201
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Li Q, Yang M, Chen C, Xiong C, Jin X, Pu Z, Huang W. Characterization and phylogenetic analysis of the complete mitochondrial genome of the medicinal fungus Laetiporus sulphureus. Sci Rep 2018; 8:9104. [PMID: 29904057 PMCID: PMC6002367 DOI: 10.1038/s41598-018-27489-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/24/2018] [Indexed: 12/22/2022] Open
Abstract
The medicinal fungus Laetiporus sulphureus is widely distributed worldwide. To screen for molecular markers potentially useful for phylogenetic analyses of this species and related species, the mitochondrial genome of L. sulphureus was sequenced and assembled. The complete circular mitochondrial genome was 101,111 bp long, and contained 38 protein-coding genes (PCGs), 2 rRNA genes, and 25 tRNA genes. Our BLAST search aligned about 6.1 kb between the mitochondrial and nuclear genomes of L. sulphureus, indicative of possible gene transfer events. Both the GC and AT skews in the L. sulphureus mitogenome were negative, in contrast to the other seven Polyporales species tested. Of the 15 PCGs conserved across the seven species of Polyporales, the lengths of 11 were unique in the L. sulphureus mitogenome. The Ka/Ks of these 15 PCGs were all less than 1, indicating that PCGs were subject to purifying selection. Our phylogenetic analysis showed that three single genes (cox1, cob, and rnl) were potentially useful as molecular markers. This study is the first publication of a mitochondrial genome in the family Laetiporaceae, and will facilitate the study of population genetics and evolution in L. sulphureus and other species in this family.
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Affiliation(s)
- Qiang Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, P.R. China
| | - Mei Yang
- Panzhihua City Academy of Agricultural and Forest Sciences, Panzhihua, 617061, Sichuan, P.R. China
| | - Cheng Chen
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Chuan Xiong
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China
| | - Xin Jin
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China
| | - Zhigang Pu
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China. .,Sichuan Academy of Agricultural Sciences, 106 # Shizishan Rd, Chengdu, 610061, Sichuan, China.
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China. .,Sichuan Academy of Agricultural Sciences, 106 # Shizishan Rd, Chengdu, 610061, Sichuan, China.
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202
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Geoghegan JL, Pirotta V, Harvey E, Smith A, Buchmann JP, Ostrowski M, Eden JS, Harcourt R, Holmes EC. Virological Sampling of Inaccessible Wildlife with Drones. Viruses 2018; 10:v10060300. [PMID: 29865228 PMCID: PMC6024715 DOI: 10.3390/v10060300] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 05/31/2018] [Accepted: 05/31/2018] [Indexed: 11/16/2022] Open
Abstract
There is growing interest in characterizing the viromes of diverse mammalian species, particularly in the context of disease emergence. However, little is known about virome diversity in aquatic mammals, in part due to difficulties in sampling. We characterized the virome of the exhaled breath (or blow) of the Eastern Australian humpback whale (Megaptera novaeangliae). To achieve an unbiased survey of virome diversity, a meta-transcriptomic analysis was performed on 19 pooled whale blow samples collected via a purpose-built Unmanned Aerial Vehicle (UAV, or drone) approximately 3 km off the coast of Sydney, Australia during the 2017 winter annual northward migration from Antarctica to northern Australia. To our knowledge, this is the first time that UAVs have been used to sample viruses. Despite the relatively small number of animals surveyed in this initial study, we identified six novel virus species from five viral families. This work demonstrates the potential of UAVs in studies of virus disease, diversity, and evolution.
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Affiliation(s)
- Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Vanessa Pirotta
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Erin Harvey
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Alastair Smith
- Heliguy Scientific Pty Ltd., Sydney, NSW 2204, Australia.
| | - Jan P Buchmann
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Martin Ostrowski
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
- Westmead Institute for Medical Research, Centre for Virus Research, Westmead, NSW 2145, Australia.
| | - Robert Harcourt
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
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203
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Burgueño A, Frabasile S, Díaz LA, Cabrera A, Pisano MB, Rivarola ME, Contigiani M, Delfraro A. Genomic Characterization and Seroprevalence Studies on Alphaviruses in Uruguay. Am J Trop Med Hyg 2018; 98:1811-1818. [PMID: 29633690 PMCID: PMC6086168 DOI: 10.4269/ajtmh.17-0980] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/23/2018] [Indexed: 11/07/2022] Open
Abstract
Alphaviruses (Togaviridae) are arboviruses frequently associated with emerging infectious diseases. In this study, we aimed to investigate the presence of alphaviruses in Uruguay by detecting the viral genome in mosquitoes and neutralizing antibodies in equines. A total of 3,575 mosquitoes were analyzed for alphavirus genome detection. Serologic studies were performed on 425 horse sera by plaque reduction neutralization test (PRNT80) against Venezuelan equine encephalitis virus (VEEV) subtype IAB, Pixuna virus (PIXV), Rio Negro virus (RNV), western equine encephalitis virus (WEEV), and Madariaga virus (MADV). Mosquitoes belonging to six genera were captured and 82.9% were identified as Culex pipiens. Two Cx. pipiens pools collected in Fray Bentos and Las Toscas localities were alphavirus positive, and phylogenetic analyses showed that the sequences grouped into two different clusters: the lineage I of eastern equine encephalitis virus and RNV (VEEV complex), respectively. Plaque reduction neutralization test assays showed antibodies against strains of the VEEV complex, MADV, and WEEV. Rio Negro virus was the most geographically widespread virus, showing higher seroprevalences (up to 20%). Seroprevalences against VEEV IAB ranged between 4.6% and 13%; antibodies against PIXV, WEEV, and MADV were less frequent (3-4%). In conclusion, RNV exhibited the highest seroprevalence in horses, a wide geographical distribution, and viral genome was detected in Cx. pipiens mosquitoes. Madariaga virus had a low seroprevalence in equines, but an epizootic lineage typical of North America was detected in Cx. pipiens mosquitoes. Taken together, our results show that alphaviruses are present in Uruguay with variable occurrence and geographical distribution being a potential threat for human and equine health.
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Affiliation(s)
- Analía Burgueño
- Sección Virología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Sandra Frabasile
- Sección Virología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Luis Adrián Díaz
- Instituto de Virología “Dr. J.M. Vanella,” Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Instituto de Investigaciones Biológicas y Tecnológicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Andrés Cabrera
- Sección Virología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - María Belén Pisano
- Instituto de Virología “Dr. J.M. Vanella,” Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - María Elisa Rivarola
- Instituto de Virología “Dr. J.M. Vanella,” Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Marta Contigiani
- Instituto de Virología “Dr. J.M. Vanella,” Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Adriana Delfraro
- Sección Virología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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204
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Expansion of cap superfamily proteins in the genome of Mesocestoides corti : An extreme case of a general bilaterian trend. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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205
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Li WX, Fu PP, Zhang D, Boyce K, Xi BW, Zou H, Li M, Wu SG, Wang GT. Comparative mitogenomics supports synonymy of the genera Ligula and Digramma (Cestoda: Diphyllobothriidae). Parasit Vectors 2018; 11:324. [PMID: 29848351 PMCID: PMC5975392 DOI: 10.1186/s13071-018-2910-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/21/2018] [Indexed: 12/19/2022] Open
Abstract
Background After observing differences in the number of reproductive complexes per proglottid within the genus Ligula, the genus Digramma was erected. However, the validity of Digramma has been previously questioned due to a low variability in the cox1, nad1 and ITS rDNA sequences between the two genera. We undertook a study to greatly increase the amount of sequence data available for resolution of this question by sequencing and characterizing the complete mitogenomes of Digramma interrupta and Ligula intestinalis. Results The circular mtDNA molecules of Digramma interrupta and Ligula intestinalis are 13,685 bp and 13,621 bp in size, respectively, both comprising 12 PCGs, 22 tRNA genes, two rRNA genes, and two mNCRs. Both mitogenomes exhibit the same gene order and share 92.7% nucleotide identity, compared with 85.8–86.5% to the most closely related genus Dibothriocephalus. Each gene from D. interrupta and L. intestinalis is almost of the same size, and the sequence identity ranges from 87.5% (trnD) to 100% (trnH, trnQ and trnV). NCR2 sequences of D. interrupta and L. intestinalis are 249 bp and 183 bp in length, respectively, which contributes to the main difference in length between their complete mitogenomes. A sliding window analysis of the 12 PCGs and two rRNAs indicated nucleotide diversity to be higher in nad5, nad6, nad2, nad4 and cox3, whereas the most conserved genes were rrnL and rrnS. Lower sequence identity was also found in nad2, nad4, nad5, nad6 and cox3 genes between the two diphyllobothriids. Within the Diphyllobothriidae, phylogenetic analysis indicated Ligula and Digramma to be most closely related to one another, forming a sister group with Dibothriocephalus. Conclusions Owing to higher nucleotide diversity, the genes nad2, nad4, nad5, nad6 and cox3 should be considered optimal candidates to use as molecular markers for population genetics and species identification between the two closely related species. The phylogenetic results in combination with the comparative analysis of the two mitogenomes, consistently support the congeneric status of L. intestinalis and D. interrupta. Electronic supplementary material The online version of this article (10.1186/s13071-018-2910-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wen X Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China
| | - Pei P Fu
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Dong Zhang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Kellyanne Boyce
- South Devon College University Centre, Long Road, Paignton, TQ4 7EJ, UK
| | - Bing W Xi
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China
| | - Ming Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China
| | - Shan G Wu
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China
| | - Gui T Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China.
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206
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Thiel D, Bauknecht P, Jékely G, Hejnol A. An ancient FMRFamide-related peptide-receptor pair induces defence behaviour in a brachiopod larva. Open Biol 2018; 7:rsob.170136. [PMID: 28835571 PMCID: PMC5577450 DOI: 10.1098/rsob.170136] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 07/25/2017] [Indexed: 11/22/2022] Open
Abstract
Animal behaviour often comprises spatially separated sub-reactions and even ciliated larvae are able to coordinate sub-reactions of complex behaviours (metamorphosis, feeding). How these sub-reactions are coordinated is currently not well understood. Neuropeptides are potential candidates for triggering larval behaviour. However, although their immunoreactivity has been widely analysed, their function in trochozoan larvae has only been studied for a few cases. Here, we investigate the role of neuropeptides in the defence behaviour of brachiopod larvae. When mechanically disturbed, the planktonic larvae of Terebratalia transversa protrude their stiff chaetae and sink down slowly. We identified endogenous FLRFamide-type neuropeptides (AFLRFamide and DFLRFamide) in T. transversa larvae and show that the protrusion of the chaetae as well as the sinking reaction can both be induced by each of these peptides. This also correlates with the presence of FLRFamidergic neurons in the apical lobe and adjacent to the trunk musculature. We deorphanized the AFLRFamide/DFLRFamide receptor and detected its expression in the same tissues. Furthermore, the ability of native and modified FLRFamide-type peptides to activate this receptor was found to correspond with their ability to trigger behavioural responses. Our results show how FLRFamide-type neuropeptides can induce two coherent sub-reactions in a larva with a simple nervous system.
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Affiliation(s)
- Daniel Thiel
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway
| | - Philipp Bauknecht
- Max Planck Institute for Developmental Biology, Spemannstraße 35, 72076 Tübingen, Germany
| | - Gáspár Jékely
- Max Planck Institute for Developmental Biology, Spemannstraße 35, 72076 Tübingen, Germany
| | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway
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207
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Yang L, Wu J, Hu T, Qin S, Deng B, Liu J, Zhang F, He B, Tu C. Genetic diversity of bat orthohepadnaviruses in China and a proposed new nomenclature. INFECTION GENETICS AND EVOLUTION 2018; 63:135-143. [PMID: 29842981 PMCID: PMC7173211 DOI: 10.1016/j.meegid.2018.05.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 05/23/2018] [Accepted: 05/25/2018] [Indexed: 01/24/2023]
Abstract
The orthohepadnaviruses, which include the major human pathogen hepatitis B virus, exist in a wide range of hosts. Since 2013, a large group of orthohepadnaviruses has been identified in bats worldwide and classified as 4 species within the genus Orthohepadnavirus. To further investigate orthohepadnaviruses in the Chinese bat population, 554 archived bat samples from 20 colonies covering 3 southern provinces were screened with results showing that 9 (1.6%) were positive. A systematic phylogenetic analysis has indicated the need for a new nomenclature for bat hepatitis B virus-like viruses: BtHBV, with the addition of 3 new species, one being divided into 6 genotypes. Viruses identified here shared 9.0–19.2% full genome divergence and classified into 3 different genotypes. This study illustrates the genetic diversity of orthohepadnaviruses in the Chinese bat population, and emphasizes need for further investigation of their public health significance. Three new orthohepadnaviral lineages were identified in Chinese bats. A new nomenclature was proposed for bat hepatitis B virus-like viruses. This study indicates genetic diversity of orthohepadnaviruses in Chinese bats.
