involved in symbioses with native symbionts in early life stages, we also investigated transcriptomic responses of Acropora larvae exposed to closely related, nonsymbiotic, and occasionally symbiotic Symbiodinium strains. We found that the number of differentially expressed genes was largest when larvae acquired native symbionts. Repertoires of differentially expressed genes indicated that corals reduced amino acid, sugar, and lipid metabolism, such that metabolic enzymes performing these functions were derived primarily from S. microadriaticum rather than from A. tenuis. Upregulated gene expression of transporters for those metabolites occurred only when coral larvae acquired their natural symbionts, suggesting active utilization of native symbionts by host corals. We also discovered that in Acropora, genes for sugar and amino acid transporters, prosaposin-like, and Notch ligand-like, were upregulated only in response to native symbionts, and included tandemly duplicated genes. Gene duplications in coral genomes may have been essential to establish genomic novelties for coral–algae symbiosis.
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Affiliation(s)
- Yuki Yoshioka
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan.,Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Hiroshi Yamashita
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Okinawa, Japan
| | - Go Suzuki
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Okinawa, Japan
| | - Yuna Zayasu
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Ipputa Tada
- Department of Genetics, SOKENDAI (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
| | - Miyuki Kanda
- DNA Sequencing Section (SQC), Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
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99818
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Zhang L, Li H, Wang S, Li S. The complete mitochondrial genome of Pseudoxenodon stejnegeri (Squamata: Colubridae: Pseudoxenodontinae) and its phylogeny. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3752-3753. [PMID: 33367087 PMCID: PMC7671704 DOI: 10.1080/23802359.2020.1835584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The mitochondrial genome sequence of Pseudoxenodon stejnegeri (Squamata: Colubridae: Pseudoxenodontinae) from Taishun County, Zhejiang Province, China, which is 18,475 bp in length and contains 25 tRNAs (including extra two tRNA-Tyr genes and extra one tRNA-Met gene), two rRNAs, 13 protein-coding genes and two identical control regions. The overall AT content of the mitogenome is 59.6% (A = 32.6%, T = 27%, C = 27%, G = 13.4%). In BI and ML phylogenetic analyses, the monophyly of the family Colubridae was well supported and P. stejnegeri was a basal clade of Colubridae.
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Affiliation(s)
- Liyue Zhang
- The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Hui Li
- College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Shengqin Wang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Shuran Li
- College of Life and Environmental Science, Wenzhou University, Wenzhou, China
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99819
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Gómez LM, Teixeira-Silva NS, Caserta R, Takita MA, Marques MOM, de Souza AA. Overexpression of Citrus reticulata SAMT in Nicotiana tabacum increases MeSA volatilization and decreases Xylella fastidiosa symptoms. PLANTA 2020; 252:103. [PMID: 33185761 DOI: 10.1007/s00425-020-03511-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/03/2020] [Indexed: 06/11/2023]
Abstract
MAIN CONCLUSION Nicotiana tabacum overexpressing CrSAMT from Citrus reticulata increased production of MeSA, which works as an airborne signal in neighboring wild-type plants, inducing PR1 and increasing resistance to the pathogen Xylella fastidiosa. Xylella fastidiosa is one of the major threats to plant health worldwide, affecting yield in many crops. Despite many efforts, the development of highly productive resistant varieties has been challenging. In studying host plant resistance, the S-adenosyl-L-methionine: salicylic acid carboxyl methyltransferase gene (SAMT) from Citrus reticulata, a X. fastidiosa resistant species, was upregulated in response to pathogen infection. SAMT is involved with the catalysis and production of methyl salicylate (MeSA), an airborne signal responsible for triggering systemic acquired resistance. Here we used tobacco as a model system and generated transgenic plants overexpressing C. reticulata SAMT (CrSAMT). We performed an in silico structural characterization of CrSAMT and investigated its biotechnological potential in modulating the immune system in transgenic plants. The increase of MeSA production in transgenic lines was confirmed by gas chromatography (GC-MS). The transgenic lines showed upregulation of PR1, and their incubation with neighboring wild-type plants activated PR1 expression, indicating that MeSA worked as an airborne signal. In addition, transgenic plants showed significantly fewer symptoms when challenged with X. fastidiosa. Altogether, these data suggest that CrSAMT plays a role in host defense response and can be used in biotechnology approaches to confer resistance against X. fastidiosa.
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Affiliation(s)
- Laura M Gómez
- Centro de Citricultura Sylvio Moreira/IAC, Rodovia Anhanguera, km 158, PO Box 04, Cordeirópolis, SP, 13490-970, Brazil
- Entomology and Plant Pathology Department, Auburn University, Auburn, AL, USA
| | - Natália S Teixeira-Silva
- Centro de Citricultura Sylvio Moreira/IAC, Rodovia Anhanguera, km 158, PO Box 04, Cordeirópolis, SP, 13490-970, Brazil
| | - Raquel Caserta
- Centro de Citricultura Sylvio Moreira/IAC, Rodovia Anhanguera, km 158, PO Box 04, Cordeirópolis, SP, 13490-970, Brazil
| | - Marco A Takita
- Centro de Citricultura Sylvio Moreira/IAC, Rodovia Anhanguera, km 158, PO Box 04, Cordeirópolis, SP, 13490-970, Brazil
| | - Márcia O M Marques
- Departamento de Fitoquímica/IAC, Avenida Doutor Theodureto Almeida Camargo 1500, Campinas, SP, 13012970, Brazil
| | - Alessandra A de Souza
- Centro de Citricultura Sylvio Moreira/IAC, Rodovia Anhanguera, km 158, PO Box 04, Cordeirópolis, SP, 13490-970, Brazil.
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99820
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Kim MS, Choi BS, Ogello EO, Kim HJ, Hagiwara A, Lee JS. Complete mitochondrial genome of the freshwater monogonont rotifer Brachionus angularis (Rotifera, Brachionidae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3754-3755. [PMID: 33367088 PMCID: PMC7671714 DOI: 10.1080/23802359.2020.1835578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The two complete mitochondrial genomes were sequenced from the freshwater monogonont rotifer Brachionus angularis. The mitochondrial genome sequences were 10,764 bp (mitochondrial DNA I) and 12,238 bp (mitochondrial DNA II) in size, respectively. The gene structure and its orientation of 12 protein-coding genes (PCGs) of complete mitochondrial genomes of B. angularis was identical to those shown in other marine rotifers and the freshwater rotifer Brachionus rubens, but was different from the freshwater rotifer Brachionus calyciflorus. Of 12 PCGs, one gene (ND5) had incomplete stop codon. Furthermore, the start codon for CO1, ND4L, ND5, and CO2 was GTG, while the start codon for ND3 and other PCGs was ATA and ATG, respectively. The base composition of 12 PCGs in B. angularis mitogenome showed 20.4% for A, 47.3% for T, 17.5% for C, and 14.8% for G, respectively. The mitochondrial genome A + T base composition (67.7%) of 12 PCGs was higher than G + C (32.3%), while the complete mitochondrial genome A + T base composition (66.3%) was higher than G + C (33.7%).
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Affiliation(s)
- Min-Sub Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon, South Korea
| | | | | | - Hee-Jin Kim
- Institute of Integrated Science and Technology, Nagasaki University, Nagasaki, Japan
| | - Atsushi Hagiwara
- Institute of Integrated Science and Technology, Nagasaki University, Nagasaki, Japan.,Organization for Marine Science and Technology, Nagasaki University, Nagasaki, Japan
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon, South Korea
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99821
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Ciubotariu II, Jones CM, Kobayashi T, Bobanga T, Muleba M, Pringle JC, Stevenson JC, Carpi G, Norris DE. Genetic Diversity of Anopheles coustani (Diptera: Culicidae) in Malaria Transmission Foci in Southern and Central Africa. JOURNAL OF MEDICAL ENTOMOLOGY 2020; 57:1782-1792. [PMID: 32614047 PMCID: PMC7899271 DOI: 10.1093/jme/tjaa132] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Indexed: 05/04/2023]
Abstract
Despite ongoing malaria control efforts implemented throughout sub-Saharan Africa, malaria remains an enormous public health concern. Current interventions such as indoor residual spraying with insecticides and use of insecticide-treated bed nets are aimed at targeting the key malaria vectors that are primarily endophagic and endophilic. Anopheles coustani s.l., an understudied vector of malaria, is a species previously thought to exhibit mostly zoophilic behavior. Like many of these understudied species, An. coustani has greater anthropophilic tendencies than previously appreciated, is often both endophagic and exophagic, and carries Plasmodium falciparum sporozoites. The aim of this study was to explore genetic variation of An. coustani mosquitoes and the potential of this species to contribute to malaria parasite transmission in high transmission settings in Zambia and the Democratic Republic of the Congo (DRC). Morphologically identified An. coustani specimens that were trapped outdoors in these study sites were analyzed by PCR and sequencing for species identification and bloodmeal sources, and malaria parasite infection was determined by ELISA and qPCR. Fifty An. coustani s.s. specimens were confirmed by analysis of mitochondrial DNA cytochrome c oxidase subunit I (COI) and ribosomal internal transcribed spacer region 2 (ITS2). Maximum likelihood phylogenetic analysis of COI and ITS2 sequences revealed two distinct phylogenetic groups within this relatively small regional collection. Our findings indicate that both An. coustani groups have anthropophilic and exophagic habits and come into frequent contact with P. falciparum, suggesting that this potential alternative malaria vector might elude current vector control measures in northern Zambia and southern DRC.
