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Villacís AG, Dujardin JP, Panzera F, Yumiseva CA, Pita S, Santillán-Guayasamín S, Orozco MI, Mosquera KD, Grijalva MJ. Chagas vectors Panstrongylus chinai (Del Ponte, 1929) and Panstrongylus howardi (Neiva, 1911): chromatic forms or true species? Parasit Vectors 2020; 13:226. [PMID: 32375868 PMCID: PMC7201598 DOI: 10.1186/s13071-020-04097-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 04/25/2020] [Indexed: 11/23/2022] Open
Abstract
Background Chagas disease is a parasitic infection transmitted by “kissing bugs” (Hemiptera: Reduviidae: Triatominae) that has a huge economic impact in Latin American countries. The vector species with the upmost epidemiological importance in Ecuador are Rhodnius ecuadoriensis (Lent & Leon, 1958) and Triatoma dimidiata (Latreille, 1811). However, other species such as Panstrongylus howardi (Neiva, 1911) and Panstrongylus chinai (Del Ponte, 1929) act as secondary vectors due to their growing adaptation to domestic structures and their ability to transmit the parasite to humans. The latter two taxa are distributed in two different regions, they are allopatric and differ mainly by their general color. Their relative morphological similarity led some authors to suspect that P. chinai is a melanic form of P. howardi. Methods The present study explored this question using different approaches: antennal phenotype; geometric morphometrics of heads, wings and eggs; cytogenetics; molecular genetics; experimental crosses; and ecological niche modeling. Results The antennal morphology, geometric morphometrics of head and wing shape and cytogenetic analysis were unable to show distinct differences between the two taxa. However, geometric morphometrics of the eggs, molecular genetics, ecological niche modeling and experimental crosses including chromosomal analyses of the F1 hybrids, in addition to their coloration and current distribution support the hypothesis that P. chinai and P. howardi are separate species. Conclusions Based on the evidence provided here, P. howardi and P. chinai should not be synonymized. They represent two valid, closely related species.![]()
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Affiliation(s)
- Anita G Villacís
- Center for Research on Health in Latin America (CISeAL), School of Biological Sciences, Pontificia Universidad Católica del Ecuador, Av. 12 de Octubre 1076 y Roca, Quito, Ecuador.,Infectious and Tropical Disease Institute, Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, 45701, USA
| | - Jean-Pierre Dujardin
- Center for Research on Health in Latin America (CISeAL), School of Biological Sciences, Pontificia Universidad Católica del Ecuador, Av. 12 de Octubre 1076 y Roca, Quito, Ecuador.,IRD, UMR 177 IRD-CIRAD INTERTRYP, Campus international de Baillarguet, Montpellier, France
| | - Francisco Panzera
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - César A Yumiseva
- Center for Research on Health in Latin America (CISeAL), School of Biological Sciences, Pontificia Universidad Católica del Ecuador, Av. 12 de Octubre 1076 y Roca, Quito, Ecuador
| | - Sebastián Pita
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Soledad Santillán-Guayasamín
- Center for Research on Health in Latin America (CISeAL), School of Biological Sciences, Pontificia Universidad Católica del Ecuador, Av. 12 de Octubre 1076 y Roca, Quito, Ecuador
| | - Marco I Orozco
- Center for Research on Health in Latin America (CISeAL), School of Biological Sciences, Pontificia Universidad Católica del Ecuador, Av. 12 de Octubre 1076 y Roca, Quito, Ecuador
| | - Katherine D Mosquera
- Center for Research on Health in Latin America (CISeAL), School of Biological Sciences, Pontificia Universidad Católica del Ecuador, Av. 12 de Octubre 1076 y Roca, Quito, Ecuador.,Carrera de Ingeniería en Biotecnología, Departamento de Ciencias de la Vida y la Agricultura, Universidad de las Fuerzas Armadas - ESPE, Sangolquí, Ecuador
| | - Mario J Grijalva
- Infectious and Tropical Disease Institute, Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, 45701, USA.
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102
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Li C, Ge X, Su B, Fu Q, Wang B, Liu X, Ren Y, Song L, Yang N. Characterization of class B scavenger receptor type 1 (SRB1) in turbot (Scophthalmus maximus L.). FISH & SHELLFISH IMMUNOLOGY 2020; 100:358-367. [PMID: 32169665 DOI: 10.1016/j.fsi.2020.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 06/10/2023]
Abstract
Class B scavenger receptor type 1 (SRB1) serves as a high-density lipoprotein (HDL) receptor essential for HDL metabolism, and plays vital roles in innate immunity. In this study, the turbot (Scophthalmus maximus) SRB1 was cloned and characterized. The gene structure consists of a coding region of 1,527 bp nucleotides dividing into 13 exons and 12 introns. Such genome structure is highly conserved among teleost fishes. The deduced SRB1 encodes 508 amino acids that mainly has a CD36 transmembrane domain. Tissue distribution of SRB1 showed the lowest expression in liver, while the highest expression was found in intestine. Significantly down-regulation pattern of SmSRB1 expression in intestine was shared after infection with Vibrio anguillarum and Streptococcus iniae. Brach and site models in CODEML program showed that SmSRB1 underwent a conservative evolutionary and three potential positive selected sites 470K, 496E, and 501Y were detected, which requires further investigation and confirmation using base-editing technologies. Subcellular localization demonstrated that turbot SRB1 was distributed in the membrane and cytoplasm. rSmSRB1 showed binding ability in vitro to bacteria, LPS, PGN, LTA and virus. Protein-protein interaction network agrees the function of SRB1 as lipoprotein receptor. Our results indicated SmSRB1 might act as co-receptors to TLRs and NLRs to modulate the immune response to pathogens. Further studies should pay attention to evaluate the specific co-receptor for SRB1 in recognition of different pathogens and selective mechanisms involved.
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Affiliation(s)
- Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xuefeng Ge
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Baofeng Su
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Qiang Fu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Beibei Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiaoli Liu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yichao Ren
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lin Song
- College of Marine Science and Biological Engineering, Qingdao University of Science & Technology, Qingdao, 266011, China
| | - Ning Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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103
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Lu A, Watkins M, Li Q, Robinson SD, Concepcion GP, Yandell M, Weng Z, Olivera BM, Safavi-Hemami H, Fedosov AE. Transcriptomic Profiling Reveals Extraordinary Diversity of Venom Peptides in Unexplored Predatory Gastropods of the Genus Clavus. Genome Biol Evol 2020; 12:684-700. [PMID: 32333764 PMCID: PMC7259678 DOI: 10.1093/gbe/evaa083] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2020] [Indexed: 12/21/2022] Open
Abstract
Predatory gastropods of the superfamily Conoidea number over 12,000 living species. The evolutionary success of this lineage can be explained by the ability of conoideans to produce complex venoms for hunting, defense, and competitive interactions. Whereas venoms of cone snails (family Conidae) have become increasingly well studied, the venoms of most other conoidean lineages remain largely uncharacterized. In the present study, we present the venom gland transcriptomes of two species of the genus Clavus that belong to the family Drilliidae. Venom gland transcriptomes of two specimens of Clavus canalicularis and two specimens of Clavus davidgilmouri were analyzed, leading to the identification of a total of 1,176 putative venom peptide toxins (drillipeptides). Based on the combined evidence of secretion signal sequence identity, entire precursor similarity search (BLAST), and the orthology inference, putative Clavus toxins were assigned to 158 different gene families. The majority of identified transcripts comprise signal, pro-, mature peptide, and post-regions, with a typically short (<50 amino acids) and cysteine-rich mature peptide region. Thus, drillipeptides are structurally similar to conotoxins. However, convincing homology with known groups of Conus toxins was only detected for very few toxin families. Among these are Clavus counterparts of Conus venom insulins (drillinsulins), porins (drilliporins), and highly diversified lectins (drillilectins). The short size of most drillipeptides and structural similarity to conotoxins were unexpected, given that most related conoidean gastropod families (Terebridae and Turridae) possess longer mature peptide regions. Our findings indicate that, similar to conotoxins, drillipeptides may represent a valuable resource for future pharmacological exploration.
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Affiliation(s)
- Aiping Lu
- Department of Central Laboratory, Shanghai Tenth People’s Hospital of Tongji University, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | | | - Qing Li
- Eccles Institute of Human Genetics, University of Utah
- High-Throughput Genomics and Bioinformatic Analysis Shared Resource, Huntsman Cancer Institute, University of Utah
| | | | - Gisela P Concepcion
- Marine Science Institute, University of the Philippines-Diliman, Quezon City, Philippines
| | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah
- Utah Center for Genetic Discovery, University of Utah
| | - Zhiping Weng
- Department of Central Laboratory, Shanghai Tenth People’s Hospital of Tongji University, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School
| | | | - Helena Safavi-Hemami
- Department of Biochemistry, University of Utah
- Department of Biology, University of Copenhagen, Denmark
| | - Alexander E Fedosov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Science, Moscow, Russia
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104
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Joffrin L, Goodman SM, Wilkinson DA, Ramasindrazana B, Lagadec E, Gomard Y, Le Minter G, Dos Santos A, Corrie Schoeman M, Sookhareea R, Tortosa P, Julienne S, Gudo ES, Mavingui P, Lebarbenchon C. Bat coronavirus phylogeography in the Western Indian Ocean. Sci Rep 2020; 10:6873. [PMID: 32327721 PMCID: PMC7181612 DOI: 10.1038/s41598-020-63799-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/31/2020] [Indexed: 12/28/2022] Open
Abstract
Bats provide key ecosystem services such as crop pest regulation, pollination, seed dispersal, and soil fertilization. Bats are also major hosts for biological agents responsible for zoonoses, such as coronaviruses (CoVs). The islands of the Western Indian Ocean are identified as a major biodiversity hotspot, with more than 50 bat species. In this study, we tested 1,013 bats belonging to 36 species from Mozambique, Madagascar, Mauritius, Mayotte, Reunion Island and Seychelles, based on molecular screening and partial sequencing of the RNA-dependent RNA polymerase gene. In total, 88 bats (8.7%) tested positive for coronaviruses, with higher prevalence in Mozambican bats (20.5% ± 4.9%) as compared to those sampled on islands (4.5% ± 1.5%). Phylogenetic analyses revealed a large diversity of α- and β-CoVs and a strong signal of co-evolution between CoVs and their bat host species, with limited evidence for host-switching, except for bat species sharing day roost sites. These results highlight that strong variation between islands does exist and is associated with the composition of the bat species community on each island. Future studies should investigate whether CoVs detected in these bats have a potential for spillover in other hosts.
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Affiliation(s)
- Léa Joffrin
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France.
| | - Steven M Goodman
- Association Vahatra, Antananarivo, Madagascar
- Field Museum of Natural History, Chicago, USA
| | - David A Wilkinson
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Beza Ramasindrazana
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
- Association Vahatra, Antananarivo, Madagascar
- Beza Ramasindrazana, Institut Pasteur de Madagascar, BP 1274, Ambatofotsikely, Antananarivo, 101, Madagascar
| | - Erwan Lagadec
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Yann Gomard
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Gildas Le Minter
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | | | - M Corrie Schoeman
- School of Life Sciences, University of Kwa-Zulu Natal, Kwa-Zulu Natal, South Africa
| | | | - Pablo Tortosa
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Simon Julienne
- Seychelles Ministry of Health, Victoria, Mahe, Seychelles
| | | | - Patrick Mavingui
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Camille Lebarbenchon
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France.
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105
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Joshi B, Lyngdoh S, Singh SK, Sharma R, Kumar V, Tiwari VP, Dar SA, Maheswari A, Pal R, Bashir T, Reshamwala HS, Shrotriya S, Sathyakumar S, Habib B, Kvist L, Goyal SP. Revisiting the Woolly wolf (Canis lupus chanco) phylogeny in Himalaya: Addressing taxonomy, spatial extent and distribution of an ancient lineage in Asia. PLoS One 2020; 15:e0231621. [PMID: 32298359 PMCID: PMC7162449 DOI: 10.1371/journal.pone.0231621] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 03/27/2020] [Indexed: 11/23/2022] Open
Abstract
Of the sub-species of Holarctic wolf, the Woolly wolf (Canis lupus chanco) is uniquely adapted to atmospheric hypoxia and widely distributed across the Himalaya, Qinghai Tibetan Plateau (QTP) and Mongolia. Taxonomic ambiguity still exists for this sub-species because of complex evolutionary history anduse of limited wild samples across its range in Himalaya. We document for the first time population genetic structure and taxonomic affinity of the wolves across western and eastern Himalayan regions from samples collected from the wild (n = 19) using mitochondrial control region (225bp). We found two haplotypes in our data, one widely distributed in the Himalaya that was shared with QTP and the other confined to Himachal Pradesh and Uttarakhand in the western Himalaya, India. After combining our data withpublished sequences (n = 83), we observed 15 haplotypes. Some of these were shared among different locations from India to QTP and a few were private to geographic locations. A phylogenetic tree indicated that Woolly wolves from India, Nepal, QTP and Mongolia are basal to other wolves with shallow divergence (K2P; 0.000-0.044) and high bootstrap values. Demographic analyses based on mismatch distribution and Bayesian skyline plots (BSP) suggested a stable population over a long time (~million years) with signs of recent declines. Regional dominance of private haplotypes across its distribution range may indicate allopatric divergence. This may be due to differences in habitat characteristics, availability of different wild prey species and differential deglaciation within the range of the Woolly wolf during historic time. Presence of basal and shallow divergence within-clade along with unique ecological requirements and adaptation to hypoxia, the Woolly wolf of Himalaya, QTP, and Mongolian regions may be considered as a distinct an Evolutionary Significant Unit (ESU). Identifying management units (MUs) is needed within its distribution range using harmonized multiple genetic data for effective conservation planning.