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Affiliation(s)
- Ling'en Yang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, Jilin Province, China; Fujian A&F University, College of Animal Science, Fuzhou, Fujian Province, China
| | - Jianmin Wu
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, Guangxi Province, China
| | - Tingsong Hu
- Centers for Disease Control and Prevention of Chengdu Military Command, Kunming, Yunnan Province, China
| | - Shaomin Qin
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, Guangxi Province, China
| | - Bo Deng
- Centers for Disease Control and Prevention of Chengdu Military Command, Kunming, Yunnan Province, China
| | - Jinfeng Liu
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, Guangxi Province, China
| | - Fuqiang Zhang
- Centers for Disease Control and Prevention of Chengdu Military Command, Kunming, Yunnan Province, China.
| | - Biao He
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, Jilin Province, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu Province, China.
| | - Changchun Tu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, Jilin Province, China; Fujian A&F University, College of Animal Science, Fuzhou, Fujian Province, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu Province, China.
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208
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Virus survey in populations of two subspecies of bent-winged bats (Miniopterus orianae bassanii and oceanensis) in south-eastern Australia reveals a high prevalence of diverse herpesviruses. PLoS One 2018; 13:e0197625. [PMID: 29795610 PMCID: PMC5967723 DOI: 10.1371/journal.pone.0197625] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/05/2018] [Indexed: 01/03/2023] Open
Abstract
While bats are often viewed as carriers of infectious disease agents, little research has been conducted on the effects these potential pathogens may have on the bat populations themselves. The southern bent-winged bat (Miniopterus orianae bassanii) is a critically endangered subspecies endemic to south-eastern Australia. Population numbers of this bat have been declining for the past 50 years, but the reasons for this are unclear. As part of a larger study to determine if disease could be a contributing factor to this decline, 351 southern bent-winged bats from four locations were captured, and oral swabs were collected and tested for the presence of potentially pathogenic viruses. Results were compared with those obtained from 116 eastern bent-winged bats (Miniopterus orianae oceanensis) from three different locations. The eastern bent-winged bat is a related but more common and widespread subspecies whose geographical range overlaps partly with southern bent-winged bats. Herpesviruses were detected in bent-winged bats from all seven locations. At least six novel herpesviruses (five betaherpesviruses and one gammaherpesvirus) were identified. The prevalence of herpesvirus infection was higher in eastern bent-winged bats (44%, 51/116), compared to southern bent-winged bats (27%, 95/351), although this varied across the locations and sampling periods. Adenoviruses and a range of different RNA viruses (lyssaviruses, filoviruses, coronaviruses and henipaviruses) were also tested for but not detected. The detected herpesviruses did not appear to be associated with obvious ill health, and may thus not be playing a role in the population decline of the southern bent-winged bat. The detection of multiple novel herpesviruses at a high prevalence of infection is consistent with our understanding of bats as hosts to a rich diversity of viruses.
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209
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Yano H, Iwamoto T, Nishiuchi Y, Nakajima C, Starkova DA, Mokrousov I, Narvskaya O, Yoshida S, Arikawa K, Nakanishi N, Osaki K, Nakagawa I, Ato M, Suzuki Y, Maruyama F. Population Structure and Local Adaptation of MAC Lung Disease Agent Mycobacterium avium subsp. hominissuis. Genome Biol Evol 2018; 9:2403-2417. [PMID: 28957464 PMCID: PMC5622343 DOI: 10.1093/gbe/evx183] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2017] [Indexed: 12/11/2022] Open
Abstract
Mycobacterium avium subsp. hominissuis (MAH) is one of the most common nontuberculous mycobacterial species responsible for chronic lung disease in humans. Despite increasing worldwide incidence, little is known about the genetic mechanisms behind the population evolution of MAH. To elucidate the local adaptation mechanisms of MAH, we assessed genetic population structure, the mutual homologous recombination, and gene content for 36 global MAH isolates, including 12 Japanese isolates sequenced in the present study. We identified five major MAH lineages and found that extensive mutual homologous recombination occurs among them. Two lineages (MahEastAsia1 and MahEastAsia2) were predominant in the Japanese isolates. We identified alleles unique to these two East Asian lineages in the loci responsible for trehalose biosynthesis (treS and mak) and in one mammalian cell entry operon, which presumably originated from as yet undiscovered mycobacterial lineages. Several genes and alleles unique to East Asian strains were located in the fragments introduced via recombination between East Asian lineages, suggesting implication of recombination in local adaptation. These patterns of MAH genomes are consistent with the signature of distribution conjugative transfer, a mode of sexual reproduction reported for other mycobacterial species.
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Affiliation(s)
- Hirokazu Yano
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.,Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Tomotada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan
| | - Yukiko Nishiuchi
- Toneyama Institute for Tuberculosis Research, Osaka City University Medical School, Osaka, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo, Japan
| | | | - Igor Mokrousov
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Olga Narvskaya
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Shiomi Yoshida
- Clinical Research Center, National Hospital Organization, Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Kentaro Arikawa
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan
| | - Noriko Nakanishi
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan
| | - Ken Osaki
- TOMY Digital Biology Co. Ltd, Taito-Ku, Tokyo, Japan
| | - Ichiro Nakagawa
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Manabu Ato
- Department of Immunology, National Institute of Infectious Diseases, Shinjuku-Ku, Tokyo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo, Japan
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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210
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Zhu Z, Yang F, He J, Li J, Cao W, Li J, Xia Y, Guo J, Jin Y, Zhang K, Zheng H, Liu X. First detection of foot-and-mouth disease virus O/ME-SA/Ind2001 in China. Transbound Emerg Dis 2018; 65:2027-2031. [PMID: 29745040 DOI: 10.1111/tbed.12895] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Indexed: 11/28/2022]
Abstract
Foot-and-mouth disease (FMD) is endemic in China and is predominantly due to foot-and-mouth disease virus (FMDV) serotype O Mya-98 lineage. In recent years, FMDV O/ME-SA/Ind2001 lineage has spread from the Indian subcontinent to South-East Asia, Middle East and Africa, which may pose potential threats for future trans-regional livestock movements. In this study, we identified the appearance of FMDV O/ME-SA/Ind2001 in China; the first time that this virus lineage has been found there. Sequencing and phylogenetic analysis of VP1 sequences revealed that this newly determined strain belongs to O/ME-SA/Ind2001 sublineage d and is closely related to strains that have caused recent outbreaks of FMD in Nepal, Myanmar, Russia and South Korea. The results suggest extensive movements of the current O/ME-SA/Ind2001 sublineage d viruses and provide essential information for an effective national FMDV control programme in China.
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Affiliation(s)
- Z Zhu
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - F Yang
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - J He
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - J Li
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - W Cao
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - J Li
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases, Taishan Medical College, Universities of Shandong, Taian, Shandong, China
| | - Y Xia
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - J Guo
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Y Jin
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - K Zhang
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - H Zheng
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - X Liu
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
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211
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Fam RR, Hiong KC, Choo CY, Wong WP, Chew SF, Ip YK. Molecular characterization of a novel algal glutamine synthetase (GS) and an algal glutamate synthase (GOGAT) from the colorful outer mantle of the giant clam, Tridacna squamosa , and the putative GS-GOGAT cycle in its symbiotic zooxanthellae. Gene 2018; 656:40-52. [DOI: 10.1016/j.gene.2018.02.062] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/09/2018] [Accepted: 02/23/2018] [Indexed: 12/25/2022]
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212
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Xu L, Lin Q, Xu S, Gu Y, Hou J, Liu Y, Dumont HJ, Han B. Daphnia diversity on the Tibetan Plateau measured by DNA taxonomy. Ecol Evol 2018; 8:5069-5078. [PMID: 29876082 PMCID: PMC5980554 DOI: 10.1002/ece3.4071] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 03/25/2018] [Accepted: 03/26/2018] [Indexed: 02/04/2023] Open
Abstract
Daphnia on the Tibetan Plateau has been little studied, and information on species diversity and biogeography is lacking. Here, we conducted a 4-year survey using the barcoding fragment of the mitochondrial COI gene to determine the distribution and diversity of Daphnia species found across the Plateau. Our results show that species richness is higher than previously thought, with total described and provisional species number doubling from 5 to 10. Six of the taxonomic units recovered by DNA taxonomy agreed well with morphology, but DNA barcoding distinguished three clades each for the D. longispina (D. galeata, D. dentifera, and D. longispina) and D. pulex (D. pulex, D. cf. tenebrosa, and D. pulicaria) complexes. The sequence divergence between congeneric species varied within a large range, from 9.25% to 30.71%. The endemic D. tibetana was the most common and widespread species, occurring in 12 hyposaline to mesosaline lakes. The lineage of D. longispina is the first confirmed occurrence in west Tibet.
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Affiliation(s)
- Lei Xu
- South China Sea Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- Institute of HydrobiologyJinan UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Fishery Ecology and EnvironmentGuangzhouChina
- Key Laboratory of South China Sea Fishery ResourcesDevelopment and UtilizationMinistry of AgricultureGuangzhouChina
| | - Qiuqi Lin
- Institute of HydrobiologyJinan UniversityGuangzhouChina
| | - Shaolin Xu
- Institute of HydrobiologyJinan UniversityGuangzhouChina
| | - Yangliang Gu
- Institute of HydrobiologyJinan UniversityGuangzhouChina
| | - Juzhi Hou
- Institute of Tibetan Plateau ResearchChinese Academy of SciencesBeijingChina
| | - Yongqin Liu
- Institute of Tibetan Plateau ResearchChinese Academy of SciencesBeijingChina
| | | | - Bo‐Ping Han
- Institute of HydrobiologyJinan UniversityGuangzhouChina
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213
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Xu L, Wang L, Ning J, Li H, Ji Y, Du F. Diversity of marine planktonic ostracods in South China Sea: a DNA taxonomy approach. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:118-125. [PMID: 29671658 DOI: 10.1080/24701394.2018.1462349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Ostracods (Crustacea, Ostracoda) are small bivalved crustaceans, contributing over 200 described species to the marine zooplankton community. They are widely distributed and are relatively abundant components of the mesozooplankton, playing an important role in the transport of organic matter to deep layers. However, identification of ostracods based on micro-morphological characters is extremely difficult and time-consuming. Previous fragmentary taxonomic studies of ostracods in the South China Sea (SCA), were based solely on morphology. Here, by analysing the mitochondrial COI gene, we explore the taxa across the SCA using molecular tools for the first time. Our results show that sequence divergence among species varies within a large range, from 12.93% to 35.82%. Sixteen of the taxonomic units recovered by DNA taxonomy agree well with morphology, but Paraconchoecia oblonga, Conchoecia magna and Halocypris brevirostris split into two clades each, each of which contains cryptic species.
