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Wang H, Chen M, Wei X, Xia R, Pei D, Huang X, Han B. Computational tools for plant genomics and breeding. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2578-6. [PMID: 38676814 DOI: 10.1007/s11427-024-2578-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/25/2024] [Indexed: 04/29/2024]
Abstract
Plant genomics and crop breeding are at the intersection of biotechnology and information technology. Driven by a combination of high-throughput sequencing, molecular biology and data science, great advances have been made in omics technologies at every step along the central dogma, especially in genome assembling, genome annotation, epigenomic profiling, and transcriptome profiling. These advances further revolutionized three directions of development. One is genetic dissection of complex traits in crops, along with genomic prediction and selection. The second is comparative genomics and evolution, which open up new opportunities to depict the evolutionary constraints of biological sequences for deleterious variant discovery. The third direction is the development of deep learning approaches for the rational design of biological sequences, especially proteins, for synthetic biology. All three directions of development serve as the foundation for a new era of crop breeding where agronomic traits are enhanced by genome design.
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Affiliation(s)
- Hai Wang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
| | - Mengjiao Chen
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xin Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Rui Xia
- College of Horticulture, South China Agricultural University, Guangzhou, 510640, China
| | - Dong Pei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Bin Han
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200233, China
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Manzano-Morales S, Liu Y, González-Bodí S, Huerta-Cepas J, Iranzo J. Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses. Genome Biol 2023; 24:250. [PMID: 37904249 PMCID: PMC10614367 DOI: 10.1186/s13059-023-03089-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 10/16/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND A key step for comparative genomics is to group open reading frames into functionally and evolutionarily meaningful gene clusters. Gene clustering is complicated by intraspecific duplications and horizontal gene transfers that are frequent in prokaryotes. In consequence, gene clustering methods must deal with a trade-off between identifying vertically transmitted representatives of multicopy gene families, which are recognizable by synteny conservation, and retrieving complete sets of species-level orthologs. We studied the implications of adopting homology, orthology, or synteny conservation as formal criteria for gene clustering by performing comparative analyses of 125 prokaryotic pangenomes. RESULTS Clustering criteria affect pangenome functional characterization, core genome inference, and reconstruction of ancestral gene content to different extents. Species-wise estimates of pangenome and core genome sizes change by the same factor when using different clustering criteria, allowing robust cross-species comparisons regardless of the clustering criterion. However, cross-species comparisons of genome plasticity and functional profiles are substantially affected by inconsistencies among clustering criteria. Such inconsistencies are driven not only by mobile genetic elements, but also by genes involved in defense, secondary metabolism, and other accessory functions. In some pangenome features, the variability attributed to methodological inconsistencies can even exceed the effect sizes of ecological and phylogenetic variables. CONCLUSIONS Choosing an appropriate criterion for gene clustering is critical to conduct unbiased pangenome analyses. We provide practical guidelines to choose the right method depending on the research goals and the quality of genome assemblies, and a benchmarking dataset to assess the robustness and reproducibility of future comparative studies.
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Affiliation(s)
- Saioa Manzano-Morales
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
- Barcelona Supercomputing Centre (BSC-CNS) - Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Yang Liu
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Sara González-Bodí
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain.
| | - Jaime Iranzo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain.
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain.
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Li R, Ma XY, Zhang YJ, Zhang YJ, Zhu H, Shao SN, Zhang DD, Klosterman SJ, Dai XF, Subbarao KV, Chen JY. Genome-wide identification and analysis of a cotton secretome reveals its role in resistance against Verticillium dahliae. BMC Biol 2023; 21:166. [PMID: 37542270 PMCID: PMC10403859 DOI: 10.1186/s12915-023-01650-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/13/2023] [Indexed: 08/06/2023] Open
Abstract
BACKGROUND The extracellular space between the cell wall and plasma membrane is a battlefield in plant-pathogen interactions. Within this space, the pathogen employs its secretome to attack the host in a variety of ways, including immunity manipulation. However, the role of the plant secretome is rarely studied for its role in disease resistance. RESULTS Here, we examined the secretome of Verticillium wilt-resistant Gossypium hirsutum cultivar Zhongzhimian No.2 (ZZM2, encoding 95,327 predicted coding sequences) to determine its role in disease resistance against the wilt causal agent, Verticillium dahliae. Bioinformatics-driven analyses showed that the ZZM2 genome encodes 2085 secreted proteins and that these display disequilibrium in their distribution among the chromosomes. The cotton secretome displayed differences in the abundance of certain amino acid residues as compared to the remaining encoded proteins due to the localization of these putative proteins in the extracellular space. The secretome analysis revealed conservation for an allotetraploid genome, which nevertheless exhibited variation among orthologs and comparable unique genes between the two sub-genomes. Secretome annotation strongly suggested its involvement in extracellular stress responses (hydrolase activity, oxidoreductase activity, and extracellular region, etc.), thus contributing to resistance against the V. dahliae infection. Furthermore, the defense response genes (immunity marker NbHIN1, salicylic acid marker NbPR1, and jasmonic acid marker NbLOX4) were activated to varying degrees when Nicotina benthamiana leaves were agro-infiltrated with 28 randomly selected members, suggesting that the secretome plays an important role in the immunity response. Finally, gene silencing assays of 11 members from 13 selected candidates in ZZM2 displayed higher susceptibility to V. dahliae, suggesting that the secretome members confer the Verticillium wilt resistance in cotton. CONCLUSIONS Our data demonstrate that the cotton secretome plays an important role in Verticillium wilt resistance, facilitating the development of the resistance gene markers and increasing the understanding of the mechanisms regulating disease resistance.