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Affiliation(s)
| | | | | | - Reeta Sharma
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | - Vinay Kumar
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | | | - S. A. Dar
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | | | - Ranjana Pal
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | - Tawqir Bashir
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | | | | | - S. Sathyakumar
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | - Bilal Habib
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | - Laura Kvist
- Department of Biology, University of Oulu, Oulu, Finland
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106
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Singh R, Lava Kumar S, Mishra SK, Gurao A, Niranjan SK, Vohra V, Dash SK, Rajesh C, Kataria RS. Mitochondrial sequence-based evolutionary analysis of riverine-swamp hybrid buffaloes of India indicates novel maternal differentiation and domestication patterns. Anim Genet 2020; 51:476-482. [PMID: 32281135 DOI: 10.1111/age.12938] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2020] [Indexed: 11/29/2022]
Abstract
In this study, mitochondrial D-loop sequence data on riverine, swamp and hybrid buffaloes from India have been generated and compared with other reported Indian riverine, Chinese and Bangladeshi swamp buffalo populations. Sequence analysis revealed the presence of 132 haplotypes, with a haplotype diversity of 0.9611 ± 0.0045 and a nucleotide diversity of 0.04801 ± 0.00126. For the first time, the existence of riverine-swamp hybrids among the Indian Chilika buffalo population has been recorded, having 49 chromosomes, which was also confirmed by mitochondrial haplotype sharing between Chilika and Indian swamp as well as Chinese swamp buffalo populations in the network analysis. Phylogenetic analysis documents the sharing of reported pre-domestication haplogroups 'SA1', 'SA2', 'SA3' and 'SB1' between the Chilika and swamp buffalo populations of India, China and Bangladesh, an indication of the migration of swamp buffaloes towards Bangladesh and adjoining lower parts of India and north towards Chinese domestication sites. The results have also been supplemented by multidimension scaling, grouping Indian and Chinese swamp buffaloes more closely together with Bangladeshi buffaloes, but into a separate quadrant, whereas Chilika grouped away from other riverine as well as swamp buffaloes. These findings thus confirm the previous reports that the northeast region of India, close to the Indo-China border, is the point of evolution of swamp buffaloes with multiple sites of domestication.
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Affiliation(s)
- R Singh
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India.,Department of Biotechnology, SGGSWU, Fatehgarh Sahib, Punjab, 140407, India
| | - S Lava Kumar
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - S K Mishra
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - A Gurao
- Department of Veterinary Microbiology and Biotechnology, College of Veterinary and Animal Sciences, Rajasthan University of Veterinary and Animal Sciences, Bikaner, Rajasthan, 334001, India
| | - S K Niranjan
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - V Vohra
- Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - S K Dash
- Department of Animal Breeding and Genetics, OUAT, Bhubaneshwar, Odisha, 751003, India
| | - C Rajesh
- Department of Biotechnology, SGGSWU, Fatehgarh Sahib, Punjab, 140407, India
| | - R S Kataria
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
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107
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Damodaran L, de Bernardi Schneider A, Chen S, Janies D. Evolution of endemic and sylvatic lineages of dengue virus. Cladistics 2020; 36:115-128. [PMID: 34618965 DOI: 10.1111/cla.12402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2019] [Indexed: 11/30/2022] Open
Abstract
Recent disease outbreaks have raised awareness of tropical pathogens, especially mosquito-borne viruses. Dengue virus (DENV) is a widely studied mammalian pathogen transmitted by various species of mosquito in the genus Aedes, especially Aedes aegypti and Aedes albopictus. The prevailing view of the research community is that endemic viral lineages that cause epidemics of DENV in humans have emerged over time from sylvatic viral lineages, which persist in wild, non-human primates. These notions have been examined by researchers through phylogenetic analyses of the envelope gene (E) from the four serotypes of DENV (serotypes DENV-1 to DENV-4). In these previous reports, researchers used visual inspection of a phylogeny in order to assert that sylvatic lineages lead to endemic clades. In making this assertion, these researchers also reasserted the model of periodic sylvatic to endemic disease outbreaks. Since that study, there has been a significant increase in data both in terms of metadata (e.g., place and host of isolation) and genetic sequences of DENV. Here, we re-examine the model of sylvatic to endemic shifts in viral lineages through a phylogenetic tree search and character evolution study of metadata on the tree. We built a dataset of nucleotide sequences for 188 isolates of DENV that have metadata on sylvatic or endemic sampling along with three orthologous sequences from West Nile virus as the outgroup for the phylogenetic analysis. In contrast to previous research, we find that there are several shifts from endemic to sylvatic lineages as well as sylvatic to endemic lineages, indicating a much more dynamic model of evolution. We propose that a model that allows oscillation between sylvatic and endemic hosts better captures the dynamics of DENV transmission.
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Affiliation(s)
- Lambodhar Damodaran
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223-0001, NC, USA.,Institute of Bioinformatics, University of Georgia, 120 Green St., Athens, 30602, GA, USA
| | - Adriano de Bernardi Schneider
- AntiViral Research Center, Department of Medicine, University of California San Diego, 220 Dickinson St, Suite A, San Diego, 92103-8208, CA, USA
| | - Shi Chen
- Department of Public Health Sciences, College of Health and Human Services, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223-0001, NC, USA
| | - Daniel Janies
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223-0001, NC, USA
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108
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Wang X, Ding J, Lin S, Liu D, Gu T, Wu H, Trigiano RN, McAvoy R, Huang J, Li Y. Evolution and roles of cytokinin genes in angiosperms 2: Do ancient CKXs play housekeeping roles while non-ancient CKXs play regulatory roles? HORTICULTURE RESEARCH 2020; 7:29. [PMID: 32140238 PMCID: PMC7049301 DOI: 10.1038/s41438-020-0246-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/27/2019] [Accepted: 01/04/2020] [Indexed: 05/23/2023]
Abstract
Cytokinin oxidase/dehydrogenase (CKX) is a key enzyme responsible for the degradation of endogenous cytokinins. However, the origins and roles of CKX genes in angiosperm evolution remain unclear. Based on comprehensive bioinformatic and transgenic plant analyses, we demonstrate that the CKXs of land plants most likely originated from an ancient chlamydial endosymbiont during primary endosymbiosis. We refer to the CKXs retaining evolutionarily ancient characteristics as "ancient CKXs" and those that have expanded and functionally diverged in angiosperms as "non-ancient CKXs". We show that the expression of some non-ancient CKXs is rapidly inducible within 15 min upon the dehydration of Arabidopsis, while the ancient CKX (AtCKX7) is not drought responsive. Tobacco plants overexpressing a non-ancient CKX display improved oxidative and drought tolerance and root growth. Previous mutant studies have shown that non-ancient CKXs regulate organ development, particularly that of flowers. Furthermore, ancient CKXs preferentially degrade cis-zeatin (cZ)-type cytokinins, while non-ancient CKXs preferentially target N6-(Δ2-isopentenyl) adenines (iPs) and trans-zeatins (tZs). Based on the results of this work, an accompanying study (Wang et al. 10.1038/s41438-019-0211-x) and previous studies, we hypothesize that non-ancient CKXs and their preferred substrates of iP/tZ-type cytokinins regulate angiosperm organ development and environmental stress responses, while ancient CKXs and their preferred substrates of cZs play a housekeeping role, which echoes the conclusions and hypothesis described in the accompanying report (Wang, X. et al. Evolution and roles of cytokinin genes in angiosperms 1: Doancient IPTs play housekeeping while non-ancient IPTs play regulatory roles? Hortic Res7, (2020). 10.1038/s41438-019-0211-x).
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Affiliation(s)
- Xiaojing Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
| | - Jing Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
| | - Shanshan Lin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
| | - Decai Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
| | - Tingting Gu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
| | - Han Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
| | - Robert N. Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996-4560 USA
| | - Richard McAvoy
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269 USA
| | - Jinling Huang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
- Department of Biology, East Carolina University, Greenville, NC 27858 USA
| | - Yi Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269 USA
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Wang X, Lin S, Liu D, Gan L, McAvoy R, Ding J, Li Y. Evolution and roles of cytokinin genes in angiosperms 1: Do ancient IPTs play housekeeping while non-ancient IPTs play regulatory roles? HORTICULTURE RESEARCH 2020; 7:28. [PMID: 32140237 PMCID: PMC7049300 DOI: 10.1038/s41438-019-0211-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 06/04/2019] [Accepted: 06/05/2019] [Indexed: 05/07/2023]
Abstract
Isopentenyltransferase (IPT) genes, including those encoding ATP/ADP-IPTs and tRNA-IPTs, control the rate-limiting steps of the biosynthesis of N 6-(Δ2-isopentenyl)adenine (iP)-type and trans-zeatin (tZ)-type cytokinins and cis-zeatin (cZ)-type cytokinins, respectively. However, the evolution and roles of these IPTs in angiosperms are not well understood. Here, we report comprehensive analyses of the origins, evolution, expression patterns, and possible roles of ATP/ADP-IPTs and tRNA-IPTs in angiosperms. We found that Class I and II tRNA-IPTs likely coexisted in the last common ancestor of eukaryotes, while ATP/ADP-IPTs likely originated from a Class II tRNA-IPT before the divergence of angiosperms. tRNA-IPTs are conservatively retained as 2-3 copies, but ATP/ADP-IPTs exhibit considerable expansion and diversification. Additionally, tRNA-IPTs are constitutively expressed throughout the plant, whereas the expression of ATP/ADP-IPTs is tissue-specific and rapidly downregulated by abiotic stresses. Furthermore, previous studies and our present study indicate that ATP/ADP-IPTs and their products, iPs/tZs, may regulate responses to environmental stresses and organ development in angiosperms. We therefore hypothesize that tRNA-IPTs and the associated cZs play a housekeeping role, whereas ATP/ADP-IPTs and the associated iP/tZ-type cytokinins play regulatory roles in organ development and stress responses in angiosperms, which echoes the conclusions and hypothesis presented in the accompanying study by Wang, X. et al Evolution and roles of cytokinin genes in angiosperms 2: Do ancient CKXs play housekeeping roles while non-ancient CKXs play regulatory roles? Hortic Res 10.1038/s41438-020-0246-z.
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Affiliation(s)
- Xiaojing Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and the College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
| | - Shanshan Lin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and the College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
| | - Decai Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and the College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
| | - Lijun Gan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, P. R. China
| | - Richard McAvoy
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269 USA
| | - Jing Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and the College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
| | - Yi Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and the College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269 USA
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110
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Lin JP, Tsai MH, Kroh A, Trautman A, Machado DJ, Chang LY, Reid R, Lin KT, Bronstein O, Lee SJ, Janies D. The first complete mitochondrial genome of the sand dollar Sinaechinocyamus mai (Echinoidea: Clypeasteroida). Genomics 2020; 112:1686-1693. [PMID: 31629878 PMCID: PMC7032948 DOI: 10.1016/j.ygeno.2019.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 09/18/2019] [Accepted: 10/08/2019] [Indexed: 11/26/2022]
Abstract
Morphologic and molecular data often lead to different hypotheses of phylogenetic relationships. Such incongruence has been found in the echinoderm class Echinoidea. In particular, the phylogenetic status of the order Clypeasteroida is not well resolved. Complete mitochondrial genomes are currently available for 29 echinoid species, but no clypeasteroid had been sequenced to date. DNA extracted from a single live individual of Sinaechinocyamus mai was sequenced with 10× Genomics technology. This first complete mitochondrial genome (mitogenome) for the order Clypeasteroida is 15,756 base pairs in length. Phylogenomic analysis based on 34 ingroup taxa belonging to nine orders of the class Echinoidea show congruence between our new genetic inference and published trees based on morphologic characters, but also includes some intriguing differences that imply the need for additional investigation.
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Affiliation(s)
- Jih-Pai Lin
- Department of Geosciences, National Taiwan University, Taipei, Taiwan.
| | - Mong-Hsun Tsai
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Andreas Kroh
- Department of Geology and Palaeontology, Natural History Museum Vienna, Vienna, Austria
| | - Aaron Trautman
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, USA
| | - Denis Jacob Machado
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, USA; Bioinformatics Graduate Program, University of São Paulo, Brazil
| | - Lo-Yu Chang
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
| | - Robert Reid
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, USA
| | - Kuan-Ting Lin
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Omri Bronstein
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel-Aviv, Israel; Steinhardt Museum of Natural History, Tel-Aviv, Israel
| | - Shyh-Jye Lee
- Department of Life Science, National Taiwan University, Taipei, Taiwan; Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Daniel Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, USA
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111
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Ezzedine JA, Jacas L, Desdevises Y, Jacquet S. Bdellovibrio and Like Organisms in Lake Geneva: An Unseen Elephant in the Room? Front Microbiol 2020; 11:98. [PMID: 32117128 PMCID: PMC7034301 DOI: 10.3389/fmicb.2020.00098] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/17/2020] [Indexed: 01/21/2023] Open
Abstract
When considering microbial biotic interactions, viruses as well as eukaryotic grazers are known to be important components of aquatic microbial food webs. It might be the same for bacterivorous bacteria but these groups have been comparatively less studied. This is typically the case of the Bdellovibrio and like organisms (BALOs), which are obligate bacterial predators of other bacteria. Recently, the abundance and distribution of three families of this functional group were investigated in perialpine lakes, revealing their presence and quantitative importance. Here, a more in-depth analysis is provided for Lake Geneva regarding the diversity of these bacterial predators at different seasons, sites and depths. We reveal a seasonal and spatial (vertical) pattern for BALOs. They were also found to be relatively diverse (especially Bdellovibrionaceae) and assigned to both known and unknown phylogenetic clusters. At last we found that most BALOs were positively correlated to other bacterial groups, mainly Gram-negative, in particular Myxococcales (among which many are predators of other microbes). This study is the first shedding light on this potentially important bacterial killing group in a large and deep lake.
