201
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Abstract
Recombination increases the local GC-content in genomic regions through GC-biased gene conversion (gBGC). The recent discovery of a large genomic region with extreme GC-content in the fat sand rat Psammomys obesus provides a model to study the effects of gBGC on chromosome evolution. Here, we compare the GC-content and GC-to-AT substitution patterns across protein-coding genes of four gerbil species and two murine rodents (mouse and rat). We find that the known high-GC region is present in all the gerbils, and is characterized by high substitution rates for all mutational categories (AT-to-GC, GC-to-AT, and GC-conservative) both at synonymous and nonsynonymous sites. A higher AT-to-GC than GC-to-AT rate is consistent with the high GC-content. Additionally, we find more than 300 genes outside the known region with outlying values of AT-to-GC synonymous substitution rates in gerbils. Of these, over 30% are organized into at least 17 large clusters observable at the megabase-scale. The unusual GC-skewed substitution pattern suggests the evolution of genomic regions with very high recombination rates in the gerbil lineage, which can lead to a runaway increase in GC-content. Our results imply that rapid evolution of GC-content is possible in mammals, with gerbil species providing a powerful model to study the mechanisms of gBGC.
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Affiliation(s)
- Rodrigo Pracana
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - John F Mulley
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
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202
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Linard B, Ebersberger I, McGlynn SE, Glover N, Mochizuki T, Patricio M, Lecompte O, Nevers Y, Thomas PD, Gabaldón T, Sonnhammer E, Dessimoz C, Uchiyama I. Ten Years of Collaborative Progress in the Quest for Orthologs. Mol Biol Evol 2021; 38:3033-3045. [PMID: 33822172 PMCID: PMC8321534 DOI: 10.1093/molbev/msab098] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/07/2021] [Accepted: 04/01/2021] [Indexed: 12/19/2022] Open
Abstract
Accurate determination of the evolutionary relationships between genes is a foundational challenge in biology. Homology-evolutionary relatedness-is in many cases readily determined based on sequence similarity analysis. By contrast, whether or not two genes directly descended from a common ancestor by a speciation event (orthologs) or duplication event (paralogs) is more challenging, yet provides critical information on the history of a gene. Since 2009, this task has been the focus of the Quest for Orthologs (QFO) Consortium. The sixth QFO meeting took place in Okazaki, Japan in conjunction with the 67th National Institute for Basic Biology conference. Here, we report recent advances, applications, and oncoming challenges that were discussed during the conference. Steady progress has been made toward standardization and scalability of new and existing tools. A feature of the conference was the presentation of a panel of accessible tools for phylogenetic profiling and several developments to bring orthology beyond the gene unit-from domains to networks. This meeting brought into light several challenges to come: leveraging orthology computations to get the most of the incoming avalanche of genomic data, integrating orthology from domain to biological network levels, building better gene models, and adapting orthology approaches to the broad evolutionary and genomic diversity recognized in different forms of life and viruses.
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Affiliation(s)
- Benjamin Linard
- LIRMM, University of Montpellier, CNRS, Montpellier, France.,SPYGEN, Le Bourget-du-Lac, France
| | - Ingo Ebersberger
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany.,Senckenberg Biodiversity and Climate Research Centre (S-BIKF), Frankfurt, Germany.,LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt, Germany
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo, Japan.,Blue Marble Space Institute of Science, Seattle, WA, USA
| | - Natasha Glover
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Tomohiro Mochizuki
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo, Japan
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Odile Lecompte
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Yannis Nevers
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Paul D Thomas
- Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BCS-CNS), Jordi Girona, Barcelona, Spain.,Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Erik Sonnhammer
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Christophe Dessimoz
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Department of Computer Science, University College London, London, United Kingdom.,Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Ikuo Uchiyama
- Department of Theoretical Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
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203
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Rodrigues JA, Espley RV, Allan AC. Genomic analysis uncovers functional variation in the C-terminus of anthocyanin-activating MYB transcription factors. HORTICULTURE RESEARCH 2021; 8:77. [PMID: 33790254 PMCID: PMC8012628 DOI: 10.1038/s41438-021-00514-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/16/2021] [Accepted: 03/01/2021] [Indexed: 05/26/2023]
Abstract
MYB transcription factors regulate diverse aspects of plant development and secondary metabolism, often by partnering in transcriptional regulatory complexes. Here, we harness genomic resources to identify novel MYBs, thereby producing an updated eudicot MYB phylogeny with revised relationships among subgroups as well as new information on sequence variation in the disordered C-terminus of anthocyanin-activating MYBs. BLAST® and hidden Markov model scans of gene annotations identified a total of 714 MYB transcription factors across the genomes of four crops that span the eudicots: apple, grape, kiwifruit and tomato. Codon model-based phylogenetic inference identified novel members of previously defined subgroups, and the function of specific anthocyanin-activating subgroup 6 members was assayed transiently in tobacco leaves. Sequence conservation within subgroup 6 highlighted one previously described and two novel short linear motifs in the disordered C-terminal region. The novel motifs have a mix of hydrophobic and acidic residues and are predicted to be relatively ordered compared with flanking protein sequences. Comparison of motifs with the Eukaryotic Linear Motif database suggests roles in protein-protein interaction. Engineering of motifs and their flanking regions from strong anthocyanin activators into weak activators, and vice versa, affected function. We conclude that, although the MYB C-terminal sequence diverges greatly even within MYB clades, variation within the C-terminus at and near relatively ordered regions offers opportunities for exploring MYB function and developing superior alleles for plant breeding.
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Affiliation(s)
- Jessica A Rodrigues
- The New Zealand Institute for Plant and Food Research Limited, 120 Mount Albert Road, Sandringham, Auckland, 1025, New Zealand
| | - Richard V Espley
- The New Zealand Institute for Plant and Food Research Limited, 120 Mount Albert Road, Sandringham, Auckland, 1025, New Zealand
| | - Andrew C Allan
- The New Zealand Institute for Plant and Food Research Limited, 120 Mount Albert Road, Sandringham, Auckland, 1025, New Zealand.
- School of Biological Sciences, University of Auckland, 3A Symonds St, Auckland, 1010, New Zealand.
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204
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He H, Yang M. Characterization of the leafhopper mitogenome of Mileewa alara (Hemiptera: Cicadellidae: Mileewinae) and its phylogenetic analysis. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1265-1266. [PMID: 33829103 PMCID: PMC8009127 DOI: 10.1080/23802359.2021.1906180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The mitogenome data of leafhopper species Mileewa alara was assembled and annotated in this study. The results shows that length of M. alara is 16020 bp, consist of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and one control region. The A + T content in the mitogenome was 77.9%. Phylogenetic analysis based on 13 PCGs of four Mileewa species and other 29 Cicadellidae species, each subfamily species well separated. And M. alara clustered with M. ponta. This study also raised mitogenome of Mileewa number in GenBank to four.
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Affiliation(s)
- Hongli He
- College of Agricultural Science, Guizhou University, Guiyang, China.,Institute of Entomology, Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guizhou University, Guiyang, China
| | - Maofa Yang
- College of Agricultural Science, Guizhou University, Guiyang, China.,Institute of Entomology, Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guizhou University, Guiyang, China.,College of Tobacco Science, Guizhou University, Guiyang, China
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205
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Castillo AI, Almeida RPP. Evidence of gene nucleotide composition favoring replication and growth in a fastidious plant pathogen. G3-GENES GENOMES GENETICS 2021; 11:6170658. [PMID: 33715000 PMCID: PMC8495750 DOI: 10.1093/g3journal/jkab076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 03/02/2021] [Indexed: 11/13/2022]
Abstract
Nucleotide composition (GC content) varies across bacteria species, genome regions, and specific genes. In Xylella fastidiosa, a vector-borne fastidious plant pathogen infecting multiple crops, GC content ranges between ∼51-52%; however, these values were gathered using limited genomic data. We evaluated GC content variations across X. fastidiosa subspecies fastidiosa (N = 194), subsp. pauca (N = 107), and subsp. multiplex (N = 39). Genomes were classified based on plant host and geographic origin; individual genes within each genome were classified based on gene function, strand, length, ortholog group, Core vs. Accessory, and Recombinant vs. Non-recombinant. GC content was calculated for each gene within each evaluated genome. The effects of genome and gene level variables were evaluated with a mixed effect ANOVA, and the marginal-GC content was calculated for each gene. Also, the correlation between gene-specific GC content vs. natural selection (dN/dS) and recombination/mutation (r/m) was estimated. Our analyses show that intra-genomic changes in nucleotide composition in X. fastidiosa are small and influenced by multiple variables. Higher AT-richness is observed in genes involved in replication and translation, and genes in the leading strand. In addition, we observed a negative correlation between high-AT and dN/dS in subsp. pauca. The relationship between recombination and GC content varied between core and accessory genes. We hypothesize that distinct evolutionary forces and energetic constraints both drive and limit these small variations in nucleotide composition.
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Affiliation(s)
- Andreina I Castillo
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
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206
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Hall ND, Patel JD, McElroy JS, Goertzen LR. Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet). BMC Genomics 2021; 22:175. [PMID: 33706694 PMCID: PMC7953713 DOI: 10.1186/s12864-021-07447-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 02/16/2021] [Indexed: 01/15/2023] Open
Abstract
Background Finger millet (Eleusine coracana 2n = 4x = 36) is a hardy, nutraceutical, climate change tolerant, orphan crop that is consumed throughout eastern Africa and India. Its genome has been sequenced multiple times, but A and B subgenomes could not be separated because no published genome for E. indica existed. The classification of A and B subgenomes is important for understanding the evolution of this crop and provide a means to improve current and future breeding programs. Results We produced subgenome calls for 704 syntenic blocks and inferred A or B subgenomic identity for 59,377 genes 81% of the annotated genes. Phylogenetic analysis of a super matrix containing 455 genes shows high support for A and B divergence within the Eleusine genus. Synonymous substitution rates between A and B genes support A and B calls. The repetitive content on highly supported B contigs is higher than that on similar A contigs. Analysis of syntenic singletons showed evidence of biased fractionation showed a pattern of A genome dominance, with 61% A, 37% B and 1% unassigned, and was further supported by the pattern of loss observed among cyto-nuclear interacting genes. Conclusion The evidence of individual gene calls within each syntenic block, provides a powerful tool for inference for subgenome classification. Our results show the utility of a draft genome in resolving A and B subgenomes calls, primarily it allows for the proper polarization of A and B syntenic blocks. There have been multiple calls for the use of phylogenetic inference in subgenome classification, our use of synteny is a practical application in a system that has only one parental genome available. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07447-y.
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Affiliation(s)
- Nathan D Hall
- Department of Crop, Soil and Environmental Science Auburn University, Auburn, AL, USA.
| | - Jinesh D Patel
- Department of Crop, Soil and Environmental Science Auburn University, Auburn, AL, USA
| | - J Scott McElroy
- Department of Crop, Soil and Environmental Science Auburn University, Auburn, AL, USA
| | - Leslie R Goertzen
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
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207
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DeGiorgio M, Assis R. Learning Retention Mechanisms and Evolutionary Parameters of Duplicate Genes from Their Expression Data. Mol Biol Evol 2021; 38:1209-1224. [PMID: 33045078 PMCID: PMC7947822 DOI: 10.1093/molbev/msaa267] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Learning about the roles that duplicate genes play in the origins of novel phenotypes requires an understanding of how their functions evolve. A previous method for achieving this goal, CDROM, employs gene expression distances as proxies for functional divergence and then classifies the evolutionary mechanisms retaining duplicate genes from comparisons of these distances in a decision tree framework. However, CDROM does not account for stochastic shifts in gene expression or leverage advances in contemporary statistical learning for performing classification, nor is it capable of predicting the parameters driving duplicate gene evolution. Thus, here we develop CLOUD, a multi-layer neural network built on a model of gene expression evolution that can both classify duplicate gene retention mechanisms and predict their underlying evolutionary parameters. We show that not only is the CLOUD classifier substantially more powerful and accurate than CDROM, but that it also yields accurate parameter predictions, enabling a better understanding of the specific forces driving the evolution and long-term retention of duplicate genes. Further, application of the CLOUD classifier and predictor to empirical data from Drosophila recapitulates many previous findings about gene duplication in this lineage, showing that new functions often emerge rapidly and asymmetrically in younger duplicate gene copies, and that functional divergence is driven by strong natural selection. Hence, CLOUD represents a major advancement in classifying retention mechanisms and predicting evolutionary parameters of duplicate genes, thereby highlighting the utility of incorporating sophisticated statistical learning techniques to address long-standing questions about evolution after gene duplication.