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Affiliation(s)
- Ran Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
| | - Xi-Yue Ma
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ye-Jing Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yong-Jun Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - He Zhu
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
- The Cotton Research Center of Liaoning Academy of Agricultural Sciences, National Cotton Industry Technology System Liaohe Comprehensive Experimental Station, Liaoning Provincial Institute of Economic Crops, Liaoyang, 111000, China
| | - Sheng-Nan Shao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Dan-Dan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
| | - Steven J Klosterman
- United States Department of Agriculture, Agricultural Research Service, Salinas, CA, USA
| | - Xiao-Feng Dai
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China.
| | - Krishna V Subbarao
- Department of Plant Pathology, University of California, Davis c/o United States Agricultural Research Station, Salinas, CA, USA.
| | - Jie-Yin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China.
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Andolfo G, Di Donato A, Ercolano MR. NB-LRR Lineage-Specific Equipment Is Sorted Out by Sequence Pattern Adaptation and Domain Segment Shuffling. Int J Mol Sci 2022; 23:ijms232214269. [PMID: 36430746 PMCID: PMC9696612 DOI: 10.3390/ijms232214269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
The nucleotide-binding and leucine-rich repeat (NB-LRR) genes, also known as resistance (R)-genes, play an important role in the activation of immune responses. In recent years, large-scale studies have been performed to highlight the diversification of plant NB-LRR repertories. It is well known that, to provide new functionalities, NB-LRR sequences are subject to duplication, domain fusions and acquisition and other kinds of mutations. Although some mechanisms that govern NB-LRR protein domain adaptations have been uncovered, to retrace the plant-lineage-specific evolution routes of R protein structure, a multi-genome comparative analysis was performed. This study allowed us to define groups of genes sharing homology relationships across different species. It is worth noting that the most populated groups contained well-characterized R proteins. The arsenal profile of such groups was investigated in five botanical families, including important crop species, to underline specific adaptation signatures. In addition, the dissection of 70 NB domains of well-characterized R-genes revealed the NB core motifs from which the three main R protein classes have been diversified. The structural remodeling of domain segments shaped the specific NB-LRR repertoires observed in each plant species. This analysis provided new evolutionary and functional insights on NB protein domain shuffling. Taken together, such findings improved our understanding of the molecular adaptive selection mechanisms occurring at plant R loci.
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Genomic and transcriptomic analyses of the subterranean termite Reticulitermes speratus: Gene duplication facilitates social evolution. Proc Natl Acad Sci U S A 2022; 119:2110361119. [PMID: 35042774 PMCID: PMC8785959 DOI: 10.1073/pnas.2110361119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2021] [Indexed: 12/26/2022] Open
Abstract
Gene duplication is a major source of evolutionary innovation and is associated with the increases in biological complexity and adaptive radiation. Termites are model social organisms characterized by a sophisticated caste system. We analyzed the genome of the Japanese subterranean termite, an ecologically and economically important insect acting as a destructive pest. The analyses revealed the significance of gene duplication in social evolution. Gene duplication associated with caste-biased gene expression was prevalent in the termite genome. Many of the duplicated genes were related to social functions, such as chemical communication, social immunity, and defense, and they were often expressed in caste-specific organs. We propose that gene duplication facilitates social evolution through regulatory diversification leading to caste-biased expression and functional specialization. Termites are model social organisms characterized by a polyphenic caste system. Subterranean termites (Rhinotermitidae) are ecologically and economically important species, including acting as destructive pests. Rhinotermitidae occupies an important evolutionary position within the clade representing a transitional taxon between the higher (Termitidae) and lower (other families) termites. Here, we report the genome, transcriptome, and methylome of the Japanese subterranean termite Reticulitermes speratus. Our analyses highlight the significance of gene duplication in social evolution in this termite. Gene duplication associated with caste-biased gene expression was prevalent in the R. speratus genome. The duplicated genes comprised diverse categories related to social functions, including lipocalins (chemical communication), cellulases (wood digestion and social interaction), lysozymes (social immunity), geranylgeranyl diphosphate synthase (social defense), and a novel class of termite lineage–specific genes with unknown functions. Paralogous genes were often observed in tandem in the genome, but their expression patterns were highly variable, exhibiting caste biases. Some of the assayed duplicated genes were expressed in caste-specific organs, such as the accessory glands of the queen ovary and the frontal glands of soldier heads. We propose that gene duplication facilitates social evolution through regulatory diversification, leading to caste-biased expression and subfunctionalization and/or neofunctionalization conferring caste-specialized functions.