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Affiliation(s)
- Lei Xu
- a South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China.,b Guangdong Provincial Key Laboratory of Fishery Ecology and Environment , Guangzhou , China.,c Key Laboratory of South China Sea Fishery Resources Development and Utilization, Ministry of Agriculture , Guangzhou , China
| | - Lianggen Wang
- a South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China.,b Guangdong Provincial Key Laboratory of Fishery Ecology and Environment , Guangzhou , China.,c Key Laboratory of South China Sea Fishery Resources Development and Utilization, Ministry of Agriculture , Guangzhou , China
| | - Jiajia Ning
- a South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China.,b Guangdong Provincial Key Laboratory of Fishery Ecology and Environment , Guangzhou , China.,c Key Laboratory of South China Sea Fishery Resources Development and Utilization, Ministry of Agriculture , Guangzhou , China
| | - Hong Li
- a South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China.,b Guangdong Provincial Key Laboratory of Fishery Ecology and Environment , Guangzhou , China.,c Key Laboratory of South China Sea Fishery Resources Development and Utilization, Ministry of Agriculture , Guangzhou , China
| | - Yingying Ji
- a South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China.,d College of Marine Sciences , Shanghai Ocean University , Shanghai , China
| | - Feiyan Du
- a South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China.,b Guangdong Provincial Key Laboratory of Fishery Ecology and Environment , Guangzhou , China.,c Key Laboratory of South China Sea Fishery Resources Development and Utilization, Ministry of Agriculture , Guangzhou , China
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214
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Singh PK, Ray S, Thakur S, Rathour R, Sharma V, Sharma TR. Co-evolutionary interactions between host resistance and pathogen avirulence genes in rice-Magnaporthe oryzae pathosystem. Fungal Genet Biol 2018; 115:9-19. [PMID: 29630984 DOI: 10.1016/j.fgb.2018.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 11/29/2022]
Abstract
Rice and Magnaporthe oryzae constitutes an ideal pathosystem for studying host-pathogen interaction in cereals crops. There are two alternative hypotheses, viz. Arms race and Trench warfare, which explain the co-evolutionary dynamics of hosts and pathogens which are under continuous confrontation. Arms race proposes that both R- and Avr- genes of host and pathogen, respectively, undergo positive selection. Alternatively, trench warfare suggests that either R- or Avr- gene in the pathosystem is under balanced selection intending to stabilize the genetic advantage gained over the opposition. Here, we made an attempt to test the above-stated hypotheses in rice-M. oryzae pathosystem at loci of three R-Avr gene pairs, Piz-t-AvrPiz-t, Pi54-AvrPi54 and Pita-AvrPita using allele mining approach. Allele mining is an efficient way to capture allelic variants existing in the population and to study the selective forces imposed on the variants during evolution. Results of nucleotide diversity, neutrality statistics and phylogenetic analyses reveal that Piz-t, Pi54 and AvrPita are diversified and under positive selection at their corresponding loci, while their counterparts, AvrPiz-t, AvrPi54 and Pita are conserved and under balancing selection, in nature. These results imply that rice-M. oryzae populations are engaged in a trench warfare at least at the three R/Avr loci studied. It is a maiden attempt to study the co-evolution of three R-Avr gene pairs in this pathosystem. Knowledge gained from this study will help in understanding the evolutionary dynamics of host-pathogen interaction in a better way and will also aid in developing new durable blast resistant rice varieties in future.
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Affiliation(s)
- Pankaj Kumar Singh
- National Research Centre on Plant Biotechnology, New Delhi 110 012, India; Department of Bioscience and Biotechnology, Banasthali University, Tonk, Rajasthan 304 022, India
| | - Soham Ray
- National Research Centre on Plant Biotechnology, New Delhi 110 012, India
| | - Shallu Thakur
- National Research Centre on Plant Biotechnology, New Delhi 110 012, India
| | - Rajeev Rathour
- Department of Agricultural Biotechnology, CSK HPKV, Palampur, H.P. 176 062, India
| | - Vinay Sharma
- Department of Bioscience and Biotechnology, Banasthali University, Tonk, Rajasthan 304 022, India
| | - Tilak Raj Sharma
- National Research Centre on Plant Biotechnology, New Delhi 110 012, India; National Agri-Food Biotechnology Institute, Mohali, Punjab 140 306, India.
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215
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Siegel SV, Rivero AV, Oberstaller J, Colon BL, de Buron I, Kyle DE. Blood flukes Cardicola parvus and C. laruei (Trematoda: Aporocotylidae): life cycles and cryptic infection in spotted seatrout, Cynoscion nebulosus (Teleost: Sciaenidae). Parasitol Int 2018; 67:150-158. [DOI: 10.1016/j.parint.2017.10.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 10/24/2017] [Accepted: 10/30/2017] [Indexed: 01/22/2023]
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216
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Richard MMS, Gratias A, Thareau V, Kim KD, Balzergue S, Joets J, Jackson SA, Geffroy V. Genomic and epigenomic immunity in common bean: the unusual features of NB-LRR gene family. DNA Res 2018; 25:161-172. [PMID: 29149287 PMCID: PMC5909424 DOI: 10.1093/dnares/dsx046] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 10/26/2017] [Indexed: 12/20/2022] Open
Abstract
In plants, a key class of genes comprising most of disease resistance (R) genes encodes Nucleotide-binding leucine-rich repeat (NL) proteins. Access to common bean (Phaseolus vulgaris) genome sequence provides unparalleled insight into the organization and evolution of this large gene family (∼400 NL) in this important crop. As observed in other plant species, most common bean NL are organized in cluster of genes. However, a particularity of common bean is that these clusters are often located in subtelomeric regions close to terminal knobs containing the satellite DNA khipu. Phylogenetically related NL are spread between different chromosome ends, suggesting frequent exchanges between non-homologous chromosomes. NL peculiar location, in proximity to heterochromatic regions, led us to study their DNA methylation status using a whole-genome cytosine methylation map. In common bean, NL genes displayed an unusual body methylation pattern since half of them are methylated in the three contexts, reminiscent of the DNA methylation pattern of repeated sequences. Moreover, 90 NL were also abundantly targeted by 24 nt siRNA, with 90% corresponding to methylated NL genes. This suggests the existence of a transcriptional gene silencing mechanism of NL through the RdDM (RNA-directed DNA methylation) pathway in common bean that has not been described in other plant species.
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Affiliation(s)
- Manon M S Richard
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Univ Paris-Saclay, Univ Paris-Sud, Univ Evry, Univ Paris-Diderot, Sorbone Paris-Cité, 91405 Orsay, France
| | - Ariane Gratias
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Univ Paris-Saclay, Univ Paris-Sud, Univ Evry, Univ Paris-Diderot, Sorbone Paris-Cité, 91405 Orsay, France
| | - Vincent Thareau
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Univ Paris-Saclay, Univ Paris-Sud, Univ Evry, Univ Paris-Diderot, Sorbone Paris-Cité, 91405 Orsay, France
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
| | - Sandrine Balzergue
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Univ Paris-Saclay, Univ Paris-Sud, Univ Evry, Univ Paris-Diderot, Sorbone Paris-Cité, 91405 Orsay, France
- IRHS, INRA, AGROCAMPUS-Ouest, Université d’Angers, SFR 4207 QUASAV, 49071 Beaucouzé cedex, France
| | - Johann Joets
- GQE – Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
| | - Valérie Geffroy
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Univ Paris-Saclay, Univ Paris-Sud, Univ Evry, Univ Paris-Diderot, Sorbone Paris-Cité, 91405 Orsay, France
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217
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Piwczyński M, Wyborska D, Gołębiewska J, Puchałka R. Phylogenetic positions of seven poorly known species of Ferula (Apiaceae) with remarks on the phylogenetic utility of the plastid trnH-psbA, trnS-trnG, and atpB-rbcL intergenic spacers. SYST BIODIVERS 2018. [DOI: 10.1080/14772000.2018.1442374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Marcin Piwczyński
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland
| | - Dominika Wyborska
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland
| | - Joanna Gołębiewska
- Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Radosław Puchałka
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland
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218
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Lee T, Alemseged Y, Mitchell A. Dropping Hints: Estimating the diets of livestock in rangelands using DNA metabarcoding of faeces. METABARCODING AND METAGENOMICS 2018. [DOI: 10.3897/mbmg.2.22467] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The introduction of domesticated animals into new environments can lead to considerable ecological disruption, and it can be difficult to predict their impact on the new ecosystem. In this study, we use faecal metabarcoding to characterize the diets of three ruminant taxa in the rangelands of south-western New South Wales, Australia. Our study organisms included goats (Capraaegagrushircus) and two breeds of sheep (Ovisaries): Merinos, which have been present in Australia for over two hundred years, and Dorpers, which were introduced in the 1990s. We used High-Throughput Sequencing methods to sequence therbcLand ITS2 genes of plants in the faecal samples, and identified the samples using the GenBank and BOLD online databases, as well as a reference collection of sequences from plants collected in the study area. We found that the diets of all three taxa were dominated by the family Malvaceae, and that the Dorper diet was more diverse than the Merino diet at both the family and the species level. We conclude that Dorpers, like Merinos, are potentially a threat to some vulnerable species in the rangelands of New South Wales.
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219
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Genome-wide identification and characterization of the RIO atypical kinase family in plants. Genes Genomics 2018; 40:669-683. [PMID: 29892951 DOI: 10.1007/s13258-018-0658-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 01/16/2018] [Indexed: 10/18/2022]
Abstract
Members of the right open reading frame (RIO) atypical kinase family are present in all three domains of life. In eukaryotes, three subfamilies have been identified: RIO1, RIO2, and RIO3. Studies have shown that the yeast and human RIO1 and RIO2 kinases are essential for the biogenesis of small ribosomal subunits. Thus far, RIO3 has been found only in multicellular eukaryotes. In this study, we systematically identified members of the RIO gene family in 37 species representing the major evolutionary lineages in Viridiplantae. A total of 84 RIO genes were identified; among them, 41 were classified as RIO1 and 43 as RIO2. However, no RIO3 gene was found in any of the species examined. Phylogenetic trees constructed for plant RIO1 and RIO2 proteins were generally congruent with the species phylogeny. Subcellular localization analyses showed that the plant RIO proteins were localized mainly in the nucleus and/or cytoplasm. Expression profile analysis of rice, maize, and Arabidopsis RIO genes in different tissues revealed similar expression patterns between RIO1 and RIO2 genes, and their expression levels were high in certain tissues. In addition, the expressions of plant RIO genes were regulated by two drugs: mycophenolic acid and actinomycin D. Function prediction using genome-wide coexpression analysis revealed that most plant RIO genes may be involved in ribosome biogenesis. Our results will be useful for the evolutionary analysis of the ancient RIO kinase family and provide a basis for further functional characterization of RIO genes in plants.
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220
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Gaunitz C, Fages A, Hanghøj K, Albrechtsen A, Khan N, Schubert M, Seguin-Orlando A, Owens IJ, Felkel S, Bignon-Lau O, de Barros Damgaard P, Mittnik A, Mohaseb AF, Davoudi H, Alquraishi S, Alfarhan AH, Al-Rasheid KAS, Crubézy E, Benecke N, Olsen S, Brown D, Anthony D, Massy K, Pitulko V, Kasparov A, Brem G, Hofreiter M, Mukhtarova G, Baimukhanov N, Lõugas L, Onar V, Stockhammer PW, Krause J, Boldgiv B, Undrakhbold S, Erdenebaatar D, Lepetz S, Mashkour M, Ludwig A, Wallner B, Merz V, Merz I, Zaibert V, Willerslev E, Librado P, Outram AK, Orlando L. Ancient genomes revisit the ancestry of domestic and Przewalski’s horses. Science 2018; 360:111-114. [DOI: 10.1126/science.aao3297] [Citation(s) in RCA: 176] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 01/31/2018] [Indexed: 12/28/2022]
Abstract
The Eneolithic Botai culture of the Central Asian steppes provides the earliest archaeological evidence for horse husbandry, ~5500 years ago, but the exact nature of early horse domestication remains controversial. We generated 42 ancient-horse genomes, including 20 from Botai. Compared to 46 published ancient- and modern-horse genomes, our data indicate that Przewalski’s horses are the feral descendants of horses herded at Botai and not truly wild horses. All domestic horses dated from ~4000 years ago to present only show ~2.7% of Botai-related ancestry. This indicates that a massive genomic turnover underpins the expansion of the horse stock that gave rise to modern domesticates, which coincides with large-scale human population expansions during the Early Bronze Age.