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Affiliation(s)
- Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431
- Institute for Human Health and Disease Intervention, Florida Atlantic University, Boca Raton, FL 33431
| | - Raquel Assis
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431
- Institute for Human Health and Disease Intervention, Florida Atlantic University, Boca Raton, FL 33431
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208
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Cissé OH, Ma L, Dekker JP, Khil PP, Youn JH, Brenchley JM, Blair R, Pahar B, Chabé M, Van Rompay KKA, Keesler R, Sukura A, Hirsch V, Kutty G, Liu Y, Peng L, Chen J, Song J, Weissenbacher-Lang C, Xu J, Upham NS, Stajich JE, Cuomo CA, Cushion MT, Kovacs JA. Genomic insights into the host specific adaptation of the Pneumocystis genus. Commun Biol 2021; 4:305. [PMID: 33686174 PMCID: PMC7940399 DOI: 10.1038/s42003-021-01799-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/04/2021] [Indexed: 11/21/2022] Open
Abstract
Pneumocystis jirovecii, the fungal agent of human Pneumocystis pneumonia, is closely related to macaque Pneumocystis. Little is known about other Pneumocystis species in distantly related mammals, none of which are capable of establishing infection in humans. The molecular basis of host specificity in Pneumocystis remains unknown as experiments are limited due to an inability to culture any species in vitro. To explore Pneumocystis evolutionary adaptations, we have sequenced the genomes of species infecting macaques, rabbits, dogs and rats and compared them to available genomes of species infecting humans, mice and rats. Complete whole genome sequence data enables analysis and robust phylogeny, identification of important genetic features of the host adaptation, and estimation of speciation timing relative to the rise of their mammalian hosts. Our data reveals insights into the evolution of P. jirovecii, the sole member of the genus able to infect humans. Cissé, Ma et al. utilize genomic data from Pneumocystis species infecting macaques, rabbit, dogs and rats to investigate the molecular basis of host specificity in Pneumocystis. Their analyses provide insight to the specific adaptations enabling the infection of humans by P. jirovecii.
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Affiliation(s)
- Ousmane H Cissé
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA.
| | - Liang Ma
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA.
| | - John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA.,Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Pavel P Khil
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA.,Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Jung-Ho Youn
- Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | | | - Robert Blair
- Tulane National Primate Research Center, Tulane University, New Orleans, LA, USA
| | - Bapi Pahar
- Tulane National Primate Research Center, Tulane University, New Orleans, LA, USA
| | - Magali Chabé
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Koen K A Van Rompay
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Rebekah Keesler
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Antti Sukura
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Vanessa Hirsch
- Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Geetha Kutty
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Yueqin Liu
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Li Peng
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jie Chen
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jun Song
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Jie Xu
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nathan S Upham
- Arizona State University, School of Life Sciences, Tempe, ARI, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology and Institute for Integrative Genome Biology, University of California, Riverside, Riverside-California, Riverside, CA, USA
| | - Christina A Cuomo
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Melanie T Cushion
- Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Joseph A Kovacs
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA.
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209
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Li X, Luo Y, Jiang J, Wang L, Tong X. Description of a new species of the genus Ameletus Eaton, 1885 (Ephemeroptera, Ameletidae) from Yunnan, China. Zookeys 2021; 1021:37-51. [PMID: 33716541 PMCID: PMC7940326 DOI: 10.3897/zookeys.1021.59927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/22/2021] [Indexed: 11/15/2022] Open
Abstract
A new species with primitive characteristics, Ameletusdaliensis Tong, sp. nov., is described, based on the morphology of imago, larva and egg with molecular data of the mitochondrial COI from Mount Cangshan, Dali, China. The new species is closely related to one of the most primitive mayflies, Ameletusprimitivus Traver, 1939, by sharing persistent mouthparts in the alate stage, but it can be distinguished from the latter by the morphological differences of the mouthpart remains, wings and genitals in the imaginal stage. Both morphological and molecular evidence support that A.daliensis Tong, sp. nov. is a new member of the genus Ameletus. The discovery of the new species could help understand the origin and evolution of the genus Ameletus.
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Affiliation(s)
- Xianfu Li
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671000, Yunnan, China Dali University Dali China.,Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali University, Dali, Yunnan, China South China Agricultural University Guangzhou China.,The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region from Dali University, Dali, Yunnan, China Dali University Dali China
| | - Yanping Luo
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510642, Guangdong, China South China Agricultural University Guangzhou China
| | - Jian Jiang
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510642, Guangdong, China South China Agricultural University Guangzhou China
| | - Lili Wang
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510642, Guangdong, China South China Agricultural University Guangzhou China
| | - Xiaoli Tong
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali University, Dali, Yunnan, China South China Agricultural University Guangzhou China.,Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510642, Guangdong, China South China Agricultural University Guangzhou China
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210
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Westbury MV, Le Duc D, Duchêne DA, Krishnan A, Prost S, Rutschmann S, Grau JH, Dalen L, Weyrich A, Norén K, Werdelin L, Dalerum F, Schöneberg T, Hofreiter M. Ecological Specialisation and Evolutionary Reticulation in Extant Hyaenidae. Mol Biol Evol 2021; 38:3884-3897. [PMID: 34426844 PMCID: PMC8382907 DOI: 10.1093/molbev/msab055] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
During the Miocene, Hyaenidae was a highly diverse family of Carnivora that has since been severely reduced to four species: the bone-cracking spotted, striped, and brown hyenas, and the specialized insectivorous aardwolf. Previous studies investigated the evolutionary histories of the spotted and brown hyenas, but little is known about the remaining two species. Moreover, the genomic underpinnings of scavenging and insectivory, defining traits of the extant species, remain elusive. Here, we generated an aardwolf genome and analyzed it together with the remaining three species to reveal their evolutionary relationships, genomic underpinnings of their scavenging and insectivorous lifestyles, and their respective genetic diversities and demographic histories. High levels of phylogenetic discordance suggest gene flow between the aardwolf lineage and the ancestral brown/striped hyena lineage. Genes related to immunity and digestion in the bone-cracking hyenas and craniofacial development in the aardwolf showed the strongest signals of selection, suggesting putative key adaptations to carrion and termite feeding, respectively. A family-wide expansion in olfactory receptor genes suggests that an acute sense of smell was a key early adaptation. Finally, we report very low levels of genetic diversity within the brown and striped hyenas despite no signs of inbreeding, putatively linked to their similarly slow decline in effective population size over the last ∼2 million years. High levels of genetic diversity and more stable population sizes through time are seen in the spotted hyena and aardwolf. Taken together, our findings highlight how ecological specialization can impact the evolutionary history, demographics, and adaptive genetic changes of an evolutionary lineage.
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Affiliation(s)
- M V Westbury
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, Germany.,Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Diana Le Duc
- Institute of Human Genetics, University Medical Center Leipzig, Leipzig, 04103, Germany.,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - David A Duchêne
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark.,Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Arunkumar Krishnan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.,Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha, 760010, India
| | - Stefan Prost
- LOEWE-Center for Translational Biodiversity Genomics, Senckenberg, 60325, Germany. Frankfurt.,South African National Biodiversity Institute, National Zoological Garden, Pretoria, 0184, South Africa
| | - Sereina Rutschmann
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, Germany
| | - Jose H Grau
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, Germany.,amedes Genetics, amedes Medizinische Dienstleistungen, Berlin, Germany
| | - Love Dalen
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm, 10691, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm, 10405, Sweden
| | - Alexandra Weyrich
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, 10315, Germany
| | - Karin Norén
- Department of Zoology, Stockholm University, Stockholm, 106 91, Sweden
| | - Lars Werdelin
- Department of Palaeobiology, Swedish Museum of Natural History, Box 50007, Stockholm, SE-10405, Sweden
| | - Fredrik Dalerum
- Department of Zoology, Stockholm University, Stockholm, 106 91, Sweden.,Research Unit of Biodiversity (UO-CSIC-PA), Mieres Campus, University of Oviedo, Mieres, Asturias, 33600, Spain.,Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, South Africa
| | - Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, Johannisallee 30, Leipzig, 04103, Germany
| | - Michael Hofreiter
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, Germany
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211
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Allio R, Tilak MK, Scornavacca C, Avenant NL, Kitchener AC, Corre E, Nabholz B, Delsuc F. High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox. eLife 2021; 10:e63167. [PMID: 33599612 PMCID: PMC7963486 DOI: 10.7554/elife.63167] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/16/2021] [Indexed: 12/26/2022] Open
Abstract
In a context of ongoing biodiversity erosion, obtaining genomic resources from wildlife is essential for conservation. The thousands of yearly mammalian roadkill provide a useful source material for genomic surveys. To illustrate the potential of this underexploited resource, we used roadkill samples to study the genomic diversity of the bat-eared fox (Otocyon megalotis) and the aardwolf (Proteles cristatus), both having subspecies with similar disjunct distributions in Eastern and Southern Africa. First, we obtained reference genomes with high contiguity and gene completeness by combining Nanopore long reads and Illumina short reads. Then, we showed that the two subspecies of aardwolf might warrant species status (P. cristatus and P. septentrionalis) by comparing their genome-wide genetic differentiation to pairs of well-defined species across Carnivora with a new Genetic Differentiation index (GDI) based on only a few resequenced individuals. Finally, we obtained a genome-scale Carnivora phylogeny including the new aardwolf species.
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Affiliation(s)
- Rémi Allio
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Marie-Ka Tilak
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Celine Scornavacca
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Nico L Avenant
- National Museum and Centre for Environmental Management, University of the Free StateBloemfonteinSouth Africa
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums ScotlandEdinburghUnited Kingdom
| | - Erwan Corre
- CNRS, Sorbonne Université, CNRS, ABiMS, Station Biologique de RoscoffRoscoffFrance
| | - Benoit Nabholz
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
- Institut Universitaire de France (IUF)ParisFrance
| | - Frédéric Delsuc
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
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212
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Huston NC, Wan H, Strine MS, de Cesaris Araujo Tavares R, Wilen CB, Pyle AM. Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms. Mol Cell 2021; 81:584-598.e5. [PMID: 33444546 PMCID: PMC7775661 DOI: 10.1016/j.molcel.2020.12.041] [Citation(s) in RCA: 177] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 11/06/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023]
Abstract
Severe-acute-respiratory-syndrome-related coronavirus 2 (SARS-CoV-2) is the positive-sense RNA virus that causes coronavirus disease 2019 (COVID-19). The genome of SARS-CoV-2 is unique among viral RNAs in its vast potential to form RNA structures, yet as much as 97% of its 30 kilobases have not been structurally explored. Here, we apply a novel long amplicon strategy to determine the secondary structure of the SARS-CoV-2 RNA genome at single-nucleotide resolution in infected cells. Our in-depth structural analysis reveals networks of well-folded RNA structures throughout Orf1ab and reveals aspects of SARS-CoV-2 genome architecture that distinguish it from other RNA viruses. Evolutionary analysis shows that several features of the SARS-CoV-2 genomic structure are conserved across β-coronaviruses, and we pinpoint regions of well-folded RNA structure that merit downstream functional analysis. The native, secondary structure of SARS-CoV-2 presented here is a roadmap that will facilitate focused studies on the viral life cycle, facilitate primer design, and guide the identification of RNA drug targets against COVID-19.