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Functional Genomics and Comparative Lineage-Specific Region Analyses Reveal Novel Insights into Race Divergence in Verticillium dahliae. Microbiol Spectr 2021; 9:e0111821. [PMID: 34937170 PMCID: PMC8694104 DOI: 10.1128/spectrum.01118-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Verticillium dahliae is a widespread soilborne fungus that causes Verticillium wilt on numerous economically important plant species. In tomato, until now, three races have been characterized based on the response of differential cultivars to V. dahliae, but the genetic basis of race divergence in V. dahliae remains undetermined. To investigate the genetic basis of race divergence, we sequenced the genomes of two race 2 strains and four race 3 strains for comparative analyses with two known race 1 genomes. The genetic basis of race divergence was described by the pathogenicity-related genes among the three races, orthologue analyses, and genomic structural variations. Global comparative genomics showed that chromosomal rearrangements are not the only source of race divergence and that race 3 should be split into two genotypes based on orthologue clustering. Lineage-specific regions (LSRs), frequently observed between genomes of the three races, encode several predicted secreted proteins that potentially function as suppressors of immunity triggered by known effectors. These likely contribute to the virulence of the three races. Two genes in particular that can act as markers for race 2 and race 3 (VdR2e and VdR3e, respectively) contribute to virulence on tomato, and the latter acts as an avirulence factor of race 3. We elucidated the genetic basis of race divergence through global comparative genomics and identified secreted proteins in LSRs that could potentially play critical roles in the differential virulence among the races in V. dahliae. IMPORTANCE Deciphering the gene-for-gene relationships during host-pathogen interactions is the basis of modern plant resistance breeding. In the Verticillium dahliae-tomato pathosystem, two races (races 1 and 2) and their corresponding avirulence (Avr) genes have been identified, but strains that lack these two Avr genes exist in nature. In this system, race 3 has been described, but the corresponding Avr gene has not been identified. We de novo-sequenced genomes of six strains and identified secreted proteins within the lineage-specific regions (LSRs) distributed among the genomes of the three races that could potentially function as manipulators of host immunity. One of the LSR genes, VdR3e, was confirmed as the Avr gene for race 3. The results indicate that differences in transcriptional regulation may contribute to race differentiation. This is the first study to describe these differences and elucidate roles of secreted proteins in LSRs that play roles in race differentiation.
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El Jeni R, Ghedira K, El Bour M, Abdelhak S, Benkahla A, Bouhaouala-Zahar B. High-quality genome sequence assembly of R.A73 Enterococcus faecium isolated from freshwater fish mucus. BMC Microbiol 2020; 20:322. [PMID: 33096980 PMCID: PMC7584074 DOI: 10.1186/s12866-020-01980-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/18/2020] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Whole-genome sequencing using high throughput technologies has revolutionized and speeded up the scientific investigation of bacterial genetics, biochemistry, and molecular biology. Lactic acid bacteria (LABs) have been extensively used in fermentation and more recently as probiotics in food products that promote health. Genome sequencing and functional genomics investigations of LABs varieties provide rapid and important information about their diversity and their evolution, revealing a significant molecular basis. This study investigated the whole genome sequences of the Enterococcus faecium strain (HG937697), isolated from the mucus of freshwater fish in Tunisian dams. Genomic DNA was extracted using the Quick-GDNA kit and sequenced using the Illumina HiSeq2500 system. Sequences quality assessment was performed using FastQC software. The complete genome annotation was carried out with the Rapid Annotation using Subsystem Technology (RAST) web server then NCBI PGAAP. RESULTS The Enterococcus faecium R.A73 assembled in 28 contigs consisting of 2,935,283 bps. The genome annotation revealed 2884 genes in total including 2834 coding sequences and 50 RNAs containing 3 rRNAs (one rRNA 16 s, one rRNA 23 s and one rRNA 5 s) and 47 tRNAs. Twenty-two genes implicated in bacteriocin production are identified within the Enterococcus faecium R.A73 strain. CONCLUSION Data obtained provide insights to further investigate the effective strategy for testing this Enterococcus faecium R.A73 strain in the industrial manufacturing process. Studying their metabolism with bioinformatics tools represents the future challenge and contribution to improving the utilization of the multi-purpose bacteria in food.