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Affiliation(s)
- Jade A Ezzedine
- Université Savoie Mont-Blanc, INRAE, CARRTEL, Thonon-les-Bains, France
| | - Louis Jacas
- Université Savoie Mont-Blanc, INRAE, CARRTEL, Thonon-les-Bains, France
| | - Yves Desdevises
- CNRS, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France
| | - Stéphan Jacquet
- Université Savoie Mont-Blanc, INRAE, CARRTEL, Thonon-les-Bains, France
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112
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Choi YJ, Fontenla S, Fischer PU, Le TH, Costábile A, Blair D, Brindley PJ, Tort JF, Cabada MM, Mitreva M. Adaptive Radiation of the Flukes of the Family Fasciolidae Inferred from Genome-Wide Comparisons of Key Species. Mol Biol Evol 2020; 37:84-99. [PMID: 31501870 DOI: 10.1093/molbev/msz204] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Liver and intestinal flukes of the family Fasciolidae cause zoonotic food-borne infections that impact both agriculture and human health throughout the world. Their evolutionary history and the genetic basis underlying their phenotypic and ecological diversity are not well understood. To close that knowledge gap, we compared the whole genomes of Fasciola hepatica, Fasciola gigantica, and Fasciolopsis buski and determined that the split between Fasciolopsis and Fasciola took place ∼90 Ma in the late Cretaceous period, and that between 65 and 50 Ma an intermediate host switch and a shift from intestinal to hepatic habitats occurred in the Fasciola lineage. The rapid climatic and ecological changes occurring during this period may have contributed to the adaptive radiation of these flukes. Expansion of cathepsins, fatty-acid-binding proteins, protein disulfide-isomerases, and molecular chaperones in the genus Fasciola highlights the significance of excretory-secretory proteins in these liver-dwelling flukes. Fasciola hepatica and Fasciola gigantica diverged ∼5 Ma near the Miocene-Pliocene boundary that coincides with reduced faunal exchange between Africa and Eurasia. Severe decrease in the effective population size ∼10 ka in Fasciola is consistent with a founder effect associated with its recent global spread through ruminant domestication. G-protein-coupled receptors may have key roles in adaptation of physiology and behavior to new ecological niches. This study has provided novel insights about the genome evolution of these important pathogens, has generated genomic resources to enable development of improved interventions and diagnosis, and has laid a solid foundation for genomic epidemiology to trace drug resistance and to aid surveillance.
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Affiliation(s)
- Young-Jun Choi
- McDonnell Genome Institute at Washington University in St. Louis, St. Louis, MO
| | - Santiago Fontenla
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Peter U Fischer
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Thanh Hoa Le
- Immunology Department, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Alicia Costábile
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - David Blair
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Paul J Brindley
- Department of Microbiology, Immunology and Tropical Medicine, and Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC
| | - Jose F Tort
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Miguel M Cabada
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Texas Medical Branch, Galveston, TX
| | - Makedonka Mitreva
- McDonnell Genome Institute at Washington University in St. Louis, St. Louis, MO.,Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO
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113
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Wang XR, Kurtti TJ, Oliver JD, Munderloh UG. The identification of tick autophagy-related genes in Ixodes scapularis responding to amino acid starvation. Ticks Tick Borne Dis 2020; 11:101402. [PMID: 32035896 DOI: 10.1016/j.ttbdis.2020.101402] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/04/2020] [Accepted: 01/27/2020] [Indexed: 12/25/2022]
Abstract
Ticks are obligate hematophagous arthropods and must tolerate starvation during off-host periods. Macroautophagy (hereafter autophagy) is a well-conserved self-eating mechanism of cell survival and is essential for recycling cellular contents during periods of starvation, stress, and injury in organisms. Although the genome sequence of Ixodes scapularis (Say) is available, the characteristics and functions of autophagy-related gene families remain largely unknown. To advance our understanding of autophagy in I. scapularis, we used comprehensive genomic approaches to identify Atg genes. Homologues of 14 Atg genes were identified, and their protein motif compositions were predicted. Phylogenetic analysis indicated that ATGs in I. scapularis were evolutionarily closely related to their homologues in Haemaphysalis longicornis and Rhipicephalus microplus ticks. Expression patterns of Atg genes differed across tick developmental stages. Immunofluorescence results by monodansylcadaverine (MDC) staining indicated that autophagy was activated after amino acid starvation treatments in I. scapularis embryo-derived cell lines ISE6 and IDE8. Subsequently, the expression of key Atg genes involved in autophagy pathway in both cell lines were examined. In ISE6 cells, the expression levels of three Atg genes (Atg4B, Atg6 and Atg8A) increased significantly after amino acid starvation; similarly, four Atg genes (Atg4A, Atg4B, Atg6 and Atg8B) were upregulated in IDE8 cells in response to starvation. In parallel, the MDC and lysotracker staining results indicated that autophagy was triggered after amino acid starvation treatments in R. microplus embryo-derived cell line BME26. Our observations showed that Atg family genes are highly conserved in ticks and function in autophagy pathway induced by amino acid starvation. These results also provide valuable insight for further autophagy-related research as a new strategy for blocking the transmission of tick-borne pathogens.
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Affiliation(s)
- Xin-Ru Wang
- Department of Entomology, University of Minnesota, St. Paul, MN, USA.
| | - Timothy J Kurtti
- Department of Entomology, University of Minnesota, St. Paul, MN, USA
| | - Jonathan D Oliver
- School of Public Health, Division of Environmental Health Sciences, University of Minnesota, Minneapolis, MN, USA
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114
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Zhang YH, Ravi V, Qin G, Dai H, Zhang HX, Han FM, Wang X, Liu YH, Yin JP, Huang LM, Venkatesh B, Lin Q. Comparative genomics reveal shared genomic changes in syngnathid fishes and signatures of genetic convergence with placental mammals. Natl Sci Rev 2020; 7:964-977. [PMID: 34692118 PMCID: PMC8289055 DOI: 10.1093/nsr/nwaa002] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 12/31/2019] [Accepted: 01/06/2020] [Indexed: 12/19/2022] Open
Abstract
Syngnathids (seahorses, pipefishes and seadragons) exhibit an array of morphological innovations including loss of pelvic fins, a toothless tubular mouth and male pregnancy. They comprise two subfamilies: Syngnathinae and Nerophinae. Genomes of three Syngnathinae members have been analyzed previously. In this study, we have sequenced the genome of a Nerophinae member, the Manado pipefish (Microphis manadensis), which has a semi-enclosed brood pouch. Comparative genomic analysis revealed that the molecular evolutionary rate of the four syngnathids is higher than that of other teleosts. The loss of all but one P/Q-rich SCPP gene in the syngnathids suggests a role for the lost genes in dentin and enameloid formation in teleosts. Genome-wide comparison identified a set of 118 genes with parallel identical amino acid substitutions in syngnathids and placental mammals. Association of some of these genes with placental and embryonic development in mammals suggests a role for them in syngnathid pregnancy.
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Affiliation(s)
- Yan-Hong Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Vydianathan Ravi
- Comparative and Medical Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR 138673, Singapore
| | - Geng Qin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - He Dai
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Hui-Xian Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Feng-Ming Han
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Yu-Hong Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Jian-Ping Yin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Liang-Min Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Byrappa Venkatesh
- Comparative and Medical Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR 138673, Singapore
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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115
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Linde AM, Sawangproh W, Cronberg N, Szövényi P, Lagercrantz U. Evolutionary History of the Marchantia polymorpha Complex. FRONTIERS IN PLANT SCIENCE 2020; 11:829. [PMID: 32670318 PMCID: PMC7332582 DOI: 10.3389/fpls.2020.00829] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/22/2020] [Indexed: 05/14/2023]
Abstract
The potential role of introgression in evolution has gained increased interest in recent years. Although some fascinating examples have been reported, more information is needed to generalize the importance of hybridization and introgression for adaptive divergence. As limited data exist on haploid dominant species, we analyzed genomes of three subspecies of the liverwort Marchantia polymorpha. We used available genomic data for subsp. ruderalis and carried out whole-genome (PacBio) sequencing for one individual each of subsp. montivagans and subsp. polymorpha as well as Illumina resequencing of additional genomes for all three subspecies. The three subspecies were compared against M. paleacea as outgroup. Our analyses revealed separation of the three taxa, but all three possible topologies were richly represented across the genomes, and the underlying divergence order less obvious. This uncertainty could be the result of the divergence of the three subspecies close in time, or that introgression has been frequent since divergence. In particular, we found that pseudo-chromosome 2 in subsp. montivagans was much more diverged than other parts of the genomes. This could either be explained by specific capture of chromosome 2 from an unknown related species through hybridization or by conservation of chromosome 2 despite intermittent or ongoing introgression affecting more permeable parts of the genomes. A higher degree of chromosomal rearrangements on pseudo-chromosome 2 support the second hypothesis. Species tree analyses recovered an overall topology where subsp. montivagans diverged first and subsp. ruderalis and subsp. polymorpha appeared as sister lineages. Each subspecies was associated with its own chloroplast and mitochondrial haplotype group. Our data suggest introgression but refute a previous hypothesis that subsp. ruderalis is a new stabilized hybrid between the other two subspecies.
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Affiliation(s)
- Anna-Malin Linde
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Weerachon Sawangproh
- Biodiversity, Department of Biology, Lund University, Lund, Sweden
- Division of Conservation Biology, School of Interdisciplinary Studies, Mahidol University, Kanchanaburi, Thailand
| | - Nils Cronberg
- Biodiversity, Department of Biology, Lund University, Lund, Sweden
- *Correspondence: Nils Cronberg,
| | - Péter Szövényi
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Ulf Lagercrantz
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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116
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Ohlweiler FP, Rossignoli TDJ, Palasio RGS, Tuan R. Taxonomic diversity of Biomphalaria (Planorbidae) in São Paulo state, Brazil. BIOTA NEOTROPICA 2020. [DOI: 10.1590/1676-0611-bn-2020-0975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract: Morphological and molecular identifications were carried out for Biomphalaria occidentalis, Biomphalaria oligoza, Biomphalaria peregrina, Biomphalaria schrammi, Biomphalaria straminea and Biomphalaria tenagophila collected from 55 sites located along the upper basin of Tietê River in the Southeast Region of Brazil. Morphological analysis considered aspects of the shell, mantle, excretory organs and reproductive system. Molecular data included 122 sequences of Cytochrome C Oxidase I gene (COI). Our results showed that some shell characters, as well as other characters related to the mantle and the reproductive system, are fundamental for the identification of the six Biomphalaria species included in this study. The use of DNA barcoding together with morphological taxonomy generated more reliable results, proving to be a very useful approach, even for malacological surveillance services.
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Affiliation(s)
| | | | | | - Roseli Tuan
- Superintendência de Controle de Endemias, Brasil
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117
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Thomas JE, Carvalho GR, Haile J, Rawlence NJ, Martin MD, Ho SYW, Sigfússon AÞ, Jósefsson VA, Frederiksen M, Linnebjerg JF, Samaniego Castruita JA, Niemann J, Sinding MHS, Sandoval-Velasco M, Soares AER, Lacy R, Barilaro C, Best J, Brandis D, Cavallo C, Elorza M, Garrett KL, Groot M, Johansson F, Lifjeld JT, Nilson G, Serjeanston D, Sweet P, Fuller E, Hufthammer AK, Meldgaard M, Fjeldså J, Shapiro B, Hofreiter M, Stewart JR, Gilbert MTP, Knapp M. Demographic reconstruction from ancient DNA supports rapid extinction of the great auk. eLife 2019; 8:e47509. [PMID: 31767056 PMCID: PMC6879203 DOI: 10.7554/elife.47509] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 10/22/2019] [Indexed: 01/23/2023] Open
Abstract
The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.
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Affiliation(s)
- Jessica E Thomas
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological SciencesBangor UniversityBangorUnited Kingdom
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Gary R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological SciencesBangor UniversityBangorUnited Kingdom
| | - James Haile
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Michael D Martin
- Department of Natural History, University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Simon YW Ho
- School of Life and Environmental SciencesUniversity of SydneySydneyAustralia
| | | | | | | | | | | | - Jonas Niemann
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Mikkel-Holger S Sinding
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- Greenland Institute of Natural ResourcesNuukGreenland
| | | | - André ER Soares
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzUnited States
| | - Robert Lacy
- Department of Conservation ScienceChicago Zoological SocietyBrookfieldUnited States
| | | | - Juila Best
- Department of Archaeology, Anthropology and Forensic Science, Faculty of Science and TechnologyBournemouth UniversityPooleUnited Kingdom
- School of History, Archaeology and ReligionCardiff UniversityCardiffUnited Kingdom
| | | | - Chiara Cavallo
- Amsterdam Centre for Ancient Studies and ArchaeologyUniversity of AmsterdamAmsterdamNetherlands
| | - Mikelo Elorza
- Arqueología PrehistóricaSociedad de Ciencias AranzadiSan SebastiánSpain
| | - Kimball L Garrett
- Natural History Museum of Los Angeles CountyLos AngelesUnited States
| | - Maaike Groot
- Institut für Prähistorische ArchäologieFreie Universität BerlinBerlinGermany
| | | | | | - Göran Nilson
- Gothenburg Museum of Natural HistoryGothenburgSweden
| | - Dale Serjeanston
- Humanities ArchaeologyUniversity of SouthamptonSouthamptonUnited Kingdom
| | - Paul Sweet
- Department of OrnithologyAmerican Museum of Natural HistoryNew YorkUnited States
| | | | | | | | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate, Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Beth Shapiro
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzUnited States
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Department of Mathematics and Natural SciencesUniversity of PotsdamPotsdamGermany
| | - John R Stewart
- Faculty of Science and TechnologyBournemouth UniversityDorsetUnited Kingdom
| | - M Thomas P Gilbert
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- Department of Natural History, University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Michael Knapp
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
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118
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Chen C, Li Q, Fu R, Wang J, Xiong C, Fan Z, Hu R, Zhang H, Lu D. Characterization of the mitochondrial genome of the pathogenic fungus Scytalidium auriculariicola (Leotiomycetes) and insights into its phylogenetics. Sci Rep 2019; 9:17447. [PMID: 31768013 PMCID: PMC6877775 DOI: 10.1038/s41598-019-53941-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/17/2019] [Indexed: 12/26/2022] Open
Abstract
Scytalidium auriculariicola is the causative pathogen of slippery scar disease in the cultivated cloud ear fungus, Auricularia polytricha. In the present study, the mitogenome of S. auriculariicola was sequenced and assembled by next-generation sequencing technology. The circular mitogenome is 96,857 bp long and contains 56 protein-coding genes, 2 ribosomal RNA genes, and 30 transfer RNA genes (tRNAs). The high frequency of A and T used in codons contributed to the high AT content (73.70%) of the S. auriculariicola mitogenome. Comparative analysis indicated that the base composition and the number of introns and protein-coding genes in the S. auriculariicola mitogenome varied from that of other Leotiomycetes mitogenomes, including a uniquely positive AT skew. Five distinct groups were found in the gene arrangements of Leotiomycetes. Phylogenetic analyses based on combined gene datasets (15 protein-coding genes) yielded well-supported (BPP = 1) topologies. A single-gene phylogenetic tree indicated that the nad4 gene may be useful as a molecular marker to analyze the phylogenetic relationships of Leotiomycetes species. This study is the first report on the mitochondrial genome of the genus Scytalidium, and it will contribute to our understanding of the population genetics and evolution of S. auriculariicola and related species.