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Affiliation(s)
- Nicholas C Huston
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Han Wan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Madison S Strine
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06519, USA
| | | | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06519, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA; Department of Chemistry, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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213
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Muyle A, Seymour D, Darzentas N, Primetis E, Gaut BS, Bousios A. Gene capture by transposable elements leads to epigenetic conflict in maize. MOLECULAR PLANT 2021; 14:237-252. [PMID: 33171302 DOI: 10.1016/j.molp.2020.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/15/2020] [Accepted: 11/05/2020] [Indexed: 06/11/2023]
Abstract
Transposable elements (TEs) regularly capture fragments of genes. When the host silences these TEs, siRNAs homologous to the captured regions may also target the genes. This epigenetic crosstalk establishes an intragenomic conflict: silencing the TEs has the cost of silencing the genes. If genes are important, however, natural selection may maintain function by moderating the silencing response, which may also advantage the TEs. In this study, we examined this model by focusing on Helitrons, Pack-MULEs, and Sirevirus LTR retrotransposons in the maize genome. We documented 1263 TEs containing exon fragments from 1629 donor genes. Consistent with epigenetic conflict, donor genes mapped more siRNAs and were more methylated than genes with no evidence of capture. However, these patterns differed between syntelog versus translocated donor genes. Syntelogs appeared to maintain function, as measured by gene expression, consistent with moderation of silencing for functionally important genes. Epigenetic marks did not spread beyond their captured regions and 24nt crosstalk siRNAs were linked with CHH methylation. Translocated genes, in contrast, bore the signature of silencing. They were highly methylated and less expressed, but also overrepresented among donor genes and located away from chromosomal arms, which suggests a link between capture and gene movement. Splitting genes into potential functional categories based on evolutionary constraint supported the synteny-based findings. TE families captured genes in different ways, but the evidence for their advantage was generally less obvious; nevertheless, TEs with captured fragments were older, mapped fewer siRNAs, and were slightly less methylated than TEs without captured fragments. Collectively, our results argue that TE capture triggers an intragenomic conflict that may not affect the function of important genes but may lead to the pseudogenization of less-constrained genes.
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Affiliation(s)
- Aline Muyle
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92697, USA
| | - Danelle Seymour
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92697, USA; Department of Botany and Plant Sciences, UC Riverside, Riverside, CA 92521, USA
| | - Nikos Darzentas
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Elias Primetis
- School of Life Sciences, University of Sussex, Brighton, UK
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92697, USA.
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214
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Island songbirds as windows into evolution in small populations. Curr Biol 2021; 31:1303-1310.e4. [PMID: 33476557 DOI: 10.1016/j.cub.2020.12.040] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 10/12/2020] [Accepted: 12/23/2020] [Indexed: 11/20/2022]
Abstract
Due to their limited ranges and inherent isolation, island species have long been recognized as crucial systems for tackling a range of evolutionary questions, including in the early study of speciation.1,2 Such species have been less studied in the understanding of the evolutionary forces driving DNA sequence evolution. Island species usually have lower census population sizes (N) than continental species and, supposedly, lower effective population sizes (Ne). Given that both the rates of change caused by genetic drift and by selection are dependent upon Ne, island species are theoretically expected to exhibit (1) lower genetic diversity, (2) less effective natural selection against slightly deleterious mutations,3,4 and (3) a lower rate of adaptive evolution.5-8 Here, we have used a large set of newly sequenced and published whole-genome sequences of Passerida species (14 insular and 11 continental) to test these predictions. We confirm that island species exhibit lower census size and Ne, supporting the hypothesis that the smaller area available on islands constrains the upper bound of Ne. In the insular species, we find lower nucleotide diversity in coding regions, higher ratios of non-synonymous to synonymous polymorphisms, and lower adaptive substitution rates. Our results provide robust evidence that the lower Ne experienced by island species has affected both the ability of natural selection to efficiently remove weakly deleterious mutations and also the adaptive potential of island species, therefore providing considerable empirical support for the nearly neutral theory. We discuss the implications for both evolutionary and conservation biology.
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215
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Derous D, Sahu J, Douglas A, Lusseau D, Wenzel M. Comparative genomics of cetartiodactyla: energy metabolism underpins the transition to an aquatic lifestyle. CONSERVATION PHYSIOLOGY 2021; 9:coaa136. [PMID: 33505701 PMCID: PMC7816800 DOI: 10.1093/conphys/coaa136] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/09/2020] [Accepted: 12/19/2020] [Indexed: 05/28/2023]
Abstract
Foraging disruption caused by human activities is emerging as a key issue in cetacean conservation because it can affect nutrient levels and the amount of energy available to individuals to invest into reproduction. Our ability to predict how anthropogenic stressors affect these ecological processes and ultimately population trajectory depends crucially on our understanding of the complex physiological mechanisms that detect nutrient availability and regulate energy metabolism, foraging behavior and life-history decisions. These physiological mechanisms are likely to differ considerably from terrestrial mammalian model systems. Here, we examine nucleotide substitution rates in cetacean and other artiodactyl genomes to identify signatures of selection in genes associated with nutrient sensing pathways. We also estimated the likely physiological consequences of adaptive amino acid substitutions for pathway functions. Our results highlight that genes involved in the insulin, mTOR and NF-ĸB pathways are subject to significant positive selection in cetaceans compared to terrestrial artiodactyla. These genes may have been positively selected to enable cetaceans to adapt to a glucose-poor diet, to overcome deleterious effects caused by hypoxia during diving (e.g. oxidative stress and inflammation) and to modify fat-depot signaling functions in a manner different to terrestrial mammals. We thus show that adaptation in cetaceans to an aquatic lifestyle significantly affected functions in nutrient sensing pathways. The use of fat stores as a condition index in cetaceans may be confounded by the multiple and critical roles fat has in regulating cetacean metabolism, foraging behavior and diving physiology.
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Affiliation(s)
- Davina Derous
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Jagajjit Sahu
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Alex Douglas
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - David Lusseau
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
- National Institute of Aquatic Resources, Technical University of Denmark, Kgs. Lyngby, Copenhagen, Denmark
| | - Marius Wenzel
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
- Centre for Genome Enabled Biology and Medicine, University of Aberdeen, Aberdeen, UK
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216
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Nagamatsu ST, Coutouné N, José J, Fiamenghi MB, Pereira GAG, Oliveira JVDC, Carazzolle MF. Ethanol production process driving changes on industrial strains. FEMS Yeast Res 2021; 21:6070656. [PMID: 33417685 DOI: 10.1093/femsyr/foaa071] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/04/2021] [Indexed: 12/16/2022] Open
Abstract
Ethanol production has key differences between the two largest producing countries of this biofuel, Brazil and the USA, such as feedstock source, sugar concentration and ethanol titers in industrial fermentation. Therefore, it is highly probable that these specificities have led to genome adaptation of the Saccharomyces cerevisiae strains employed in each process to tolerate different environments. In order to identify particular adaptations, in this work, we have compared the genomes of industrial yeast strains widely used to produce ethanol from sugarcane, corn and sweet sorghum, and also two laboratory strains as reference. The genes were predicted and then 4524 single-copy orthologous were selected to build the phylogenetic tree. We found that the geographic location and industrial process were shown as the main evolutionary drivers: for sugarcane fermentation, positive selection was identified for metal homeostasis and stress response genes, whereas genes involved in membrane modeling have been connected with corn fermentation. In addition, the corn specialized strain Ethanol Red showed an increased number of copies of MAL31, a gene encoding a maltose transporter. In summary, our work can help to guide new strain chassis selection for engineering strategies, to produce more robust strains for biofuel production and other industrial applications.
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Affiliation(s)
- Sheila Tiemi Nagamatsu
- Division of Human Genetics, Department of Psychiatry, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA.,Laboratório de Genômica e BioEnergia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, 13083-970, Brazil
| | - Natalia Coutouné
- Laboratório Nacional de Biorrenováveis (LNBR), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), CEP 13083-970, Campinas, São Paulo, Brazil
| | - Juliana José
- Laboratório de Genômica e BioEnergia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, 13083-970, Brazil
| | - Mateus Bernabe Fiamenghi
- Laboratório de Genômica e BioEnergia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, 13083-970, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Laboratório de Genômica e BioEnergia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, 13083-970, Brazil
| | - Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Biorrenováveis (LNBR), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), CEP 13083-970, Campinas, São Paulo, Brazil
| | - Marcelo Falsarella Carazzolle
- Laboratório de Genômica e BioEnergia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, 13083-970, Brazil
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217
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Jacquet S, Pontier D, Etienne L. Rapid Evolution of HERC6 and Duplication of a Chimeric HERC5/6 Gene in Rodents and Bats Suggest an Overlooked Role of HERCs in Mammalian Immunity. Front Immunol 2021; 11:605270. [PMID: 33391270 PMCID: PMC7775381 DOI: 10.3389/fimmu.2020.605270] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022] Open
Abstract
Studying the evolutionary diversification of mammalian antiviral defenses is of main importance to better understand our innate immune repertoire. The small HERC proteins are part of a multigene family, including HERC5 and HERC6, which have probably diversified through complex evolutionary history in mammals. Here, we performed mammalian-wide phylogenetic and genomic analyses of HERC5 and HERC6, using 83 orthologous sequences from bats, rodents, primates, artiodactyls, and carnivores—the top five representative groups of mammalian evolution. We found that HERC5 has been under weak and differential positive selection in mammals, with only primate HERC5 showing evidences of pathogen-driven selection. In contrast, HERC6 has been under strong and recurrent adaptive evolution in mammals, suggesting past and widespread genetic arms-races with viral pathogens. Importantly, the rapid evolution of mammalian HERC6 spacer domain suggests that it might be a host-pathogen interface, targeting viral proteins and/or being the target of virus antagonists. Finally, we identified a HERC5/6 chimeric gene that arose from independent duplication in rodent and bat lineages and encodes for a conserved HERC5 N-terminal domain and divergent HERC6 spacer and HECT domains. This duplicated chimeric gene highlights adaptations that potentially contribute to rodent and bat immunity. Our findings open new research avenues on the functions of HERC6 and HERC5/6 in mammals, and on their implication in antiviral innate immunity.
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Affiliation(s)
- Stéphanie Jacquet
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, Villeurbanne, France.,CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France.,LabEx Ecofect, Université de Lyon, Lyon, France
| | - Dominique Pontier
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, Villeurbanne, France.,LabEx Ecofect, Université de Lyon, Lyon, France
| | - Lucie Etienne
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France.,LabEx Ecofect, Université de Lyon, Lyon, France
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218
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Abstract
Most genomic and evolutionary comparative analyses rely on accurate multiple sequence alignments. With their underlying codon structure, protein-coding nucleotide sequences pose a specific challenge for multiple sequence alignment. Multiple Alignment of Coding Sequences (MACSE) is a multiple sequence alignment program that provided the first automatic solution for aligning protein-coding gene datasets containing both functional and nonfunctional sequences (pseudogenes). Through its unique features, reliable codon alignments can be built in the presence of frameshifts and stop codons suitable for subsequent analysis of selection based on the ratio of nonsynonymous to synonymous substitutions. Here we offer a practical overview and guidelines on the use of MACSE v2. This major update of the initial algorithm now comes with a graphical interface providing user-friendly access to different subprograms to handle multiple alignments of protein-coding sequences. We also present new pipelines based on MACSE v2 subprograms to handle large datasets and distributed as Singularity containers. MACSE and associated pipelines are available at: https://bioweb.supagro.inra.fr/macse/ .