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Affiliation(s)
- Rim El Jeni
- Laboratory of Microbiology and Pathology of Aquatic Organisms, Institut National des Sciences et Technologies de la Mer (INSTM), Tunis, Tunisia
- Laboratory of Venoms and Therapeutic Molecules, Pasteur Institute of Tunis, Tunis, Tunisia
| | - Kais Ghedira
- Bioinformatics and Biostatistics Laboratory (LR16IPT09), Pasteur Institute of Tunis, Tunis, Tunisia
| | - Monia El Bour
- Laboratory of Microbiology and Pathology of Aquatic Organisms, Institut National des Sciences et Technologies de la Mer (INSTM), Tunis, Tunisia
| | - Sonia Abdelhak
- Biomedical Genomics and Oncogenetics Laboratory LR16IPT05, Pasteur Institute of Tunis, Tunis, Tunisia
| | - Alia Benkahla
- Bioinformatics and Biostatistics Laboratory (LR16IPT09), Pasteur Institute of Tunis, Tunis, Tunisia
| | - Balkiss Bouhaouala-Zahar
- Laboratory of Venoms and Therapeutic Molecules, Pasteur Institute of Tunis, Tunis, Tunisia
- Medical School of Tunis, University of Tunis El Manar, 1007 Tunis, Tunisia
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Ferretti L, Krämer-Eis A, Schiffer PH. Conserved Patterns in Developmental Processes and Phases, Rather than Genes, Unite the Highly Divergent Bilateria. Life (Basel) 2020; 10:E182. [PMID: 32899936 PMCID: PMC7555945 DOI: 10.3390/life10090182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 01/03/2023] Open
Abstract
Bilateria are the predominant clade of animals on Earth. Despite having evolved a wide variety of body plans and developmental modes, they are characterized by common morphological traits. By default, researchers have tried to link clade-specific genes to these traits, thus distinguishing bilaterians from non-bilaterians, by their gene content. Here we argue that it is rather biological processes that unite Bilateria and set them apart from their non-bilaterian sisters, with a less complex body morphology. To test this hypothesis, we compared proteomes of bilaterian and non-bilaterian species in an elaborate computational pipeline, aiming to search for a set of bilaterian-specific genes. Despite the limited confidence in their bilaterian specificity, we nevertheless detected Bilateria-specific functional and developmental patterns in the sub-set of genes conserved in distantly related Bilateria. Using a novel multi-species GO-enrichment method, we determined the functional repertoire of genes that are widely conserved among Bilateria. Analyzing expression profiles in three very distantly related model species-D. melanogaster, D. rerio and C. elegans-we find characteristic peaks at comparable stages of development and a delayed onset of expression in embryos. In particular, the expression of the conserved genes appears to peak at the phylotypic stage of different bilaterian phyla. In summary, our study illustrate how development connects distantly related Bilateria after millions of years of divergence, pointing to processes potentially separating them from non-bilaterians. We argue that evolutionary biologists should return from a purely gene-centric view of evolution and place more focus on analyzing and defining conserved developmental processes and periods.
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Affiliation(s)
- Luca Ferretti
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Andrea Krämer-Eis
- Institut für Genetik, Universität zu Köln, Zülpicher Straße 47a, 50674 Köln, Germany;
| | - Philipp H. Schiffer
- Institut für Zoologie, Universität zu Köln, Zülpicher Straße 47b, 50674 Köln, Germany
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Galperin MY, Kristensen DM, Makarova KS, Wolf YI, Koonin EV. Microbial genome analysis: the COG approach. Brief Bioinform 2020; 20:1063-1070. [PMID: 28968633 DOI: 10.1093/bib/bbx117] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/01/2017] [Indexed: 11/15/2022] Open
Abstract
For the past 20 years, the Clusters of Orthologous Genes (COG) database had been a popular tool for microbial genome annotation and comparative genomics. Initially created for the purpose of evolutionary classification of protein families, the COG have been used, apart from straightforward functional annotation of sequenced genomes, for such tasks as (i) unification of genome annotation in groups of related organisms; (ii) identification of missing and/or undetected genes in complete microbial genomes; (iii) analysis of genomic neighborhoods, in many cases allowing prediction of novel functional systems; (iv) analysis of metabolic pathways and prediction of alternative forms of enzymes; (v) comparison of organisms by COG functional categories; and (vi) prioritization of targets for structural and functional characterization. Here we review the principles of the COG approach and discuss its key advantages and drawbacks in microbial genome analysis.
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Feng JM, Yang CL, Tian HF, Wang JX, Wen JF. Identification and evolutionary analysis of the nucleolar proteome of Giardia lamblia. BMC Genomics 2020; 21:269. [PMID: 32228450 PMCID: PMC7104513 DOI: 10.1186/s12864-020-6679-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/16/2020] [Indexed: 01/05/2023] Open
Abstract
Background The nucleoli, including their proteomes, of higher eukaryotes have been extensively studied, while few studies about the nucleoli of the lower eukaryotes – protists were reported. Giardia lamblia, a protist with the controversy of whether it is an extreme primitive eukaryote or just a highly evolved parasite, might be an interesting object for carrying out the nucleolar proteome study of protists and for further examining the controversy. Results Using bioinformatics methods, we reconstructed G. lamblia nucleolar proteome (GiNuP) and the common nucleolar proteome of the three representative higher eukaryotes (human, Arabidopsis, yeast) (HEBNuP). Comparisons of the two proteomes revealed that: 1) GiNuP is much smaller than HEBNuP, but 78.4% of its proteins have orthologs in the latter; 2) More than 68% of the GiNuP proteins are involved in the “Ribosome related” function, and the others participate in the other functions, and these two groups of proteins are much larger and much smaller than those in HEBNuP, respectively; 3) Both GiNuP and HEBNuP have their own specific proteins, but HEBNuP has a much higher proportion of such proteins to participate in more categories of nucleolar functions. Conclusion For the first time the nucleolar proteome of a protist - Giardia was reconstructed. The results of comparison of it with the common proteome of three representative higher eukaryotes -- HEBNuP indicated that the simplicity of GiNuP is most probably a reflection of primitiveness but not just parasitic reduction of Giardia, and simultaneously revealed some interesting evolutionary phenomena about the nucleolus and even the eukaryotic cell, compositionally and functionally.