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Affiliation(s)
- Ilinca I Ciubotariu
- The Department of Biological Sciences, Purdue University, West Lafayette, IN
| | - Christine M Jones
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Tamaki Kobayashi
- The Department of Epidemiology, Division of Infectious Disease Epidemiology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Thierry Bobanga
- The Department of Family Medicine, School of Medicine, Université Protestante au Congo, Kinshasa, Democratic Republic of Congo
- The Department of Tropical Medicine, School of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | | | - Julia C Pringle
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Jennifer C Stevenson
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
- Macha Research Trust, Choma, Zambia
| | - Giovanna Carpi
- The Department of Biological Sciences, Purdue University, West Lafayette, IN
| | - Douglas E Norris
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
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99822
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Cassal MC, Fukushima A, Nishi O, Iiyama K, Fiuza LM, Yasunaga-Aoki C. Identification and characterization of three microsporidian genera concurrently infecting a silkworm, Bombyx mori, in Brazil. J Invertebr Pathol 2020; 177:107502. [PMID: 33197450 DOI: 10.1016/j.jip.2020.107502] [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: 08/04/2020] [Revised: 11/05/2020] [Accepted: 11/07/2020] [Indexed: 11/28/2022]
Abstract
Microsporidia are important entomopathogens known for infecting insects such as the silkworm (Bombyx mori) thus impairing global silk production. This study aimed to identify and characterize the microsporidia isolated from a diseased larva of silkworm, collected from a sericulture farm in southern Brazil. Identification was performed by phylogenetic analysis of the nucleotide sequences of the SSU rRNA genes. Characterization was performed by analyzing spore sizes, tissue tropism, internal and external symptoms, and pathogenicity against B. mori. Microsporidia belonging to three different genera were identified, namely, Endoreticulatus, Nosema and Tubulinosema. After inoculation of the mixed spores of the microsporidian isolates into B. mori larvae, a high prevalence of Tubulinosema spp. was observed. This isolate showed high prevalence on the silk glands and a late mortality, initially of around 10% until the 20th day post-inoculation but reaching 91.5% upon pupation. Therefore, we demonstrated that Tubulinosema spp. causes chronic infection with slow pathogenicity. We identified for the first time three different microsporidians concurrently infecting B. mori in Brazil. Tubulinosema is of particular interest because of its potential threat to silk production; it affects the formation of silk glands in B. mori while not presenting distinguishable external symptoms or causing the immediate death of these insects. Further studies focusing on this species, mainly regarding its life cycle within the host and the sublethal effects of surviving individuals, demonstrate the importance of describing it as a new species and improving the characterization of the disease in order to prevent its spread.
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Affiliation(s)
- Maximiano Corrêa Cassal
- Laboratory of Insect Pathology and Microbial Control, Institute of Biological Control, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, 819-0395 Fukuoka, Japan.
| | - Airi Fukushima
- Laboratory of Insect Pathology and Microbial Control, Institute of Biological Control, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, 819-0395 Fukuoka, Japan.
| | - Oumi Nishi
- Laboratory of Insect Pathology and Microbial Control, Institute of Biological Control, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, 819-0395 Fukuoka, Japan.
| | - Kazuhiro Iiyama
- Laboratory of Plant Pathology, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, 819-0395 Fukuoka, Japan.
| | - Lidia Mariana Fiuza
- CABIO - Control Agro Bio Agricultural Research and Defence Ltd., 90670-100 Porto Alegre, RS, Brazil.
| | - Chisa Yasunaga-Aoki
- Laboratory of Insect Pathology and Microbial Control, Institute of Biological Control, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, 819-0395 Fukuoka, Japan.
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99823
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Lee YG, Lee JY, Kim J, Kim YJ. Insertion variants missing in the human reference genome are widespread among human populations. BMC Biol 2020; 18:167. [PMID: 33187521 PMCID: PMC7666470 DOI: 10.1186/s12915-020-00894-1] [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] [Received: 05/13/2020] [Accepted: 10/09/2020] [Indexed: 01/07/2023] Open
Abstract
Background Structural variants comprise diverse genomic arrangements including deletions, insertions, inversions, and translocations, which can generally be detected in humans through sequence comparison to the reference genome. Among structural variants, insertions are the least frequently identified variants, mainly due to ascertainment bias in the reference genome, lack of previous sequence knowledge, and low complexity of typical insertion sequences. Though recent developments in long-read sequencing deliver promise in annotating individual non-reference insertions, population-level catalogues on non-reference insertion variants have not been identified and the possible functional roles of these hidden variants remain elusive. Results To detect non-reference insertion variants, we developed a pipeline, InserTag, which generates non-reference contigs by local de novo assembly and then infers the full-sequence of insertion variants by tracing contigs from non-human primates and other human genome assemblies. Application of the pipeline to data from 2535 individuals of the 1000 Genomes Project helped identify 1696 non-reference insertion variants and re-classify the variants as retention of ancestral sequences or novel sequence insertions based on the ancestral state. Genotyping of the variants showed that individuals had, on average, 0.92-Mbp sequences missing from the reference genome, 92% of the variants were common (allele frequency > 5%) among human populations, and more than half of the variants were major alleles. Among human populations, African populations were the most divergent and had the most non-reference sequences, which was attributed to the greater prevalence of high-frequency insertion variants. The subsets of insertion variants were in high linkage disequilibrium with phenotype-associated SNPs and showed signals of recent continent-specific selection. Conclusions Non-reference insertion variants represent an important type of genetic variation in the human population, and our developed pipeline, InserTag, provides the frameworks for the detection and genotyping of non-reference sequences missing from human populations. Supplementary information Supplementary information accompanies this paper at 10.1186/s12915-020-00894-1.
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Affiliation(s)
- Young-Gun Lee
- Department of Integrated Omics for Biomedical Science, WCU Graduate School, Yonsei University, Seoul, Republic of Korea
| | - Jin-Young Lee
- Department of Biochemistry, College of Life Science and Technology, Yonsei University, Seoul, Republic of Korea
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Young-Joon Kim
- Department of Integrated Omics for Biomedical Science, WCU Graduate School, Yonsei University, Seoul, Republic of Korea. .,Department of Biochemistry, College of Life Science and Technology, Yonsei University, Seoul, Republic of Korea.
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99824
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Brachiocephalic Muscular Arrangements in Cavioid Rodents (Caviomorpha): a Functional, Anatomical, and Evolutionary Study. J MAMM EVOL 2020. [DOI: 10.1007/s10914-020-09529-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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99825
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Choi SC, Kim S. A chloroplast genome of Forsythia saxatilis (Nakai) Nakai, an endemic species in Korea. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3743-3745. [PMID: 33367083 PMCID: PMC7671593 DOI: 10.1080/23802359.2020.1834889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Forsythia saxatilis (Nakai) Nakai is an endemic species in Korea. We present the second complete chloroplast genome sequence of F. saxatilis showing that the chloroplast genome is 156,376 bp in length containing four subregions: a large single-copy (LSC) region of 87,097 bp, a small single-copy (SSC) region of 17,859 bp, and a pair of inverted repeat regions (IRs) of 25,710 bp. The genome contains 131 genes including 88 protein-coding genes, 35 tRNAs, and eight rRNAs. We found 40 base differences in 17 sites between our chloroplast genome and the previously reported chloroplast genome sequences of F. saxatilis. All of the differences were found in a region of 832 bp in the LSC region except for one site, which indicated potential sequencing errors in building the previously reported genome because of little substitutions in the homologous region of the other Forsythia species and even of Abeliophyllum distichum, a sister to Forsythia. The new chloroplast genomes of F. saxatilis and those of F. x intermedia and F. viridissima are identical, which suggests that F. saxatilis is maternally closely related to the other two species.
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Affiliation(s)
- Sang Chul Choi
- Department of Biotechnology, Sungshin University, Seoul, Korea
| | - Sangtae Kim
- Department of Biotechnology, Sungshin University, Seoul, Korea
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99826
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In silico studies on structural, functional, and evolutionary analysis of bacterial chromate reductase family responsible for high chromate bioremediation efficiency. SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-020-03830-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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99827
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Xie C, Bekpen C, Künzel S, Keshavarz M, Krebs-Wheaton R, Skrabar N, Ullrich KK, Zhang W, Tautz D. Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines. PLoS Comput Biol 2020; 16:e1008354. [PMID: 33180766 PMCID: PMC7685438 DOI: 10.1371/journal.pcbi.1008354] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 11/24/2020] [Accepted: 09/20/2020] [Indexed: 12/26/2022] Open
Abstract
Systematic knockout studies in mice have shown that a large fraction of the gene replacements show no lethal or other overt phenotypes. This has led to the development of more refined analysis schemes, including physiological, behavioral, developmental and cytological tests. However, transcriptomic analyses have not yet been systematically evaluated for non-lethal knockouts. We conducted a power analysis to determine the experimental conditions under which even small changes in transcript levels can be reliably traced. We have applied this to two gene disruption lines of genes for which no function was known so far. Dedicated phenotyping tests informed by the tissues and stages of highest expression of the two genes show small effects on the tested phenotypes. For the transcriptome analysis of these stages and tissues, we used a prior power analysis to determine the number of biological replicates and the sequencing depth. We find that under these conditions, the knockouts have a significant impact on the transcriptional networks, with thousands of genes showing small transcriptional changes. GO analysis suggests that A930004D18Rik is involved in developmental processes through contributing to protein complexes, and A830005F24Rik in extracellular matrix functions. Subsampling analysis of the data reveals that the increase in the number of biological replicates was more important that increasing the sequencing depth to arrive at these results. Hence, our proof-of-principle experiment suggests that transcriptomic analysis is indeed an option to study gene functions of genes with weak or no traceable phenotypic effects and it provides the boundary conditions under which this is possible. Knockout mice benefit the understanding of gene functions in mammals. However, it has proven difficult for many genes to identify clear phenotypes, related due to lack of sufficient assays. As Lewis Wolpert put it in a famous quote “But did you take them to the opera?”, thus metaphorically alluding to the need to extend phenotyping efforts. This insight led to the establishment of phenotyping pipelines that are nowadays routinely used to characterize knock-out lines. However, transcriptomic approaches based on RNA-Seq have been much less explored for such deep-level studies. We conducted here both, a theoretical power analysis and practical RNA-Seq experiments on two knockout lines with small phenotypic effects to investigate the parameters including sample size, sequencing depth, fold change, and dispersion. Our dedicated RNA-Seq studies discovered thousands of genes with small transcriptional changes and enriched in specific functions in both knockout lines. We find that it is more important to increase the number of samples than to increase the sequencing depth. Our work shows that a deep RNA-Seq study on knockouts is powerful for understanding gene functions in cases of weak phenotypic effects, and provides a guideline for the experimental design of such studies.