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Affiliation(s)
- Vincent Ranwez
- AGAP, University of Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
| | - Nathalie Chantret
- AGAP, University of Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Frédéric Delsuc
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
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219
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Abstract
The number of complete genome sequences explodes more and more with each passing year. Thus, methods for genome annotation need to be honed constantly to handle the deluge of information. Annotation of pseudogenes (i.e., gene copies that appear not to make a functional protein) in genomes is a persistent problem; here, we overview pseudogene annotation methods that are based on the detection of sequence homology in genomic DNA.
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Affiliation(s)
- Paul M Harrison
- Department of Biology, McGill University, Montreal, QC, Canada.
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220
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Florez-Rueda AM, Scharmann M, Roth M, Städler T. Population Genomics of the "Arcanum" Species Group in Wild Tomatoes: Evidence for Separate Origins of Two Self-Compatible Lineages. FRONTIERS IN PLANT SCIENCE 2021; 12:624442. [PMID: 33815438 PMCID: PMC8018279 DOI: 10.3389/fpls.2021.624442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/24/2021] [Indexed: 05/07/2023]
Abstract
Given their diverse mating systems and recent divergence, wild tomatoes (Solanum section Lycopersicon) have become an attractive model system to study ecological divergence, the build-up of reproductive barriers, and the causes and consequences of the breakdown of self-incompatibility. Here we report on a lesser-studied group of species known as the "Arcanum" group, comprising the nominal species Solanum arcanum, Solanum chmielewskii, and Solanum neorickii. The latter two taxa are self-compatible but are thought to self-fertilize at different rates, given their distinct manifestations of the morphological "selfing syndrome." Based on experimental crossings and transcriptome sequencing of a total of 39 different genotypes from as many accessions representing each species' geographic range, we provide compelling evidence for deep genealogical divisions within S. arcanum; only the self-incompatible lineage known as "var. marañón" has close genealogical ties to the two self-compatible species. Moreover, there is evidence under multiple inference schemes for different geographic subsets of S. arcanum var. marañón being closest to S. chmielewskii and S. neorickii, respectively. To broadly characterize the population-genomic consequences of these recent mating-system transitions and their associated speciation events, we fit demographic models indicating strong reductions in effective population size, congruent with reduced nucleotide and S-locus diversity in the two independently derived self-compatible species.
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221
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Koenen EJ, Kidner C, de Souza ÉR, Simon MF, Iganci JR, Nicholls JA, Brown GK, de Queiroz LP, Luckow M, Lewis GP, Pennington RT, Hughes CE. Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation. AMERICAN JOURNAL OF BOTANY 2020; 107:1710-1735. [PMID: 33253423 PMCID: PMC7839790 DOI: 10.1002/ajb2.1568] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/07/2020] [Indexed: 05/05/2023]
Abstract
PREMISE Targeted enrichment methods facilitate sequencing of hundreds of nuclear loci to enhance phylogenetic resolution and elucidate why some parts of the "tree of life" are difficult (if not impossible) to resolve. The mimosoid legumes are a prominent pantropical clade of ~3300 species of woody angiosperms for which previous phylogenies have shown extensive lack of resolution, especially among the species-rich and taxonomically challenging ingoids. METHODS We generated transcriptomes to select low-copy nuclear genes, enrich these via hybrid capture for representative species of most mimosoid genera, and analyze the resulting data using de novo assembly and various phylogenomic tools for species tree inference. We also evaluate gene tree support and conflict for key internodes and use phylogenetic network analysis to investigate phylogenetic signal across the ingoids. RESULTS Our selection of 964 nuclear genes greatly improves phylogenetic resolution across the mimosoid phylogeny and shows that the ingoid clade can be resolved into several well-supported clades. However, nearly all loci show lack of phylogenetic signal for some of the deeper internodes within the ingoids. CONCLUSIONS Lack of resolution in the ingoid clade is most likely the result of hyperfast diversification, potentially causing a hard polytomy of six or seven lineages. The gene set for targeted sequencing presented here offers great potential to further enhance the phylogeny of mimosoids and the wider Caesalpinioideae with denser taxon sampling, to provide a framework for taxonomic reclassification, and to study the ingoid radiation.
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Affiliation(s)
- Erik J. M. Koenen
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Catherine Kidner
- School of Biological SciencesUniversity of EdinburghKing’s Buildings, Mayfield RoadEdinburghUK
- Royal Botanic Gardens Edinburgh20a Inverleith RowEdinburghEH3 5LRUK
| | - Élvia R. de Souza
- Departamento Ciências BiológicasUniversidade Estadual de Feira de SantanaAvenida Transnordestina s/n—Novo Horizonte44036‐900Feira de SantanaBrazil
| | - Marcelo F. Simon
- Embrapa Recursos Genéticos e BiotecnologiaParque Estação Biológica (PqEB)Avenida W5 norte70770‐917BrasíliaBrazil
| | - João R. Iganci
- Instituto de BiologiaUniversidade Federal de PelotasCampus Universitário Capão do LeãoTravessa André Dreyfus s/nCapão do Leão96010‐900Rio Grande do SulBrazil
| | - James A. Nicholls
- School of Biological SciencesUniversity of EdinburghKing’s Buildings, Mayfield RoadEdinburghUK
- Australian National Insect CollectionCSIROClunies Ross StActonACT 2601Australia
| | - Gillian K. Brown
- Queensland HerbariumBrisbane Botanic GardensMount Coot‐tha, Mt Coot‐tha RoadToowong4066QueenslandAustralia
| | - Luciano P. de Queiroz
- Departamento Ciências BiológicasUniversidade Estadual de Feira de SantanaAvenida Transnordestina s/n—Novo Horizonte44036‐900Feira de SantanaBrazil
| | - Melissa Luckow
- L.H. Bailey HortoriumDepartment of Plant BiologyCornell University412 Mann Library BuildingIthacaNew York14853USA
| | - Gwilym P. Lewis
- Comparative Plant and Fungal Biology DepartmentRoyal Botanic GardensKew, RichmondSurreyTW9 3AEUK
| | - R. Toby Pennington
- Royal Botanic Gardens Edinburgh20a Inverleith RowEdinburghEH3 5LRUK
- GeographyUniversity of ExeterAmory Building, Rennes DriveExeterEX4 4RJUK
| | - Colin E. Hughes
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
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222
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Hughes LC, Ortí G, Saad H, Li C, White WT, Baldwin CC, Crandall KA, Arcila D, Betancur-R R. Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics. Mol Ecol Resour 2020; 21:816-833. [PMID: 33084200 DOI: 10.1111/1755-0998.13287] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 10/09/2020] [Indexed: 11/28/2022]
Abstract
Exon markers have a long history of use in phylogenetics of ray-finned fishes, the most diverse clade of vertebrates with more than 35,000 species. As the number of published genomes increases, it has become easier to test exons and other genetic markers for signals of ancient duplication events and filter out paralogues that can mislead phylogenetic analysis. We present seven new probe sets for current target-capture phylogenomic protocols that capture 1,104 exons explicitly filtered for paralogues using gene trees. These seven probe sets span the diversity of teleost fishes, including four sets that target five hyperdiverse percomorph clades which together comprise ca. 17,000 species (Carangaria, Ovalentaria, Eupercaria, and Syngnatharia + Pelagiaria combined). We additionally included probes to capture legacy nuclear exons and mitochondrial markers that have been commonly used in fish phylogenetics (despite some exons being flagged for paralogues) to facilitate integration of old and new molecular phylogenetic matrices. We tested these probes experimentally for 56 fish species (eight species per probe set) and merged new exon-capture sequence data into an existing data matrix of 1,104 exons and 300 ray-finned fish species. We provide an optimized bioinformatics pipeline to assemble exon capture data from raw reads to alignments for downstream analysis. We show that legacy loci with known paralogues are at risk of assembling duplicated sequences with target-capture, but we also assembled many useful orthologous sequences that can be integrated with many PCR-generated matrices. These probe sets are a valuable resource for advancing fish phylogenomics because targeted exons can easily be extracted from increasingly available whole genome and transcriptome data sets, and also may be integrated with existing PCR-based exon and mitochondrial data.
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Affiliation(s)
- Lily C Hughes
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Computational Biology Institute, Milken Institute of Public Health, George Washington University, Washington, DC, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Guillermo Ortí
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Hadeel Saad
- Department of Biological Sciences, George Washington University, Washington, DC, USA
| | - Chenhong Li
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - William T White
- CSIRO Australian National Fish Collection, National Research Collections of Australia, Hobart, TAS, Australia
| | - Carole C Baldwin
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Keith A Crandall
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Computational Biology Institute, Milken Institute of Public Health, George Washington University, Washington, DC, USA
| | - Dahiana Arcila
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Sam Noble Oklahoma Museum of Natural History, Norman, OK, USA.,Department of Biology, University of Oklahoma, Norman, OK, USA
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223
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Drivers and dynamics of a massive adaptive radiation in cichlid fishes. Nature 2020; 589:76-81. [DOI: 10.1038/s41586-020-2930-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 08/20/2020] [Indexed: 12/29/2022]
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224
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Cohen ZP, Brevik K, Chen YH, Hawthorne DJ, Weibel BD, Schoville SD. Elevated rates of positive selection drive the evolution of pestiferousness in the Colorado potato beetle (Leptinotarsa decemlineata, Say). Mol Ecol 2020; 30:237-254. [PMID: 33095936 DOI: 10.1111/mec.15703] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 09/28/2020] [Accepted: 10/15/2020] [Indexed: 12/16/2022]
Abstract
Contextualizing evolutionary history and identifying genomic features of an insect that might contribute to its pest status is important in developing early detection and control tactics. In order to understand the evolution of pestiferousness, which we define as the accumulation of traits that contribute to an insect population's success in an agroecosystem, we tested the importance of known genomic properties associated with rapid adaptation in the Colorado potato beetle (CPB), Leptinotarsa decemlineata Say. Within the leaf beetle genus Leptinotarsa, only CPB, and a few populations therein, has risen to pest status on cultivated nightshades, Solanum. Using whole genomes from ten closely related Leptinotarsa species native to the United States, we reconstructed a high-quality species tree and used this phylogenetic framework to assess evolutionary patterns in four genomic features of rapid adaptation: standing genetic variation, gene family expansion and contraction, transposable element abundance and location, and positive selection at protein-coding genes. Throughout approximately 20 million years of history, Leptinotarsa species show little evidence of gene family turnover and transposable element variation. However, there is a clear pattern of CPB experiencing higher rates of positive selection on protein-coding genes. We determine that these rates are associated with greater standing genetic variation due to larger effective population size, which supports the theory that the demographic history contributes to rates of protein evolution. Furthermore, we identify a suite of coding genes under positive selection that are putatively associated with pestiferousness in the Colorado potato beetle lineage. They are involved in the biological processes of xenobiotic detoxification, chemosensation and hormone function.