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221
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Fedosov A, Puillandre N, Herrmann M, Kantor Y, Oliverio M, Dgebuadze P, Modica MV, Bouchet P. The collapse of Mitra: molecular systematics and morphology of the Mitridae (Gastropoda: Neogastropoda). Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zlx073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Alexander Fedosov
- A.N. Severtzov Institute of Ecology and Evolution of Russian Academy of Sciences, Leninskiy Prospect, Moscow, Russia
- Institut de Systématique, Évolution, Biodiversité ISYEB – UMR 7205 – CNRS, MNHN, UPMC, EPHE, Muséum National d’Histoire Naturelle, Sorbonne Universités, Paris, France
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité ISYEB – UMR 7205 – CNRS, MNHN, UPMC, EPHE, Muséum National d’Histoire Naturelle, Sorbonne Universités, Paris, France
| | | | - Yuri Kantor
- A.N. Severtzov Institute of Ecology and Evolution of Russian Academy of Sciences, Leninskiy Prospect, Moscow, Russia
- Institut de Systématique, Évolution, Biodiversité ISYEB – UMR 7205 – CNRS, MNHN, UPMC, EPHE, Muséum National d’Histoire Naturelle, Sorbonne Universités, Paris, France
| | - Marco Oliverio
- Department of Biology and Biotechnologies ‘Charles Darwin’, ‘Sapienza’ University of Rome, Viale dell’Università, Roma, Italy
| | - Polina Dgebuadze
- A.N. Severtzov Institute of Ecology and Evolution of Russian Academy of Sciences, Leninskiy Prospect, Moscow, Russia
| | | | - Philippe Bouchet
- Institut de Systématique, Évolution, Biodiversité ISYEB – UMR 7205 – CNRS, MNHN, UPMC, EPHE, Muséum National d’Histoire Naturelle, Sorbonne Universités, Paris, France
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222
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Ritchie AM, Lo N, Ho SYW. The Impact of the Tree Prior on Molecular Dating of Data Sets Containing a Mixture of Inter- and Intraspecies Sampling. Syst Biol 2018; 66:413-425. [PMID: 27798404 DOI: 10.1093/sysbio/syw095] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 10/14/2016] [Indexed: 11/12/2022] Open
Abstract
In Bayesian phylogenetic analyses of genetic data, prior probability distributions need to be specified for the model parameters, including the tree. When Bayesian methods are used for molecular dating, available tree priors include those designed for species-level data, such as the pure-birth and birth-death priors, and coalescent-based priors designed for population-level data. However, molecular dating methods are frequently applied to data sets that include multiple individuals across multiple species. Such data sets violate the assumptions of both the speciation and coalescent-based tree priors, making it unclear which should be chosen and whether this choice can affect the estimation of node times. To investigate this problem, we used a simulation approach to produce data sets with different proportions of within- and between-species sampling under the multispecies coalescent model. These data sets were then analyzed under pure-birth, birth-death, constant-size coalescent, and skyline coalescent tree priors. We also explored the ability of Bayesian model testing to select the best-performing priors. We confirmed the applicability of our results to empirical data sets from cetaceans, phocids, and coregonid whitefish. Estimates of node times were generally robust to the choice of tree prior, but some combinations of tree priors and sampling schemes led to large differences in the age estimates. In particular, the pure-birth tree prior frequently led to inaccurate estimates for data sets containing a mixture of inter- and intraspecific sampling, whereas the birth-death and skyline coalescent priors produced stable results across all scenarios. Model testing provided an adequate means of rejecting inappropriate tree priors. Our results suggest that tree priors do not strongly affect Bayesian molecular dating results in most cases, even when severely misspecified. However, the choice of tree prior can be significant for the accuracy of dating results in the case of data sets with mixed inter- and intraspecies sampling. [Bayesian phylogenetic methods; model testing; molecular dating; node time; tree prior.].
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Affiliation(s)
- Andrew M Ritchie
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
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223
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Bai J, Xu S, Nie Z, Wang Y, Zhu C, Wang Y, Min W, Cai Y, Zou J, Zhou X. The complete mitochondrial genome of Huananpotamon lichuanense (Decapoda: Brachyura) with phylogenetic implications for freshwater crabs. Gene 2018; 646:217-226. [PMID: 29307851 DOI: 10.1016/j.gene.2018.01.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 11/22/2017] [Accepted: 01/03/2018] [Indexed: 10/18/2022]
Abstract
In the present study, we determined the complete mitochondrial genome of Huananpotamon lichuanense (Decapoda: Brachyura) for the first time. The genome is 15,380bp in length and typically consists of 37 genes. When the gene order was compared to the ancestral crustacean type, two tRNA genes (tRNAHis and tRNAGln) were rearranged in H. lichuanense, and the translocation of tRNAGln appeared only in Potamoidea crabs, such as Geothelphusa dehaani and Sinopotamon xiushuiense, supporting the monophyly of the Potamoidea superfamily. Thirteen protein-coding genes and 2 rRNA genes were divided into five complexes to perform the phylogenetic analysis, and the results showed that the trees constructed by complex I (ND1-ND6 and ND4L), complex IV (COX1-COX3) and rRNA genes better accord with the morphological classification system, suggesting that molecular markers of higher-level phylogeny can be developed in these three complexes in the future. The estimated divergence time for freshwater crabs is approximately 133.58Ma, and G. dehaani from Japan diverged from the freshwater crabs of mainland China approximately 60.66Ma. A selective pressure analysis based on current data revealed obviously increasing dN/dS ratios (except for ATP6 and ND4L) of freshwater crabs, and the accumulation of nonsynonymous mutations suggests that terrestrial habitats provide a relatively relaxed selective pressure environment for this group.
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Affiliation(s)
- Jun Bai
- Research lab of Freshwater Crustacean Decapoda &Paragonimus, School of Basic Medical Sciences, Nanchang University, 461 Bayi Avenue, Nanchang City, Jiangxi Province 330006, People's Republic of China
| | - Shuxin Xu
- Research lab of Freshwater Crustacean Decapoda &Paragonimus, School of Basic Medical Sciences, Nanchang University, 461 Bayi Avenue, Nanchang City, Jiangxi Province 330006, People's Republic of China
| | - Zongheng Nie
- Research lab of Freshwater Crustacean Decapoda &Paragonimus, School of Basic Medical Sciences, Nanchang University, 461 Bayi Avenue, Nanchang City, Jiangxi Province 330006, People's Republic of China
| | - Yifan Wang
- Institute of Pathogen Biology, Jiangxi Academy of Medical Sciences, 461 Bayi Avenue, Nanchang City, Jiangxi Province 330006, People's Republic of China
| | - Chunchao Zhu
- Research lab of Freshwater Crustacean Decapoda &Paragonimus, School of Basic Medical Sciences, Nanchang University, 461 Bayi Avenue, Nanchang City, Jiangxi Province 330006, People's Republic of China
| | - Yan Wang
- Research lab of Freshwater Crustacean Decapoda &Paragonimus, School of Basic Medical Sciences, Nanchang University, 461 Bayi Avenue, Nanchang City, Jiangxi Province 330006, People's Republic of China
| | - Weiping Min
- Institute of Pathogen Biology, Jiangxi Academy of Medical Sciences, 461 Bayi Avenue, Nanchang City, Jiangxi Province 330006, People's Republic of China
| | - Yixiong Cai
- National Biodiversity Centre, National Parks Board, 1 Cluny Road, Singapore 259569, Republic of Singapore
| | - Jiexin Zou
- Research lab of Freshwater Crustacean Decapoda &Paragonimus, School of Basic Medical Sciences, Nanchang University, 461 Bayi Avenue, Nanchang City, Jiangxi Province 330006, People's Republic of China.
| | - Xianmin Zhou
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, 1299 Xuefu Avenue, Nanchang City, Jiangxi Province 330031, People's Republic of China.
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224
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Yinda CK, Ghogomu SM, Conceição-Neto N, Beller L, Deboutte W, Vanhulle E, Maes P, Van Ranst M, Matthijnssens J. Cameroonian fruit bats harbor divergent viruses, including rotavirus H, bastroviruses, and picobirnaviruses using an alternative genetic code. Virus Evol 2018; 4:vey008. [PMID: 29644096 PMCID: PMC5888411 DOI: 10.1093/ve/vey008] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Most human emerging infectious diseases originate from wildlife and bats are a major reservoir of viruses, a few of which have been highly pathogenic to humans. In some regions of Cameroon, bats are hunted and eaten as a delicacy. This close proximity between human and bats provides ample opportunity for zoonotic events. To elucidate the viral diversity of Cameroonian fruit bats, we collected and metagenomically screened eighty-seven fecal samples of Eidolon helvum and Epomophorus gambianus fruit bats. The results showed a plethora of known and novel viruses. Phylogenetic analyses of the eleven gene segments of the first complete bat rotavirus H genome, showed clearly separated clusters of human, porcine, and bat rotavirus H strains, not indicating any recent interspecies transmission events. Additionally, we identified and analyzed a bat bastrovirus genome (a novel group of recently described viruses, related to astroviruses and hepatitis E viruses), confirming their recombinant nature, and provide further evidence of additional recombination events among bat bastroviruses. Interestingly, picobirnavirus-like RNA-dependent RNA polymerase gene segments were identified using an alternative mitochondrial genetic code, and further principal component analyses suggested that they may have a similar lifestyle to mitoviruses, a group of virus-like elements known to infect the mitochondria of fungi. Although identified bat coronavirus, parvovirus, and cyclovirus strains belong to established genera, most of the identified partitiviruses and densoviruses constitute putative novel genera in their respective families. Finally, the results of the phage community analyses of these bats indicate a very diverse geographically distinct bat phage population, probably reflecting different diets and gut bacterial ecosystems.
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Affiliation(s)
- Claude Kwe Yinda
- Laboratory of Viral Metagenomics
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, B-3000 Leuven, Belgium
| | - Stephen Mbigha Ghogomu
- Molecular and Cell Biology Laboratory, Biotechnology Unit, Department of Biochemistry and Molecular Biology, University of Buea, Buea, 237, Cameroon
| | - Nádia Conceição-Neto
- Laboratory of Viral Metagenomics
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, B-3000 Leuven, Belgium
| | | | | | | | - Piet Maes
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, B-3000 Leuven, Belgium
| | - Marc Van Ranst
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, B-3000 Leuven, Belgium
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225
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Fan Y, Yu M, Liu M, Zhang R, Sun W, Qian M, Duan H, Chang W, Ma J, Qu C, Zhang K, Lei B, Lu K. Genome-Wide Identification, Evolutionary and Expression Analyses of the GALACTINOL SYNTHASE Gene Family in Rapeseed and Tobacco. Int J Mol Sci 2017; 18:E2768. [PMID: 29261107 PMCID: PMC5751367 DOI: 10.3390/ijms18122768] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/16/2017] [Accepted: 12/17/2017] [Indexed: 11/16/2022] Open
Abstract
Galactinol synthase (GolS) is a key enzyme in raffinose family oligosaccharide (RFO) biosynthesis. The finding that GolS accumulates in plants exposed to abiotic stresses indicates RFOs function in environmental adaptation. However, the evolutionary relationships and biological functions of GolS family in rapeseed (Brassica napus) and tobacco (Nicotiana tabacum) remain unclear. In this study, we identified 20 BnGolS and 9 NtGolS genes. Subcellular localization predictions showed that most of the proteins are localized to the cytoplasm. Phylogenetic analysis identified a lost event of an ancient GolS copy in the Solanaceae and an ancient duplication event leading to evolution of GolS4/7 in the Brassicaceae. The three-dimensional structures of two GolS proteins were conserved, with an important DxD motif for binding to UDP-galactose (uridine diphosphate-galactose) and inositol. Expression profile analysis indicated that BnGolS and NtGolS genes were expressed in most tissues and highly expressed in one or two specific tissues. Hormone treatments strongly induced the expression of most BnGolS genes and homologous genes in the same subfamilies exhibited divergent-induced expression. Our study provides a comprehensive evolutionary analysis of GolS genes among the Brassicaceae and Solanaceae as well as an insight into the biological function of GolS genes in hormone response in plants.
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Affiliation(s)
- Yonghai Fan
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China.
| | - Mengna Yu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China.
| | - Miao Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China.
| | - Rui Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China.
| | - Wei Sun
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China.
| | - Mingchao Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China.
| | - Huichun Duan
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China.
| | - Wei Chang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China.
| | - Jinqi Ma
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China.
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China.
| | - Kai Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China.
| | - Bo Lei
- Key Laboratory of Molecular Genetics, China National Tobacco Corporation, Guizhou Academy of Tobacco Science, Guiyang 550081, China.
- Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China.
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China.