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Affiliation(s)
- Chen Xie
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- * E-mail:
| | - Cemalettin Bekpen
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Sven Künzel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Maryam Keshavarz
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Rebecca Krebs-Wheaton
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Neva Skrabar
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Kristian K. Ullrich
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Wenyu Zhang
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Diethard Tautz
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
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99828
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Doherty SJ, Barbato RA, Grandy AS, Thomas WK, Monteux S, Dorrepaal E, Johansson M, Ernakovich JG. The Transition From Stochastic to Deterministic Bacterial Community Assembly During Permafrost Thaw Succession. Front Microbiol 2020; 11:596589. [PMID: 33281795 PMCID: PMC7691490 DOI: 10.3389/fmicb.2020.596589] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/27/2020] [Indexed: 01/04/2023] Open
Abstract
The Northern high latitudes are warming twice as fast as the global average, and permafrost has become vulnerable to thaw. Changes to the environment during thaw leads to shifts in microbial communities and their associated functions, such as greenhouse gas emissions. Understanding the ecological processes that structure the identity and abundance (i.e., assembly) of pre- and post-thaw communities may improve predictions of the functional outcomes of permafrost thaw. We characterized microbial community assembly during permafrost thaw using in situ observations and a laboratory incubation of soils from the Storflaket Mire in Abisko, Sweden, where permafrost thaw has occurred over the past decade. In situ observations indicated that bacterial community assembly was driven by randomness (i.e., stochastic processes) immediately after thaw with drift and dispersal limitation being the dominant processes. As post-thaw succession progressed, environmentally driven (i.e., deterministic) processes became increasingly important in structuring microbial communities where homogenizing selection was the only process structuring upper active layer soils. Furthermore, laboratory-induced thaw reflected assembly dynamics immediately after thaw indicated by an increase in drift, but did not capture the long-term effects of permafrost thaw on microbial community dynamics. Our results did not reflect a link between assembly dynamics and carbon emissions, likely because respiration is the product of many processes in microbial communities. Identification of dominant microbial community assembly processes has the potential to improve our understanding of the ecological impact of permafrost thaw and the permafrost-climate feedback.
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Affiliation(s)
- Stacey Jarvis Doherty
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
- Cold Regions Research and Engineering Laboratory, Engineer Research Development Center, United States Army Corps of Engineers, Hanover, NH, United States
| | - Robyn A. Barbato
- Cold Regions Research and Engineering Laboratory, Engineer Research Development Center, United States Army Corps of Engineers, Hanover, NH, United States
| | - A. Stuart Grandy
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, United States
| | - W. Kelley Thomas
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Sylvain Monteux
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ellen Dorrepaal
- Climate Impacts Research Centre, Department of Ecology and Environmental Sciences, Umeå University, Abisko, Sweden
| | - Margareta Johansson
- Department of Physical Geography and Ecosystem Science, Lund University, Lund, Sweden
| | - Jessica G. Ernakovich
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, United States
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99829
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Mutanen M, Huemer P, Autto J, Karsholt O, Kaila L. Monopis jussii, a new species (Lepidoptera, Tineidae) inhabiting nests of the Boreal owl ( Aegolius funereus). Zookeys 2020; 992:157-181. [PMID: 33223909 PMCID: PMC7677292 DOI: 10.3897/zookeys.992.53975] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/26/2020] [Indexed: 11/12/2022] Open
Abstract
Monopis jussii Kaila, Mutanen, Huemer, Karsholt & Autto, sp. nov. (Lepidoptera, Tineidae) is described as a new species. It is closely related to the widespread and common M. laevigella ([Denis & Schiffermüller], 1775), but differs in its distinct COI DNA barcode sequences, four examined nuclear loci as well as details in forewing coloration and pattern. Most reared specimens of M. jussii have emerged from the nest remnants of the Boreal owl (Aegolius funereus (Linnaeus, 1758)), but also nests of the Ural owl (Strix uralensis Pallas, 1771) and the Great tit (Parus major Linnaeus, 1758) have been observed as suitable habitats. Based on the present knowledge, the new species has a boreo-montane distribution as it is recorded only from northern Europe and the Alps. Several extensive rearing experiments from Strix spp. nest remnants from southern Finland did not produce any M. jussii, but thousands of M. laevigella, suggesting that the species is lacking in the area or, more unlikely, that the nest of these owl species do not serve as good habitat for the new species. This unexpected species discovery highlights, once again, the usefulness of DNA barcoding in revealing the cryptic layers of biodiversity. To serve stability we select a neotype for Tinea laevigella [Denis & Schiffermüller], 1775, and discuss the complicated synonymy and nomenclature of this species.
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Affiliation(s)
- Marko Mutanen
- Ecology and Genetics Research Unit, P.O.Box 3000, FI-90014 University of Oulu, Finland University of Oulu Oulu Finland
| | - Peter Huemer
- Tiroler Landesmuseen-Betriebsgesellschaft m.b.H., Innsbruck, Austria Tiroler Landesmuseen-Betriebsgesellschaft m.b.H. Innsbruck Austria
| | - Jonna Autto
- Apajatie 11, FI-96800 Rovaniemi, Finland Unaffiliated Rovaniemi Finland
| | - Ole Karsholt
- Zoological Museum, Natural History Museum of Denmark, Universitetsparken 15, DK-2100 Copenhagen, Denmark Natural History Museum of Denmark Copenhagen Denmark
| | - Lauri Kaila
- Finnish Museum of Natural History, Zoology Unit, P.O.Box 17, FI-00014 University of Helsinki, Finland University of Helsinki Helsinki Finland
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99830
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Zhuang W, Shu X, Zhang M, Wang T, Zhang F, Wang N, Wang Z. Characterization of the complete chloroplast genome of Populus deltoides Zhonglin 2025. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3723-3724. [PMID: 33367076 PMCID: PMC7671709 DOI: 10.1080/23802359.2020.1833773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The complete chloroplast genome of Populus deltoides was characterized by reference-based assembly using whole-genome sequencing data. The total chloroplast genome size of Populus deltoides included a pair of inverted repeat regions (IRs) of 27,649 bp each, a small single-copy region (SSC) of 16,563 bp, and large single-copy region (LSC) of 85,096 bp, which was 156,957 bp in length. A total of 109 genes were predicted from the chloroplast genome, including 83 protein-coding genes, 22 tRNA genes, and four rRNA genes. The GC content of chloroplast genome for Populus deltoides was 36.68%. The phylogenetic analysis based on the reported chloroplast genomes of Populus showed that the chloroplast of the Populus deltoides is most closely related to the Populus fremontii. The complete chloroplast genome of Populus deltoides provides new insights into Populus evolutionary and genomic studies.
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Affiliation(s)
- Weibing Zhuang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, PR China
| | - Xiaochun Shu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, PR China
| | - Ming Zhang
- Jiangsu Forest Resources Inspect Center, Nanjing, PR China
| | - Tao Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, PR China
| | - Fengjiao Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, PR China
| | - Ning Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, PR China
| | - Zhong Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, PR China
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99831
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Vorobieva NV, Makunin AI, Druzhkova AS, Kusliy MA, Trifonov VA, Popova KO, Polosmak NV, Molodin VI, Vasiliev SK, Shunkov MV, Graphodatsky AS. High genetic diversity of ancient horses from the Ukok Plateau. PLoS One 2020; 15:e0241997. [PMID: 33180850 PMCID: PMC7660532 DOI: 10.1371/journal.pone.0241997] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 10/24/2020] [Indexed: 11/18/2022] Open
Abstract
A growing number of researchers studying horse domestication come to a conclusion that this process happened in multiple locations and involved multiple wild maternal lines. The most promising approach to address this problem involves mitochondrial haplotype comparison of wild and domestic horses from various locations coupled with studies of possible migration routes of the ancient shepherds. Here, we sequenced complete mitochondrial genomes of six horses from burials of the Ukok plateau (Russia, Altai Mountains) dated from 2.7 to 1.4 thousand years before present and a single late Pleistocene wild horse from the neighboring region (Denisova cave). Sequencing data indicates that the wild horse belongs to an extinct pre-domestication lineage. Integration of the domestic horse data with known Eurasian haplotypes of a similar age revealed two distinct groups: the first one widely distributed in Europe and presumably imported to Altai, and the second one specific for Altai Mountains and surrounding area.