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Affiliation(s)
- Zachary P Cohen
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Kristian Brevik
- Department of Plant and Soil Sciences, University of Vermont, Burlington, VT, USA
| | - Yolanda H Chen
- Department of Plant and Soil Sciences, University of Vermont, Burlington, VT, USA
| | - David J Hawthorne
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Benjamin D Weibel
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
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225
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Santos-Garcia D, Mestre-Rincon N, Ouvrard D, Zchori-Fein E, Morin S. Portiera Gets Wild: Genome Instability Provides Insights into the Evolution of Both Whiteflies and Their Endosymbionts. Genome Biol Evol 2020; 12:2107-2124. [PMID: 33049039 PMCID: PMC7821994 DOI: 10.1093/gbe/evaa216] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2020] [Indexed: 12/12/2022] Open
Abstract
Whiteflies (Hemiptera: Sternorrhyncha: Aleyrodidae) are a superfamily of small phloem-feeding insects. They rely on their primary endosymbionts "Candidatus Portiera aleyrodidarum" to produce essential amino acids not present in their diet. Portiera has been codiverging with whiteflies since their origin and therefore reflects its host's evolutionary history. Like in most primary endosymbionts, the genome of Portiera stays stable across the Aleyrodidae superfamily after millions of years of codivergence. However, Portiera of the whitefly Bemisia tabaci has lost the ancestral genome order, reflecting a rare event in the endosymbiont evolution: the appearance of genome instability. To gain a better understanding of Portiera genome evolution, identify the time point in which genome instability appeared and contribute to the reconstruction of whitefly phylogeny, we developed a new phylogenetic framework. It targeted five Portiera genes and determined the presence of the DNA polymerase proofreading subunit (dnaQ) gene, previously associated with genome instability, and two alternative gene rearrangements. Our results indicated that Portiera gene sequences provide a robust tool for studying intergenera phylogenetic relationships in whiteflies. Using these new framework, we found that whitefly species from the Singhiella, Aleurolobus, and Bemisia genera form a monophyletic tribe, the Aleurolobini, and that their Portiera exhibit genome instability. This instability likely arose once in the common ancestor of the Aleurolobini tribe (at least 70 Ma), drawing a link between the appearance of genome instability in Portiera and the switch from multibacteriocyte to a single-bacteriocyte mode of inheritance in this tribe.
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Affiliation(s)
- Diego Santos-Garcia
- Department of Entomology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Natividad Mestre-Rincon
- Department of Entomology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - David Ouvrard
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Entomology and Invasive Plants Unit, Plant Health Laboratory, ANSES, Montferrier-sur-Lez, France
| | - Einat Zchori-Fein
- Department of Entomology, Newe-Ya'ar Research Center, ARO, Ramat-Yishai, Israel
| | - Shai Morin
- Department of Entomology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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226
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Cheng S, Wu H, Chen Z. Evolution of Transmissible Gastroenteritis Virus (TGEV): A Codon Usage Perspective. Int J Mol Sci 2020; 21:E7898. [PMID: 33114322 PMCID: PMC7660598 DOI: 10.3390/ijms21217898] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/18/2020] [Accepted: 10/21/2020] [Indexed: 12/14/2022] Open
Abstract
Transmissible gastroenteritis virus (TGEV) is a coronavirus associated with diarrhea and high mortality in piglets. To gain insight into the evolution and adaptation of TGEV, a comprehensive analysis of phylogeny and codon usage bias was performed. The phylogenetic analyses of maximum likelihood and Bayesian inference displayed two distinct genotypes: genotypes I and II, and genotype I was classified into subtypes Ia and Ib. The compositional properties revealed that the coding sequence contained a higher number of A/U nucleotides than G/C nucleotides, and that the synonymous codon third position was A/U-enriched. The principal component analysis based on the values of relative synonymous codon usage (RSCU) showed the genotype-specific codon usage patterns. The effective number of codons (ENC) indicated moderate codon usage bias in the TGEV genome. Dinucleotide analysis showed that CpA and UpG were over-represented and CpG was under-represented in the coding sequence of the TGEV genome. The analyses of Parity Rule 2 plot, ENC-plot, and neutrality plot displayed that natural selection was the dominant evolutionary driving force in shaping codon usage preference in genotypes Ia and II. In addition, natural selection played a major role, while mutation pressure had a minor role in driving the codon usage bias in genotype Ib. The codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses suggested that genotype I might be more adaptive to pigs than genotype II. Current findings contribute to understanding the evolution and adaptation of TGEV.
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Affiliation(s)
- Saipeng Cheng
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China;
| | - Huiguang Wu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China;
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Zhenhai Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China;
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
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227
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Dai Y, Pracana R, Holland PWH. Divergent genes in gerbils: prevalence, relation to GC-biased substitution, and phenotypic relevance. BMC Evol Biol 2020; 20:134. [PMID: 33076817 PMCID: PMC7574485 DOI: 10.1186/s12862-020-01696-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/29/2020] [Indexed: 11/25/2022] Open
Abstract
Background Two gerbil species, sand rat (Psammomys obesus) and Mongolian jird (Meriones unguiculatus), can become obese and show signs of metabolic dysregulation when maintained on standard laboratory diets. The genetic basis of this phenotype is unknown. Recently, genome sequencing has uncovered very unusual regions of high guanine and cytosine (GC) content scattered across the sand rat genome, most likely generated by extreme and localized biased gene conversion. A key pancreatic transcription factor PDX1 is encoded by a gene in the most extreme GC-rich region, is remarkably divergent and exhibits altered biochemical properties. Here, we ask if gerbils have proteins in addition to PDX1 that are aberrantly divergent in amino acid sequence, whether they have also become divergent due to GC-biased nucleotide changes, and whether these proteins could plausibly be connected to metabolic dysfunction exhibited by gerbils. Results We analyzed ~ 10,000 proteins with 1-to-1 orthologues in human and rodents and identified 50 proteins that accumulated unusually high levels of amino acid change in the sand rat and 41 in Mongolian jird. We show that more than half of the aberrantly divergent proteins are associated with GC biased nucleotide change and many are in previously defined high GC regions. We highlight four aberrantly divergent gerbil proteins, PDX1, INSR, MEDAG and SPP1, that may plausibly be associated with dietary metabolism. Conclusions We show that through the course of gerbil evolution, many aberrantly divergent proteins have accumulated in the gerbil lineage, and GC-biased nucleotide substitution rather than positive selection is the likely cause of extreme divergence in more than half of these. Some proteins carry putatively deleterious changes that could be associated with metabolic and physiological phenotypes observed in some gerbil species. We propose that these animals provide a useful model to study the ‘tug-of-war’ between natural selection and the excessive accumulation of deleterious substitutions mutations through biased gene conversion.
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Affiliation(s)
- Yichen Dai
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Rodrigo Pracana
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Peter W H Holland
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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228
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Chang CH, Wang YC, Shao YT, Liu SH. Phylogenetic analysis and ontogenetic changes in the cone opsins of the western mosquitofish (Gambusia affinis). PLoS One 2020; 15:e0240313. [PMID: 33048954 PMCID: PMC7553354 DOI: 10.1371/journal.pone.0240313] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/23/2020] [Indexed: 11/25/2022] Open
Abstract
To convert external light into internal neural signal, vertebrates rely on a special group of proteins, the visual opsins. Four of the five types of visual opsins—short-wavelength sensitive 1 (Sws1), short-wavelength sensitive 2 (Sws2), medium-wavelength sensitive (Rh2), and long-wavelength sensitive (Lws)—are expressed in cone cells for scotopic vision, with the fifth, rhodopsin (Rh1), being expressed in rod cells for photopic vision. Fish often display differing ontogenetic cone opsin expression profiles, which may be related to dietary and/or habitat ontogenetic shift. The western mosquitofish (Gambusia affinis) is an aggressive invader that has successfully colonized every continent except Antarctica. The strong invasiveness of this species may be linked to its visual acuity since it can inhabit turbid waters better than other fishes. By genome screening and transcriptome analysis, we identify seven cone opsin genes in the western mosquitofish, including one sws1, two sws2, one rh2, and three lws. The predicted maximal absorbance wavelength (λmax) values of the respective proteins are 353 nm for Sws1, 449 nm for Sws2a, 408 nm for Sws2b, 516 nm for Rh2-1, 571 nm for Lws-1, and 519 nm for Lws-3. Retention of an intron in the lws-r transcript likely renders this visual opsin gene non-functional. Our real-time quantitative PCR demonstrates that adult male and female western mosquitofish do not differ in their cone opsin expression profiles, but we do reveal an ontogenetic shift in cone opsin expression. Compared to adults, larvae express proportionally more sws1 and less lws-1, suggesting that the western mosquitofish is more sensitive to shorter wavelengths in the larval stage, but becomes more sensitive to longer wavelengths in adulthood.
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Affiliation(s)
- Chia-Hao Chang
- TIGP Biodiversity Program, Tunghai University, Taichung City, Taiwan
- Center for Ecology and Environment, Tunghai University, Taichung City, Taiwan
| | - Yu-Chun Wang
- Planning and Information Division, Fisheries Research Institute, Keelung City, Taiwan
| | - Yi Ta Shao
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan
| | - Shih-Hui Liu
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung City, Taiwan
- * E-mail: ,
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229
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Aguilera-Uribe M, Meza-Lázaro RN, Kieran TJ, Ibarra-Cerdeña CN, Zaldívar-Riverón A. Phylogeny of the North-Central American clade of blood-sucking reduviid bugs of the tribe Triatomini (Hemiptera: Triatominae) based on the mitochondrial genome. INFECTION GENETICS AND EVOLUTION 2020; 84:104373. [DOI: 10.1016/j.meegid.2020.104373] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/19/2022]
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230
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Assis R. Out of the testis, into the ovary: biased outcomes of gene duplication and deletion in Drosophila. Evolution 2020; 73:1850-1862. [PMID: 31418820 DOI: 10.1111/evo.13820] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/28/2019] [Accepted: 07/03/2019] [Indexed: 12/30/2022]
Abstract
Gene turnover is a key source of adaptive variation. Yet most evolutionary studies have focused on gene duplication, dismissing gene deletion as a mechanism that simply eradicates redundancy. Here, I use genome-scale sequence and multi-tissue expression data from Drosophila melanogaster and Drosophila pseudoobscura to simultaneously assess the evolutionary outcomes of gene duplication and deletion in Drosophila. I find that gene duplication is more frequent than gene deletion in both species, indicating that it may play a more important role in Drosophila evolution. However, examination of several genic properties reveals that genes likely possess distinct functions after duplication that diverge further before deletion, suggesting that loss of redundancy cannot explain a majority of gene deletion events in Drosophila. Moreover, in addition to providing support for the well-known "out of the testis" origin of young duplicate genes, analyses of gene expression profiles uncover a preferential bias against deletion of old ovary-expressed genes. Therefore, I propose a novel "into the ovary" hypothesis for gene deletion in Drosophila, in which gene deletion may promote adaptation by salvaging genes that contribute to the evolution of female reproductive phenotypes. Under this combined "out of the testis, into the ovary" evolutionary model, gene duplication and deletion work in concert to generate and maintain a balanced repertoire of genes that promote sex-specific adaptation in Drosophila.