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226
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Alves BM, Siqueira JD, Garrido MM, Botelho OM, Prellwitz IM, Ribeiro SR, Soares EA, Soares MA. Characterization of HIV-1 Near Full-Length Proviral Genome Quasispecies from Patients with Undetectable Viral Load Undergoing First-Line HAART Therapy. Viruses 2017; 9:v9120392. [PMID: 29257103 PMCID: PMC5744166 DOI: 10.3390/v9120392] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 12/16/2017] [Accepted: 12/18/2017] [Indexed: 12/16/2022] Open
Abstract
Increased access to highly active antiretroviral therapy (HAART) by human immunodeficiency virus postive (HIV+) individuals has become a reality worldwide. In Brazil, HAART currently reaches over half of HIV-infected subjects. In the context of a remarkable HIV-1 genetic variability, highly related variants, called quasispecies, are generated. HIV quasispecies generated during infection can influence virus persistence and pathogenicity, representing a challenge to treatment. However, the clinical relevance of minority quasispecies is still uncertain. In this study, we have determined the archived proviral sequences, viral subtype and drug resistance mutations from a cohort of HIV+ patients with undetectable viral load undergoing HAART as first-line therapy using next-generation sequencing for near full-length virus genome (NFLG) assembly. HIV-1 consensus sequences representing NFLG were obtained for eleven patients, while for another twelve varying genome coverage rates were obtained. Phylogenetic analysis showed the predominance of subtype B (83%; 19/23). Considering the minority variants, 18 patients carried archived virus harboring at least one mutation conferring antiretroviral resistance; for six patients, the mutations correlated with the current ARVs used. These data highlight the importance of monitoring HIV minority drug resistant variants and their clinical impact, to guide future regimen switches and improve HIV treatment success.
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Affiliation(s)
- Brunna M Alves
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
| | - Juliana D Siqueira
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
| | - Marianne M Garrido
- Serviço de Doenças Infecciosas, Hospital Federal de Ipanema, Rio de Janeiro 22411-020, Brazil.
| | - Ornella M Botelho
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
| | - Isabel M Prellwitz
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
| | - Sayonara R Ribeiro
- Serviço de Doenças Infecciosas, Hospital Federal de Ipanema, Rio de Janeiro 22411-020, Brazil.
| | - Esmeralda A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
| | - Marcelo A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21944-970, Brazil.
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227
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Central European Woolly Mammoth Population Dynamics: Insights from Late Pleistocene Mitochondrial Genomes. Sci Rep 2017; 7:17714. [PMID: 29255197 PMCID: PMC5735091 DOI: 10.1038/s41598-017-17723-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/21/2017] [Indexed: 01/13/2023] Open
Abstract
The population dynamics of the Pleistocene woolly mammoth (Mammuthus primigenius) has been the subject of intensive palaeogenetic research. Although a large number of mitochondrial genomes across Eurasia have been reconstructed, the available data remains geographically sparse and mostly focused on eastern Eurasia. Thus, population dynamics in other regions have not been extensively investigated. Here, we use a multi-method approach utilising proteomic, stable isotope and genetic techniques to identify and generate twenty woolly mammoth mitochondrial genomes, and associated dietary stable isotopic data, from highly fragmentary Late Pleistocene material from central Europe. We begin to address region-specific questions regarding central European woolly mammoth populations, highlighting parallels with a previous replacement event in eastern Eurasia ten thousand years earlier. A high number of shared derived mutations between woolly mammoth mitochondrial clades are identified, questioning previous phylogenetic analysis and thus emphasizing the need for nuclear DNA studies to explicate the increasingly complex genetic history of the woolly mammoth.
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228
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Lee C, Moroldo M, Perdomo-Sabogal A, Mach N, Marthey S, Lecardonnel J, Wahlberg P, Chong AY, Estellé J, Ho SYW, Rogel-Gaillard C, Gongora J. Inferring the evolution of the major histocompatibility complex of wild pigs and peccaries using hybridisation DNA capture-based sequencing. Immunogenetics 2017; 70:401-417. [PMID: 29256177 DOI: 10.1007/s00251-017-1048-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/25/2017] [Indexed: 12/20/2022]
Abstract
The major histocompatibility complex (MHC) is a key genomic model region for understanding the evolution of gene families and the co-evolution between host and pathogen. To date, MHC studies have mostly focused on species from major vertebrate lineages. The evolution of MHC classical (Ia) and non-classical (Ib) genes in pigs has attracted interest because of their antigen presentation roles as part of the adaptive immune system. The pig family Suidae comprises over 18 extant species (mostly wild), but only the domestic pig has been extensively sequenced and annotated. To address this, we used a DNA-capture approach, with probes designed from the domestic pig genome, to generate MHC data for 11 wild species of pigs and their closest living family, Tayassuidae. The approach showed good efficiency for wild pigs (~80% reads mapped, ~87× coverage), compared to tayassuids (~12% reads mapped, ~4× coverage). We retrieved 145 MHC loci across both families. Phylogenetic analyses show that the class Ia and Ib genes underwent multiple duplications and diversifications before suids and tayassuids diverged from their common ancestor. The histocompatibility genes mostly form orthologous groups and there is genetic differentiation for most of these genes between Eurasian and sub-Saharan African wild pigs. Tests of selection showed that the peptide-binding region of class Ib genes was under positive selection. These findings contribute to better understanding of the evolutionary history of the MHC, specifically, the class I genes, and provide useful data for investigating the immune response of wild populations against pathogens.
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Affiliation(s)
- Carol Lee
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, Australia
| | - Marco Moroldo
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Alvaro Perdomo-Sabogal
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, Australia.,Institute of Animal Science (460i), Department of Bioinformatics, University of Hohenheim, Stuttgart, Germany
| | - Núria Mach
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Sylvain Marthey
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jérôme Lecardonnel
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Per Wahlberg
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Amanda Y Chong
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, Australia.,Earlham Institute, Norwich Research Park, Norwich, UK
| | - Jordi Estellé
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Simon Y W Ho
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
| | | | - Jaime Gongora
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, Australia.
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229
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Ilgová J, Jedličková L, Dvořáková H, Benovics M, Mikeš L, Janda L, Vorel J, Roudnický P, Potěšil D, Zdráhal Z, Gelnar M, Kašný M. A novel type I cystatin of parasite origin with atypical legumain-binding domain. Sci Rep 2017; 7:17526. [PMID: 29235483 PMCID: PMC5727476 DOI: 10.1038/s41598-017-17598-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 11/28/2017] [Indexed: 12/26/2022] Open
Abstract
Parasite inhibitors of cysteine peptidases are known to influence a vast range of processes linked to a degradation of either the parasites' own proteins or proteins native to their hosts. We characterise a novel type I cystatin (stefin) found in a sanguinivorous fish parasite Eudiplozoon nipponicum (Platyhelminthes: Monogenea). We have identified a transcript of its coding gene in the transcriptome of adult worms. Its amino acid sequence is similar to other stefins except for containing a legumain-binding domain, which is in this type of cystatins rather unusual. As expected, the recombinant form of E. nipponicum stefin (rEnStef) produced in Escherichia coli inhibits clan CA peptidases - cathepsins L and B of the worm - via the standard papain-binding domain. It also blocks haemoglobinolysis by cysteine peptidases in the worm's excretory-secretory products and soluble extracts. Furthermore, we had confirmed its ability to inhibit clan CD asparaginyl endopeptidase (legumain). The presence of a native EnStef in the excretory-secretory products of adult worms, detected by mass spectrometry, suggests that this protein has an important biological function at the host-parasite interface. We discuss the inhibitor's possible role in the regulation of blood digestion, modulation of antigen presentation, and in the regeneration of host tissues.
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Affiliation(s)
- Jana Ilgová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic.
| | - Lucie Jedličková
- Department of Parasitology, Faculty of Science, Charles University, Prague, 128 44, Czech Republic
| | - Hana Dvořáková
- Department of Parasitology, Faculty of Science, Charles University, Prague, 128 44, Czech Republic
| | - Michal Benovics
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic
| | - Libor Mikeš
- Department of Parasitology, Faculty of Science, Charles University, Prague, 128 44, Czech Republic
| | - Lubomír Janda
- Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Jiří Vorel
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic
| | - Pavel Roudnický
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Milan Gelnar
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic
| | - Martin Kašný
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic.,Department of Parasitology, Faculty of Science, Charles University, Prague, 128 44, Czech Republic
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230
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Xin Y, Lu Y, Lee YY, Wei L, Jia J, Wang Q, Wang D, Bai F, Hu H, Hu Q, Liu J, Li Y, Xu J. Producing Designer Oils in Industrial Microalgae by Rational Modulation of Co-evolving Type-2 Diacylglycerol Acyltransferases. MOLECULAR PLANT 2017; 10:1523-1539. [PMID: 29107033 DOI: 10.1016/j.molp.2017.10.011] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/17/2017] [Accepted: 10/21/2017] [Indexed: 05/03/2023]
Abstract
Microalgal oils, depending on their degree of unsaturation, can be utilized as either nutritional supplements or fuels; thus, a feedstock with genetically designed and tunable degree of unsaturation is desirable to maximize process efficiency and product versatility. Systematic profiling of ex vivo (in yeast), in vitro, and in vivo activities of type-2 diacylglycerol acyltransferases in Nannochloropsis oceanica (NoDGAT2s or NoDGTTs), via reverse genetics, revealed that NoDGAT2A prefers saturated fatty acids (SFAs), NoDGAT2D prefers monounsaturated fatty acids (MUFAs), and NoDGAT2C exhibits the strongest activity toward polyunsaturated fatty acids (PUFAs). As NoDGAT2A, 2C, and 2D originated from the green alga, red alga, and eukaryotic host ancestral participants of secondary endosymbiosis, respectively, a mechanistic model of oleaginousness was unveiled, in which the indigenous and adopted NoDGAT2s formulated functional complementarity and specific transcript abundance ratio that underlie a rigid SFA:MUFA:PUFA hierarchy in triacylglycerol (TAG). By rationally modulating the ratio of NoDGAT2A:2C:2D transcripts, a bank of N. oceanica strains optimized for nutritional supplement or fuel production with a wide range of degree of unsaturation were created, in which proportion of SFAs, MUFAs, and PUFAs in TAG varied by 1.3-, 3.7-, and 11.2-fold, respectively. This established a novel strategy to simultaneously improve productivity and quality of oils from industrial microalgae.
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Affiliation(s)
- Yi Xin
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yandu Lu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Ying Lee
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science and University of Maryland, Baltimore County, Baltimore, MD 21202, USA
| | - Li Wei
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Jia
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qintao Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongmei Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fali Bai
- Core Laboratory, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanhua Hu
- Diatom Biology Group, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Hu
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin Liu
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science and University of Maryland, Baltimore County, Baltimore, MD 21202, USA; Institute for Food and Bioresource Engineering and Department of Energy and Resource Engineering, College of Engineering, Peking University, Beijing 100871, China.
| | - Yantao Li
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science and University of Maryland, Baltimore County, Baltimore, MD 21202, USA.
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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231
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Pečnerová P, Palkopoulou E, Wheat CW, Skoglund P, Vartanyan S, Tikhonov A, Nikolskiy P, van der Plicht J, Díez-Del-Molino D, Dalén L. Mitogenome evolution in the last surviving woolly mammoth population reveals neutral and functional consequences of small population size. Evol Lett 2017; 1:292-303. [PMID: 30283657 PMCID: PMC6121868 DOI: 10.1002/evl3.33] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 11/06/2017] [Indexed: 01/25/2023] Open
Abstract
The onset of the Holocene was associated with a global temperature increase, which led to a rise in sea levels and isolation of the last surviving population of woolly mammoths on Wrangel Island. Understanding what happened with the population's genetic diversity at the time of the isolation and during the ensuing 6000 years can help clarify the effects of bottlenecks and subsequent limited population sizes in species approaching extinction. Previous genetic studies have highlighted questions about how the Holocene Wrangel population was established and how the isolation event affected genetic diversity. Here, we generated high‐quality mitogenomes from 21 radiocarbon‐dated woolly mammoths to compare the ancestral large and genetically diverse Late Pleistocene Siberian population and the small Holocene Wrangel population. Our results indicate that mitogenome diversity was reduced to one single haplotype at the time of the isolation, and thus that the Holocene Wrangel Island population was established by a single maternal lineage. Moreover, we show that the ensuing small effective population size coincided with fixation of a nonsynonymous mutation, and a comparative analysis of mutation rates suggests that the evolutionary rate was accelerated in the Holocene population. These results suggest that isolation on Wrangel Island led to an increase in the frequency of deleterious genetic variation, and thus are consistent with the hypothesis that strong genetic drift in small populations leads to purifying selection being less effective in removing deleterious mutations.