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Affiliation(s)
- Cheng Chen
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, 610066, Sichuan, P.R. China
| | - Qiang Li
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, P.R. China
| | - Rongtao Fu
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Jian Wang
- 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
| | - Zhonghan Fan
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Rongping Hu
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Hong Zhang
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Daihua Lu
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China.
- Sichuan Academy of Agricultural Sciences, 20 # Jingjusi Rd, Chengdu, 610066, Sichuan, P.R. China.
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119
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Jugovic J, Zakšek V, Petković M, Sket B. A shrimp out of place. New genus of Atyidae (Crustacea: Decapoda) in subterranean waters of southeastern Europe, with some remarks on Atyidae taxonomy. ZOOL ANZ 2019. [DOI: 10.1016/j.jcz.2019.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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120
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Salvo M, Mir D, Tort LFL, Lizasoain A, Colina R, Victoria M. Description of a human Bocavirus recombinant strain in the Americas. Mem Inst Oswaldo Cruz 2019; 114:e190219. [PMID: 31644704 PMCID: PMC6804322 DOI: 10.1590/0074-02760190219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/08/2019] [Indexed: 12/24/2022] Open
Abstract
Human bocaviruses (HBoV) are mainly associated with respiratory and gastroenteric
infections. These viruses belong to the family Parvoviridae,
genus Bocaparvovirus and are classified in four subtypes
(HBoV1-4). Recombination and point mutation have been described as basis of
parvovirus evolution. In this study three viral sequences were obtained from
positives HBoV sewage samples collected in two Uruguayan cities and were
characterised by different methods as recombinant strains. This recombination
event was localised in the 5’ end of VP1 gene and the parental strains belonged
to subtypes 3 and 4. These three Uruguayan strains are identical at the
nucleotide sequences in the analysed genome region of the virus. As far as we
known, this study represents the first detection of HBoV recombinants strains in
the Americas.
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Affiliation(s)
- Matías Salvo
- Universidad de la República, Centro Universitario Regional Litoral Norte, Laboratory of Molecular Virology, Salto, Uruguay
| | - Daiana Mir
- Universidad de la República, Centro Universitario Regional Litoral Norte, Genomics and Bioinformatics Unit, Salto, Uruguay
| | - Luis Fernando López Tort
- Universidad de la República, Centro Universitario Regional Litoral Norte, Laboratory of Molecular Virology, Salto, Uruguay
| | - Andrés Lizasoain
- Universidad de la República, Centro Universitario Regional Litoral Norte, Laboratory of Molecular Virology, Salto, Uruguay
| | - Rodney Colina
- Universidad de la República, Centro Universitario Regional Litoral Norte, Laboratory of Molecular Virology, Salto, Uruguay
| | - Matías Victoria
- Universidad de la República, Centro Universitario Regional Litoral Norte, Laboratory of Molecular Virology, Salto, Uruguay
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121
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The global diversity of Haemonchus contortus is shaped by human intervention and climate. Nat Commun 2019; 10:4811. [PMID: 31641125 PMCID: PMC6805936 DOI: 10.1038/s41467-019-12695-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 09/23/2019] [Indexed: 12/14/2022] Open
Abstract
Haemonchus contortus is a haematophagous parasitic nematode of veterinary interest. We have performed a survey of its genome-wide diversity using single-worm whole genome sequencing of 223 individuals sampled from 19 isolates spanning five continents. We find an African origin for the species, together with evidence for parasites spreading during the transatlantic slave trade and colonisation of Australia. Strong selective sweeps surrounding the β-tubulin locus, a target of benzimidazole anthelmintic drug, are identified in independent populations. These sweeps are further supported by signals of diversifying selection enriched in genes involved in response to drugs and other anthelmintic-associated biological functions. We also identify some candidate genes that may play a role in ivermectin resistance. Finally, genetic signatures of climate-driven adaptation are described, revealing a gene acting as an epigenetic regulator and components of the dauer pathway. These results begin to define genetic adaptation to climate in a parasitic nematode. Based on single worm whole genome sequencing, the authors here characterise the global evolution of the gastrointestinal parasite Haemonchus contortus and identify genes that play a role in drug resistance as well as climate-driven adaptations involving an epigenetic regulator.
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122
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Braun EL. An evolutionary model motivated by physicochemical properties of amino acids reveals variation among proteins. Bioinformatics 2019; 34:i350-i356. [PMID: 29950007 PMCID: PMC6022633 DOI: 10.1093/bioinformatics/bty261] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Motivation The relative rates of amino acid interchanges over evolutionary time are likely to vary among proteins. Variation in those rates has the potential to reveal information about constraints on proteins. However, the most straightforward model that could be used to estimate relative rates of amino acid substitution is parameter-rich and it is therefore impractical to use for this purpose. Results A six-parameter model of amino acid substitution that incorporates information about the physicochemical properties of amino acids was developed. It showed that amino acid side chain volume, polarity and aromaticity have major impacts on protein evolution. It also revealed variation among proteins in the relative importance of those properties. The same general approach can be used to improve the fit of empirical models such as the commonly used PAM and LG models. Availability and implementation Perl code and test data are available from https://github.com/ebraun68/sixparam. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Edward L Braun
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL, USA
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123
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Sympatric western lowland gorillas, central chimpanzees and humans are infected with different trichomonads. Parasitology 2019; 147:225-230. [PMID: 31559930 DOI: 10.1017/s0031182019001343] [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: 01/02/2023]
Abstract
We investigated intestinal trichomonads in western lowland gorillas, central chimpanzees and humans cohabiting the forest ecosystem of Dzanga-Sangha Protected Area in Central African Republic, using the internal transcribed spacer (ITS) region and SSU rRNA gene sequences. Trichomonads belonging to the genus Tetratrichomonas were detected in 23% of the faecal samples and in all host species. Different hosts were infected with different genotypes of Tetratrichomonas. In chimpanzees, we detected tetratrichomonads from 'novel lineage 2', which was previously reported mostly in captive and wild chimpanzees. In gorillas, we found two different genotypes of Tetratrichomonas. The ITS region sequences of the more frequent genotype were identical to the sequence found in a faecal sample of a wild western lowland gorilla from Cameroon. Sequences of the second genotype from gorillas were almost identical to sequences previously obtained from an anorexic French woman. We provide the first report of the presence of intestinal tetratrichomonads in asymptomatic, apparently healthy humans. Human tetratrichomonads belonged to the lineage 7, which was previously reported in domestic and wild pigs and a domestic horse. Our findings suggest that the ecology and spatial overlap among hominids in the tropical forest ecosystem has not resulted in exchange of intestinal trichomonads among these hosts.
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124
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Li Q, Xiang D, Wan Y, Wu Q, Wu X, Ma C, Song Y, Zhao G, Huang W. The complete mitochondrial genomes of five important medicinal Ganoderma species: Features, evolution, and phylogeny. Int J Biol Macromol 2019; 139:397-408. [DOI: 10.1016/j.ijbiomac.2019.08.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/10/2019] [Accepted: 08/01/2019] [Indexed: 12/31/2022]
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125
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Ding H, Zhu R, Dong J, Bi D, Jiang L, Zeng J, Huang Q, Liu H, Xu W, Wu L, Kan X. Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales. PLANTS (BASEL, SWITZERLAND) 2019; 8:E386. [PMID: 31569538 PMCID: PMC6843225 DOI: 10.3390/plants8100386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/27/2019] [Accepted: 09/28/2019] [Indexed: 01/21/2023]
Abstract
The genus Sedum, with about 470 recognized species, is classified in the family Crassulaceae of the order Saxifragales. Phylogenetic relationships within the Saxifragales are still unresolved and controversial. In this study, the plastome of S. plumbizincicola was firstly presented, with a focus on the structural analysis of rrn operon and phylogenetic implications within the order Saxifragaceae. The assembled complete plastome of S. plumbizincicola is 149,397 bp in size, with a typical circular, double-stranded, and quadripartite structure of angiosperms. It contains 133 genes, including 85 protein-coding genes (PCGs), 36 tRNA genes, 8 rRNA genes, and four pseudogenes (one ycf1, one rps19, and two ycf15). The predicted secondary structure of S. plumbizincicola 16S rRNA includes three main domains organized in 74 helices. Further, our results confirm that 4.5S rRNA of higher plants is associated with fragmentation of 23S rRNA progenitor. Notably, we also found the sequence of putative rrn5 promoter has some evolutionary implications within the order Saxifragales. Moreover, our phylogenetic analyses suggested that S. plumbizincicola had a closer relationship with S. sarmentosum than S. oryzifolium, and supported the taxonomic revision of Phedimus. Our findings of the present study will be useful for further investigation of the evolution of plastid rRNA operon and phylogenetic relationships within Saxifragales.
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Affiliation(s)
- Hengwu Ding
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China.
- The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu 241000, Anhui, China.
| | - Ran Zhu
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China.
| | - Jinxiu Dong
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China.
| | - De Bi
- National Engineering Laboratory of Soil Pollution Control and Remediation Technologies, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, Jiangsu, China.
| | - Lan Jiang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China.
| | - Juhua Zeng
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China.
| | - Qingyu Huang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China.
| | - Huan Liu
- National Engineering Laboratory of Soil Pollution Control and Remediation Technologies, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, Jiangsu, China.
| | - Wenzhong Xu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Longhua Wu
- National Engineering Laboratory of Soil Pollution Control and Remediation Technologies, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, Jiangsu, China.
| | - Xianzhao Kan
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China.
- The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu 241000, Anhui, China.
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126
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Chen SG, Li J, Zhang F, Xiao B, Hu JM, Cui YQ, Hofreiter M, Hou XD, Sheng GL, Lai XL, Yuan JX. Different maternal lineages revealed by ancient mitochondrial genome of Camelus bactrianus from China. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:786-793. [PMID: 31542986 DOI: 10.1080/24701394.2019.1659250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Domestic Bactrian camel (Camelus bactrianus) used to be one of the most important livestock species in Chinese history, as well as the major transport carrier on the ancient Silk Road. However, archeological studies on Chinese C. bactrianus are still limited, and molecular biology research on this species is mainly focused on modern specimens. In this study, we retrieved the complete mitochondrial genome from a C. bactrianus specimen, which was excavated from northwestern China and dated at 1290-1180 cal. years before present (yBP). Phylogenetic analyses using 18 mitochondrial genomes indicated that the C. bactrianus clade was divided into two maternal lineages. The majority of samples originating from Iran to Japan and Mongolia belong to subclade A1, while our sample together with two Mongolian individuals formed the much smaller subclade A2. Furthermore, the divergence time of these two maternal lineages was estimated as 165 Kya (95% credibility interval 117-222 Kya), this might indicate that several different evolutionary lineages were incorporated into the domestic gene pool during the initial domestication process. Bayesian skyline plot (BSP) analysis suggest a slow increase in female effective population size of C. bactrianus from 5000 years ago, which corresponds to the beginning of domestication of C. bactrianus. The present study also revealed that there were extensive exchanges of genetic information among C. bactrianus populations in regions along the Silk Road.
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Affiliation(s)
- Shun-Gang Chen
- Faculty of Materials Science and Chemistry, China University of Geosciences , Wuhan , China.,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Ji Li
- Insitute of Silk Road Studies, Northwest University , Xi'an , China
| | - Fan Zhang
- Ancient DNA Lab, School of Life Science, Jilin University , Changchun , China
| | - Bo Xiao
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Jia-Ming Hu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Yin-Qiu Cui
- Ancient DNA Lab, School of Life Science, Jilin University , Changchun , China
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse , Potsdam , Germany
| | - Xin-Dong Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Gui-Lian Sheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Xu-Long Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Jun-Xia Yuan
- Faculty of Materials Science and Chemistry, China University of Geosciences , Wuhan , China.,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
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127
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da Costa ZP, Cauz-Santos LA, Ragagnin GT, Van Sluys MA, Dornelas MC, Berges H, de Mello Varani A, Vieira MLC. Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis. Mol Biol Rep 2019; 46:6117-6133. [DOI: 10.1007/s11033-019-05047-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/28/2019] [Indexed: 12/23/2022]
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128
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Wang X, Lin S, Liu D, Wang Q, McAvoy R, Ding J, Li Y. Characterization and Expression Analysis of ERF Genes in Fragaria vesca Suggest Different Divergences of Tandem ERF Duplicates. Front Genet 2019; 10:805. [PMID: 31572436 PMCID: PMC6752658 DOI: 10.3389/fgene.2019.00805] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 07/31/2019] [Indexed: 01/26/2023] Open
Abstract
Ethylene-responsive factors (ERFs) play important roles in plant growth and development and in responses to abiotic stresses. However, little information was available about the ERF genes in woodland strawberry (Fragaria vesca), a genetic model plant for the Fragaria genus and Rosaceae family. In this study, 91 FveERF genes were identified, including 35 arrayed in tandem, indicating that tandem duplication is a major mechanism for the expansion of the FveERF family. According to their phylogenetic relationships with AtERFs from Arabidopsis thaliana, the tandem FveERF genes could be grouped into ancestral and lineage-specific tandem ones. The ancestral tandem FveERFs are likely derived from tandem duplications that occurred in the common ancestor of F. vesca and A. thaliana, whereas the lineage-specific ones are specifically present in the F. vesca lineage. The lineage-specific tandem FveERF duplicates are more conserved than the ancestral ones in sequence and structure. However, their expression in flowers and fruits is similarly diversified, indicating that tandem FveERFs have diverged rapidly after duplication in this respect. The lineage-specific tandem FveERFs display the same response patterns with only one exception under drought or cold, whereas the ancestral tandem ones are largely differentially expressed, suggesting that divergence of tandem FveERF expression under stress may have occurred later in the reproductive development. Our results provide evidence that the retention of tandem FveERF duplicates soon after their duplication may be related to their divergence in the regulation of reproductive development. In contrast, their further divergence in expression pattern likely contributes to plant response to abiotic stress.