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Affiliation(s)
- Raquel Assis
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, 16801
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231
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Smith CH, Pfeiffer JM, Johnson NA. Comparative phylogenomics reveal complex evolution of life history strategies in a clade of bivalves with parasitic larvae (Bivalvia: Unionoida: Ambleminae). Cladistics 2020; 36:505-520. [DOI: 10.1111/cla.12423] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2020] [Indexed: 01/27/2023] Open
Affiliation(s)
| | - John M. Pfeiffer
- National Museum of Natural History Smithsonian Institution Washington DC USA
| | - Nathan A. Johnson
- U.S. Geological Survey, Wetland and Aquatic Research Center 7920 NW 71st Street Gainesville FL32653 USA
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232
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Huston NC, Wan H, de Cesaris Araujo Tavares R, Wilen C, Pyle AM. Comprehensive in-vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.07.10.197079. [PMID: 32676598 PMCID: PMC7359520 DOI: 10.1101/2020.07.10.197079] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
SARS-CoV-2 is the positive-sense RNA virus that causes COVID-19, a disease that has triggered a major human health and economic crisis. The genome of SARS-CoV-2 is unique among viral RNAs in its vast potential to form stable RNA structures and yet, as much as 97% of its 30 kilobases have not been structurally explored in the context of a viral infection. Our limited knowledge of SARS-CoV-2 genomic architecture is a fundamental limitation to both our mechanistic understanding of coronavirus life cycle and the development of COVID-19 RNA-based therapeutics. Here, we apply a novel long amplicon strategy to determine for the first time the secondary structure of the SARS-CoV-2 RNA genome probed in infected cells. In addition to the conserved structural motifs at the viral termini, we report new structural features like a conformationally flexible programmed ribosomal frameshifting pseudoknot, and a host of novel RNA structures, each of which highlights the importance of studying viral structures in their native genomic context. Our in-depth structural analysis reveals extensive networks of well-folded RNA structures throughout Orf1ab and reveals new aspects of SARS-CoV-2 genome architecture that distinguish it from other single-stranded, positive-sense RNA viruses. Evolutionary analysis of RNA structures in SARS-CoV-2 shows that several features of its genomic structure are conserved across beta coronaviruses and we pinpoint individual regions of well-folded RNA structure that merit downstream functional analysis. The native, complete secondary structure of SAR-CoV-2 presented here is a roadmap that will facilitate focused studies on mechanisms of replication, translation and packaging, and guide the identification of new RNA drug targets against COVID-19.
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Affiliation(s)
- Nicholas C. Huston
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Han Wan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
| | | | - Craig Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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233
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Alves LQ, Ruivo R, Fonseca MM, Lopes-Marques M, Ribeiro P, Castro L. PseudoChecker: an integrated online platform for gene inactivation inference. Nucleic Acids Res 2020; 48:W321-W331. [PMID: 32449938 PMCID: PMC7319564 DOI: 10.1093/nar/gkaa408] [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: 03/10/2020] [Revised: 04/22/2020] [Accepted: 05/06/2020] [Indexed: 01/21/2023] Open
Abstract
The rapid expansion of high-quality genome assemblies, exemplified by ongoing initiatives such as the Genome-10K and i5k, demands novel automated methods to approach comparative genomics. Of these, the study of inactivating mutations in the coding region of genes, or pseudogenization, as a source of evolutionary novelty is mostly overlooked. Thus, to address such evolutionary/genomic events, a systematic, accurate and computationally automated approach is required. Here, we present PseudoChecker, the first integrated online platform for gene inactivation inference. Unlike the few existing methods, our comparative genomics-based approach displays full automation, a built-in graphical user interface and a novel index, PseudoIndex, for an empirical evaluation of the gene coding status. As a multi-platform online service, PseudoChecker simplifies access and usability, allowing a fast identification of disruptive mutations. An analysis of 30 genes previously reported to be eroded in mammals, and 30 viable genes from the same lineages, demonstrated that PseudoChecker was able to correctly infer 97% of loss events and 95% of functional genes, confirming its reliability. PseudoChecker is freely available, without login required, at http://pseudochecker.ciimar.up.pt.
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Affiliation(s)
- Luís Q Alves
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Matosinhos, 4450-208, Portugal
| | - Raquel Ruivo
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Matosinhos, 4450-208, Portugal
| | - Miguel M Fonseca
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Matosinhos, 4450-208, Portugal
| | - Mónica Lopes-Marques
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Matosinhos, 4450-208, Portugal
| | - Pedro Ribeiro
- CRACS & INESC-TEC Department of Computer Science, FCUP, Porto, 4169-007, Portugal
| | - L Filipe C Castro
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Matosinhos, 4450-208, Portugal
- Department of Biology, FCUP, Porto, 4169-007, Portugal
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234
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A genome-wide survey of copy number variations reveals an asymmetric evolution of duplicated genes in rice. BMC Biol 2020; 18:73. [PMID: 32591023 PMCID: PMC7318451 DOI: 10.1186/s12915-020-00798-0] [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: 01/24/2020] [Accepted: 05/20/2020] [Indexed: 11/21/2022] Open
Abstract
Background Copy number variations (CNVs) are an important type of structural variations in the genome that usually affect gene expression levels by gene dosage effect. Understanding CNVs as part of genome evolution may provide insights into the genetic basis of important agricultural traits and contribute to the crop breeding in the future. While available methods to detect CNVs utilizing next-generation sequencing technology have helped shed light on prevalence and effects of CNVs, the complexity of crop genomes poses a major challenge and requires development of additional tools. Results Here, we generated genomic and transcriptomic data of 93 rice (Oryza sativa L.) accessions and developed a comprehensive pipeline to call CNVs in this large-scale dataset. We analyzed the correlation between CNVs and gene expression levels and found that approximately 13% of the identified genes showed a significant correlation between their expression levels and copy numbers. Further analysis showed that about 36% of duplicate pairs were involved in pseudogenetic events while only 5% of them showed functional differentiation. Moreover, the offspring copy mainly contributed to the expression levels and seemed more likely to become a pseudogene, whereas the parent copy tended to maintain the function of ancestral gene. Conclusion We provide a high-accuracy CNV dataset that will contribute to functional genomics studies and molecular breeding in rice. We also showed that gene dosage effect of CNVs in rice is not exponential or linear. Our work demonstrates that the evolution of duplicated genes is asymmetric in both expression levels and gene fates, shedding a new insight into the evolution of duplicated genes.
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235
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Antiviral Activity and Adaptive Evolution of Avian Tetherins. J Virol 2020; 94:JVI.00416-20. [PMID: 32238588 DOI: 10.1128/jvi.00416-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 03/26/2020] [Indexed: 02/07/2023] Open
Abstract
Tetherin/BST-2 is an antiviral protein that blocks the release of enveloped viral particles by linking them to the membrane of producing cells. At first, BST-2 genes were described only in humans and other mammals. Recent work identified BST-2 orthologs in nonmammalian vertebrates, including birds. Here, we identify the BST-2 sequence in domestic chicken (Gallus gallus) for the first time and demonstrate its activity against avian sarcoma and leukosis virus (ASLV). We generated a BST-2 knockout in chicken cells and showed that BST-2 is a major determinant of an interferon-induced block of ASLV release. Ectopic expression of chicken BST-2 blocks the release of ASLV in chicken cells and of human immunodeficiency virus type 1 (HIV-1) in human cells. Using metabolic labeling and pulse-chase analysis of HIV-1 Gag proteins, we verified that chicken BST-2 blocks the virus at the release stage. Furthermore, we describe BST-2 orthologs in multiple avian species from 12 avian orders. Previously, some of these species were reported to lack BST-2, highlighting the difficulty of identifying sequences of this extremely variable gene. We analyzed BST-2 genes in the avian orders Galliformes and Passeriformes and showed that they evolve under positive selection. This indicates that avian BST-2 is involved in host-virus evolutionary arms races and suggests that BST-2 antagonists exist in some avian viruses. In summary, we show that chicken BST-2 has the potential to act as a restriction factor against ASLV. Characterizing the interaction of avian BST-2 with avian viruses is important in understanding innate antiviral defenses in birds.IMPORTANCE Birds are important hosts of viruses that have the potential to cause zoonotic infections in humans. However, only a few antiviral genes (called viral restriction factors) have been described in birds, mostly because birds lack counterparts of highly studied mammalian restriction factors. Tetherin/BST-2 is a restriction factor, originally described in humans, that blocks the release of newly formed virus particles from infected cells. Recent work identified BST-2 in nonmammalian vertebrate species, including birds. Here, we report the BST-2 sequence in domestic chicken and describe its antiviral activity against a prototypical avian retrovirus, avian sarcoma and leukosis virus (ASLV). We also identify BST-2 genes in multiple avian species and show that they evolve rapidly in birds, which is an important indication of their relevance for antiviral defense. Analysis of avian BST-2 genes will shed light on defense mechanisms against avian viral pathogens.
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236
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Wang JJ, Wu YF, Yang MF, Dai RH. The Phylogenetic Implications of the Mitochondrial Genomes of Macropsis notata and Oncopsis nigrofasciata. Front Genet 2020; 11:443. [PMID: 32508875 PMCID: PMC7251781 DOI: 10.3389/fgene.2020.00443] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/09/2020] [Indexed: 11/13/2022] Open
Abstract
Macropsinae are forest pests that feed on woody plants. They can damage the growth of trees and crops, and some species can also spread plant pathogens. Due to their widespread effects, these leafhoppers are of great economic significance, which is why there is a need to study their genomes. To fill the gap in the mitochondrial genomic data of the subfamily Macropsinae, we sequenced the complete mitochondrial genomes of Macropsis notata and Oncopsis nigrofasciata (which were 16,323 and 15,927 bp long, respectively). These two species are representative species of the leafhoppers group (Cicadellidae); the mitochondrial genomes of these species range from a length of 15,131 bp (Trocnadella arisana) to 16,811 bp (Parocerus laurifoliae). Both mitogenomes contained 37 typical insect mitochondrial genes and a control region; there were no long non-coding sequences. The genes within the mitogenome were very compact. The mitogenomes from both species contained two kinds of parallel repeat units in the control region. The whole mitogenomes of Macropsinae showed a heavy AT nucleotide bias (M. notata 76.8% and O. nigrofasciata 79.0%), a positive AT Skew (0.15 and 0.12), and a negative GC Skew (-0.14 and -0.08). Upon comparative ML and BI analysis, some clade relationships were consistent among the six trees. Most subfamilies were reconstructed into monophyletic groups with strong support in all analyses, with the exception of Evacanthinae and Cicadellinae. Unlike the results of previous research, it was shown that although all Deltocephalinae species are grouped into one clade, they were not the sister group to all other leafhoppers. Further, Cicadellinae and Evacanthinae were occasionally reconstructed as a polyphyletic and a paraphyletic group, respectively, possibly due to the limited numbers of samples and sequences. This mitogenome information for M. notata and O. nigrofasciata could facilitate future studies on the mitogenomic diversity and evolution of the related Membracoidea, and eventually help to control their effects on plants for the betterment of society at large.
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Affiliation(s)
| | | | | | - Ren-Huai Dai
- The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, China
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237
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Allio R, Schomaker-Bastos A, Romiguier J, Prosdocimi F, Nabholz B, Delsuc F. MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics. Mol Ecol Resour 2020; 20:892-905. [PMID: 32243090 PMCID: PMC7497042 DOI: 10.1111/1755-0998.13160] [Citation(s) in RCA: 560] [Impact Index Per Article: 140.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 02/21/2020] [Accepted: 03/12/2020] [Indexed: 11/27/2022]
Abstract
Thanks to the development of high-throughput sequencing technologies, target enrichment sequencing of nuclear ultraconserved DNA elements (UCEs) now allows routine inference of phylogenetic relationships from thousands of genomic markers. Recently, it has been shown that mitochondrial DNA (mtDNA) is frequently sequenced alongside the targeted loci in such capture experiments. Despite its broad evolutionary interest, mtDNA is rarely assembled and used in conjunction with nuclear markers in capture-based studies. Here, we developed MitoFinder, a user-friendly bioinformatic pipeline, to efficiently assemble and annotate mitogenomic data from hundreds of UCE libraries. As a case study, we used ants (Formicidae) for which 501 UCE libraries have been sequenced whereas only 29 mitogenomes are available. We compared the efficiency of four different assemblers (IDBA-UD, MEGAHIT, MetaSPAdes, and Trinity) for assembling both UCE and mtDNA loci. Using MitoFinder, we show that metagenomic assemblers, in particular MetaSPAdes, are well suited to assemble both UCEs and mtDNA. Mitogenomic signal was successfully extracted from all 501 UCE libraries, allowing us to confirm species identification using CO1 barcoding. Moreover, our automated procedure retrieved 296 cases in which the mitochondrial genome was assembled in a single contig, thus increasing the number of available ant mitogenomes by an order of magnitude. By utilizing the power of metagenomic assemblers, MitoFinder provides an efficient tool to extract complementary mitogenomic data from UCE libraries, allowing testing for potential mitonuclear discordance. Our approach is potentially applicable to other sequence capture methods, transcriptomic data and whole genome shotgun sequencing in diverse taxa. The MitoFinder software is available from GitHub (https://github.com/RemiAllio/MitoFinder).