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Affiliation(s)
- Patrícia Pečnerová
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden.,Department of Zoology Stockholm University Stockholm Sweden
| | - Eleftheria Palkopoulou
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden.,Department of Zoology Stockholm University Stockholm Sweden.,Department of Genetics Harvard Medical School Boston Massachusetts 02115
| | | | - Pontus Skoglund
- Department of Genetics Harvard Medical School Boston Massachusetts 02115.,Broad Institute of Harvard and MIT Cambridge Massachusetts 02142
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute N.A.N.A. Shilo Far East Branch, Russian Academy of Sciences (NEISRI FEB RAS) Magadan Russia
| | - Alexei Tikhonov
- Zoological Institute of Russian Academy of Sciences Saint-Petersburg Russia.,Institute of Applied Ecology of the North North-Eastern Federal University Yakutsk Russia
| | - Pavel Nikolskiy
- Geological Institute of the Russian Academy of Sciences Moscow Russia
| | - Johannes van der Plicht
- Centre for Isotope Research Groningen University Groningen The Netherlands.,Faculty of Archaeology Leiden University Leiden The Netherlands
| | - David Díez-Del-Molino
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
| | - Love Dalén
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
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232
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Pool deconvolution approach for high-throughput gene mining from Bacillus thuringiensis. Appl Microbiol Biotechnol 2017; 102:1467-1482. [DOI: 10.1007/s00253-017-8633-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/24/2017] [Accepted: 11/05/2017] [Indexed: 11/27/2022]
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Gordeeva NV, Salmenkova EA. Genetic markers of adaptive processes in the Far Eastern pink salmon Oncorhynchus gorbuscha: Allelic diversity at the locus of major histocompatibility complex MHC I-A1. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417110035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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234
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Genomic, Network, and Phylogenetic Analysis of the Oomycete Effector Arsenal. mSphere 2017; 2:mSphere00408-17. [PMID: 29202039 PMCID: PMC5700374 DOI: 10.1128/msphere.00408-17] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 11/02/2017] [Indexed: 02/07/2023] Open
Abstract
The oomycetes are a class of microscopic, filamentous eukaryotes and include ecologically significant animal and plant pathogens. Oomycetes secrete large arsenals of effector proteins that degrade host cell components, manipulate host immune responses, and induce necrosis, enabling parasitic colonization. In this study, we catalogued the number and evolution of effectors in 37 oomycete species whose genomes have been completely sequenced. Large expansions of effector protein families in Phytophthora species, including glycoside hydrolases, pectinases, and necrosis-inducing proteins, were observed. Species-specific expansions were detected, including chitinases in Aphanomyces astaci and Pythium oligandrum. Novel effectors which may be involved in suppressing animal immune responses were identified in Ap. astaci and Py. oligandrum. Type 2 necrosis-inducing proteins with an unusual phylogenetic history were also located. This work represents an up-to-date in silico catalogue of the effector arsenal of the oomycetes based on the 37 genomes currently available. The oomycetes are a class of microscopic, filamentous eukaryotes within the stramenopiles-alveolate-Rhizaria (SAR) supergroup and include ecologically significant animal and plant pathogens. Oomycetes secrete large arsenals of effector proteins that degrade host cell components, manipulate host immune responses, and induce necrosis, enabling parasitic colonization. This study investigated the expansion and evolution of effectors in 37 oomycete species in 4 oomycete orders, including Albuginales, Peronosporales, Pythiales, and Saprolegniales species. Our results highlight the large expansions of effector protein families, including glycoside hydrolases, pectinases, and necrosis-inducing proteins, in Phytophthora species. Species-specific expansions, including expansions of chitinases in Aphanomyces astaci and Pythium oligandrum, were detected. Novel effectors which may be involved in suppressing animal immune responses in Ap. astaci and Py. insidiosum were also identified. Type 2 necrosis-inducing proteins with an unusual phylogenetic history were also located in a number of oomycete species. We also investigated the "RxLR" effector complement of all 37 species and, as expected, observed large expansions in Phytophthora species numbers. Our results provide in-depth sequence information on all putative RxLR effectors from all 37 species. This work represents an up-to-date in silico catalogue of the effector arsenal of the oomycetes based on the 37 genomes currently available. IMPORTANCE The oomycetes are a class of microscopic, filamentous eukaryotes and include ecologically significant animal and plant pathogens. Oomycetes secrete large arsenals of effector proteins that degrade host cell components, manipulate host immune responses, and induce necrosis, enabling parasitic colonization. In this study, we catalogued the number and evolution of effectors in 37 oomycete species whose genomes have been completely sequenced. Large expansions of effector protein families in Phytophthora species, including glycoside hydrolases, pectinases, and necrosis-inducing proteins, were observed. Species-specific expansions were detected, including chitinases in Aphanomyces astaci and Pythium oligandrum. Novel effectors which may be involved in suppressing animal immune responses were identified in Ap. astaci and Py. oligandrum. Type 2 necrosis-inducing proteins with an unusual phylogenetic history were also located. This work represents an up-to-date in silico catalogue of the effector arsenal of the oomycetes based on the 37 genomes currently available.
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Andrades Valtueña A, Mittnik A, Key FM, Haak W, Allmäe R, Belinskij A, Daubaras M, Feldman M, Jankauskas R, Janković I, Massy K, Novak M, Pfrengle S, Reinhold S, Šlaus M, Spyrou MA, Szécsényi-Nagy A, Tõrv M, Hansen S, Bos KI, Stockhammer PW, Herbig A, Krause J. The Stone Age Plague and Its Persistence in Eurasia. Curr Biol 2017; 27:3683-3691.e8. [PMID: 29174893 DOI: 10.1016/j.cub.2017.10.025] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/31/2017] [Accepted: 10/09/2017] [Indexed: 12/20/2022]
Abstract
Yersinia pestis, the etiologic agent of plague, is a bacterium associated with wild rodents and their fleas. Historically it was responsible for three pandemics: the Plague of Justinian in the 6th century AD, which persisted until the 8th century [1]; the renowned Black Death of the 14th century [2, 3], with recurrent outbreaks until the 18th century [4]; and the most recent 19th century pandemic, in which Y. pestis spread worldwide [5] and became endemic in several regions [6]. The discovery of molecular signatures of Y. pestis in prehistoric Eurasian individuals and two genomes from Southern Siberia suggest that Y. pestis caused some form of disease in humans prior to the first historically documented pandemic [7]. Here, we present six new European Y. pestis genomes spanning the Late Neolithic to the Bronze Age (LNBA; 4,800 to 3,700 calibrated years before present). This time period is characterized by major transformative cultural and social changes that led to cross-European networks of contact and exchange [8, 9]. We show that all known LNBA strains form a single putatively extinct clade in the Y. pestis phylogeny. Interpreting our data within the context of recent ancient human genomic evidence that suggests an increase in human mobility during the LNBA, we propose a possible scenario for the early spread of Y. pestis: the pathogen may have entered Europe from Central Eurasia following an expansion of people from the steppe, persisted within Europe until the mid-Bronze Age, and moved back toward Central Eurasia in parallel with human populations.
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Affiliation(s)
| | - Alissa Mittnik
- Max Planck Institute for the Science of Human History, Jena, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Felix M Key
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Wolfgang Haak
- Max Planck Institute for the Science of Human History, Jena, Germany; School of Biological Sciences, The University of Adelaide, Adelaide SA 5005, South Australia, Australia
| | - Raili Allmäe
- Archaeological Research Collection, Tallinn University, Tallinn, Estonia
| | | | - Mantas Daubaras
- Department of Archaeology, Lithuanian Institute of History, Vilnius, Lithuania
| | - Michal Feldman
- Max Planck Institute for the Science of Human History, Jena, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Rimantas Jankauskas
- Department of Anatomy, Histology and Anthropology, Vilnius University, Vilnius, Lithuania
| | - Ivor Janković
- Institute for Anthropological Research, Zagreb, Croatia; Department of Anthropology, University of Wyoming, Laramie, WY, USA
| | - Ken Massy
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilians-University Munich, Munich, Germany; Heidelberg Academy of Sciences, Heidelberg, Germany
| | - Mario Novak
- Institute for Anthropological Research, Zagreb, Croatia
| | - Saskia Pfrengle
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Mario Šlaus
- Anthropological Center, Croatian Academy of Sciences and Arts, Zagreb, Croatia
| | - Maria A Spyrou
- Max Planck Institute for the Science of Human History, Jena, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Anna Szécsényi-Nagy
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | - Mari Tõrv
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu, Estonia
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Kirsten I Bos
- Max Planck Institute for the Science of Human History, Jena, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Philipp W Stockhammer
- Max Planck Institute for the Science of Human History, Jena, Germany; Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Jena, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany.
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany.
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Zou H, Jakovlić I, Chen R, Zhang D, Zhang J, Li WX, Wang GT. The complete mitochondrial genome of parasitic nematode Camallanus cotti: extreme discontinuity in the rate of mitogenomic architecture evolution within the Chromadorea class. BMC Genomics 2017; 18:840. [PMID: 29096600 PMCID: PMC5669012 DOI: 10.1186/s12864-017-4237-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 10/24/2017] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Complete mitochondrial genomes are much better suited for the taxonomic identification and phylogenetic studies of nematodes than morphology or traditionally-used molecular markers, but they remain unavailable for the entire Camallanidae family (Chromadorea). As the only published mitogenome in the Camallanina suborder (Dracunculoidea superfamily) exhibited a unique gene order, the other objective of this research was to study the evolution of mitochondrial architecture in the Spirurida order. Thus, we sequenced the complete mitogenome of the Camallanus cotti fish parasite and conducted structural and phylogenomic comparative analyses with all available Spirurida mitogenomes. RESULTS The mitogenome is exceptionally large (17,901 bp) among the Chromadorea and, with 46 (pseudo-) genes, exhibits a unique architecture among nematodes. Six protein-coding genes (PCGs) and six tRNAs are duplicated. An additional (seventh) tRNA (Trp) was probably duplicated by the remolding of tRNA-Ser2 (missing). Two pairs of these duplicated PCGs might be functional; three were incomplete and one contained stop codons. Apart from Ala and Asp, all other duplicated tRNAs are conserved and probably functional. Only 19 unique tRNAs were found. Phylogenomic analysis included Gnathostomatidae (Spirurina) in the Camallanina suborder. CONCLUSIONS Within the Nematoda, comparable PCG duplications were observed only in the enoplean Mermithidae family, but those result from mitochondrial recombination, whereas characteristics of the studied mitogenome suggest that likely rearrangement mechanisms are either a series of duplications, transpositions and random loss events, or duplication, fragmentation and subsequent reassembly of the mitogenome. We put forward a hypothesis that the evolution of mitogenomic architecture is extremely discontinuous, and that once a long period of stasis in gene order and content has been punctuated by a rearrangement event, such a destabilised mitogenome is much more likely to undergo subsequent rearrangement events, resulting in an exponentially accelerated evolutionary rate of mitogenomic rearrangements. Implications of this model are particularly important for the application of gene order similarity as an additive source of phylogenetic information. Chromadorean nematodes, and particularly Camallanina clade (with C. cotti as an example of extremely accelerated rate of rearrangements), might be a good model to further study this discontinuity in the dynamics of mitogenomic evolution.