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Affiliation(s)
- Xiaojing Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Shanshan Lin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Decai Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Quanzhi Wang
- Engineering and Technology Center for Modern Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang, China
| | - Richard McAvoy
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, United States
| | - Jing Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yi Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, China.,Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, United States
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129
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Walker CH, Siu-Ting K, Taylor A, O'Connell MJ, Bennett T. Strigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation. BMC Biol 2019; 17:70. [PMID: 31488154 PMCID: PMC6728956 DOI: 10.1186/s12915-019-0689-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/13/2019] [Indexed: 11/10/2022] Open
Abstract
Background Strigolactones (SLs) are an important class of carotenoid-derived signalling molecule in plants, which function both as exogenous signals in the rhizosphere and as endogenous plant hormones. In flowering plants, SLs are synthesized by a core pathway of four enzymes and are perceived by the DWARF14 (D14) receptor, leading to degradation of SMAX1-LIKE7 (SMXL7) target proteins in a manner dependent on the SCFMAX2 ubiquitin ligase. The evolutionary history of SLs is poorly understood, and it is not clear whether SL synthesis and signalling are present in all land plant lineages, nor when these traits evolved. Results We have utilized recently-generated genomic and transcriptomic sequences from across the land plant clade to resolve the origin of each known component of SL synthesis and signalling. We show that all enzymes in the core SL synthesis pathway originated at or before the base of land plants, consistent with the previously observed distribution of SLs themselves in land plant lineages. We also show that the late-acting enzyme LATERAL BRANCHING OXIDOREDUCTASE (LBO) may be considerably more ancient than previously thought. We perform a detailed phylogenetic analysis of SMXL proteins and show that specific SL target proteins only arose in flowering plants. We also assess diversity and protein structure in the SMXL family, identifying several previously unknown clades. Conclusions Overall, our results suggest that SL synthesis is much more ancient than canonical SL signalling, consistent with the idea that SLs first evolved as rhizosphere signals and were only recruited much later as hormonal signals. Electronic supplementary material The online version of this article (10.1186/s12915-019-0689-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Catriona H Walker
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Karen Siu-Ting
- Institute for Global Food Security, School of Biological Sciences, Queens University, Belfast, BT7 1NN, UK.,Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3FD, UK
| | - Alysha Taylor
- Computational and Molecular Evolutionary Biology Research Group, School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Mary J O'Connell
- Computational and Molecular Evolutionary Biology Research Group, School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.,Computational and Molecular Evolutionary Biology Research Group, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Tom Bennett
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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130
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Beinart RA, Luo C, Konstantinidis KT, Stewart FJ, Girguis PR. The Bacterial Symbionts of Closely Related Hydrothermal Vent Snails With Distinct Geochemical Habitats Show Broad Similarity in Chemoautotrophic Gene Content. Front Microbiol 2019; 10:1818. [PMID: 31474946 PMCID: PMC6702916 DOI: 10.3389/fmicb.2019.01818] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/23/2019] [Indexed: 12/29/2022] Open
Abstract
Symbiosis has evolved between a diversity of invertebrate taxa and chemosynthetic bacterial lineages. At the broadest level, these symbioses share primary function: the bacterial symbionts use the energy harnessed from the oxidation of reduced chemicals to power the fixation of inorganic carbon and/or other nutrients, providing the bulk of host nutrition. However, it is unclear to what extent the ecological niche of the host species is influenced by differences in symbiont traits, particularly those involved in chemoautotrophic function and interaction with the geochemical environment. Hydrothermal vents in the Lau Basin (Tonga) are home to four morphologically and physiologically similar snail species from the sister genera Alviniconcha and Ifremeria. Here, we assembled nearly complete genomes from their symbionts to determine whether differences in chemoautotrophic capacity exist among these symbionts that could explain the observed distribution of these snail species into distinct geochemical habitats. Phylogenomic analyses confirmed that the symbionts have evolved from four distinct lineages in the classes γ-proteobacteria or Campylobacteria. The genomes differed with respect to genes related to motility, adhesion, secretion, and amino acid uptake or excretion, though were quite similar in chemoautotrophic function, with all four containing genes for carbon fixation, sulfur and hydrogen oxidation, and oxygen and nitrate respiration. This indicates that differences in the presence or absence of symbiont chemoautotrophic functions does not likely explain the observed geochemical habitat partitioning. Rather, differences in gene expression and regulation, biochemical differences among these chemoautotrophic pathways, and/or differences in host physiology could all influence the observed patterns of habitat partitioning.
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Affiliation(s)
- Roxanne A. Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, United States
| | - Chengwei Luo
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Frank J. Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Peter R. Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
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131
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Morgan CC, Hart MW. Molecular evolution of mammalian genes with epistatic interactions in fertilization. BMC Evol Biol 2019; 19:154. [PMID: 31345177 PMCID: PMC6659299 DOI: 10.1186/s12862-019-1480-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/16/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Genes that encode proteins associated with sperm competition, fertilization, and sexual conflicts of interest are often among the most rapidly evolving parts of animal genomes. One family of sperm-expressed genes (Zp3r, C4bpa) in the mammalian gene cluster called the regulator of complement activation (RCA) encodes proteins that bind eggs and mediate reproductive success, and are therefore expected to show high relative rates of nonsynonymous nucleotide substitution in response to sexual selection in comparison to other genes not involved in gamete binding at fertilization. We tested that working hypothesis by using phylogenetic models of codon evolution to identify episodes of diversifying positive selection. We used a comparative approach to quantify the evidence for episodic diversifying selection acting on RCA genes with known functions in fertilization (and sensitivity to sexual selection), and contrast them with other RCA genes in the same gene family that function in innate immunity (and are not sensitive to sexual selection). RESULTS We expected but did not find evidence for more episodes of positive selection on Zp3r in Glires (the rodents and lagomorphs) or on C4BPA in Primates, in comparison to other paralogous RCA genes in the same taxon, or in comparison to the same orthologous RCA gene in the other taxon. That result was not unique to RCA genes: we also found little evidence for more episodes of diversifying selection on genes that encode selective sperm-binding molecules in the egg coat or zona pellucida (Zp2, Zp3) in comparison to members of the same gene family that encode structural elements of the egg coat (Zp1, Zp4). Similarly, we found little evidence for episodic diversifying selection acting on two other recently discovered genes (Juno, Izumo1) that encode essential molecules for sperm-egg fusion. CONCLUSIONS These negative results help to illustrate the importance of a comparative context for this type of codon model analysis. The results may also point to other phylogenetic contexts in which the effects of selection acting on these fertilization proteins might be more readily discovered and documented in mammals and other taxa.
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Affiliation(s)
- Claire C. Morgan
- Department of Medicine, Imperial College London, London, W12 0NN UK
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Michael W. Hart
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia V5A 1S6 Canada
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132
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Xu M, Lawrence JG, Durand D. Selection, periodicity and potential function for Highly Iterative Palindrome-1 (HIP1) in cyanobacterial genomes. Nucleic Acids Res 2019; 46:2265-2278. [PMID: 29432573 PMCID: PMC5861425 DOI: 10.1093/nar/gky075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 01/25/2018] [Indexed: 02/05/2023] Open
Abstract
Highly Iterated Palindrome 1 (HIP1, GCGATCGC) is hyper-abundant in most cyanobacterial genomes. In some cyanobacteria, average HIP1 abundance exceeds one motif per gene. Such high abundance suggests a significant role in cyanobacterial biology. However, 20 years of study have not revealed whether HIP1 has a function, much less what that function might be. We show that HIP1 is 15- to 300-fold over-represented in genomes analyzed. More importantly, HIP1 sites are conserved both within and between open reading frames, suggesting that their overabundance is maintained by selection rather than by continual replenishment by neutral processes, such as biased DNA repair. This evidence for selection suggests a functional role for HIP1. No evidence was found to support a functional role as a peptide or RNA motif or a role in the regulation of gene expression. Rather, we demonstrate that the distribution of HIP1 along cyanobacterial chromosomes is significantly periodic, with periods ranging from 10 to 90 kb, consistent in scale with periodicities reported for co-regulated, co-expressed and evolutionarily correlated genes. The periodicity we observe is also comparable in scale to chromosomal interaction domains previously described in other bacteria. In this context, our findings imply HIP1 functions associated with chromosome and nucleoid structure.
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Affiliation(s)
- Minli Xu
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Jeffrey G Lawrence
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Dannie Durand
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA.,Department of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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133
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Siu-Ting K, Torres-Sánchez M, San Mauro D, Wilcockson D, Wilkinson M, Pisani D, O'Connell MJ, Creevey CJ. Inadvertent Paralog Inclusion Drives Artifactual Topologies and Timetree Estimates in Phylogenomics. Mol Biol Evol 2019; 36:1344-1356. [PMID: 30903171 PMCID: PMC6526904 DOI: 10.1093/molbev/msz067] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Increasingly, large phylogenomic data sets include transcriptomic data from nonmodel organisms. This not only has allowed controversial and unexplored evolutionary relationships in the tree of life to be addressed but also increases the risk of inadvertent inclusion of paralogs in the analysis. Although this may be expected to result in decreased phylogenetic support, it is not clear if it could also drive highly supported artifactual relationships. Many groups, including the hyperdiverse Lissamphibia, are especially susceptible to these issues due to ancient gene duplication events and small numbers of sequenced genomes and because transcriptomes are increasingly applied to resolve historically conflicting taxonomic hypotheses. We tested the potential impact of paralog inclusion on the topologies and timetree estimates of the Lissamphibia using published and de novo sequencing data including 18 amphibian species, from which 2,656 single-copy gene families were identified. A novel paralog filtering approach resulted in four differently curated data sets, which were used for phylogenetic reconstructions using Bayesian inference, maximum likelihood, and quartet-based supertrees. We found that paralogs drive strongly supported conflicting hypotheses within the Lissamphibia (Batrachia and Procera) and older divergence time estimates even within groups where no variation in topology was observed. All investigated methods, except Bayesian inference with the CAT-GTR model, were found to be sensitive to paralogs, but with filtering convergence to the same answer (Batrachia) was observed. This is the first large-scale study to address the impact of orthology selection using transcriptomic data and emphasizes the importance of quality over quantity particularly for understanding relationships of poorly sampled taxa.
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Affiliation(s)
- Karen Siu-Ting
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom.,School of Biotechnology, Dublin City University, Glasnevin, Dublin, Ireland.,Dpto. de Herpetología, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - María Torres-Sánchez
- Department of Biodiversity, Ecology, and Evolution, Complutense University of Madrid, Madrid, Spain.,Department of Neuroscience, Spinal Cord and Brain Injury Research Center and Ambystoma Genetic Stock Center, University of Kentucky, Lexington, KY
| | - Diego San Mauro
- Department of Biodiversity, Ecology, and Evolution, Complutense University of Madrid, Madrid, Spain
| | - David Wilcockson
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Mark Wilkinson
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Davide Pisani
- Life Sciences Building, University of Bristol, Bristol, United Kingdom
| | - Mary J O'Connell
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.,School of Life Sciences, University of Nottingham, University Park, United Kingdom
| | - Christopher J Creevey
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
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134
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Tuteja R, McKeown PC, Ryan P, Morgan CC, Donoghue MTA, Downing T, O'Connell MJ, Spillane C. Paternally Expressed Imprinted Genes under Positive Darwinian Selection in Arabidopsis thaliana. Mol Biol Evol 2019; 36:1239-1253. [PMID: 30913563 PMCID: PMC6526901 DOI: 10.1093/molbev/msz063] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genomic imprinting is an epigenetic phenomenon where autosomal genes display uniparental expression depending on whether they are maternally or paternally inherited. Genomic imprinting can arise from parental conflicts over resource allocation to the offspring, which could drive imprinted loci to evolve by positive selection. We investigate whether positive selection is associated with genomic imprinting in the inbreeding species Arabidopsis thaliana. Our analysis of 140 genes regulated by genomic imprinting in the A. thaliana seed endosperm demonstrates they are evolving more rapidly than expected. To investigate whether positive selection drives this evolutionary acceleration, we identified orthologs of each imprinted gene across 34 plant species and elucidated their evolutionary trajectories. Increased positive selection was sought by comparing its incidence among imprinted genes with nonimprinted controls. Strikingly, we find a statistically significant enrichment of imprinted paternally expressed genes (iPEGs) evolving under positive selection, 50.6% of the total, but no such enrichment for positive selection among imprinted maternally expressed genes (iMEGs). This suggests that maternally- and paternally expressed imprinted genes are subject to different selective pressures. Almost all positively selected amino acids were fixed across 80 sequenced A. thaliana accessions, suggestive of selective sweeps in the A. thaliana lineage. The imprinted genes under positive selection are involved in processes important for seed development including auxin biosynthesis and epigenetic regulation. Our findings support a genomic imprinting model for plants where positive selection can affect paternally expressed genes due to continued conflict with maternal sporophyte tissues, even when parental conflict is reduced in predominantly inbreeding species.