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Affiliation(s)
- Nadezhda V. Vorobieva
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Novosibirsk Oblast, Russia
- Paleogenomics Laboratory, Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia
| | - Alexey I. Makunin
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Novosibirsk Oblast, Russia
| | - Anna S. Druzhkova
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Novosibirsk Oblast, Russia
| | - Mariya A. Kusliy
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Novosibirsk Oblast, Russia
- * E-mail:
| | - Vladimir A. Trifonov
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Novosibirsk Oblast, Russia
| | - Kseniya O. Popova
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Novosibirsk Oblast, Russia
| | - Natalia V. Polosmak
- Paleometal Archeology Department, Institute of Archaeology and Ethnography SB RAS, Novosibirsk, Novosibirsk Oblast, Russia
| | - Vyacheslav I. Molodin
- Paleometal Archeology Department, Institute of Archaeology and Ethnography SB RAS, Novosibirsk, Novosibirsk Oblast, Russia
| | - Sergei K. Vasiliev
- Paleometal Archeology Department, Institute of Archaeology and Ethnography SB RAS, Novosibirsk, Novosibirsk Oblast, Russia
| | - Michael V. Shunkov
- Paleometal Archeology Department, Institute of Archaeology and Ethnography SB RAS, Novosibirsk, Novosibirsk Oblast, Russia
| | - Alexander S. Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Novosibirsk Oblast, Russia
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99832
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Hashem AH, Suleiman WB, Abu-Elrish GM, El-Sheikh HH. Consolidated Bioprocessing of Sugarcane Bagasse to Microbial Oil by Newly Isolated Oleaginous Fungus: Mortierella wolfii. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2020. [DOI: 10.1007/s13369-020-05076-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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99833
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Shaughnessy CA, Breves JP. Molecular mechanisms of Cl
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transport in fishes: New insights and their evolutionary context. JOURNAL OF EXPERIMENTAL ZOOLOGY PART 2020; 335:207-216. [DOI: 10.1002/jez.2428] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022]
Affiliation(s)
| | - Jason P. Breves
- Department of Biology Skidmore College Saratoga Springs New York USA
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99834
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Targueta CP, Krylov V, Nondilo TE, Lima J, Lourenço LB. Sex chromosome evolution in frogs-helpful insights from chromosome painting in the genus Engystomops. Heredity (Edinb) 2020; 126:396-409. [PMID: 33184505 DOI: 10.1038/s41437-020-00385-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/27/2020] [Accepted: 10/28/2020] [Indexed: 12/29/2022] Open
Abstract
The differentiation of sex chromosomes is thought to be interrupted by relatively frequent sex chromosome turnover and/or occasional recombination between sex chromosomes (fountain-of-youth model) in some vertebrate groups as fishes, amphibians, and lizards. As a result, we observe the prevalence of homomorphic sex chromosomes in these groups. Here, we provide evidence for the loss of sex chromosome heteromorphism in the Amazonian frogs of the genus Engystomops, which harbors an intriguing history of sex chromosome evolution. In this species complex composed of two named species, two confirmed unnamed species, and up to three unconfirmed species, highly divergent karyotypes are present, and heteromorphic X and Y chromosomes were previously found in two species. We describe the karyotype of a lineage estimated to be the sister of all remaining Amazonian Engystomops (named Engystomops sp.) and perform chromosome painting techniques using one probe for the Y chromosome and one probe for the non-centromeric heterochromatic bands of the X chromosome of E. freibergi to compare three Engystomops karyotypes. The Y probe detected the Y chromosomes of E. freibergi and E. petersi and one homolog of chromosome pair 11 of Engystomops sp., suggesting their common evolutionary origin. The X probe showed no interspecific hybridization, revealing that X chromosome heterochromatin is strongly divergent among the studied species. In the light of the phylogenetic relationships, our data suggest that sex chromosome heteromorphism may have occurred early in the evolution of the Amazonian Engystomops and have been lost in two unnamed but confirmed candidate species.
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Affiliation(s)
- Cíntia P Targueta
- Department of Structural and Functional Biology, Institute of Biology, State University of Campinas, Campinas, São Paulo, 13083-863, Brazil.,Department of Genetics, Institute of Biology Science, Federal University of Goiás, Goiânia, 74960-000, Brazil
| | - Vladimir Krylov
- Faculty of Science, Department of Cell Biology, Charles University, Vinicna 7, Prague 2, 128 44, Czech Republic
| | - Tobias E Nondilo
- Department of Structural and Functional Biology, Institute of Biology, State University of Campinas, Campinas, São Paulo, 13083-863, Brazil
| | - Jucivaldo Lima
- Institute of Scientific and Technological Research of Amapá-IEPA, Nucleus of Biodiversity (NUBIO); Rodovia Juscelino Kubitschek, s/n, Distrito da Fazendinha, Macapá, Amapá, Brazil
| | - Luciana B Lourenço
- Department of Structural and Functional Biology, Institute of Biology, State University of Campinas, Campinas, São Paulo, 13083-863, Brazil.
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99835
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Post-Flood Impacts on Occurrence and Distribution of Mycotoxin-Producing Aspergilli from the Sections Circumdati, Flavi, and Nigri in Indoor Environment. J Fungi (Basel) 2020; 6:jof6040282. [PMID: 33198357 PMCID: PMC7711759 DOI: 10.3390/jof6040282] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/03/2020] [Accepted: 11/10/2020] [Indexed: 01/11/2023] Open
Abstract
Mycotoxin-producing Aspergilli (Circumdati, Flavi, and Nigri), usually associated with contaminated food, may also cause respiratory disorders and are insufficiently studied in water-damaged indoor environments. Airborne (N = 71) and dust borne (N = 76) Aspergilli collected at post-flood and control locations in Croatia resulted in eleven different species based on their calmodulin marker: A. ochraceus, A. ostianus, A. pallidofulvus, A. sclerotiorum, and A. westerdijkiae (Circumdati); A. flavus (Flavi); and A. tubingensis, A. welwitschiae, A. niger, A. piperis, and A. uvarum (Nigri). Most of the airborne (73%) and dust borne (54%) isolates were found at post-flood locations, and the highest concentrations measured in indoor air (5720 colony-forming units (CFU)/m3) and dust (2.5 × 105 CFU/g) were up to twenty times higher than in the control locations. A. flavus dominated among airborne isolates (25%) at the unrepaired locations, while 56% of the dust borne Aspergilli were identified as A. tubingensis and A. welwitschiae. The ability of identified isolates to produce mycotoxins aflatoxin B1 (AFB1), fumonisin B2 (FB2), and ochratoxin A were assessed by LC-MS analysis. All ochratoxin A (OTA)-producing Circumdati belonged to A. westerdijkiae (13.7 ± 15.81 µg/mL); in the section, FlaviA. flavus produced AFB1 (2.51 ± 5.31 µg/mL), while A. welwitschiae and A. niger (section Nigri) produced FB2 (6.76 ± 13.51 µg/mL and 11.24 ± 18.30 µg/mL, respectively). Water damage dominantly supported the occurrence of aflatoxigenic A. flavus in indoor environments. Yet unresolved, the causal relationship of exposure to indoor Aspergilli and adverse health effects may support the significance of this research.
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99836
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Zając KS, Stec D. Molecular Approach to Identifying Three Closely Related Slug Species of the genus Deroceras (Gastropoda: Eupulmonata: Agriolimacidae). Zool Stud 2020; 59:e55. [PMID: 34140973 PMCID: PMC8181155 DOI: 10.6620/zs.2020.59-55] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/06/2020] [Indexed: 11/18/2022]
Abstract
Some species of slugs belonging to the genus Deroceras are invasive and cause severe agricultural damage. Despite extensive knowledge about their invasiveness, data on the molecular differentiation of these morphologically similar species are lacking. Here we present a molecular approach to identifying three closely related species of the genus Deroceras-D. agreste (L., 1758), D. reticulatum (O. F. Müller, 1774) and D. turcicum (Simroth, 1894) (Gastropoda: Eupulmonata: Agriolimacidae)-based on sequences of multiple molecular markers: cytochrome c oxidase subunit I (COI), cytochrome b (cyt-b), internal transcribed spacer 2 (ITS-2) and 28S ribosomal RNA (28S rRNA). We also provide detailed photomicrographs of the penis and penial gland of the three species, as it is the latter that holds the most important phenotypic characters for distinguishing between these taxa. Since identification of the studied species based solely on morphology is considered challenging, contributing a means of molecular differentiation will aid further ecological and biodiversity surveys of these important pests.
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Affiliation(s)
- Kamila S Zając
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland. (Zając)
| | - Daniel Stec
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland. E-mail: (Stec)
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99837
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Piza-Buitrago A, Rincón V, Donato J, Saavedra SY, Duarte C, Morero J, Falquet L, Reguero MT, Barreto-Hernández E. Genome-based characterization of two Colombian clinical Providencia rettgeri isolates co-harboring NDM-1, VIM-2, and other β-lactamases. BMC Microbiol 2020; 20:345. [PMID: 33183231 PMCID: PMC7664025 DOI: 10.1186/s12866-020-02030-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 11/02/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Providencia rettgeri is a nosocomial pathogen associated with urinary tract infections and related to Healthcare-Associated Infection (HAI). In recent years isolates producing New Delhi Metallo-β-lactamase (NDM) and other β-lactamases have been reported that reduce the efficiency of clinical antimicrobial treatments. In this study, we analyzed antibiotic resistance, the presence of resistance genes and the clonal relationship of two P. rettgeri isolates obtained from male patients admitted to the same hospital in Bogotá - Colombia, 2015. RESULTS Antibiotic susceptibility profile evaluated by the Kirby-Bauer method revealed that both isolates were resistant to third-generation carbapenems and cephalosporins. Whole-genome sequencing (Illumina HiSeq) followed by SPAdes assembling, Prokka annotation in combination with an in-house Python program and resistance gene detection by ResFinder identified the same six β-lactamase genes in both isolates: blaNDM-1, blaVIM-2, blaCTX-M-15, blaOXA-10, blaCMY-2 and blaTEM-1. Additionally, various resistance genes associated with antibiotic target alteration (arnA, PmrE, PmrF, LpxA, LpxC, gyrB, folP, murA, rpoB, rpsL, tet34) were found and four efflux pumps (RosAB, EmrD, mdtH and cmlA). The additional resistance to gentamicin in one of the two isolates could be explained by a detected SNP in CpxA (Cys191Arg) which is involved in the stress response of the bacterial envelope. Genome BLAST comparison using CGView, the ANI value (99.99%) and the pangenome (using Roary) phylogenetic tree (same clade, small distance) showed high similarity between the isolates. The rMLST analysis indicated that both isolates were typed as rST-61,696, same as the RB151 isolate previously isolated in Bucaramanga, Colombia, 2013, and the FDAARGOS_330 isolate isolated in the USA, 2015. CONCLUSIONS We report the coexistence of the carbapenemase genes blaNDM-1, and blaVIM-2, together with the β-lactamase genes blaCTX-M-15, blaOXA-10, blaCMY-2 and blaTEM-1, in P. rettgeri isolates from two patients in Colombia. Whole-genome sequence analysis indicated a circulation of P. rettgeri rST-61,696 strains in America that needs to be investigated further.