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Affiliation(s)
- Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Wuhan Institute of Biotechnology, Wuhan, 430075 People’s Republic of China
| | - Rong Chen
- Bio-Transduction Lab, Wuhan Institute of Biotechnology, Wuhan, 430075 People’s Republic of China
| | - Dong Zhang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Jin Zhang
- Bio-Transduction Lab, Wuhan Institute of Biotechnology, Wuhan, 430075 People’s Republic of China
| | - Wen-Xiang Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
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Gene Acquisition by a Distinct Phyletic Group within Streptococcus pneumoniae Promotes Adhesion to the Ocular Epithelium. mSphere 2017; 2:mSphere00213-17. [PMID: 29085912 PMCID: PMC5656748 DOI: 10.1128/msphere.00213-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 09/14/2017] [Indexed: 11/20/2022] Open
Abstract
Streptococcus pneumoniae (pneumococcus) displays broad tissue tropism and infects multiple body sites in the human host. However, infections of the conjunctiva are limited to strains within a distinct phyletic group with multilocus sequence types ST448, ST344, ST1186, ST1270, and ST2315. In this study, we sequenced the genomes of six pneumococcal strains isolated from eye infections. The conjunctivitis isolates are grouped in a distinct phyletic group together with a subset of nasopharyngeal isolates. The keratitis (infection of the cornea) and endophthalmitis (infection of the vitreous body) isolates are grouped with the remainder of pneumococcal strains. Phenotypic characterization is consistent with morphological differences associated with the distinct phyletic group. Specifically, isolates from the distinct phyletic group form aggregates in planktonic cultures and chain-like structures in biofilms grown on abiotic surfaces. To begin to investigate the association between genotype and epidemiology, we focused on a predicted surface-exposed adhesin (SspB) encoded exclusively by this distinct phyletic group. Phylogenetic analysis of the gene encoding SspB in the context of a streptococcal species tree suggests that sspB was acquired by lateral gene transfer from Streptococcus suis. Furthermore, an sspB deletion mutant displays decreased adherence to cultured cells from the ocular epithelium compared to the isogenic wild-type and complemented strains. Together these findings suggest that acquisition of genes from outside the species has contributed to pneumococcal tissue tropism by enhancing the ability of a subset of strains to infect the ocular epithelium causing conjunctivitis. IMPORTANCE Changes in the gene content of pathogens can modify their ability to colonize and/or survive in different body sites in the human host. In this study, we investigate a gene acquisition event and its role in the pathogenesis of Streptococccus pneumoniae (pneumococcus). Our findings suggest that the gene encoding the predicted surface protein SspB has been transferred from Streptococcus suis (a distantly related streptococcal species) into a distinct set of pneumococcal strains. This group of strains distinguishes itself from the remainder of pneumococcal strains by extensive differences in genomic composition and by the ability to cause conjunctivitis. We find that the presence of sspB increases adherence of pneumococcus to the ocular epithelium. Thus, our data support the hypothesis that a subset of pneumococcal strains has gained genes from neighboring species that enhance their ability to colonize the epithelium of the eye, thus expanding into a new niche.
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Takatsuka J, Nakai M, Shinoda T. A virus carries a gene encoding juvenile hormone acid methyltransferase, a key regulatory enzyme in insect metamorphosis. Sci Rep 2017; 7:13522. [PMID: 29051595 PMCID: PMC5648886 DOI: 10.1038/s41598-017-14059-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/05/2017] [Indexed: 12/29/2022] Open
Abstract
Microbial parasitism, infection, and symbiosis in animals often modulate host endocrine systems, resulting in alterations of phenotypic traits of the host that can have profound effects on the ecology and evolution of both the microorganisms and their hosts. Information about the mechanisms and genetic bases of such modulations by animal parasites is available from studies of steroid hormones. However, reports involving other hormones are scarce. We found that an insect virus, a betaentomopoxvirus, encodes a juvenile hormone acid methyltransferase that can synthesize an important insect hormone, the sesquiterpenoid juvenile hormone. Phylogenetic analysis suggested that this gene is of bacterial origin. Our study challenges the conventional view that functional enzymes in the late phase of the juvenile hormone biosynthesis pathway are almost exclusive to insects or arthropods, and shed light on juvenoid hormone synthesis beyond Eukaryota. This striking example demonstrates that even animal parasites having no metabolic pathways for molecules resembling host hormones can nevertheless influence the synthesis of such hormones, and provides a new context for studying animal parasite strategies in diverse systems such as host-parasite, host-symbiont or host-vector-parasite.
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Affiliation(s)
- Jun Takatsuka
- Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan.
| | - Madoka Nakai
- Institute of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Tetsuro Shinoda
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
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Echeverría AI, Becerra F, Buezas GN, Vassallo AI. Bite it forward … bite it better? Incisor procumbency and mechanical advantage in the chisel-tooth and scratch-digger genus Ctenomys (Caviomorpha, Rodentia). ZOOLOGY 2017; 125:53-68. [PMID: 29029899 DOI: 10.1016/j.zool.2017.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 06/06/2017] [Accepted: 08/03/2017] [Indexed: 11/24/2022]
Abstract
The subterranean genus Ctenomys (∼60 species, ∼100-1000g) constructs its burrows by using both forefeet and teeth throughout a wide range of habitats in South America. They show a high variation in the incisors' angle of attack (procumbency) and a mostly conserved skull morphology, not only amongst their congeners, but within the caviomorph rodents. Traditionally, procumbency has been largely related to tooth-digging. Looking for the possible influence of incisor procumbency on the mechanical advantage (MA) of each of the seven jaw adductor muscles in the genus, we examined 165 skulls representing 24 species. We also evaluated the role of two other relevant traits - i.e. mandibular width and diastema length - in jaw biomechanics and the existence of a relationship between procumbency angle and soil hardness. The in- and out-lever arms (Li and Lo) of the involve muscles were determined based on their insertion's 3D-coordinates and integrated to calculate their MA. Interspecific scaling relationships for skull and muscle measurements were analyzed through reduced major axis regression performed with phylogenetically independent standardized contrasts. Although the procumbency angle ranged between ∼92.5° (C. mendocinus) and ∼107.2 (C. occultus), we found that it was not significantly correlated with the MA of any jaw adductor muscle. This study also showed that the incisor procumbency variation was not associated with the relative rostral length or soil hardness. This result contradicts previous generalizations about a correlation between habitat conditions and the procumbency of the incisors in subterranean rodents. In sum, our results suggest that, within Ctenomys, possessing more procumbent incisors may not represent a biomechanical advantage, but might be beneficial in other aspects related to chisel-tooth digging or food processing behaviors.
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Affiliation(s)
- Alejandra I Echeverría
- Grupo Morfología Funcional y Comportamiento, Instituto de Investigaciones Marinas y Costeras (IIMyC), Universidad Nacional de Mar del Plata (UNMdP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Funes 3250, 7600 Mar del Plata, Buenos Aires, Argentina.
| | - Federico Becerra
- Grupo Morfología Funcional y Comportamiento, Instituto de Investigaciones Marinas y Costeras (IIMyC), Universidad Nacional de Mar del Plata (UNMdP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Funes 3250, 7600 Mar del Plata, Buenos Aires, Argentina; Max Planck Weizmann Center for Integrative Archaeology and Anthropology (MPWC), Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
| | - Guido N Buezas
- Grupo Morfología Funcional y Comportamiento, Instituto de Investigaciones Marinas y Costeras (IIMyC), Universidad Nacional de Mar del Plata (UNMdP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Funes 3250, 7600 Mar del Plata, Buenos Aires, Argentina
| | - Aldo I Vassallo
- Grupo Morfología Funcional y Comportamiento, Instituto de Investigaciones Marinas y Costeras (IIMyC), Universidad Nacional de Mar del Plata (UNMdP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Funes 3250, 7600 Mar del Plata, Buenos Aires, Argentina
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Gomez-Gil L, Camara Almiron J, Rodriguez Carrillo PL, Olivares Medina CN, Bravo Ruiz G, Romo Rodriguez P, Corrales Escobosa AR, Gutierrez Corona F, Roncero MI. Nitrate assimilation pathway (NAP): role of structural (nit) and transporter (ntr1) genes in Fusarium oxysporum f.sp. lycopersici growth and pathogenicity. Curr Genet 2017; 64:493-507. [DOI: 10.1007/s00294-017-0766-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 10/06/2017] [Accepted: 10/10/2017] [Indexed: 01/12/2023]
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241
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Herman E, Siegesmund MA, Bottery MJ, van Aerle R, Shather MM, Caler E, Dacks JB, van der Giezen M. Membrane Trafficking Modulation during Entamoeba Encystation. Sci Rep 2017; 7:12854. [PMID: 28993644 PMCID: PMC5634486 DOI: 10.1038/s41598-017-12875-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 09/11/2017] [Indexed: 12/15/2022] Open
Abstract
Entamoeba histolytica is an intestinal parasite that infects 50-100 million people and causes up to 55,000 deaths annually. The transmissive form of E. histolytica is the cyst, with a single infected individual passing up to 45 million cysts per day, making cyst production an attractive target for infection control. Lectins and chitin are secreted to form the cyst wall, although little is known about the underlying membrane trafficking processes supporting encystation. As E. histolytica does not readily form cysts in vitro, we assessed membrane trafficking gene expression during encystation in the closely related model Entamoeba invadens. Genes involved in secretion are up-regulated during cyst formation, as are some trans-Golgi network-to-endosome trafficking genes. Furthermore, endocytic and general trafficking genes are up-regulated in the mature cyst, potentially preserved as mRNA in preparation for excystation. Two divergent dynamin-related proteins found in Entamoeba are predominantly expressed during cyst formation. Phylogenetic analyses indicate that they are paralogous to, but quite distinct from, classical dynamins found in human, suggesting that they may be potential drug targets to block encystation. The membrane-trafficking machinery is clearly regulated during encystation, providing an additional facet to understanding this crucial parasitic process.
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Affiliation(s)
- Emily Herman
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, T6G 2H7, Edmonton, Alberta, Canada
| | | | - Michael J Bottery
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Ronny van Aerle
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Centre for Environment, Fisheries, and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, Dorset, DT4 8UB, UK
| | | | - Elisabet Caler
- J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD, 20850, USA
- National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), 6701, Rockledge Drive, Room 9144, Bethesda, MD, 20892-7950, USA
| | - Joel B Dacks
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, T6G 2H7, Edmonton, Alberta, Canada.
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Cooke TF, Fischer CR, Wu P, Jiang TX, Xie KT, Kuo J, Doctorov E, Zehnder A, Khosla C, Chuong CM, Bustamante CD. Genetic Mapping and Biochemical Basis of Yellow Feather Pigmentation in Budgerigars. Cell 2017; 171:427-439.e21. [PMID: 28985565 PMCID: PMC5951300 DOI: 10.1016/j.cell.2017.08.016] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/14/2017] [Accepted: 08/08/2017] [Indexed: 12/31/2022]
Abstract
Parrot feathers contain red, orange, and yellow polyene pigments called psittacofulvins. Budgerigars are parrots that have been extensively bred for plumage traits during the last century, but the underlying genes are unknown. Here we use genome-wide association mapping and gene-expression analysis to map the Mendelian blue locus, which abolishes yellow pigmentation in the budgerigar. We find that the blue trait maps to a single amino acid substitution (R644W) in an uncharacterized polyketide synthase (MuPKS). When we expressed MuPKS heterologously in yeast, yellow pigments accumulated. Mass spectrometry confirmed that these yellow pigments match those found in feathers. The R644W substitution abolished MuPKS activity. Furthermore, gene-expression data from feathers of different bird species suggest that parrots acquired their colors through regulatory changes that drive high expression of MuPKS in feather epithelia. Our data also help formulate biochemical models that may explain natural color variation in parrots. VIDEO ABSTRACT.
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Affiliation(s)
- Thomas F Cooke
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Curt R Fischer
- ChEM-H, Stanford University, Stanford, CA 94305, USA; Stanford Genome Technology Center, Stanford University, Stanford, CA 94305, USA
| | - Ping Wu
- Department of Pathology, University of Southern California, Los Angeles, CA 90033, USA
| | - Ting-Xin Jiang
- Department of Pathology, University of Southern California, Los Angeles, CA 90033, USA
| | - Kathleen T Xie
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - James Kuo
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Elizabeth Doctorov
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ashley Zehnder
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chaitan Khosla
- ChEM-H, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; Departments of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Cheng-Ming Chuong
- Department of Pathology, University of Southern California, Los Angeles, CA 90033, USA; Integrative Stem Cell Center, China Medical University, Taichung 404, Taiwan; Center for the Integrative and Evolutionary Galliformes Genomics, National Chung Hsing University, Taichung 402, Taiwan
| | - Carlos D Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Nascimento FF, Reis MD, Yang Z. A biologist's guide to Bayesian phylogenetic analysis. Nat Ecol Evol 2017; 1:1446-1454. [PMID: 28983516 PMCID: PMC5624502 DOI: 10.1038/s41559-017-0280-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 07/17/2017] [Indexed: 11/09/2022]
Abstract
Bayesian methods have become very popular in molecular phylogenetics due to the availability of user-friendly software implementing sophisticated models of evolution. However, Bayesian phylogenetic models are complex, and analyses are often carried out using default settings, which may not be appropriate. Here, we summarize the major features of Bayesian phylogenetic inference and discuss Bayesian computation using Markov chain Monte Carlo (MCMC), the diagnosis of an MCMC run, and ways of summarising the MCMC sample. We discuss the specification of the prior, the choice of the substitution model, and partitioning of the data. Finally, we provide a list of common Bayesian phylogenetic software and provide recommendations as to their use.