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Affiliation(s)
- Reetu Tuteja
- Genetics & Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), School of Natural Sciences, Ryan Institute, National University of Ireland Galway, Galway, Ireland.,Center for Genomics and Systems Biology, New York University, New York, NY
| | - Peter C McKeown
- Genetics & Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), School of Natural Sciences, Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Pat Ryan
- Genetics & Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), School of Natural Sciences, Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Claire C Morgan
- School of Biotechnology, Faculty of Biological Sciences, Dublin City University, Dublin, Ireland.,Division of Diabetes, Endocrinology and Metabolism, Imperial College London, London, United Kingdom
| | - Mark T A Donoghue
- Genetics & Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), School of Natural Sciences, Ryan Institute, National University of Ireland Galway, Galway, Ireland.,Memorial Sloan Kettering Cancer Center, New York, NY
| | - Tim Downing
- School of Biotechnology, Faculty of Biological Sciences, Dublin City University, Dublin, Ireland
| | - Mary J O'Connell
- Computational and Molecular Evolutionary Biology Research Group, School of Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, United Kingdom.,Computational and Molecular Evolutionary Biology Group, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Charles Spillane
- Genetics & Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), School of Natural Sciences, Ryan Institute, National University of Ireland Galway, Galway, Ireland
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135
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Song R, Zhang D, Gao JW, Cheng XF, Xie M, Li H, Wu YA. Characterization of the complete mitochondrial genome of Brentisentisyangtzensis Yu & Wu, 1989 (Acanthocephala, Illiosentidae). Zookeys 2019; 861:1-14. [PMID: 31363345 PMCID: PMC6656981 DOI: 10.3897/zookeys.861.34809] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 05/31/2019] [Indexed: 11/12/2022] Open
Abstract
The mitogenome of Brentisentisyangtzensis is 13,864 bp in length and has the circular structure typical of metazoans. It contains 36 genes: 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and 12 protein-encoding genes (PCGs). All genes are transcribed from the same strand. Thirteen overlapping regions were found in the mitochondrial genome. The overall A+T content of B.yangtzensis is 68.3% versus 31.7% of G+C content (A = 27.8%, T = 40.5%, C = 9.0%, G = 22.7%). B.yangtzenensis (Illiosentidae) and Leptorhynchoidesthecatus (Rhadinorhynchidae) form a sister clade, showing the relatively close relationship between the Illiosentidae and the Rhadinorhynchidae. The mitochondrial gene arrangements of acanthocephalan species are relatively conserved, with only a few translocations of tRNAs (trnS1, trnS2, trnV, and trnK) detected. An identical gene order was found both in a sister clade (Centrorhynchusaluconis and Plagiorhynchustransversus) and across different classes (B.yangtzensis (Palaeacanthocephala), Acanthosentischeni (Eoacanthocephala) and Macracanthorhynchushirudinaceus (Archiacanthocephala), Oncicolaluehei and L.thecatus (Palaeacanthocephala)). More studies and more sequences of acanthocephalan species are needed to gain a clear understanding of the phylogenetic relationships.
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Affiliation(s)
- Rui Song
- Hunan Fisheries Science Institute, Changsha 410153, ChinaHunan Fisheries Science InstituteChangshaChina
- Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde, 415000, ChinaCollaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan ProvinceChangdeChina
| | - 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, ChinaInstitute of Hydrobiology, Chinese Academy of SciencesWuhanChina
| | - Jin-Wei Gao
- Hunan Fisheries Science Institute, Changsha 410153, ChinaHunan Fisheries Science InstituteChangshaChina
| | - Xiao-Fei Cheng
- Hunan Fisheries Science Institute, Changsha 410153, ChinaHunan Fisheries Science InstituteChangshaChina
| | - Min Xie
- Hunan Fisheries Science Institute, Changsha 410153, ChinaHunan Fisheries Science InstituteChangshaChina
| | - Hong Li
- Hunan Fisheries Science Institute, Changsha 410153, ChinaHunan Fisheries Science InstituteChangshaChina
| | - Yuan-An Wu
- Hunan Fisheries Science Institute, Changsha 410153, ChinaHunan Fisheries Science InstituteChangshaChina
- Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde, 415000, ChinaCollaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan ProvinceChangdeChina
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136
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Characterization and phylogenomics of the complete mitochondrial genome of the polyzoic cestode Gangesia oligonchis (Platyhelminthes: Onchoproteocephalidea). J Helminthol 2019; 94:e58. [PMID: 31272516 DOI: 10.1017/s0022149x19000452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The order Onchoproteocephalidea (Eucestoda) was recently erected to accommodate the hook-bearing tetraphyllideans and the proteocephalideans, which are characterized by internal proglottization and a tetra-acetabulate scolex. The recognized subfamilies in the Proteocephalidae appeared to be non-monophyletic based on 28S recombinant DNA (rDNA) sequence data. Other molecular markers with higher phylogenetic resolution, such as large mitochondrial DNA fragments and multiple genes, are obviously needed. Thus the mitochondrial genome of Gangesia oligonchis, belonging to the putative earliest diverging group of the Proteocephalidae, was sequenced. The circular mitogenome of G. oligonchis was 13,958 bp in size, and contained the standard 36 genes: 22 transfer RNA genes, two rRNA genes and 12 protein-coding genes, as well as two major non-coding regions. A short NCR and a large NCR (lNCR) region were 216 bp and 419 bp in size, respectively. Highly repetitive regions in the lNCR region were detected with that of 11 repeat units. The mitogenome of G. oligonchis shared 71.1% nucleotide identity with Testudotaenia sp. WL-2016. Phylogenetic analyses of the complete mitochondrial genomes with Bayesian inference and maximum likelihood methods indicated that G. oligonchis formed a sister clade with Testudotaenia sp. WL-2016 with maximum support. The ordinal topology is (Caryophyllidea, (Diphyllobothriidea, (Bothriocephalidea, (Onchoproteocephalidea, Cyclophyllidea)))). The mitogenomic gene arrangement of G. oligonchis was identical to that of Testudotaenia sp. WL-2016. Both mitogenomic and nuclear sequence data for many more taxa are required to effectively explore the inter-relationships among the Onchoproteocephalidea.
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137
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Gowthaman V, Singh SD, Dhama K, Ramakrishnan MA, Malik YPS, Gopala Krishna Murthy TR, Chitra R, Munir M. Co-infection of Newcastle disease virus genotype XIII with low pathogenic avian influenza exacerbates clinical outcome of Newcastle disease in vaccinated layer poultry flocks. Virusdisease 2019; 30:441-452. [PMID: 31803812 DOI: 10.1007/s13337-019-00533-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/09/2019] [Indexed: 01/30/2023] Open
Abstract
Newcastle disease (ND) and avian influenza (AI) are economically important infectious diseases of poultry. Sometime, concomitant secondary viral/or bacterial infections significantly alters the pathobiology of ND and AI in poultry. As of now, the disease patterns and dynamics of co-infections caused by ND virus (NDV, genotype XIII) and Low Pathogenic AI viruses (LPAI, H9N2) are explicitly elusive. Thus, we examined the clinicopathological disease conditions due to these two economically important viruses to understand the complex disease outcomes by virus-virus interactions in vaccinated flocks. The findings of clinicopathological and molecular investigations carried on 37 commercial ND vaccinated poultry flocks revealed simultaneous circulation of NDV and AIV in same flock/bird. Further, molecular characterization of hemagglutinin (HA) and neuraminidase (NA) genes confirmed that all the identified AIVs were of low pathogenicity H9N2 subtype and fusion (F) gene analysis of detected NDVs belong to NDV class II, genotype XIII, a virulent type. The NDV and H9N2 alone or co-infected flocks (NDV + LPAI) exhibit clinical signs and lesions similar to that of virulent NDV except the degree of severity, which was higher in H9N2-NDV co-infected flocks. Additionally, avian pathogenic E. coli and mycoplasma infections were detected in majority of the ailing/dead birds from the co-infected flocks during progression of the clinical disease. Overall, the findings highlight the multi-factorial disease complexity in commercial poultry and suggest the importance of NDV genotype XIII in intensifying the clinical disease in vaccinated birds.
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Affiliation(s)
- V Gowthaman
- 1Avian Diseases Section, Indian Veterinary Research Institute, Izatnagar, 243 122 India
- 2Present Address: Poultry Disease Diagnosis and Surveillance Laboratory, Veterinary College and Research Institute Campus, Namakkal, 637 002 India
| | - S D Singh
- 1Avian Diseases Section, Indian Veterinary Research Institute, Izatnagar, 243 122 India
| | - K Dhama
- 1Avian Diseases Section, Indian Veterinary Research Institute, Izatnagar, 243 122 India
| | - M A Ramakrishnan
- 3Division of Virology, Indian Veterinary Research Institute, Mukteswar, Uttarakhand 263138 India
| | - Y P S Malik
- 4Division of Biological Standardisation, Indian Veterinary Research Institute, Izatnagar, 243 122 India
| | - T R Gopala Krishna Murthy
- 2Present Address: Poultry Disease Diagnosis and Surveillance Laboratory, Veterinary College and Research Institute Campus, Namakkal, 637 002 India
| | - R Chitra
- 5Department of Animal Husbandry Statistics and Computer Applications, Veterinary College and Research Institute, Namakkal, 637 002 India
| | - M Munir
- 6Department of Biomedical and Life Sciences, Lancaster University, Lancaster, LA1 4YG UK
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138
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Two new mitogenomes of Picidae (Aves, Piciformes): Sequence, structure and phylogenetic analyses. Int J Biol Macromol 2019; 133:683-692. [DOI: 10.1016/j.ijbiomac.2019.04.157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/21/2019] [Accepted: 04/22/2019] [Indexed: 02/06/2023]
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139
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Weber CC, Whelan S. Physicochemical Amino Acid Properties Better Describe Substitution Rates in Large Populations. Mol Biol Evol 2019; 36:679-690. [PMID: 30668757 DOI: 10.1093/molbev/msz003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Substitutions between chemically distant amino acids are known to occur less frequently than those between more similar amino acids. This knowledge, however, is not reflected in most codon substitution models, which treat all nonsynonymous changes as if they were equivalent in terms of impact on the protein. A variety of methods for integrating chemical distances into models have been proposed, with a common approach being to divide substitutions into radical or conservative categories. Nevertheless, it remains unclear whether the resulting models describe sequence evolution better than their simpler counterparts. We propose a parametric codon model that distinguishes between radical and conservative substitutions, allowing us to assess if radical substitutions are preferentially removed by selection. Applying our new model to a range of phylogenomic data, we find differentiating between radical and conservative substitutions provides significantly better fit for large populations, but see no equivalent improvement for smaller populations. Comparing codon and amino acid models using these same data shows that alignments from large populations tend to select phylogenetic models containing information about amino acid exchangeabilities, whereas the structure of the genetic code is more important for smaller populations. Our results suggest selection against radical substitutions is, on average, more pronounced in large populations than smaller ones. The reduced observable effect of selection in smaller populations may be due to stronger genetic drift making it more challenging to detect preferences. Our results imply an important connection between the life history of a phylogenetic group and the model that best describes its evolution.
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Affiliation(s)
- Claudia C Weber
- Center for Computational Genetics and Genomics, Department of Biology, Temple University, Philadelphia, PA.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Simon Whelan
- Evolutionary Biology Center, Uppsala University, Uppsala, Sweden
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140
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Wang W, Zheng Y, Zhao J, Yao M. Low genetic diversity in a critically endangered primate: shallow evolutionary history or recent population bottleneck? BMC Evol Biol 2019; 19:134. [PMID: 31242851 PMCID: PMC6595580 DOI: 10.1186/s12862-019-1451-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/31/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Current patterns of population genetic variation may have been shaped by long-term evolutionary history and contemporary demographic processes. Understanding the underlying mechanisms that yield those patterns is crucial for informed conservation of endangered species. The critically endangered white-headed langur, Trachypithecus leucocephalus, is endemic to a narrow range in southwest China. This species shows very low genetic diversity in its 2 main relict populations, Fusui and Chongzuo. Whether this has been caused by a short evolutionary history or recent population declines is unknown. Therefore, we investigated the contributions of historical and recent population demographic changes to population genetic diversity by using 15 nuclear microsatellite markers and mitochondrial DNA (mtDNA) control region sequences. RESULTS Using genetic data from 214 individuals we found a total of 9 mtDNA haplotypes in the Fusui population but only 1 haplotype in the Chongzuo population, and we found an overall low genetic diversity (haplotype and nucleotide diversities: h = 0.486 ± 0.036; π = 0.0028 ± 0.0003). The demographic history inferred from mtDNA and microsatellite markers revealed no evidence for historical population size fluctuations or recent population bottlenecks. Simulations of possible population divergence histories inferred by DIYABC analysis supported a recent divergence of the Chongzuo population from the Fusui population and no population bottlenecks. CONCLUSIONS Despite severe population declines caused by anthropogenic activities in the last century, the low genetic diversity of the extant white-headed langur populations is most likely primarily due to the species' shallow evolutionary history and to a recent, local population founder event.
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Affiliation(s)
- Weiran Wang
- School of Life Sciences, Peking University, Beijing, 100871, China.,Institute of Ecology, Peking University, Beijing, 100871, China.,Beijing National Day School, Beijing, 100871, China
| | - Yitao Zheng
- School of Life Sciences, Peking University, Beijing, 100871, China.,Institute of Ecology, Peking University, Beijing, 100871, China
| | - Jindong Zhao
- School of Life Sciences, Peking University, Beijing, 100871, China.,Institute of Ecology, Peking University, Beijing, 100871, China
| | - Meng Yao
- School of Life Sciences, Peking University, Beijing, 100871, China. .,Institute of Ecology, Peking University, Beijing, 100871, China.
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141
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Li G, Zhang W, Wang R, Xing G, Wang S, Ji X, Wang N, Su S, Zhou J. Genetic Analysis and Evolutionary Changes of the Torque teno sus Virus. Int J Mol Sci 2019; 20:E2881. [PMID: 31200479 PMCID: PMC6628323 DOI: 10.3390/ijms20122881] [Citation(s) in RCA: 13] [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: 04/26/2019] [Revised: 06/05/2019] [Accepted: 06/10/2019] [Indexed: 01/03/2023] Open
Abstract
The torque teno sus virus (TTSuV) is an emerging virus threating the Suidae species of unclear pathogenicity, although it was previously reported as a worsening factor of other porcine diseases, in particular, porcine circovirus associated disease (PCVAD). Here, a comprehensive codon usage analysis of the open reading frame 1 (ORF1), which encodes the viral capsid protein, was undertaken for the first time to reveal its evolutionary history. We revealed independent phylogenetic processes for the two genera during TTSuV evolution, which was confirmed by principal component analysis (PCA). A low codon usage bias was observed in different genera and different species, with Kappatorquevirus a (TTSuVk2a) displaying the highest, which was mainly driven by mutation pressure and natural selection, especially natural selection. Overall, ATs were more abundant than GCs, along with more A-ended synonymous codons in relative synonymous codon usage (RSCU) analysis. To further confirm the role of natural selection and TTSuV adaptation to the Suidae species, codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses were performed, which showed different adaptations for different TTSuVs. Importantly, we identified a more dominant role of Sus scrofa in the evolution of Iotatorquevirus (TTSuV1), with the highest CAI values and lowest RCDI values compared to Sus scrofa domestica. However, in TTSuVk2, the roles of Sus scrofa and Sus scrofa domestica were the same, regarding codon usage, with similar CAI and RCDI values. Our study provides a new perspective of the evolution of TTSuV and valuable information to develop control measures against TTSuV.