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Affiliation(s)
- Adriana Piza-Buitrago
- Bioinformatics Group, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia
- Molecular Epidemiology Laboratory, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Verónica Rincón
- Bioinformatics Group, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia
- Molecular Epidemiology Laboratory, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - John Donato
- Bioinformatics Group, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia
- Molecular Epidemiology Laboratory, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | | | - Carolina Duarte
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | - Jaime Morero
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | - Laurent Falquet
- Biochemistry/Bioinformatics Unit, Université de Fribourg and Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - María Teresa Reguero
- Bioinformatics Group, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia
- Molecular Epidemiology Laboratory, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Emiliano Barreto-Hernández
- Bioinformatics Group, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia.
- Molecular Epidemiology Laboratory, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia.
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99838
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Kandinov I, Dementieva E, Kravtsov D, Chestkov A, Kubanov A, Solomka V, Deryabin D, Gryadunov D, Shaskolskiy B. Molecular Typing of Neisseria gonorrhoeae Clinical Isolates in Russia, 2018-2019: A Link Between penA Alleles and NG-MAST Types. Pathogens 2020; 9:pathogens9110941. [PMID: 33198126 PMCID: PMC7696878 DOI: 10.3390/pathogens9110941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/03/2020] [Accepted: 11/11/2020] [Indexed: 02/05/2023] Open
Abstract
This work aimed to study penA gene polymorphisms in clinical isolates of Neisseria gonorrhoeae collected in Russia in 2018-2019 and the contribution of the penA allele type to susceptibility to β-lactam antibiotics. A total of 182 isolates were analyzed. penA allele types were determined by sequencing, and the minimum inhibitory concentrations (MICs) of benzylpenicillin and ceftriaxone were measured. The influence of genetic factors on MICs was evaluated by regression analysis. All isolates were susceptible to ceftriaxone, and 40.1% of isolates were susceptible to penicillin. Eleven penA allele types were identified. The mosaic type XXXIV penA allele and the Gly120Lys substitution in PorB made the greatest contributions to increasing the ceftriaxone MIC; the presence of the blaTEM plasmid, Gly120Asp, Ala121Gly/Asn substitutions in PorB, and the adenine deletion in the promoter region of the mtrR gene caused an increase in the penicillin MIC. Among 61 NG-MAST types identified, the most frequent were types 228, 807, 9486, 1993, and 6226. A link between penA alleles and Neisseria gonorrhoeae multi-antigen sequence typing (NG-MAST) types was established. Resistance to two groups of β-lactam antibiotics was associated with non-identical changes in penA alleles. To prevent the emergence of ceftriaxone resistance in Russia, NG-MAST genotyping must be supplemented with penA allele analysis.
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Affiliation(s)
- Ilya Kandinov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (I.K.); (E.D.); (D.K.); (D.G.)
| | - Ekaterina Dementieva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (I.K.); (E.D.); (D.K.); (D.G.)
| | - Dmitry Kravtsov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (I.K.); (E.D.); (D.K.); (D.G.)
| | - Alexander Chestkov
- State Research Center of Dermatovenerology and Cosmetology, Russian Ministry of Health, 107076 Moscow, Russia; (A.C.); (A.K.); (V.S.); (D.D.)
| | - Alexey Kubanov
- State Research Center of Dermatovenerology and Cosmetology, Russian Ministry of Health, 107076 Moscow, Russia; (A.C.); (A.K.); (V.S.); (D.D.)
| | - Victoria Solomka
- State Research Center of Dermatovenerology and Cosmetology, Russian Ministry of Health, 107076 Moscow, Russia; (A.C.); (A.K.); (V.S.); (D.D.)
| | - Dmitry Deryabin
- State Research Center of Dermatovenerology and Cosmetology, Russian Ministry of Health, 107076 Moscow, Russia; (A.C.); (A.K.); (V.S.); (D.D.)
| | - Dmitry Gryadunov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (I.K.); (E.D.); (D.K.); (D.G.)
| | - Boris Shaskolskiy
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (I.K.); (E.D.); (D.K.); (D.G.)
- Correspondence:
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99839
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Ricarte A, Souba-Dols GJ, Skevington JH, Quinto J, García MÁM. Morphological, Genetic and Biological Evidences to Understand Meromacrus Rondani Diversity: New Species and Early Stages (Diptera: Syrphidae). INSECTS 2020; 11:insects11110791. [PMID: 33198182 PMCID: PMC7698139 DOI: 10.3390/insects11110791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 11/25/2022]
Abstract
Simple Summary Hoverflies or flower flies, technically known as syrphids, are insects providing important ecosystem services. They are used as indicators of biodiversity and habitat quality, as well as models for evolution studies. The better syrphids are known the better can be used with different aims. Meromacrus is a genus of showy syrphids that pollinate plants and decompose organic materials in the Americas. However, their classification and biology are still being investigated. In this study, morphology and DNA were used in combination to define species concepts. Two species new to science were discovered, one from Mexico and the other from Peru. The immatures (e.g., larvae or pupae) and breeding sites of these species were also described, with the larva of the Peruvian species happening to be the first ever found in a rotting cactus. To assist those working with immatures, we provide here an identification key to Meromacrus species. Our work represents the starting point for a modern revision of the Meromacrus classification and provides data that, in future, can be used to interpret evolutionary relationships within this genus. Abstract Meromacrus is a genus of conspicuous syrphids with saprophagous larvae, ranging from the southern United States to Argentina and Chile. However, this genus is in need of a taxonomic revision. Adults reared from larvae collected in Mexico and Peru, and other material available at different institutional collections were examined. Meromacrus cactorum sp. nov., from Peru, Meromacrus yucatense sp. nov., from Mexico, their puparia and breeding sites were described. A key to Meromacrus puparia is provided. The holotypes of Meromacrus canusium, Meromacrus gloriosus, Meromacrus laconicus and Meromacrus melmoth were also examined. The name Meromacrus draco is proposed as a junior synonym of M. gloriosus. Larvae of M. cactorum sp. nov. were found in decaying columnar cacti in Peru, while those of M. yucatense sp. nov. in a rot-hole of a Ceiba pentandra stump. Obtained results on both taxonomy and biology of these species serve as a first step towards a revision of the entire genus.
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Affiliation(s)
- Antonio Ricarte
- CIBIO Research Institute (Centro Iberoamericano de la Biodiversidad), Universidad de Alicante, Carretera San Vicente s/n, 03690 San Vicente del Raspeig, Alicante, Spain; (G.J.S.-D.); (M.Á.M.G.)
- Correspondence:
| | - Gabriel J. Souba-Dols
- CIBIO Research Institute (Centro Iberoamericano de la Biodiversidad), Universidad de Alicante, Carretera San Vicente s/n, 03690 San Vicente del Raspeig, Alicante, Spain; (G.J.S.-D.); (M.Á.M.G.)
| | - Jeffrey H. Skevington
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, 960 Carling Avenue, K.W. Neatby Building, Ottawa, ON K1A 0C6, Canada;
| | - Javier Quinto
- Instituto de Investigación y Formación Agraria, Pesquera, Alimentaria y de la Producción Ecológica (IFAPA), Centro Málaga (Churriana), s/n, 29140 Cortijo de la Cruz, Málaga, Spain;
- Departamento de Ecología Tropical, Universidad Autónoma de Yucatán (UADY), Km. 15.5 Carretera de Mérida-X’matkuil, Mérida, Yucatán 4-116, Mexico
| | - Mª Ángeles Marcos García
- CIBIO Research Institute (Centro Iberoamericano de la Biodiversidad), Universidad de Alicante, Carretera San Vicente s/n, 03690 San Vicente del Raspeig, Alicante, Spain; (G.J.S.-D.); (M.Á.M.G.)