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Affiliation(s)
- Fabrícia F Nascimento
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
- Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK.
| | - Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK.
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244
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Brosson S, Bottu G, Pays E, Bousbata S, Salmon D. Identification and preliminary characterization of a putative C-type lectin receptor-like protein in the T. cruzi tomato lectin endocytic-enriched proteome. Microbiol Res 2017; 205:73-79. [PMID: 28942847 DOI: 10.1016/j.micres.2017.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 06/23/2017] [Accepted: 07/05/2017] [Indexed: 11/17/2022]
Abstract
Trypanosoma cruzi, the etiological agent of the Chagas' disease in Latin America undergoes a complex life cycle involving two hosts, a mammalian host and a reduviid insect vector (triatomine). In the insect midgut the parasite multiplies as epimastigote forms, which rely on endocytosis for their energy requirement. We recently showed that posttranslational modification of endocytic N-glycoproteins by tomato lectin (TL) binding-N-glycans is crucial for receptor-mediated endocytosis (RME) in epimastigote forms. In an attempt to characterize the endocytic proteome we used a TL affinity chromatography, which significantly enriched glycoproteins of the trypanosomal endocytic pathway. In addition to various lysosomal hydrolases, we found an endosomal C-type lectin-like protein, which displays some structural and topological characteristics of the mammalian lectin receptor superfamily. This lectin encoding a large transmembrane protein of around 375kDa contained three putative extracellular N-terminal C-type lectin domains (CTLD) and located inside the flagellar pocket (FP)/cytostome and endosomal compartments of the insect stage of the parasite and on the surface of the plasma membrane of intracellular amastigote parasites. Noteworthy, this endogenous lectin displayed similar sugar-binding specificity to that of TL and therefore could be important in either the N-glycan mediated endocytosis or parasite adhesion to host cells. We postulated that during the evolution of trypanosomatids, genes encoding lectin harboring 3 CTDLs represent an old acquisition present in free-living, monoxenic and heteroxenic trypanosomatids, which would have been secondarily lost in extracellular parasites from the T. brucei clade.
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Affiliation(s)
- Sébastien Brosson
- Laboratory of Molecular Parasitology, Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, 12 rue des Professeurs Jeener et Brachet, B-6041 Gosselies, Belgium
| | - Guy Bottu
- VIB BioInformatics Training and Services (BITS), Rijvisschestraat 126 3/R, Ghent B-9052, Belgium
| | - Etienne Pays
- Laboratory of Molecular Parasitology, Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, 12 rue des Professeurs Jeener et Brachet, B-6041 Gosselies, Belgium
| | - Sabrina Bousbata
- Laboratory of Molecular Parasitology, Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, 12 rue des Professeurs Jeener et Brachet, B-6041 Gosselies, Belgium
| | - Didier Salmon
- Institute of Medical Biochemistry Leopoldo de Meis, Centro de Ciências e da Saúde, Federal University of Rio de Janeiro, Av. Brigadeiro Trompowsky, Rio de Janeiro, 21941-590, Brazil.
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245
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Tomasco IH, Boullosa N, Tandonnet S, Hoffmann FG, Lessa EP. Nucleotide sequence and results of test of adaptive evolution in the α-globin gene of octodontoid rodents. Data Brief 2017; 15:517-521. [PMID: 29085872 PMCID: PMC5650648 DOI: 10.1016/j.dib.2017.09.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/04/2017] [Accepted: 09/12/2017] [Indexed: 11/30/2022] Open
Abstract
The data presented in this article are related to the research article entitled “Molecular adaptive convergence in the α-globin gene in subterranean octodontid rodents” (Tomasco et al., 2017) [1]. This article shows the nucleotide sequences of α-globin subunit gene of hemoglobin of several South American caviomorph rodents, including subterranean and fossorial species. These sequences are deposited in Genbank, with accession numbers ranging from MF169881 to MF169898. Of a total of 429 nucleotides analyzed (143 codons), 100 variable sites and 43 amino acid replacements were reported. In this article we also show the results of TreeSaap (Woolley et al., 2003) [2] and MEME (Murrell et al., 2012) [3], that identified some replacement changes as interesting for future studies of adaptive evolution in this large rodent radiation.
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Affiliation(s)
- I H Tomasco
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - N Boullosa
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | | | - F G Hoffmann
- Department of Biochemistry and Molecular Biology, Mississippi State University, MS, USA.,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, MS, USA
| | - E P Lessa
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
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246
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Wang R, Ming M, Li J, Shi D, Qiao X, Li L, Zhang S, Wu J. Genome-wide identification of the MADS-box transcription factor family in pear ( Pyrus bretschneideri) reveals evolution and functional divergence. PeerJ 2017; 5:e3776. [PMID: 28924499 PMCID: PMC5598432 DOI: 10.7717/peerj.3776] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 08/17/2017] [Indexed: 11/21/2022] Open
Abstract
MADS-box transcription factors play significant roles in plant developmental processes such as floral organ conformation, flowering time, and fruit development. Pear (Pyrus), as the third-most crucial temperate fruit crop, has been fully sequenced. However, there is limited information about the MADS family and its functional divergence in pear. In this study, a total of 95 MADS-box genes were identified in the pear genome, and classified into two types by phylogenetic analysis. Type I MADS-box genes were divided into three subfamilies and type II genes into 14 subfamilies. Synteny analysis suggested that whole-genome duplications have played key roles in the expansion of the MADS family, followed by rearrangement events. Purifying selection was the primary force driving MADS-box gene evolution in pear, and one gene pairs presented three codon sites under positive selection. Full-scale expression information for PbrMADS genes in vegetative and reproductive organs was provided and proved by transcriptional and reverse transcription PCR analysis. Furthermore, the PbrMADS11(12) gene, together with partners PbMYB10 and PbbHLH3 was confirmed to activate the promoters of the structural genes in anthocyanin pathway of red pear through dual luciferase assay. In addition, the PbrMADS11 and PbrMADS12 were deduced involving in the regulation of anthocyanin synthesis response to light and temperature changes. These results provide a solid foundation for future functional analysis of PbrMADS genes in different biological processes, especially of pigmentation in pear.
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Affiliation(s)
- Runze Wang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Meiling Ming
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Jiaming Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Dongqing Shi
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Xin Qiao
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Leiting Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Jun Wu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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247
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Fontenla S, Rinaldi G, Smircich P, Tort JF. Conservation and diversification of small RNA pathways within flatworms. BMC Evol Biol 2017; 17:215. [PMID: 28893179 PMCID: PMC5594548 DOI: 10.1186/s12862-017-1061-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 09/05/2017] [Indexed: 02/04/2023] Open
Abstract
Background Small non-coding RNAs, including miRNAs, and gene silencing mediated by RNA interference have been described in free-living and parasitic lineages of flatworms, but only few key factors of the small RNA pathways have been exhaustively investigated in a limited number of species. The availability of flatworm draft genomes and predicted proteomes allowed us to perform an extended survey of the genes involved in small non-coding RNA pathways in this phylum. Results Overall, findings show that the small non-coding RNA pathways are conserved in all the analyzed flatworm linages; however notable peculiarities were identified. While Piwi genes are amplified in free-living worms they are completely absent in all parasitic species. Remarkably all flatworms share a specific Argonaute family (FL-Ago) that has been independently amplified in different lineages. Other key factors such as Dicer are also duplicated, with Dicer-2 showing structural differences between trematodes, cestodes and free-living flatworms. Similarly, a very divergent GW182 Argonaute interacting protein was identified in all flatworm linages. Contrasting to this, genes involved in the amplification of the RNAi interfering signal were detected only in the ancestral free living species Macrostomum lignano. We here described all the putative small RNA pathways present in both free living and parasitic flatworm lineages. Conclusion These findings highlight innovations specifically evolved in platyhelminths presumably associated with novel mechanisms of gene expression regulation mediated by small RNA pathways that differ to what has been classically described in model organisms. Understanding these phylum-specific innovations and the differences between free living and parasitic species might provide clues to adaptations to parasitism, and would be relevant for gene-silencing technology development for parasitic flatworms that infect hundreds of million people worldwide. Electronic supplementary material The online version of this article (10.1186/s12862-017-1061-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Santiago Fontenla
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UDELAR), Gral. Flores 2125, CP11800, Montevideo, MVD, Uruguay
| | - Gabriel Rinaldi
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Pablo Smircich
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UDELAR), Gral. Flores 2125, CP11800, Montevideo, MVD, Uruguay.,Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Jose F Tort
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UDELAR), Gral. Flores 2125, CP11800, Montevideo, MVD, Uruguay.
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248
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Ni Z, Ye Y, Bai T, Xu M, Xu LA. Complete Chloroplast Genome of Pinus massoniana (Pinaceae): Gene Rearrangements, Loss of ndh Genes, and Short Inverted Repeats Contraction, Expansion. Molecules 2017; 22:E1528. [PMID: 28891993 PMCID: PMC6151703 DOI: 10.3390/molecules22091528] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/08/2017] [Accepted: 09/10/2017] [Indexed: 11/17/2022] Open
Abstract
The chloroplast genome (CPG) of Pinus massoniana belonging to the genus Pinus (Pinaceae), which is a primary source of turpentine, was sequenced and analyzed in terms of gene rearrangements, ndh genes loss, and the contraction and expansion of short inverted repeats (IRs). P. massoniana CPG has a typical quadripartite structure that includes large single copy (LSC) (65,563 bp), small single copy (SSC) (53,230 bp) and two IRs (IRa and IRb, 485 bp). The 108 unique genes were identified, including 73 protein-coding genes, 31 tRNAs, and 4 rRNAs. Most of the 81 simple sequence repeats (SSRs) identified in CPG were mononucleotides motifs of A/T types and located in non-coding regions. Comparisons with related species revealed an inversion (21,556 bp) in the LSC region; P. massoniana CPG lacks all 11 intact ndh genes (four ndh genes lost completely; the five remained truncated as pseudogenes; and the other two ndh genes remain as pseudogenes because of short insertions or deletions). A pair of short IRs was found instead of large IRs, and size variations among pine species were observed, which resulted from short insertions or deletions and non-synchronized variations between "IRa" and "IRb". The results of phylogenetic analyses based on whole CPG sequences of 16 conifers indicated that the whole CPG sequences could be used as a powerful tool in phylogenetic analyses.
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Affiliation(s)
- ZhouXian Ni
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
| | - YouJu Ye
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
| | - Tiandao Bai
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
- Forestry College, Guangxi University, Nanning 530004, China.
| | - Meng Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
| | - Li-An Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
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249
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Wang Q, Sun H, Huang J. Re-analyses of "Algal" Genes Suggest a Complex Evolutionary History of Oomycetes. FRONTIERS IN PLANT SCIENCE 2017; 8:1540. [PMID: 28932232 PMCID: PMC5592239 DOI: 10.3389/fpls.2017.01540] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/22/2017] [Indexed: 06/07/2023]
Abstract
The spread of photosynthesis is one of the most important but constantly debated topics in eukaryotic evolution. Various hypotheses have been proposed to explain the plastid distribution in extant eukaryotes. Notably, the chromalveolate hypothesis suggested that multiple eukaryotic lineages were derived from a photosynthetic ancestor that had a red algal endosymbiont. As such, genes of plastid/algal origin in aplastidic chromalveolates, such as oomycetes, were considered to be important supporting evidence. Although the chromalveolate hypothesis has been seriously challenged, some of its supporting evidence has not been carefully investigated. In this study, we re-evaluate the "algal" genes from oomycetes with a larger sampling and careful phylogenetic analyses. Our data provide no conclusive support for a common photosynthetic ancestry of stramenopiles, but show that the initial estimate of "algal" genes in oomycetes was drastically inflated due to limited genome data available then for certain eukaryotic lineages. These findings also suggest that the evolutionary histories of these "algal" genes might be attributed to complex scenarios such as differential gene loss, serial endosymbioses, or horizontal gene transfer.
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Affiliation(s)
- Qia Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
| | - Jinling Huang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, Henan UniversityKaifeng, China
- Department of Biology, East Carolina University, GreenvilleNC, United States
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250
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Ascunce MS, Huguet-Tapia JC, Ortiz-Urquiza A, Keyhani NO, Braun EL, Goss EM. Phylogenomic analysis supports multiple instances of polyphyly in the oomycete peronosporalean lineage. Mol Phylogenet Evol 2017. [DOI: 10.1016/j.ympev.2017.06.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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