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Affiliation(s)
- Rémi Allio
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
| | - Alex Schomaker-Bastos
- Laboratório Multidisciplinar para Análise de Dados (LAMPADA), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jonathan Romiguier
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
| | - Francisco Prosdocimi
- Laboratório Multidisciplinar para Análise de Dados (LAMPADA), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Benoit Nabholz
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
| | - Frédéric Delsuc
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
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238
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Shen J, Zhang X, Landis JB, Zhang H, Deng T, Sun H, Wang H. Plastome Evolution in Dolomiaea (Asteraceae, Cardueae) Using Phylogenomic and Comparative Analyses. FRONTIERS IN PLANT SCIENCE 2020; 11:376. [PMID: 32351518 PMCID: PMC7174903 DOI: 10.3389/fpls.2020.00376] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 03/16/2020] [Indexed: 05/24/2023]
Abstract
Dolomiaea is a medicinally important genus of Asteraceae endemic to alpine habitats of the Qinghai-Tibet Plateau (QTP) and adjacent areas. Despite significant medicinal value, genomic resources of Dolomiaea are still lacking, impeding our understanding of its evolutionary history. Here, we sequenced and annotated plastomes of four Dolomiaea species. All analyzed plastomes share the gene content and structure of most Asteraceae plastomes, indicating the conservation of plastome evolutionary history of Dolomiaea. Eight highly divergent regions (rps16-trnQ, trnC-petN, trnE-rpoB, trnT-trnL-trnF, psbE-petL, ndhF-rpl32-trnL, rps15-ycf1, and ycf1), along with a total of 51-61 simple sequence repeats (SSRs) were identified as valuable molecular markers for further species delimitation and population genetic studies. Phylogenetic analyses confirmed the evolutionary position of Dolomiaea as a clade within the subtribe Saussureinae, while revealing the discordance between the molecular phylogeny and morphological treatment. Our analysis also revealed that the plastid genes, rpoC2 and ycf1, which are rarely used in Asteraceae phylogenetic inference, exhibit great phylogenetic informativeness and promise in further phylogenetic studies of tribe Cardueae. Analysis for signatures of selection identified four genes that contain sites undergoing positive selection (atpA, ndhF, rbcL, and ycf4). These genes may play important roles in the adaptation of Dolomiaea to alpine environments. Our study constitutes the first investigation on the sequence and structural variation, phylogenetic utility and positive selection of plastomes of Dolomiaea, which will facilitate further studies of its taxonomy, evolution and conservation.
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Affiliation(s)
- Jun Shen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jacob B. Landis
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Huajie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Tao Deng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
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239
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Portik DM, Wiens JJ. SuperCRUNCH: A bioinformatics toolkit for creating and manipulating supermatrices and other large phylogenetic datasets. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13392] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Daniel M. Portik
- Department of Ecology and Evolutionary Biology University of Arizona Tucson AZ USA
- California Academy of Sciences San Francisco CA USA
| | - John J. Wiens
- Department of Ecology and Evolutionary Biology University of Arizona Tucson AZ USA
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240
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Álvarez-Padilla F, Kallal RJ, Hormiga G. Taxonomy and Phylogenetics of Nanometinae and Other Australasian Orb-Weaving Spiders (Araneae: Tetragnathidae). BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2020. [DOI: 10.1206/0003-0090.438.1.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Fernando Álvarez-Padilla
- Departamento de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México
| | - Robert J. Kallal
- Department of Biological Sciences, The George Washington University
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University
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241
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Wang J, Wu Y, Dai R, Yang M. Comparative mitogenomes of six species in the subfamily Iassinae (Hemiptera: Cicadellidae) and phylogenetic analysis. Int J Biol Macromol 2020; 149:1294-1303. [PMID: 32004599 DOI: 10.1016/j.ijbiomac.2020.01.270] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/09/2020] [Accepted: 01/27/2020] [Indexed: 11/16/2022]
Abstract
For elucidating phylogenetic relationships among members of the family Cicadellidae, mitogenomes of six members of the subfamily Iassinae, including Batracomorphus lateprocessus, Iassus dorsalis, Krisna concava, Krisna rufimarginata, Gessius rufidorsus, and Trocnadella arisana, were sequenced. The mitogenomes are 14,724-15,356-bp long. Moreover, typical 37 genes in mitogenomes were identified; arrangement of these genes in the studied species was consistent with that in the inferred ancestral insects, except for tRNA genes, with a simple switch between the positions of trnI and trnQ in Trocnadella arisana. Most protein-coding genes in the Iassinae mitogenomes showed typical ATN start codons (ATA/ATT/ATC/ATG) and TAR (TAA/TAG) or an incomplete stop codon T--; ATP8 of all sequenced species showed the start codon TTG. The secondary structures of 16S rRNA and 12S rRNA were predicted. 16S rRNA comprised 6 domains with 43 helices, and 12S rRNA comprised 3 domains with 25 helices. All subfamilies, except Cicadellinae and Evacanthinae, were recovered as monophyletic. As reported previously, treehoppers originated from paraphyletic Cicadellidae. Iassinae and Coelidiinae, Megophthalminae and treehoppers, and Cicadellinae and Evacanthinae were sister groups with high nodal support.
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Affiliation(s)
- Jiajia Wang
- Institute of Entomology, Guizhou University, The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Guiyang, Guizhou 550025, People's Republic of China
| | - Yunfei Wu
- Institute of Entomology, Guizhou University, The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Guiyang, Guizhou 550025, People's Republic of China
| | - Renhuai Dai
- Institute of Entomology, Guizhou University, The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Guiyang, Guizhou 550025, People's Republic of China.
| | - Maofa Yang
- Institute of Entomology, Guizhou University, The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Guiyang, Guizhou 550025, People's Republic of China
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242
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Expanded complement of Niemann-Pick type C2-like protein genes in Clonorchis sinensis suggests functions beyond sterol binding and transport. Parasit Vectors 2020; 13:38. [PMID: 31973758 PMCID: PMC6979364 DOI: 10.1186/s13071-020-3910-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 01/15/2020] [Indexed: 01/04/2023] Open
Abstract
Background The parasitic flatworm Clonorchis sinensis inhabits the biliary tree of humans and other piscivorous mammals. This parasite can survive and thrive in the bile duct, despite exposure to bile constituents and host immune attack. Although the precise biological mechanisms underlying this adaptation are unknown, previous work indicated that Niemann-pick type C2 (NPC2)-like sterol-binding proteins might be integral in the host-parasite interplay. Expansions of this family in some invertebrates, such as arthropods, have shown functional diversification, including novel forms of chemoreception. Thus, here we curated the NPC2-like protein gene complement in C. sinensis, and predicted their conserved and/or divergent functional roles. Methods We used an established comparative genomic-bioinformatic approach to curate NPC2-like proteins encoded in published genomes of Korean and Chinese isolates of C. sinensis. Protein sequence and structural homology, presence of conserved domains and phylogeny were used to group and functionally classify NPC2-like proteins. Furthermore, transcription levels of NPC2-like protein-encoding genes were explored in different developmental stages and tissues. Results Totals of 35 and 32 C. sinensis NPC2-like proteins were predicted to be encoded in the genomes of the Korean and Chinese isolates, respectively. Overall, these proteins had low sequence homology and high variability of sequence alignment coverage when compared with curated NPC2s. Most C. sinensis proteins were predicted to retain a conserved ML domain and a conserved fold conformation, with a large cavity within the protein. Only one protein sequence retained the conserved amino acid residues required in bovine NPC2 to bind cholesterol. Non-canonical C. sinensis NPC2-like protein-coding domains clustered into four distinct phylogenetic groups with members of a group frequently encoded on the same genome scaffolds. Interestingly, NPC2-like protein-encoding genes were predicted to be variably transcribed in different developmental stages and adult tissues, with most being transcribed in the metacercarial stage. Conclusions The results of the present investigation confirms an expansion of NPC2-like proteins in C. sinensis, suggesting a diverse array of functions beyond sterol binding and transport. Functional explorations of this protein family should elucidate the mechanisms enabling the establishment and survival of C. sinensis and related flukes in the biliary systems of mammalian hosts.![]()
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243
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Kallal RJ, Hormiga G. Phylogenetic placement of the stone-nest orb-weaving spider Nemoscolus Simon, 1895 (Araneae : Araneidae) and the description of the first species from Australia. INVERTEBR SYST 2020. [DOI: 10.1071/is20035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The spider genus Nemoscolus Simon, 1895 (Araneidae) has been neglected taxonomically despite the unique retreat that several species construct in their horizontal orb-webs, composed of pebbles and other detritus. The distribution of Nemoscolus is poorly known and the genus includes species from Africa and Europe. Nemoscolus is placed in Simon’s Cycloseae species group along with Cyclosa Menge, 1866, Acusilas Simon, 1895, Arachnura Vinson, 1863, Witica O. Pickard-Cambridge, 1895, among others. Here we describe a new species from Queensland, Australia, N. sandersi, sp. nov., drastically expanding the distribution range of the genus. We use nucleotide sequence data to phylogenetically place Nemoscolus using model-based inference methods within Araneidae and to explore its affinities to Simon’s Cycloseae. The data support propinquity of Nemoscolus with Acusilas and Arachnura but not with Cyclosa. Our analyses suggest that Cycloseae is not a clade, with Cyclosa, Acusilas, Witica and Nemoscolus not sharing a recent common ancestor. This use of an integrated granular retreat represents at least the second independent evolution of such a structure within Araneidae. These results improve our understanding of both phylogeny and retreat evolution in araneid spiders.
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244
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Kuitche E, Jammali S, Ouangraoua A. SimSpliceEvol: alternative splicing-aware simulation of biological sequence evolution. BMC Bioinformatics 2019; 20:640. [PMID: 31842741 PMCID: PMC6916212 DOI: 10.1186/s12859-019-3207-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Background It is now well established that eukaryotic coding genes have the ability to produce more than one type of transcript thanks to the mechanisms of alternative splicing and alternative transcription. Because of the lack of gold standard real data on alternative splicing, simulated data constitute a good option for evaluating the accuracy and the efficiency of methods developed for splice-aware sequence analysis. However, existing sequence evolution simulation methods do not model alternative splicing, and so they can not be used to test spliced sequence analysis methods. Results We propose a new method called SimSpliceEvol for simulating the evolution of sets of alternative transcripts along the branches of an input gene tree. In addition to traditional sequence evolution events, the simulation also includes gene exon-intron structure evolution events and alternative splicing events that modify the sets of transcripts produced from genes. SimSpliceEvol was implemented in Python. The source code is freely available at https://github.com/UdeS-CoBIUS/SimSpliceEvol. Conclusions Data generated using SimSpliceEvol are useful for testing spliced RNA sequence analysis methods such as methods for spliced alignment of cDNA and genomic sequences, multiple cDNA alignment, orthologous exons identification, splicing orthology inference, transcript phylogeny inference, which requires to know the real evolutionary relationships between the sequences.