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Affiliation(s)
- Jin-Mei Feng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan Province, China.,Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan, 430056, Hubei Province, China
| | - Chun-Lin Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan Province, China
| | - Hai-Feng Tian
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan Province, China
| | - Jiang-Xin Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan Province, China.,College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518006, Guangdong Province, China
| | - Jian-Fan Wen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan Province, China.
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Phylogeny and highland adaptation of Chinese species in Allium section Daghestanica (Amaryllidaceae) revealed by transcriptome sequencing. Mol Phylogenet Evol 2020; 146:106737. [PMID: 31982455 DOI: 10.1016/j.ympev.2020.106737] [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: 08/26/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 01/27/2023]
Abstract
Allium L. is one of the largest monocotyledonous genera with extensive distribution in the Northern Hemisphere. The fundamental phylogenies of Allium have been investigated using many morphological and molecular characters. However, the morphological characters may not agree with the molecular results in some Allium groups or sections (such as the Chinese Allium section Daghestanica), which may result in ambiguous species relationships and hinder further evolutionary and adaptive researches. Here, transcriptome sequences of the six Chinese endemics from Allium section Daghestanica were collected, with their single-copy genes (SCGs) were extracted. The interspecies relationships were analyzed using concatenation and coalescent methods. The branch-site model (BSM) was conducted to detect the positively selected genes (PSGs) in five highland species of this section. Based on 1644, 1281 and 1580 SCGs in flowers, leaves, and flowers-leaves combination respectively, a robust consistent and well-resolved phylogeny was generated from the concatenation method. Strong conflicts among individual gene trees were detected in the coalescent method, and morphological characters were incongruent with molecular relationships to some degree. Many PSGs were involved in responses of various stresses and stimuli (e.g. hypoxia, low temperature, aridity), DNA repair, metabolism, nutrient or energy intake, photosynthesis, and signal transduction. Our study revealed a clear interspecies relationship of Chinese endemics in Allium section Daghestanica and suggested that the discordance between morphological characters and molecular relationships might result from that the former are more susceptible to convergence compared with the latter. PSGs detected in our study may provide some insights into highland adaptation in Allium species.
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Cosentino S, Iwasaki W. SonicParanoid: fast, accurate and easy orthology inference. Bioinformatics 2019; 35:149-151. [PMID: 30032301 PMCID: PMC6298048 DOI: 10.1093/bioinformatics/bty631] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/18/2018] [Indexed: 11/18/2022] Open
Abstract
Motivation Orthology inference constitutes a common base of many genome-based studies, as a pre-requisite for annotating new genomes, finding target genes for biotechnological applications and revealing the evolutionary history of life. Although its importance keeps rising with the ever-growing number of sequenced genomes, existing tools are computationally demanding and difficult to employ. Results Here, we present SonicParanoid, which is faster than, but comparably accurate to, the well-established tools with a balanced precision-recall trade-off. Furthermore, SonicParanoid substantially relieves the difficulties of orthology inference for those who need to construct and maintain their own genomic datasets. Availability and implementation SonicParanoid is available with a GNU GPLv3 license on the Python Package Index and BitBucket. Documentation is available at http://iwasakilab.bs.s.u-tokyo.ac.jp/sonicparanoid. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Salvatore Cosentino
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.,Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
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13
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Hu X, Friedberg I. SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier. Gigascience 2019; 8:giz118. [PMID: 31648300 PMCID: PMC6812468 DOI: 10.1093/gigascience/giz118] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/07/2019] [Accepted: 09/05/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Gene homology type classification is required for many types of genome analyses, including comparative genomics, phylogenetics, and protein function annotation. Consequently, a large variety of tools have been developed to perform homology classification across genomes of different species. However, when applied to large genomic data sets, these tools require high memory and CPU usage, typically available only in computational clusters. FINDINGS Here we present a new graph-based orthology analysis tool, SwiftOrtho, which is optimized for speed and memory usage when applied to large-scale data. SwiftOrtho uses long k-mers to speed up homology search, while using a reduced amino acid alphabet and spaced seeds to compensate for the loss of sensitivity due to long k-mers. In addition, it uses an affinity propagation algorithm to reduce the memory usage when clustering large-scale orthology relationships into orthologous groups. In our tests, SwiftOrtho was the only tool that completed orthology analysis of proteins from 1,760 bacterial genomes on a computer with only 4 GB RAM. Using various standard orthology data sets, we also show that SwiftOrtho has a high accuracy. CONCLUSIONS SwiftOrtho enables the accurate comparative genomic analyses of thousands of genomes using low-memory computers. SwiftOrtho is available at https://github.com/Rinoahu/SwiftOrtho.