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Affiliation(s)
- Gairu Li
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210000, China.
| | - Wenyan Zhang
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210000, China.
| | - Ruyi Wang
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210000, China.
| | - Gang Xing
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou 310027, China.
| | - Shilei Wang
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210000, China.
| | - Xiang Ji
- Department of Biomathematics, University of California, Los Angeles, CA 90095, USA.
| | - Ningning Wang
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210000, China.
| | - Shuo Su
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210000, China.
| | - Jiyong Zhou
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou 310027, China.
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Fages A, Hanghøj K, Khan N, Gaunitz C, Seguin-Orlando A, Leonardi M, McCrory Constantz C, Gamba C, Al-Rasheid KAS, Albizuri S, Alfarhan AH, Allentoft M, Alquraishi S, Anthony D, Baimukhanov N, Barrett JH, Bayarsaikhan J, Benecke N, Bernáldez-Sánchez E, Berrocal-Rangel L, Biglari F, Boessenkool S, Boldgiv B, Brem G, Brown D, Burger J, Crubézy E, Daugnora L, Davoudi H, de Barros Damgaard P, de Los Ángeles de Chorro Y de Villa-Ceballos M, Deschler-Erb S, Detry C, Dill N, do Mar Oom M, Dohr A, Ellingvåg S, Erdenebaatar D, Fathi H, Felkel S, Fernández-Rodríguez C, García-Viñas E, Germonpré M, Granado JD, Hallsson JH, Hemmer H, Hofreiter M, Kasparov A, Khasanov M, Khazaeli R, Kosintsev P, Kristiansen K, Kubatbek T, Kuderna L, Kuznetsov P, Laleh H, Leonard JA, Lhuillier J, Liesau von Lettow-Vorbeck C, Logvin A, Lõugas L, Ludwig A, Luis C, Arruda AM, Marques-Bonet T, Matoso Silva R, Merz V, Mijiddorj E, Miller BK, Monchalov O, Mohaseb FA, Morales A, Nieto-Espinet A, Nistelberger H, Onar V, Pálsdóttir AH, Pitulko V, Pitskhelauri K, Pruvost M, Rajic Sikanjic P, Rapan Papeša A, Roslyakova N, Sardari A, Sauer E, Schafberg R, Scheu A, Schibler J, Schlumbaum A, Serrand N, Serres-Armero A, Shapiro B, Sheikhi Seno S, Shevnina I, Shidrang S, Southon J, Star B, Sykes N, Taheri K, Taylor W, Teegen WR, Trbojević Vukičević T, Trixl S, Tumen D, Undrakhbold S, Usmanova E, Vahdati A, Valenzuela-Lamas S, Viegas C, Wallner B, Weinstock J, Zaibert V, Clavel B, Lepetz S, Mashkour M, Helgason A, Stefánsson K, Barrey E, Willerslev E, Outram AK, Librado P, Orlando L. Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series. Cell 2019; 177:1419-1435.e31. [PMID: 31056281 PMCID: PMC6547883 DOI: 10.1016/j.cell.2019.03.049] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 02/14/2019] [Accepted: 03/27/2019] [Indexed: 11/30/2022]
Abstract
Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN "speed gene," only rose in popularity within the last millennium. Finally, the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management.
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Affiliation(s)
- Antoine Fages
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Kristian Hanghøj
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Naveed Khan
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark; Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Charleen Gaunitz
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Michela Leonardi
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark; Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Christian McCrory Constantz
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark; Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Cristina Gamba
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Khaled A S Al-Rasheid
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Silvia Albizuri
- Seminari d'Estudis i Recerques Prehistoriques, HAR2017-87695-P, Universitat de Barcelona, Barcelona, Spain
| | - Ahmed H Alfarhan
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Morten Allentoft
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Saleh Alquraishi
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - David Anthony
- Anthropology Department, Hartwick College 1, Oneonta, NY 13820, USA
| | | | - James H Barrett
- McDonald Institute for Archaeological Research, Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, UK
| | | | - Norbert Benecke
- Deutsches Archäologisches Institut (DAI), 14195 Berlin, Germany
| | - Eloísa Bernáldez-Sánchez
- Laboratorio de Paleontologia y Paleobiologia, Instituto Andaluz del Patrimonio Historico, Sevilla, Spain
| | - Luis Berrocal-Rangel
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Fereidoun Biglari
- Department of Paleolithic, National Museum of Iran, 1136918111, Tehran, Iran
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Postbox 1066, Blindern, 0316 Oslo, Norway
| | - Bazartseren Boldgiv
- Ecology Group, Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, Veterinary University of Vienna, 1210 Vienna, Austria
| | - Dorcas Brown
- Anthropology Department, Hartwick College 1, Oneonta, NY 13820, USA
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | - Eric Crubézy
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Linas Daugnora
- Osteological material research laboratory, Klaipėda university, Klaipėda 92294, Lithuania
| | - Hossein Davoudi
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Department of Archaeology, Faculty of Humanities, Tarbiat Modares University, Tehran, Iran
| | | | | | - Sabine Deschler-Erb
- Integrative prähistorische und naturwissenschaftliche Archäologie (IPNA), 4055 Basel, Switzerland
| | - Cleia Detry
- Uniarq, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, 1600-214 Lisboa, Portugal
| | - Nadine Dill
- Integrative prähistorische und naturwissenschaftliche Archäologie (IPNA), 4055 Basel, Switzerland
| | - Maria do Mar Oom
- CE3C-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Anna Dohr
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilians-University Munich, 80539 München, Germany; ArchaeoBioCenter, Ludwig-Maximilians-University Munich, 80539 München, Germany; Institute of Palaeoanatomy, Domestication Research and History of Veterinary Medicine, Ludwig-Maximilians-University Munich, 80539 München, Germany
| | | | | | - Homa Fathi
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran
| | - Sabine Felkel
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, Veterinary University of Vienna, 1210 Vienna, Austria
| | | | - Esteban García-Viñas
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Mietje Germonpré
- Operational Direction, Earth and History of Life, Royal Belgian Institute of Natural Sciences, 1000, Brussels, Belgium
| | - José D Granado
- Integrative prähistorische und naturwissenschaftliche Archäologie (IPNA), 4055 Basel, Switzerland
| | - Jón H Hallsson
- Faculty of Agricultural and Environmental Sciences, The Agricultural University of Iceland, Keldnaholti - Árleyni 22, 112 Reykjavík, Iceland
| | - Helmut Hemmer
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | - Michael Hofreiter
- University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, 14476 Potsdam, Germany
| | - Aleksei Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg 191186, Russia
| | | | - Roya Khazaeli
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran
| | - Pavel Kosintsev
- Institute of Plant and Animal Ecology, Urals Branch of the Russian Academy of Sciences, Ekaterinburg 620144, Russia
| | | | - Tabaldiev Kubatbek
- Department of History, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
| | - Lukas Kuderna
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Catalonia 08003, Spain
| | - Pavel Kuznetsov
- Samara State University of Social Science and Education, Samara, Russia
| | - Haeedeh Laleh
- Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran; Department of Archaeology, Faculty of Humanities, University of Tehran, Iran
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), 41092 Sevilla, Spain
| | - Johanna Lhuillier
- Laboratoire Archéorient, UMR 5133, Maison de l'Orient et de la Méditerranée, 69365 Lyon Cedex 7, France
| | | | - Andrey Logvin
- Laboratory for Archaeological Research, Faculty of History and Law, Kostanay State University, Kostanay, Kazakhstan
| | - Lembi Lõugas
- Archaeological Research Collection, Tallinn University, 10130 Tallinn, Estonia
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany; Faculty of Life Sciences, Albrecht Daniel Thaer-Institute, Humboldt University Berlin, 10115 Berlin, Germany
| | - Cristina Luis
- Museu Nacional de História Natural e da Ciência, Universidade de Lisboa, Lisboa, Portugal; Centro Interuniversitário de História das Ciências e da Tecnologia (CIUHCT), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Instituto Universitário de Lisboa (ISCTE-IUL), CIES-IUL, Lisboa, Portugal
| | - Ana Margarida Arruda
- Uniarq, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, 1600-214 Lisboa, Portugal
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Catalonia 08003, Spain; Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | | | - Victor Merz
- S.Toraighyrov Pavlodar State University, Joint Research Center for Archeological Studies, 637000 Pavlodar, Kazakhstan
| | - Enkhbayar Mijiddorj
- Department of Archaeology, Ulaanbaatar State University, Ulaanbaatar 51, Mongolia
| | - Bryan K Miller
- University of Oxford, Faculty of History, George Street, Oxford, OX1 2RL, UK
| | - Oleg Monchalov
- Samara State University of Social Science and Education, Samara, Russia
| | - Fatemeh A Mohaseb
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran; Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France
| | - Arturo Morales
- Laboratory of Archaeozoology, Department Biología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ariadna Nieto-Espinet
- Archaeology of Social Dynamics Group (ADS), Institució Milà i Fontanals-Consejo Superior de Investigaciones Científicas (IMF-CSIC), 08001 Barcelona, Spain; Grup d'Investigació Prehistòrica, HAR2016-78277-R, Universitat de Lleida, 25003 Lleida, Spain
| | - Heidi Nistelberger
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Postbox 1066, Blindern, 0316 Oslo, Norway
| | - Vedat Onar
- Osteoarchaeology Practice and Research Center and Department of Anatomy, Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, 34320, Avcılar, Istanbul, Turkey
| | - Albína H Pálsdóttir
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Postbox 1066, Blindern, 0316 Oslo, Norway; Faculty of Agricultural and Environmental Sciences, The Agricultural University of Iceland, Keldnaholti - Árleyni 22, 112 Reykjavík, Iceland
| | - Vladimir Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg 191186, Russia
| | | | - Mélanie Pruvost
- Université de Bordeaux, CNRS, UMR 5199-PACEA, 33615 Pessac Cedex, France
| | | | | | | | - Alireza Sardari
- Iranian Center for Archaeological Research (ICAR), Iranian Cultural Heritage, Handicrafts, and Tourism Organization (ICHHTO), 1136918111, Tehran, Iran
| | - Eberhard Sauer
- School of History, Classics and Archaeology, The University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Renate Schafberg
- Central Natural Science Collections (ZNS), Martin Luther University Halle-Wittenberg, Domplatz 4, 06108 Halle (Saale), Germany
| | - Amelie Scheu
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | - Jörg Schibler
- Integrative prähistorische und naturwissenschaftliche Archäologie (IPNA), 4055 Basel, Switzerland
| | - Angela Schlumbaum
- Integrative prähistorische und naturwissenschaftliche Archäologie (IPNA), 4055 Basel, Switzerland
| | - Nathalie Serrand
- Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France; INRAP Guadeloupe, Centre de recherches archéologiques, UMR 7209 CNRS/MNHN, 97113 Gourbeyre, Guadeloupe
| | - Aitor Serres-Armero
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Catalonia 08003, Spain
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology and Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Shiva Sheikhi Seno
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran; Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France
| | - Irina Shevnina
- Laboratory for Archaeological Research, Faculty of History and Law, Kostanay State University, Kostanay, Kazakhstan
| | - Sonia Shidrang
- Saeedi Institute for Advanced Studies, University of Kashan, Kashan 87317-51167, Iran
| | - John Southon
- Department Earth System Science, University of California, Irvine, Irvine, CA 92697, USA
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Postbox 1066, Blindern, 0316 Oslo, Norway
| | - Naomi Sykes
- Department of Archaeology, University of Nottingham, Nottingham, NG7 2RD, UK; Department of Archaeology, University of Exeter, Exeter, EX4 4QE, UK
| | - Kamal Taheri
- Kermanshah Regional Water Authority, Kermanshah 67145-1466, Iran
| | - William Taylor
- Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Wolf-Rüdiger Teegen
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilians-University Munich, 80539 München, Germany; ArchaeoBioCenter, Ludwig-Maximilians-University Munich, 80539 München, Germany
| | - Tajana Trbojević Vukičević
- Department of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, University of Zagreb, 10 000 Zagreb, Croatia
| | - Simon Trixl
- Institute of Palaeoanatomy, Domestication Research and History of Veterinary Medicine, Ludwig-Maximilians-University Munich, 80539 München, Germany
| | - Dashzeveg Tumen
- Department of Anthropology and Archaeology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia
| | - Sainbileg Undrakhbold
- Ecology Group, Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia
| | - Emma Usmanova
- Saryarka Archaeological Institute of Buketov Karaganda State University, Karaganda 100074, Kazakhstan
| | - Ali Vahdati
- Iranian Center for Archaeological Research (ICAR), Iranian Cultural Heritage, Handicrafts, and Tourism Organization (ICHHTO), 1136918111, Tehran, Iran
| | - Silvia Valenzuela-Lamas
- Archaeology of Social Dynamics Group (ADS), Institució Milà i Fontanals-Consejo Superior de Investigaciones Científicas (IMF-CSIC), 08001 Barcelona, Spain
| | - Catarina Viegas
- Uniarq, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, 1600-214 Lisboa, Portugal
| | - Barbara Wallner
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, Veterinary University of Vienna, 1210 Vienna, Austria
| | - Jaco Weinstock
- Faculty of Humanities (Archaeology), University of Southampton, Avenue Campus, Highfield, Southampton SO17 1BF, UK
| | - Victor Zaibert
- Scientific Research Institute of Archaeology and Steppe Civilizations, Al Farabi Kazakh National University, 050040 Almaty, Kazakhstan
| | - Benoit Clavel
- Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France
| | - Sébastien Lepetz
- Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France
| | - Marjan Mashkour
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran; Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France
| | | | | | - Eric Barrey
- GABI UMR1313, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Alan K Outram
- Department of Archaeology, University of Exeter, Exeter, EX4 4QE, UK
| | - Pablo Librado
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark.