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99840
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Chakraborty J, Ghosh P. Advancement of research on plant NLRs evolution, biochemical activity, structural association, and engineering. PLANTA 2020; 252:101. [PMID: 33180185 DOI: 10.1007/s00425-020-03512-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 11/03/2020] [Indexed: 06/11/2023]
Abstract
In this review, we have included evolution of plant intracellular immune receptors, oligomeric complex formation, enzymatic action, engineering, and mechanisms of immune inspection for appropriate defense outcomes. NLR (Nucleotide binding oligomerization domain containing leucine-rich repeat) proteins are the intracellular immune receptors that recognize pathogen-derived virulence factors to confer effector-triggered immunity (ETI). Activation of plant defense by the NLRs are often conveyed through N-terminal Toll-like/ IL-1 receptor (TIR) or non-TIR (coiled-coils or CC) domains. Homodimerization or self-association property of CC/ TIR domains of plant NLRs contribute to their auto-activity and induction of in planta ectopic cell death. High resolution crystal structures of Arabidopsis thaliana RPS4TIR, L6TIR, SNC1TIR, RPP1TIR and Muscadinia rotundifolia RPV1TIR showed that interaction is mediated through one or two distinct interfaces i.e., αA and αE helices comprise AE interface and αD and αE helices were found to form DE interface. By contrast, conserved helical regions were determined for CC domains of plant NLRs. Evolutionary history of NLRs diversification has shown that paired forms were originated from NLR singletons. Plant TIRs executed NAD+ hydrolysis activity for cell death promotion. Plant NLRs were found to form large oligomeric complexes as observed in animal inflammasomes. We have also discussed different protein engineering methods includes domain shuffling, and decoy modification that increase effector recognition spectrum of plant NLRs. In summary, our review highlights structural basis of perception of the virulence factors by NLRs or NLR pairs to design novel classes of plant immune receptors.
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Affiliation(s)
| | - Prithwi Ghosh
- Department of Botany, Narajole Raj College, Narajole, Paschim Medinipur, 721211, West Bengal, India
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99841
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Rymen B, Ferrafiat L, Blevins T. Non-coding RNA polymerases that silence transposable elements and reprogram gene expression in plants. Transcription 2020; 11:172-191. [PMID: 33180661 PMCID: PMC7714444 DOI: 10.1080/21541264.2020.1825906] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Multisubunit RNA polymerase (Pol) complexes are the core machinery for gene expression in eukaryotes. The enzymes Pol I, Pol II and Pol III transcribe distinct subsets of nuclear genes. This family of nuclear RNA polymerases expanded in terrestrial plants by the duplication of Pol II subunit genes. Two Pol II-related enzymes, Pol IV and Pol V, are highly specialized in the production of regulatory, non-coding RNAs. Pol IV and Pol V are the central players of RNA-directed DNA methylation (RdDM), an RNA interference pathway that represses transposable elements (TEs) and selected genes. Genetic and biochemical analyses of Pol IV/V subunits are now revealing how these enzymes evolved from ancestral Pol II to sustain non-coding RNA biogenesis in silent chromatin. Intriguingly, Pol IV-RdDM regulates genes that influence flowering time, reproductive development, stress responses and plant–pathogen interactions. Pol IV target genes vary among closely related taxa, indicating that these regulatory circuits are often species-specific. Data from crops like maize, rice, tomato and Brassicarapa suggest that dynamic repositioning of TEs, accompanied by Pol IV targeting to TE-proximal genes, leads to the reprogramming of plant gene expression over short evolutionary timescales.
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Affiliation(s)
- Bart Rymen
- Institut de biologie moléculaire des plantes, Université de Strasbourg , Strasbourg, France
| | - Laura Ferrafiat
- Institut de biologie moléculaire des plantes, Université de Strasbourg , Strasbourg, France
| | - Todd Blevins
- Institut de biologie moléculaire des plantes, Université de Strasbourg , Strasbourg, France
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99842
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Thorat V, Kirdat K, Tiwarekar B, DaCosta E, Debbarma P, Shouche Y, Sathe S, Goel R, Lodha T, Yadav A. Pseudomonas lalkuanensis sp. nov., isolated from a bacterial consortia of contaminated soil enriched for the remediation of e-waste. Int J Syst Evol Microbiol 2020; 70:6468-6475. [PMID: 33174829 DOI: 10.1099/ijsem.0.004559] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel e-waste-degrading strain, PE08T, was isolated from contaminated soil collected from a paper mill yard in Lalkuan, Uttarakhand, India. Strain PE08T was Gram-stain-negative, rod-shaped, aerobic, oxidase-positive and catalase-positive. Optimum growth was observed at 30 °C (range, 5-40 °C), with 1-2 % NaCl (range, 0-3 %) and at pH 7 (range 6-11). The phylogeny based on 16S rRNA gene sequences delineated strain PE08T to the genus Pseudomonas and showed highest sequence similarity to Pseudomonas furukawaii KF707T (98.70 %), followed by Pseudomonas aeruginosa DSM 50071T (98.62 %) and Pseudomonas resinovorans DSM 21078T (97.93 %). The genome of strain PE08T was sequenced and had one scaffold of 6056953 bp, 99.84 % completeness and 182× coverage were obtained. The G+C content in the genome was 64.24 mol%. The DNA-DNA hybridization and average nucleotide identity values between strain PE08T and its closely related type strain, P. resinovorans DSM 21078T were below 34.8 % and 87.96 %, respectively. The phylogenetic analysis based on whole-genome sequence and concatenated GyrB and RpoB proteins revealed that strain PE08T forms a district clade in the family Pseudomonadaceae. The predominant fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 :1 ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C12 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The phenotypic, chemotaxonomic and genetic analysis, including overall genome relatedness index values, indicated that strain PE08T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas lalkuanensis sp. nov. is proposed. The type strain is PE08T (=MCC 3792=KCTC 72454=CCUG 73691).
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Affiliation(s)
- Vipool Thorat
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Kiran Kirdat
- Department of Microbiology, Tuljaram Chaturchand College, Baramati, Maharashtra 413 102, India.,National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Bhavesh Tiwarekar
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Elaine DaCosta
- Department of Biotechnology, Fergusson College, Shivajinagar, Pune 411 004, India.,National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Prasenjit Debbarma
- Department of Microbiology College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Uttarakhand, Pantnagar 263 145, India
| | - Yogesh Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Shivaji Sathe
- Department of Microbiology, Tuljaram Chaturchand College, Baramati, Maharashtra 413 102, India
| | - Reeta Goel
- Department of Microbiology College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Uttarakhand, Pantnagar 263 145, India
| | - Tushar Lodha
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Amit Yadav
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
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99843
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Dong J, Li J, Hu J, Sun C, Tian Y, Li W, Yan N, Sun C, Sheng X, Yang S, Shi Q, Ye X. Comparative Genomics Studies on the dmrt Gene Family in Fish. Front Genet 2020; 11:563947. [PMID: 33281869 PMCID: PMC7689362 DOI: 10.3389/fgene.2020.563947] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/16/2020] [Indexed: 01/15/2023] Open
Abstract
Doublesex and mab-3-related transcription factor (dmrt) genes are widely distributed across various biological groups and play critical roles in sex determination and neural development. Here, we applied bioinformatics methods to exam cross-species changes in the dmrt family members and evolutionary relationships of the dmrt genes based on genomes of 17 fish species. All the examined fish species have dmrt1-5 while only five species contained dmrt6. Most fish harbored two dmrt2 paralogs (dmrt2a and dmrt2b), with dmrt2b being unique to fish. In the phylogenetic tree, 147 DMRT are categorized into eight groups (DMRT1-DMRT8) and then clustered in three main groups. Selective evolutionary pressure analysis indicated purifying selections on dmrt1-3 genes and the dmrt1-3-2(2a) gene cluster. Similar genomic conservation patterns of the dmrt1-dmrt3-dmrt2(2a) gene cluster with 20-kb upstream/downstream regions in fish with various sex-determination systems were observed except for three regions with remarkable diversity. Synteny analysis revealed that dmrt1, dmrt2a, dmrt2b, and dmrt3-5 were relatively conserved in fish during the evolutionary process. While dmrt6 was lost in most species during evolution. The high conservation of the dmrt1-dmrt3-dmrt2(2a) gene cluster in various fish genomes suggests their crucial biological functions while various dmrt family members and sequences across fish species suggest different biological roles during evolution. This study provides a molecular basis for fish dmrt functional analysis and may serve as a reference for in-depth phylogenomics.
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Affiliation(s)
- Junjian Dong
- Key Laboratory of Tropical and Subtropical Fisheries Resources Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jia Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI Group, Shenzhen, China
| | - Jie Hu
- Key Laboratory of Tropical and Subtropical Fisheries Resources Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Chengfei Sun
- Key Laboratory of Tropical and Subtropical Fisheries Resources Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Yuanyuan Tian
- Key Laboratory of Tropical and Subtropical Fisheries Resources Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Wuhui Li
- Key Laboratory of Tropical and Subtropical Fisheries Resources Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Ningning Yan
- Key Laboratory of Tropical and Subtropical Fisheries Resources Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Chengxi Sun
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Xihui Sheng
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Song Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI Group, Shenzhen, China
| | - Xing Ye
- Key Laboratory of Tropical and Subtropical Fisheries Resources Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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99844
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da Silva ÉB, Savage RM, Biddle AS, Polukis SA, Smith ML, Kung L. Effects of a chemical additive on the fermentation, microbial communities, and aerobic stability of corn silage with or without air stress during storage. J Anim Sci 2020; 98:5881359. [PMID: 32756961 DOI: 10.1093/jas/skaa246] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/30/2020] [Indexed: 02/01/2023] Open
Abstract
We evaluated the effects of a chemical additive on the microbial communities, fermentation profile, and aerobic stability of whole-plant corn silage with or without air stress during storage. Whole-plant corn was either untreated or treated with a chemical additive containing sodium benzoate, potassium sorbate, and sodium nitrite at 2 or 3 liters/t of fresh forage weight. Ten individually treated and replicated silos (7.5 liters) were made for each treatment. Half of the silos remained sealed throughout a 63-d storage period, and the other half was subjected to air stress for 2 h/wk. The composition of the bacterial and fungal communities of fresh forage and silages untreated or treated with 2 liters/t of fresh forage weight was analyzed by Illumina Miseq sequencing. Treated silage had greater (P < 0.05) aerobic stability than untreated, even when subjected to air stress during storage, but the numbers of yeasts culturable on selective agar were not affected. However, the additive reduced the relative abundance (RA) of the lactating-assimilating yeast Candida tropicalis (P < 0.01). In air-stressed silages, untreated silage had a greater (P < 0.05) RA of Pichia kudriavzevii (also a lactate assimilator) than treated silage, whereas treated silage was dominated by Candida humilis, which is usually unable to assimilate lactate or assimilates it slowly. The additive improved the aerobic stability by specifically preventing the dominance of yeast species that can consume lactate and initiate aerobic spoilage. To the best of our knowledge, this is the first work that identifies the specific action of this additive on shifting the microbial communities in corn silage.