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Affiliation(s)
- Xiao Hu
- Department of Veterinary Microbiology and Preventive Medicine, 2118 Veterinary Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Iddo Friedberg
- Department of Veterinary Microbiology and Preventive Medicine, 2118 Veterinary Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
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14
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D'Esposito D, Cappetta E, Andolfo G, Ferriello F, Borgonuovo C, Caruso G, De Natale A, Frusciante L, Ercolano MR. Deciphering the biological processes underlying tomato biomass production and composition. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 143:50-60. [PMID: 31479882 DOI: 10.1016/j.plaphy.2019.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/19/2019] [Accepted: 08/13/2019] [Indexed: 05/20/2023]
Abstract
The huge amounts of biomass residues, remaining in the field after tomato fruits harvesting, can be utilized to produce bioenergy. A multiple level approach aimed to characterize two Solanum pennellii introgression lines (ILs), with contrasting phenotypes for plant architecture and biomass was carried out. The study of gene expression dynamics, microscopy cell traits and qualitative and quantitative cell wall chemical compounds variation enabled the discovery of key genes and cell processes involved biomass accumulation and composition. Enhanced biomass production observed in IL2-6 line is due to a more effective coordination of chloroplasts and mitochondria energy fluxes. Microscopy analysis revealed a higher number of cells and chloroplasts in leaf epidermis in the high biomass line whilst chemical measurements on the two lines pointed out striking differences in the cell wall composition and organization. Taken together, our findings shed light on the mechanisms underlying the tomato biomass production and processability.
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Affiliation(s)
- Daniela D'Esposito
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Elisa Cappetta
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Giuseppe Andolfo
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Francesca Ferriello
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Camilla Borgonuovo
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Gianluca Caruso
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Antonino De Natale
- Department of Biology, University of Naples 'Federico II', Via Cinthia, Monte Sant'Angelo, Building 7, 80126, Naples, Italy.
| | - Luigi Frusciante
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Maria Raffaella Ercolano
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
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15
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Sriswasdi S, Takashima M, Manabe RI, Ohkuma M, Iwasaki W. Genome and transcriptome evolve separately in recently hybridized Trichosporon fungi. Commun Biol 2019; 2:263. [PMID: 31341962 PMCID: PMC6642101 DOI: 10.1038/s42003-019-0515-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 06/25/2019] [Indexed: 11/28/2022] Open
Abstract
Genome hybridization is an important evolutionary event that gives rise to species with novel capabilities. However, the merging of distinct genomes also brings together incompatible regulatory networks that must be resolved during the course of evolution. Understanding of the early stages of post-hybridization evolution is particularly important because changes in these stages have long-term evolutionary consequences. Here, via comparative transcriptomic analyses of two closely related, recently hybridized Trichosporon fungi, T. coremiiforme and T. ovoides, and three extant relatives, we show that early post-hybridization evolutionary processes occur separately at the gene sequence and gene expression levels but together contribute to the stabilization of hybrid genome and transcriptome. Our findings also highlight lineage-specific consequences of genome hybridization, revealing that the transcriptional regulatory dynamics in these hybrids responded completely differently to gene loss events: one involving both subgenomes and another that is strictly subgenome-specific.
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Affiliation(s)
- Sira Sriswasdi
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 Japan
- Research Affairs, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathum Wan, Bangkok 10330 Thailand
- Computational Molecular Biology Group, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathum Wan, Bangkok 10330 Thailand
| | - Masako Takashima
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1, Koyadai, Tsukuba-shi, Ibaraki 305-0074 Japan
- Department of Microbiology, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588 Japan
| | - Ri-ichiroh Manabe
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1, Koyadai, Tsukuba-shi, Ibaraki 305-0074 Japan
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8568 Japan
- Atmosphere and Ocean Research Institute, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8564 Japan
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16
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Lin G, Huang Z, Wang L, Chen Z, Zhang T, Gillman LN, Zhao F. Evolutionary Rates of Bumblebee Genomes Are Faster at Lower Elevations. Mol Biol Evol 2019; 36:1215-1219. [PMID: 30865278 PMCID: PMC6526908 DOI: 10.1093/molbev/msz057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The importance of climate in determining biodiversity patterns has been well documented. However, the relationship between climate and rates of genetic evolution remains controversial. Latitude and elevation have been associated with rates of change in genetic markers such as cytochrome b. What is not known, however, is the strength of such associations and whether patterns found among these genes apply across entire genomes. Here, using bumblebee genetic data from seven subgenera of Bombus, we demonstrate that all species occupying warmer elevations have undergone faster genome-wide evolution than those in the same subgenera occupying cooler elevations. Our findings point to a critical biogeographic role in the relative rates of whole species evolution, potentially influencing global biodiversity patterns.