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Affiliation(s)
- Esaie Kuitche
- Department of Computer Science, University of Sherbrooke, 2500 Boulevard de l'Université, Quebec, J1K2R1, Canada.
| | - Safa Jammali
- Department of Computer Science, University of Sherbrooke, 2500 Boulevard de l'Université, Quebec, J1K2R1, Canada.,Department of Biochemistry, University of Sherbrooke, 3001 12e avenue Nord, Quebec, J1H5N4, Canada
| | - Aïda Ouangraoua
- Department of Computer Science, University of Sherbrooke, 2500 Boulevard de l'Université, Quebec, J1K2R1, Canada
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245
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Zhang D, Gao F, Jakovlić I, Zou H, Zhang J, Li WX, Wang GT. PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol Ecol Resour 2019; 20:348-355. [DOI: 10.1111/1755-0998.13096] [Citation(s) in RCA: 825] [Impact Index Per Article: 165.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/12/2019] [Accepted: 09/24/2019] [Indexed: 01/12/2023]
Affiliation(s)
- 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 China
- University of Chinese Academy of Sciences Beijing China
| | - Fangluan Gao
- Institute of Plant Virology Fujian Agriculture and Forestry University Fuzhou Fujian China
| | | | - Hong Zou
- Key Laboratory of Aquaculture Disease Control Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | | | - Wen X. Li
- Key Laboratory of Aquaculture Disease Control Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Gui T. Wang
- Key Laboratory of Aquaculture Disease Control Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
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246
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Bentz AB, Thomas GWC, Rusch DB, Rosvall KA. Tissue-specific expression profiles and positive selection analysis in the tree swallow (Tachycineta bicolor) using a de novo transcriptome assembly. Sci Rep 2019; 9:15849. [PMID: 31676844 PMCID: PMC6825141 DOI: 10.1038/s41598-019-52312-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 10/09/2019] [Indexed: 12/17/2022] Open
Abstract
Tree swallows (Tachycineta bicolor) are one of the most commonly studied wild birds in North America. They have advanced numerous research areas, including life history, physiology, and organismal responses to global change; however, transcriptomic resources are scarce. To further advance the utility of this system for biologists across disciplines, we generated a transcriptome for the tree swallow using six tissues (brain, blood, ovary, spleen, liver, and muscle) collected from breeding females. We de novo assembled 207,739 transcripts, which we aligned to 14,717 high confidence protein-coding genes. We then characterized each tissue with regard to its unique genes and processes and applied this transcriptome to two fundamental questions in evolutionary biology and endocrinology. First, we analyzed 3,015 single-copy orthologs and identified 46 genes under positive selection in the tree swallow lineage, including those with putative links to adaptations in this species. Second, we analyzed tissue-specific expression patterns of genes involved in sex steroidogenesis and processing. Enzymes capable of synthesizing these behaviorally relevant hormones were largely limited to the ovary, whereas steroid binding genes were found in nearly all other tissues, highlighting the potential for local regulation of sex steroid-mediated traits. These analyses provide new insights into potential sources of phenotypic variation in a free-living female bird and advance our understanding of fundamental questions in evolutionary and organismal biology.
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Affiliation(s)
- Alexandra B Bentz
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA. .,Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN, 47405, USA.
| | - Gregg W C Thomas
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.,Department of Computer Science, Indiana University, Bloomington, IN, 47405, USA
| | - Douglas B Rusch
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.,Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - Kimberly A Rosvall
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.,Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN, 47405, USA
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247
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Barrett CF, Sinn BT, Kennedy AH. Unprecedented Parallel Photosynthetic Losses in a Heterotrophic Orchid Genus. Mol Biol Evol 2019; 36:1884-1901. [PMID: 31058965 PMCID: PMC6736286 DOI: 10.1093/molbev/msz111] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Heterotrophic plants are evolutionary experiments in genomic, morphological, and physiological change. Yet, genomic sampling gaps exist among independently derived heterotrophic lineages, leaving unanswered questions about the process of genome modification. Here, we have sequenced complete plastid genomes for all species of the leafless orchid genus Hexalectris, including multiple individuals for most, and leafy relatives Basiphyllaea and Bletia. Our objectives are to determine the number of independent losses of photosynthesis and to test hypotheses on the process of genome degradation as a result of relaxed selection. We demonstrate four to five independent losses of photosynthesis in Hexalectris based on degradation of the photosynthetic apparatus, with all but two species displaying evidence of losses, and variation in gene loss extending below the species level. Degradation in the atp complex is advanced in Hexalectris warnockii, whereas only minimal degradation (i.e., physical loss) has occurred among some "housekeeping" genes. We find genomic rearrangements, shifts in Inverted Repeat boundaries including complete loss in one accession of H. arizonica, and correlations among substitutional and genomic attributes. Our unprecedented finding of multiple, independent transitions to a fully mycoheterotrophic lifestyle in a single genus reveals that the number of such transitions among land plants is likely underestimated. This study underscores the importance of dense taxon sampling, which is highly informative for advancing models of genome evolution in heterotrophs. Mycoheterotrophs such as Hexalectris provide forward-genetic opportunities to study the consequences of radical genome evolution beyond what is possible with mutational studies in model organisms alone.
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Affiliation(s)
- Craig F Barrett
- Department of Biology, West Virginia University, Morgantown, WV
| | - Brandon T Sinn
- Department of Biology, West Virginia University, Morgantown, WV
| | - Aaron H Kennedy
- Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA-APHIS, Beltsville, MD
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248
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Vogan AA, Ament-Velásquez SL, Granger-Farbos A, Svedberg J, Bastiaans E, Debets AJ, Coustou V, Yvanne H, Clavé C, Saupe SJ, Johannesson H. Combinations of Spok genes create multiple meiotic drivers in Podospora. eLife 2019; 8:46454. [PMID: 31347500 PMCID: PMC6660238 DOI: 10.7554/elife.46454] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/09/2019] [Indexed: 11/13/2022] Open
Abstract
Meiotic drive is the preferential transmission of a particular allele during sexual reproduction. The phenomenon is observed as spore killing in multiple fungi. In natural populations of Podospora anserina, seven spore killer types (Psks) have been identified through classical genetic analyses. Here we show that the Spok gene family underlies the Psks. The combination of Spok genes at different chromosomal locations defines the spore killer types and creates a killing hierarchy within a population. We identify two novel Spok homologs located within a large (74–167 kbp) region (the Spok block) that resides in different chromosomal locations in different strains. We confirm that the SPOK protein performs both killing and resistance functions and show that these activities are dependent on distinct domains, a predicted nuclease and kinase domain. Genomic and phylogenetic analyses across ascomycetes suggest that the Spok genes disperse through cross-species transfer, and evolve by duplication and diversification within lineages. In many organisms, most cells carry two versions of a given gene, one coming from the mother and the other from the father. An exception is sexual cells such as eggs, sperm, pollen or spores, which should only contain one variant of a gene. During their formation, these cells usually have an equal chance of inheriting one of the two gene versions. However, a certain class of gene variants called meiotic drivers can cheat this process and end up in more than half of the sexual cells; often, the cells that contain the drivers can kill sibling cells that do not carry these variants. This results in the selfish genetic elements spreading through populations at a higher rate, sometimes with severe consequences such as shifting the ratio of males to females. Meiotic drivers have been discovered in a wide range of organisms, from corn to mice to fruit flies and bread mold. They also exist in the fungus Podospora anserina, where they are called ‘spore killers’. Fungi are often used to study complex genetic processes, yet the identity and mode of action of spore killers in P. anserina were still unknown. Vogan, Ament-Velásquez et al. used a combination of genetic methods to identify three genes from the Spok family which are responsible for certain spores being able to kill their siblings. Two of these were previously unknown, and they could be found in different locations throughout the genome as part of a larger genetic region. Depending on the combination of Spok genes it carries, a spore can kill or be protected against other spores that contain different permutations of the genes. Copies of these genes were also shown to be present in other fungi, including species that are a threat to crops. Scientists have already started to create synthetic meiotic drivers to manipulate how certain traits are inherited within a population. This could be useful to control or eradicate pests and insects that transmit dangerous diseases. The results by Vogan, Ament-Velásquez et al. shine a light on the complex ways that natural meiotic drivers work, including how they can be shared between species; this knowledge could inform how to safely deploy synthetic drivers in the wild.
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Affiliation(s)
- Aaron A Vogan
- Organismal biology, Uppsala University, Uppsala, Sweden
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Abduriyim S, Zou D, Zhao H. Origin and evolution of the major histocompatibility complex class I region in eutherian mammals. Ecol Evol 2019; 9:7861-7874. [PMID: 31346446 PMCID: PMC6636196 DOI: 10.1002/ece3.5373] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 05/27/2019] [Accepted: 05/27/2019] [Indexed: 01/09/2023] Open
Abstract
Major histocompatibility complex (MHC) genes in vertebrates are vital in defending against pathogenic infections. To gain new insights into the evolution of MHC Class I (MHCI) genes and test competing hypotheses on the origin of the MHCI region in eutherian mammals, we studied available genome assemblies of nine species in Afrotheria, Xenarthra, and Laurasiatheria, and successfully characterized the MHCI region in six species. The following numbers of putatively functional genes were detected: in the elephant, four, one, and eight in the extended class I region, and κ and β duplication blocks, respectively; in the tenrec, one in the κ duplication block; and in the four bat species, one or two in the β duplication block. Our results indicate that MHCI genes in the κ and β duplication blocks may have originated in the common ancestor of eutherian mammals. In the elephant, tenrec, and all four bats, some MHCI genes occurred outside the MHCI region, suggesting that eutherians may have a more complex MHCI genomic organization than previously thought. Bat-specific three- or five-amino-acid insertions were detected in the MHCI α1 domain in all four bats studied, suggesting that pathogen defense in bats relies on MHCIs having a wider peptide-binding groove, as previously assayed by a bat MHCI gene with a three-amino-acid insertion showing a larger peptide repertoire than in other mammals. Our study adds to knowledge on the diversity of eutherian MHCI genes, which may have been shaped in a taxon-specific manner.
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Affiliation(s)
- Shamshidin Abduriyim
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life ScienceWuhan UniversityWuhanChina
| | - Da‐Hu Zou
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life ScienceWuhan UniversityWuhanChina
| | - Huabin Zhao
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life ScienceWuhan UniversityWuhanChina
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Scornavacca C, Belkhir K, Lopez J, Dernat R, Delsuc F, Douzery EJP, Ranwez V. OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes. Mol Biol Evol 2019; 36:861-862. [PMID: 30698751 PMCID: PMC6445298 DOI: 10.1093/molbev/msz015] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We present version 10 of OrthoMaM, a database of orthologous mammalian markers. OrthoMaM is already 11 years old and since the outset it has kept on improving, providing alignments and phylogenetic trees of high-quality computed with state-of-the-art methods on up-to-date data. The main contribution of this version is the increase in the number of taxa: 116 mammalian genomes for 14,509 one-to-one orthologous genes. This has been made possible by the combination of genomic data deposited in Ensembl complemented by additional good-quality genomes only available in NCBI. Version 10 users will benefit from pipeline improvements and a completely redesigned web-interface.
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Affiliation(s)
- Celine Scornavacca
- Institut des Sciences de l'Evolution (ISEM), Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Khalid Belkhir
- Institut des Sciences de l'Evolution (ISEM), Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Jimmy Lopez
- Institut des Sciences de l'Evolution (ISEM), Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Rémy Dernat
- Institut des Sciences de l'Evolution (ISEM), Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Frédéric Delsuc
- Institut des Sciences de l'Evolution (ISEM), Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Emmanuel J P Douzery
- Institut des Sciences de l'Evolution (ISEM), Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Vincent Ranwez
- AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
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