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Affiliation(s)
- Érica B da Silva
- Department of Animal and Food Sciences, University of Delaware, Newark, DE
| | - Rebecca M Savage
- Department of Animal and Food Sciences, University of Delaware, Newark, DE
| | - Amy S Biddle
- Department of Animal and Food Sciences, University of Delaware, Newark, DE
| | | | - Megan L Smith
- Department of Animal and Food Sciences, University of Delaware, Newark, DE
| | - Limin Kung
- Department of Animal and Food Sciences, University of Delaware, Newark, DE
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99845
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Valdisser PAMR, Müller BSF, de Almeida Filho JE, Morais Júnior OP, Guimarães CM, Borba TCO, de Souza IP, Zucchi MI, Neves LG, Coelho ASG, Brondani C, Vianello RP. Genome-Wide Association Studies Detect Multiple QTLs for Productivity in Mesoamerican Diversity Panel of Common Bean Under Drought Stress. FRONTIERS IN PLANT SCIENCE 2020; 11:574674. [PMID: 33343591 PMCID: PMC7738703 DOI: 10.3389/fpls.2020.574674] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/22/2020] [Indexed: 05/26/2023]
Abstract
Drought stress is an important abiotic factor limiting common bean yield, with great impact on the production worldwide. Understanding the genetic basis regulating beans' yield and seed weight (SW) is a fundamental prerequisite for the development of superior cultivars. The main objectives of this work were to conduct genome-wide marker discovery by genotyping a Mesoamerican panel of common bean germplasm, containing cultivated and landrace accessions of broad origin, followed by the identification of genomic regions associated with productivity under two water regimes using different genome-wide association study (GWAS) approaches. A total of 11,870 markers were genotyped for the 339 genotypes, of which 3,213 were SilicoDArT and 8,657 SNPs derived from DArT and CaptureSeq. The estimated linkage disequilibrium extension, corrected for structure and relatedness (r 2 sv ), was 98.63 and 124.18 kb for landraces and breeding lines, respectively. Germplasm was structured into landraces and lines/cultivars. We carried out GWASs for 100-SW and yield in field environments with and without water stress for 3 consecutive years, using single-, segment-, and gene-based models. Higher number of associations at high stringency was identified for the SW trait under irrigation, totaling ∼185 QTLs for both single- and segment-based, whereas gene-based GWASs showed ∼220 genomic regions containing ∼650 genes. For SW under drought, 18 QTLs were identified for single- and segment-based and 35 genes by gene-based GWASs. For yield, under irrigation, 25 associations were identified, whereas under drought the total was 10 using both approaches. In addition to the consistent associations detected across experiments, these GWAS approaches provided important complementary QTL information (∼221 QTLs; 650 genes; r 2 from 0.01% to 32%). Several QTLs were mined within or near candidate genes playing significant role in productivity, providing better understanding of the genetic mechanisms underlying these traits and making available molecular tools to be used in marker-assisted breeding. The findings also allowed the identification of genetic material (germplasm) with better yield performance under drought, promising to a common bean breeding program. Finally, the availability of this highly diverse Mesoamerican panel is of great scientific value for the analysis of any relevant traits in common bean.
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Affiliation(s)
- Paula Arielle Mendes Ribeiro Valdisser
- Biotechnology Laboratory, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, Brazil
- Genetics and Molecular Biology Graduate Program, Institute of Biology, UNICAMP, Campinas, Brazil
| | - Bárbara S. F. Müller
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | | | | | | | - Tereza C. O. Borba
- Biotechnology Laboratory, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, Brazil
| | - Isabela Pavanelli de Souza
- Biotechnology Laboratory, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, Brazil
- Postgraduate Program in Biological Sciences, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | - Maria Imaculada Zucchi
- Genetics and Molecular Biology Graduate Program, Institute of Biology, UNICAMP, Campinas, Brazil
- Agribusiness Technology Agency of São Paulo State, Agriculture and Food Supply Secretary of São Paulo, Piracicaba, Brazil
| | | | | | - Claudio Brondani
- Biotechnology Laboratory, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, Brazil
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99846
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Guo X, Xie Z, Zhang Y, Wang S. The FvCYP714C2 gene plays an important role in gibberellin synthesis in the woodland strawberry. Genes Genomics 2020; 43:11-16. [PMID: 33174086 DOI: 10.1007/s13258-020-01011-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/13/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Fragaria vesca, the woodland strawberry, is a diploid relative of the cultivated strawberry. A GA-deficient mutant was found in ethyl methanesulfonate (EMS)-mutagenized lines of the Fragaria vesca accession 'Yellow Wonder'. OBJECTIVE CYP714C2 was found to be differentially expressed using RNA-seq analysis. It is necessary to identify the function of this gene. METHODS In order to identify the function of this gene, it was cloned and transformed into Arabidopsis thaliana. RESULTS The DNA sequence of CYP714C2 was found to be 1940 bp in length, with an open reading frame (ORF) of 1539 bp that is predicted to encode a protein of 512 amino acids. The hydrophilicity of this protein is low and it is unstable. The highest relative expression of FvCYP714C2 was found in the leaves, followed by the pedicels, and low expression levels were found in the other tissues examined. Constitutive expression of FvCYP714C2 significantly promoted the growth of transgenic A. thaliana plants; transgenic Arabidopsis plants grew faster and grew well than wild type Col-0 plants. GA1+3 contents of the genetically modified Arabidopsis lines were significantly higher than that in the wild type. CONCLUSION We conclude that FvCYP714C2 is a gene that functions in the gibberellin biosynthesis pathway in strawberry.
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Affiliation(s)
- Xiaofan Guo
- School of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China.,Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, Xiaogan, 432000, China
| | - Zhibing Xie
- School of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China.,Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, Xiaogan, 432000, China
| | - Yang Zhang
- School of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China.,Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, Xiaogan, 432000, China
| | - Shouming Wang
- School of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China. .,Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, Xiaogan, 432000, China.
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99847
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Brussel KV, Wang X, Shi M, Carrai M, Li J, Martella V, Beatty JA, Holmes EC, Barrs VR. Identification of Novel Astroviruses in the Gastrointestinal Tract of Domestic Cats. Viruses 2020; 12:E1301. [PMID: 33198334 PMCID: PMC7697530 DOI: 10.3390/v12111301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/31/2020] [Accepted: 11/09/2020] [Indexed: 01/13/2023] Open
Abstract
Astroviruses, isolated from numerous avian and mammalian species including humans, are commonly associated with enteritis and encephalitis. Two astroviruses have previously been identified in cats, and while definitive evidence is lacking, an association with enteritis is suggested. Using metagenomic next-generation sequencing of viral nucleic acids from faecal samples, we identified two novel feline astroviruses termed Feline astrovirus 3 and 4. These viruses were isolated from healthy shelter-housed kittens (Feline astrovirus 3; 6448 bp) and from a kitten with diarrhoea that was co-infected with Feline parvovirus (Feline astrovirus 4, 6549 bp). Both novel astroviruses shared a genome arrangement of three open reading frames (ORFs) comparable to that of other astroviruses. Phylogenetic analysis of the concatenated ORFs, ORF1a, ORF1b and capsid protein revealed that both viruses were phylogenetically distinct from other feline astroviruses, although their precise evolutionary history could not be accurately determined due to a lack of resolution at key nodes. Large-scale molecular surveillance studies of healthy and diseased cats are needed to determine the pathogenicity of feline astroviruses as single virus infections or in co-infections with other enteric viruses.
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Affiliation(s)
- Kate Van Brussel
- School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW 2006, Australia; (K.V.B.); (J.A.B.)
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW 2006, Australia; (M.S.); (E.C.H.)
| | - Xiuwan Wang
- Department of Infectious Diseases and Public Health, Jockey Club of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, China; (X.W.); (J.L.)
| | - Mang Shi
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW 2006, Australia; (M.S.); (E.C.H.)
- School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Maura Carrai
- Department of Veterinary Clinical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, China;
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, China; (X.W.); (J.L.)
- School of Data Science, City University of Hong Kong, Hong Kong, China
| | - Vito Martella
- Department of Veterinary Medicine, University of Aldo Moro of Bari, 70010 Valenzano, Italy;
| | - Julia A. Beatty
- School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW 2006, Australia; (K.V.B.); (J.A.B.)
- Department of Veterinary Clinical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, China;
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW 2006, Australia; (M.S.); (E.C.H.)
| | - Vanessa R. Barrs
- School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW 2006, Australia; (K.V.B.); (J.A.B.)