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Affiliation(s)
- Gonghua Lin
- School of Life Sciences, Jinggangshan University, Ji'an, China.,Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Zuhao Huang
- School of Life Sciences, Jinggangshan University, Ji'an, China
| | - Lei Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Zhenhua Chen
- Qinghai-CAS Institute of Apicultural Research, Xining, Qinghai, China
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Lennard N Gillman
- Institute for Applied Ecology New Zealand, School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Fang Zhao
- School of Life Sciences, Jinggangshan University, Ji'an, China
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17
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McCarthy CGP, Fitzpatrick DA. Pangloss: A Tool for Pan-Genome Analysis of Microbial Eukaryotes. Genes (Basel) 2019; 10:E521. [PMID: 31295964 PMCID: PMC6678930 DOI: 10.3390/genes10070521] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/05/2019] [Accepted: 07/05/2019] [Indexed: 12/27/2022] Open
Abstract
Although the pan-genome concept originated in prokaryote genomics, an increasing number of eukaryote species pan-genomes have also been analysed. However, there is a relative lack of software intended for eukaryote pan-genome analysis compared to that available for prokaryotes. In a previous study, we analysed the pan-genomes of four model fungi with a computational pipeline that constructed pan-genomes using the synteny-dependent Pan-genome Ortholog Clustering Tool (PanOCT) approach. Here, we present a modified and improved version of that pipeline which we have called Pangloss. Pangloss can perform gene prediction for a set of genomes from a given species that the user provides, constructs and optionally refines a species pan-genome from that set using PanOCT, and can perform various functional characterisation and visualisation analyses of species pan-genome data. To demonstrate Pangloss's capabilities, we constructed and analysed a species pan-genome for the oleaginous yeast Yarrowialipolytica and also reconstructed a previously-published species pan-genome for the opportunistic respiratory pathogen Aspergillus fumigatus. Pangloss is implemented in Python, Perl and R and is freely available under an open source GPLv3 licence via GitHub.
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Affiliation(s)
- Charley G P McCarthy
- Genome Evolution Laboratory, Department of Biology, Maynooth University, W23 F2K8 Maynooth, Co. Kildare, Ireland.
- Human Health Research Institute, Maynooth University, W23 F2K8 Maynooth, Co. Kildare, Ireland.
| | - David A Fitzpatrick
- Genome Evolution Laboratory, Department of Biology, Maynooth University, W23 F2K8 Maynooth, Co. Kildare, Ireland
- Human Health Research Institute, Maynooth University, W23 F2K8 Maynooth, Co. Kildare, Ireland
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18
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A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons. Nat Ecol Evol 2019; 3:691-701. [DOI: 10.1038/s41559-019-0813-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 01/16/2019] [Indexed: 02/02/2023]
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19
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Bilyk KT, Vargas-Chacoff L, Cheng CHC. Evolution in chronic cold: varied loss of cellular response to heat in Antarctic notothenioid fish. BMC Evol Biol 2018; 18:143. [PMID: 30231868 PMCID: PMC6146603 DOI: 10.1186/s12862-018-1254-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/24/2018] [Indexed: 12/02/2022] Open
Abstract
Background Confined within the freezing Southern Ocean, the Antarctic notothenioids have evolved to become both cold adapted and cold specialized. A marked signature of cold specialization is an apparent loss of the cellular heat shock response (HSR). As the HSR has been examined in very few notothenioid species to-date, it remains unknown whether HSR loss pervades the Antarctic radiation, or whether the broader cellular responses to heat stress has sustained similar loss. Understanding the evolutionary status of these responses in this stenothermal taxon is crucial for evaluating its adaptive potential to ocean warming under climate change. Results In this study, we used an acute heat stress protocol followed by RNA-Seq analyses to study the evolution of cellular-wide transcriptional responses to heat stress across three select notothenioid lineages - the basal temperate and nearest non-Antarctic sister species Eleginops maclovinus serving as ancestral proxy, the cryopelagic Pagothenia borchgrevinki and the icefish Chionodraco rastrospinosus representing cold-adapted red-blooded and hemoglobinless Antarctic notothenioids respectively. E. maclovinus displayed robust cellular stress responses including the ER Unfolded Protein Response and the cytosolic HSR, cementing the HSR as a plesiomorphy that preceded Antarctic notothenioid radiation. While the transcriptional response to heat stress was minimal in P. borchgrevinki, C. rastrospinosus exhibited robust responses in the broader cellular networks especially in inflammatory responses despite lacking the classic HSR and UPR. Conclusion The disparate patterns observed in these two archetypal Antarctic species indicate the evolutionary status in cellular ability to mitigate acute heat stress varies even among Antarctic lineages, which may affect their adaptive potential in coping with a warming world. Electronic supplementary material The online version of this article (10.1186/s12862-018-1254-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kevin T Bilyk
- Department of Biology, Western Kentucky University, 1906 College Heights Blvd, Bowling Green, KY, 42101, USA. .,School of Integrative Biology, University of Illinois, Urbana-Champaign, USA.