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Chen J, Toh X, Ong J, Wang Y, Teo XH, Lee B, Wong PS, Khor D, Chong SM, Chee D, Wee A, Wang Y, Ng MK, Tan BH, Huangfu T. Detection and characterization of a novel marine birnavirus isolated from Asian seabass in Singapore. Virol J 2019; 16:71. [PMID: 31138237 PMCID: PMC6537170 DOI: 10.1186/s12985-019-1174-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/03/2019] [Indexed: 11/11/2022] Open
Abstract
Background Lates calcarifer, known as seabass in Asia and barramundi in Australia, is a widely farmed species internationally and in Southeast Asia and any disease outbreak will have a great economic impact on the aquaculture industry. Through disease investigation of Asian seabass from a coastal fish farm in 2015 in Singapore, a novel birnavirus named Lates calcarifer Birnavirus (LCBV) was detected and we sought to isolate and characterize the virus through molecular and biochemical methods. Methods In order to propagate the novel birnavirus LCBV, the virus was inoculated into the Bluegill Fry (BF-2) cell line and similar clinical signs of disease were reproduced in an experimental fish challenge study using the virus isolate. Virus morphology was visualized using transmission electron microscopy (TEM). Biochemical analysis using chloroform and 5-Bromo-2′-deoxyuridine (BUDR) sensitivity assays were employed to characterize the virus. Next-Generation Sequencing (NGS) was also used to obtain the virus genome for genetic and phylogenetic analyses. Results The LCBV-infected BF-2 cell line showed cytopathic effects such as rounding and granulation of cells, localized cell death and detachment of cells observed at 3 to 5 days’ post-infection. The propagated virus, when injected intra-peritoneally into naïve Asian seabass under experimental conditions, induced lesions similar to fish naturally infected with LCBV. Morphology of LCBV, visualized under TEM, revealed icosahedral particles around 50 nm in diameter. Chloroform and BUDR sensitivity assays confirmed the virus to be a non-enveloped RNA virus. Further genome analysis using NGS identified the virus to be a birnavirus with two genome segments. Phylogenetic analyses revealed that LCBV is more closely related to the Blosnavirus genus than to the Aquabirnavirus genus within the Birnaviridae family. Conclusions These findings revealed the presence of a novel birnavirus that could be linked to the disease observed in the Asian seabass from the coastal fish farms in Singapore. This calls for more studies on disease transmission and enhanced surveillance programs to be carried out to understand pathogenicity and epidemiology of this novel virus. The gene sequences data obtained from the study can also pave way to the development of PCR-based diagnostic test methods that will enable quick and specific identification of the virus in future disease investigations.
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Affiliation(s)
- Jing Chen
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore, 259569, Singapore
| | - Xinyu Toh
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore, 259569, Singapore
| | - Jasmine Ong
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore, 259569, Singapore
| | - Yahui Wang
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore, 259569, Singapore
| | - Xuan-Hui Teo
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore, 259569, Singapore
| | - Bernett Lee
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Pui-San Wong
- DSO National Laboratories, 27 Medical Drive, Singapore, 117510, Singapore
| | - Denyse Khor
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore, 259569, Singapore
| | - Shin-Min Chong
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore, 259569, Singapore
| | - Diana Chee
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore, 259569, Singapore
| | - Alvin Wee
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore, 259569, Singapore
| | - Yifan Wang
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore, 259569, Singapore
| | - Mee-Keun Ng
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore, 259569, Singapore
| | - Boon-Huan Tan
- DSO National Laboratories, 27 Medical Drive, Singapore, 117510, Singapore
| | - Taoqi Huangfu
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore, 259569, Singapore.
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Lunina AA, Nikitin MA, Shiian AS, Ereskovsky AV, Kovtun OA, Vereshchaka AL, Ivanenko VN. Integrative taxonomy of the cave-dwelling mysids of the genus Hemimysis. SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1596175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Anastasia A. Lunina
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36, Nahimovskiy prospekt, Moscow, 117997, Russia
| | - Mikhail A. Nikitin
- Belozersky Institute of Physico-chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 1-12, Moscow, 119992, Russia
| | - Aleksandra S. Shiian
- Department of Invertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Leninskie Gory, 1-12, Moscow, 119992, Russia
| | - Alexander V. Ereskovsky
- Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE), Aix Marseille University, CNRS, IRD, Avignon Université, Station marine d'Endoume, rue de la Batterie des Lions, Marseille, 13007, France
- Biological Faculty, Saint-Petersburg State University, 199034 Universitetskaya nab. 7/9, St. Petersburg, Russia
| | - Oleg A. Kovtun
- Hydrobiology and General Ecology Department, Odessa National I. I. Mechnikov University, Marine Research Station, st. Dvoryanska, 2, Odessa, 65026, Ukraine
| | - Alexander L. Vereshchaka
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36, Nahimovskiy prospekt, Moscow, 117997, Russia
| | - Viatcheslav N. Ivanenko
- Department of Invertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Leninskie Gory, 1-12, Moscow, 119992, Russia
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145
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Siqueira JD, Curty G, Xutao D, Hofer CB, Machado ES, Seuánez HN, Soares MA, Delwart E, Soares EA. Composite Analysis of the Virome and Bacteriome of HIV/HPV Co-Infected Women Reveals Proxies for Immunodeficiency. Viruses 2019; 11:v11050422. [PMID: 31067713 PMCID: PMC6563245 DOI: 10.3390/v11050422] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/26/2019] [Accepted: 05/02/2019] [Indexed: 02/07/2023] Open
Abstract
The human cervical microbiome is complex, and its role in health and disease has just begun to be elucidated. In this study, 57 cervical swab samples from 19 HIV/HPV co-infected women were analyzed for both virome and bacteriome composition. Virome analysis focused on circular DNA viruses through rolling circle amplification followed by next-generation sequencing (NGS). Data were assigned to virus families and genera, and HPV types were identified. NGS data of bacterial 16S from a subset of 24 samples were assigned to operational taxonomic units and classified according to vaginal microbiome community state types (CSTs). Four viral families were found: Papillomaviridae, Anelloviridae, Genomoviridae, and Herpesviridae. Papillomavirus reads were more abundant in women with premalignant cervical lesions, which were also strongly associated with multiple (≥3) high-risk HPV infection. Anellovirus read abundance was negatively correlated with host CD4+ T-cell counts. The bacteriome revealed the presence of CST III and CST IV, and women with ≥1% frequency of genomovirus or herpesvirus reads displayed an increased risk of carrying CST IV. By characterizing the composition of the cervical circular DNA viruses and the bacteriome of HIV/HPV co-infected women, we identified putative interactions between these two microorganism communities and their associations with patients’ clinical characteristics, notably immunodeficiency status.
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Affiliation(s)
- Juliana D Siqueira
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
| | - Gislaine Curty
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
| | - Deng Xutao
- Vitalant Research Institute, San Francisco, CA 94118, USA.
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Cristina B Hofer
- Instituto de Ginecologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 20211-340, Brazil.
| | - Elizabeth S Machado
- Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-912, Brazil.
| | - Héctor N Seuánez
- Programa de Genética, 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.
| | - 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.
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA 94118, USA.
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Esmeralda A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
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146
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Alves BM, Siqueira JD, Prellwitz IM, Botelho OM, Da Hora VP, Sanabani S, Recordon-Pinson P, Fleury H, Soares EA, Soares MA. Estimating HIV-1 Genetic Diversity in Brazil Through Next-Generation Sequencing. Front Microbiol 2019; 10:749. [PMID: 31024510 PMCID: PMC6465556 DOI: 10.3389/fmicb.2019.00749] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/25/2019] [Indexed: 12/26/2022] Open
Abstract
Approximately 36.7 million people were living with the human immunodeficiency virus (HIV) at the end of 2016 according to UNAIDS, representing a global prevalence rate of 0.8%. In Brazil, an HIV prevalence of 0.24% has been estimated, which represents approximately 830,000 individuals living with the virus. As a touristic and commercial hub in Latin America, Brazil harbors an elevated HIV genetic variability, further contributed by the selective pressure exerted by the host immune system and by antiretroviral treatment. Through the progress of the next-generation sequencing (NGS) techniques, it has been possible to expand the study of HIV genetic diversity, evolutionary, and epidemic processes, allowing the generation of HIV complete or near full-length genomes (NFLG) and improving the characterization of intra- and interhost diversity of viral populations. Greater sensitivity in the detection of viral recombinant forms represents one of the major improvements associated with this development. It is possible to identify unique or circulating recombinant forms using the near full-length viral genomes with increasing accuracy. It also permits the characterization of multiple viral infections within individual hosts. Previous Brazilian studies using NGS to analyze HIV diversity were able to identify several distinct unique and circulating recombinant forms and evidenced dual infections. These data unveiled unprecedented high rates of viral recombination and highlighted that novel recombinants are continually arising in the Brazilian epidemic. In the pooled analysis depicted in this report, HIV subtypes have been determined from HIV-positive patients in five states of Brazil with some of the highest HIV prevalence, three in the Southeast (Rio de Janeiro, São Paulo, and Minas Gerais), one in the Northeast (Pernambuco) and one in the South (Rio Grande do Sul). Combined data analysis showed a significant prevalence of recombinant forms (29%; 101/350), and a similar 26% when only NFLGs were considered. Moreover, the analysis was able to evidence the occurrence of multiple infections in some individuals. Our data highlight the great HIV genetic diversity found in Brazil and unveils a more accurate scenario of the HIV evolutionary dynamics in the region.
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Affiliation(s)
- Brunna M Alves
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Juliana D Siqueira
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Isabel M Prellwitz
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Ornella M Botelho
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Vanusa P Da Hora
- Laboratório de Biologia Molecular, Escola de Medicina, Universidade Federal do Rio Grande, Rio Grande do Sul, Brazil
| | - Sabri Sanabani
- LIM-3, Hospital das Clinicas FMUSP, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | | | - Hervé Fleury
- CNRS MFP-UMR 5234, University Hospital of Bordeaux, University of Bordeaux, Bordeaux, France
| | - Esmeralda A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Marcelo A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.,Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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147
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Ion uptake pathways in European sea bass Dicentrarchus labrax. Gene 2019; 692:126-137. [DOI: 10.1016/j.gene.2019.01.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/12/2018] [Accepted: 01/02/2019] [Indexed: 01/20/2023]
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148
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de Sousa F, Foster PG, Donoghue PCJ, Schneider H, Cox CJ. Nuclear protein phylogenies support the monophyly of the three bryophyte groups (Bryophyta Schimp.). THE NEW PHYTOLOGIST 2019; 222:565-575. [PMID: 30411803 DOI: 10.1111/nph.15587] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 10/31/2018] [Indexed: 05/05/2023]
Abstract
Unraveling the phylogenetic relationships between the four major lineages of terrestrial plants (mosses, liverworts, hornworts, and vascular plants) is essential for an understanding of the evolution of traits specific to land plants, such as their complex life cycles, and the evolutionary development of stomata and vascular tissue. Well supported phylogenetic hypotheses resulting from different data and methods are often incongruent due to processes of nucleotide evolution that are difficult to model, for example substitutional saturation and composition heterogeneity. We reanalysed a large published dataset of nuclear data and modelled these processes using degenerate-codon recoding and tree-heterogeneous composition substitution models. Our analyses resolved bryophytes as a monophyletic group and showed that the nonnonmonophyly of the clade that is supported by the analysis of nuclear nucleotide data is due solely to fast-evolving synonymous substitutions. The current congruence among phylogenies of both nuclear and chloroplast analyses lent considerable support to the conclusion that the bryophytes are a monophyletic group. An initial split between bryophytes and vascular plants implies that the bryophyte life cycle (with a dominant gametophyte nurturing an unbranched sporophyte) may not be ancestral to all land plants and that stomata are likely to be a symplesiomorphy among embryophytes.
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Affiliation(s)
- Filipe de Sousa
- Centro de Ciências do Mar, Universidade do Algarve, Gambelas, Faro, 8005-319, Portugal
| | - Peter G Foster
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
| | | | - Harald Schneider
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
- School of Earth Sciences, University of Bristol, Bristol, BS8 1TQ, UK
- Center of Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, 666303, China
| | - Cymon J Cox
- Centro de Ciências do Mar, Universidade do Algarve, Gambelas, Faro, 8005-319, Portugal
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149
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Lü H, Li J, Huang Y, Zhang M, Zhang S, Wu J. Genome-wide identification, expression and functional analysis of the phosphofructokinase gene family in Chinese white pear (Pyrus bretschneideri). Gene 2019; 702:133-142. [PMID: 30904717 DOI: 10.1016/j.gene.2019.03.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 12/29/2022]
Abstract
Phosphofructokinase plays an essential role in sugar metabolism in plants. Plants possess two types of phosphofructokinase proteins for phosphorylation of fructose-6-phosphate, the pyrophosphate-dependent fructose-6-phosphate phosphotransferase (PFP), and the ATP-dependent phosphofructokinase (PFK). Until now, the gene evolution, expression patterns, and functions of phosphofructokinase proteins were unknown in pear. In this report, 14 phosphofructokinase genes were identified in pear. The phylogenetic tree indicated that the phosphofructokinase gene family could be grouped into two subfamilies, with 10 genes belonging to the PbPFK subfamily, and 4 genes belonging to the PbPFP subfamily. Conserved motifs and exon numbers of the phosphofructokinase were found in pear and other six species. The evolution analysis indicated that WGD/Segmental and dispersed duplications were the main duplication models for the phosphofructokinase genes expansion in pear and other six species. Analysis of cis-regulatory element sequences of all phosphofructokinase genes identified light regulation and the MYB binding site in the promoter of all pear phosphofructokinase genes, suggesting that phosphofructokinase might could be regulated by light and MYB transcription factors (TFs). Gene expression patterns revealed that PbPFP1 showed similar pattern with sorbitol contents, suggesting important contributions to sugar accumulation during fruit development. Further functional analysis indicated that the phosphofructokinase gene PbPFP1 was localized on plasma membrane compartment, indicating that PbPFP1 had function in plasma membrane. Transient transformation of PbPFP1 in pear fruits led to significant increases of fructose and sorbitol compared to controls. Overall, our study provides important insights into the gene expression patterns and important potential functions of phosphofructokinase for sugar accumulation in pear fruits, which will help to enrich understanding of sugar-related bio-pathways and lay the molecular basis for fruit quality improvement.
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Affiliation(s)
- Hongmei Lü
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiaming Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuhua Huang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Mingyue Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Wu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
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150
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Adaptive evolution of the ACSL gene family in Carnivora. Genetica 2019; 147:141-148. [DOI: 10.1007/s10709-019-00057-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/06/2019] [Indexed: 10/27/2022]
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