- Department of Veterinary Clinical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, China;
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99848
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Xu Y, Magwanga RO, Jin D, Cai X, Hou Y, Juyun Z, Agong SG, Wang K, Liu F, Zhou Z. Comparative transcriptome analysis reveals evolutionary divergence and shared network of cold and salt stress response in diploid D-genome cotton. BMC PLANT BIOLOGY 2020; 20:518. [PMID: 33183239 PMCID: PMC7664088 DOI: 10.1186/s12870-020-02726-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 10/31/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Wild species of cotton are excellent resistance to abiotic stress. Diploid D-genome cotton showed abundant phenotypic diversity and was the putative donor species of allotetraploid cotton which produce the largest textile natural fiber. RESULTS A total of 41,053 genes were expressed in all samples by mapping RNA-seq Illumina reads of G. thurberi (D1), G. klotzschianum (D3-k), G. raimondii (D5) and G. trilobum (D8) to reference genome. The numbers of differently expressed genes (DEGs) were significantly higher under cold stress than salt stress. However, 34.1% DEGs under salt stress were overlapped with cold stress in four species. Notably, a potential shared network (cold and salt response, including 16 genes) was mined out by gene co-expression analysis. A total of 47,180-55,548 unique genes were identified in four diploid species by De novo assembly. Furthermore, 163, 344, 330, and 161 positively selected genes (PSGs) were detected in thurberi, G. klotzschianum, G. raimondii and G. trilobum by evolutionary analysis, respectively, and 9.5-17% PSGs of four species were DEGs in corresponding species under cold or salt stress. What's more, most of PSGs were enriched GO term related to response to stimulation. G. klotzschianum showed the best tolerance under both cold and salt stress. Interestingly, we found that a RALF-like protein coding gene not only is PSGs of G. klotzschianum, but also belongs to the potential shared network. CONCLUSION Our study provided new evidence that gene expression variations of evolution by natural selection were essential drivers of the morphological variations related to environmental adaptation during evolution. Additionally, there exist shared regulated networks under cold and salt stress, such as Ca2+ signal transduction and oxidation-reduction mechanisms. Our work establishes a transcriptomic selection mechanism for altering gene expression of the four diploid D-genome cotton and provides available gene resource underlying multi-abiotic resistant cotton breeding strategy.
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Affiliation(s)
- Yanchao Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 40070 China
| | - Richard Odongo Magwanga
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
- School of Biological, Physical, Mathematics and Actuarial sciences (SBPMAS), Main campus, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), P.O Box 210-40601, Bondo, Kenya
| | - Dingsha Jin
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Zheng Juyun
- Economic Crops Research Institute of Xinjiang Academy of Agricultural Science, Urumqi, Xinjiang province China
| | - Stephen Gaya Agong
- School of Biological, Physical, Mathematics and Actuarial sciences (SBPMAS), Main campus, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), P.O Box 210-40601, Bondo, Kenya
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
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99849
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Gil-Fernández A, Saunders PA, Martín-Ruiz M, Ribagorda M, López-Jiménez P, Jeffries DL, Parra MT, Viera A, Rufas JS, Perrin N, Veyrunes F, Page J. Meiosis reveals the early steps in the evolution of a neo-XY sex chromosome pair in the African pygmy mouse Mus minutoides. PLoS Genet 2020; 16:e1008959. [PMID: 33180767 PMCID: PMC7685469 DOI: 10.1371/journal.pgen.1008959] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/24/2020] [Accepted: 10/06/2020] [Indexed: 01/30/2023] Open
Abstract
Sex chromosomes of eutherian mammals are highly different in size and gene content, and share only a small region of homology (pseudoautosomal region, PAR). They are thought to have evolved through an addition-attrition cycle involving the addition of autosomal segments to sex chromosomes and their subsequent differentiation. The events that drive this process are difficult to investigate because sex chromosomes in almost all mammals are at a very advanced stage of differentiation. Here, we have taken advantage of a recent translocation of an autosome to both sex chromosomes in the African pygmy mouse Mus minutoides, which has restored a large segment of homology (neo-PAR). By studying meiotic sex chromosome behavior and identifying fully sex-linked genetic markers in the neo-PAR, we demonstrate that this region shows unequivocal signs of early sex-differentiation. First, synapsis and resolution of DNA damage intermediates are delayed in the neo-PAR during meiosis. Second, recombination is suppressed or largely reduced in a large portion of the neo-PAR. However, the inactivation process that characterizes sex chromosomes during meiosis does not extend to this region. Finally, the sex chromosomes show a dual mechanism of association at metaphase-I that involves the formation of a chiasma in the neo-PAR and the preservation of an ancestral achiasmate mode of association in the non-homologous segments. We show that the study of meiosis is crucial to apprehend the onset of sex chromosome differentiation, as it introduces structural and functional constrains to sex chromosome evolution. Synapsis and DNA repair dynamics are the first processes affected in the incipient differentiation of X and Y chromosomes, and they may be involved in accelerating their evolution. This provides one of the very first reports of early steps in neo-sex chromosome differentiation in mammals, and for the first time a cellular framework for the addition-attrition model of sex chromosome evolution. Sex chromosomes seem to evolve and differentiate at different rates in different taxa. The reasons for this variability are still debated. It is well established that recombination suppression around the sex-determining region triggers differentiation, and several studies have investigated this process from a genetic point of view. However, the cellular context in which recombination arrest occurs has received little attention so far. In this report, we show that meiosis, the cellular division in which pairing and recombination between chromosomes takes place, can affect the incipient differentiation of X and Y chromosomes. Combining cytogenetic and genomic approaches, we found that in the African pygmy mouse Mus minutoides, which has recently undergone sex chromosome-autosome fusions, synapsis and DNA repair dynamics are disturbed along the newly added region of the sex chromosomes. We argue that these alterations are a by-product of the fusion itself, and cause recombination suppression across a large region of the neo-sex chromosome pair. Therefore, we propose that the meiotic context in which sex or neo-sex chromosomes arise is crucial to understand the very early stages of their differentiation, as it could promote or hinder recombination suppression, and therefore impact the rate at which these chromosomes differentiate.
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Affiliation(s)
- Ana Gil-Fernández
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Paul A. Saunders
- Institut des Sciences de l'Evolution, ISEM UMR 5554 (CNRS/Université Montpellier/IRD/EPHE), Montpellier, France
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Marta Martín-Ruiz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marta Ribagorda
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Pablo López-Jiménez
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Daniel L. Jeffries
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - María Teresa Parra
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Alberto Viera
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Julio S. Rufas
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Frederic Veyrunes
- Institut des Sciences de l'Evolution, ISEM UMR 5554 (CNRS/Université Montpellier/IRD/EPHE), Montpellier, France
| | - Jesús Page
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
- * E-mail:
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99850
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Wei Q, Chen R, Wei X, Liu Y, Zhao S, Yin X, Xie T. Genome-wide identification of R2R3-MYB family in wheat and functional characteristics of the abiotic stress responsive gene TaMYB344. BMC Genomics 2020; 21:792. [PMID: 33183233 PMCID: PMC7659103 DOI: 10.1186/s12864-020-07175-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/22/2020] [Indexed: 01/19/2023] Open
Abstract
Background MYB superfamily is one of the most abundant families in plants, which plays important roles in plant growth, development, and productivity. However, to date, researches on MYBs in wheat (Triticum aestivum L.) are scattered mostly, not comprehensive. Results In this study, a total of 393 R2R3-MYBs and 12 R1R2R3-MYBs were identified and analyzed including gene structure, chromosomal distribution, synteny relationship, and evolutionary relationship. Then, 29 clusters tandem duplication and 8 clusters segmental duplication genes were discovered. The expression profile of the identified genes under abiotic and biotic stress was analyzed using RNA-seq data. Based on expression patterns analysis, we screened many candidate genes involved in plant response to abiotic and biotic stress. Among them, the functional characteristics of TaMYB344 were further studied. TaMYB344 was localized in the nucleus and functioned as a weak transcriptional activator. We demonstrated that TaMYB344-overexpressing transgenic tobacco plants had enhanced tolerance to drought, heat, and high salt stress. Conclusions In this study, 393 R2R3-MYBs and 12 R1R2R3-MYBs in wheat were systemically identified and analyzed. Differential expression analysis indicated that many R2R3-MYBs were involved in abiotic and biotic stress response. We identified a potential candidate gene TaMYB344, overexpression of which in tobacco plants enhanced drought, heat, and salt stress tolerance. These results will provide abundant molecular data for breeding new varieties of wheat in the future. Supplementary Information Supplementary information accompanies this paper at 10.1186/s12864-020-07175-9.
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Affiliation(s)
- Qiuhui Wei
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province, Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Holistic Integrative Pharmacy Institutes, School of Medicine, Hangzhou Normal University, No.2318 Yuhangtang Road, Hangzhou, 311121, People's Republic of China.
| | - Rong Chen
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province, Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Holistic Integrative Pharmacy Institutes, School of Medicine, Hangzhou Normal University, No.2318 Yuhangtang Road, Hangzhou, 311121, People's Republic of China
| | - Xin Wei
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province, Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Holistic Integrative Pharmacy Institutes, School of Medicine, Hangzhou Normal University, No.2318 Yuhangtang Road, Hangzhou, 311121, People's Republic of China
| | - Yuheng Liu
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province, Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Holistic Integrative Pharmacy Institutes, School of Medicine, Hangzhou Normal University, No.2318 Yuhangtang Road, Hangzhou, 311121, People's Republic of China
| | - Shujuan Zhao
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province, Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Holistic Integrative Pharmacy Institutes, School of Medicine, Hangzhou Normal University, No.2318 Yuhangtang Road, Hangzhou, 311121, People's Republic of China
| | - Xiaopu Yin
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province, Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Holistic Integrative Pharmacy Institutes, School of Medicine, Hangzhou Normal University, No.2318 Yuhangtang Road, Hangzhou, 311121, People's Republic of China.
| | - Tian Xie
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province, Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Holistic Integrative Pharmacy Institutes, School of Medicine, Hangzhou Normal University, No.2318 Yuhangtang Road, Hangzhou, 311121, People's Republic of China.
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