| | - Luis Vargas-Chacoff
- Instituto de Ciencias Marinas y Limnológicas, Laboratorio de Fisiología de Peces, Centro Fondap de Investigación de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile
| | - C-H Christina Cheng
- School of Integrative Biology, University of Illinois, Urbana-Champaign, USA
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20
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Zribi Zghal R, Ghedira K, Elleuch J, Kharrat M, Tounsi S. Genome sequence analysis of a novel Bacillus thuringiensis strain BLB406 active against Aedes aegypti larvae, a novel potential bioinsecticide. Int J Biol Macromol 2018; 116:1153-1162. [DOI: 10.1016/j.ijbiomac.2018.05.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 04/13/2018] [Accepted: 05/16/2018] [Indexed: 10/16/2022]
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21
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Chen X, Zhang Y, Zhang Z, Zhao Y, Sun C, Yang M, Wang J, Liu Q, Zhang B, Chen M, Yu J, Wu J, Jin Z, Xiao J. PGAweb: A Web Server for Bacterial Pan-Genome Analysis. Front Microbiol 2018; 9:1910. [PMID: 30186253 PMCID: PMC6110895 DOI: 10.3389/fmicb.2018.01910] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 07/30/2018] [Indexed: 01/22/2023] Open
Abstract
An astronomical increase in microbial genome data in recent years has led to strong demand for bioinformatic tools for pan-genome analysis within and across species. Here, we present PGAweb, a user-friendly, web-based tool for bacterial pan-genome analysis, which is composed of two main pan-genome analysis modules, PGAP and PGAP-X. PGAweb provides key interactive and customizable functions that include orthologous clustering, pan-genome profiling, sequence variation and evolution analysis, and functional classification. PGAweb presents features of genomic structural dynamics and sequence diversity with different visualization methods that are helpful for intuitively understanding the dynamics and evolution of bacterial genomes. PGAweb has an intuitive interface with one-click setting of parameters and is freely available at http://PGAweb.vlcc.cn/.
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Affiliation(s)
- Xinyu Chen
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Yadong Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhewen Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yongbing Zhao
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Chen Sun
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, United States
| | - Ming Yang
- Office of General Affairs, Chinese Academy of Sciences, Beijing, China
| | - Jinyue Wang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qian Liu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.,Center of Scientific Computing Applications and Research, Chinese Academy of Sciences, Beijing, China
| | - Baohua Zhang
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.,Center of Scientific Computing Applications and Research, Chinese Academy of Sciences, Beijing, China
| | - Meili Chen
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jiayan Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Zhong Jin
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.,Center of Scientific Computing Applications and Research, Chinese Academy of Sciences, Beijing, China
| | - Jingfa Xiao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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22
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Lan Y, Sun J, Xu T, Chen C, Tian R, Qiu JW, Qian PY. De novo transcriptome assembly and positive selection analysis of an individual deep-sea fish. BMC Genomics 2018; 19:394. [PMID: 29793428 PMCID: PMC5968573 DOI: 10.1186/s12864-018-4720-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 04/23/2018] [Indexed: 11/20/2022] Open
Abstract
Background High hydrostatic pressure and low temperatures make the deep sea a harsh environment for life forms. Actin organization and microtubules assembly, which are essential for intracellular transport and cell motility, can be disrupted by high hydrostatic pressure. High hydrostatic pressure can also damage DNA. Nucleic acids exposed to low temperatures can form secondary structures that hinder genetic information processing. To study how deep-sea creatures adapt to such a hostile environment, one of the most straightforward ways is to sequence and compare their genes with those of their shallow-water relatives. Results We captured an individual of the fish species Aldrovandia affinis, which is a typical deep-sea inhabitant, from the Okinawa Trough at a depth of 1550 m using a remotely operated vehicle (ROV). We sequenced its transcriptome and analyzed its molecular adaptation. We obtained 27,633 protein coding sequences using an Illumina platform and compared them with those of several shallow-water fish species. Analysis of 4918 single-copy orthologs identified 138 positively selected genes in A. affinis, including genes involved in microtubule regulation. Particularly, functional domains related to cold shock as well as DNA repair are exposed to positive selection pressure in both deep-sea fish and hadal amphipod. Conclusions Overall, we have identified a set of positively selected genes related to cytoskeleton structures, DNA repair and genetic information processing, which shed light on molecular adaptation to the deep sea. These results suggest that amino acid substitutions of these positively selected genes may contribute crucially to the adaptation of deep-sea animals. Additionally, we provide a high-quality transcriptome of a deep-sea fish for future deep-sea studies. Electronic supplementary material The online version of this article (10.1186/s12864-018-4720-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yi Lan
- Department of Ocean Science and Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Jin Sun
- Department of Ocean Science and Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Ting Xu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Chong Chen
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Renmao Tian
- Department of Ocean Science and Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Pei-Yuan Qian
- Department of Ocean Science and Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
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23
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Galpert D, Fernández A, Herrera F, Antunes A, Molina-Ruiz R, Agüero-Chapin G. Surveying alignment-free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers. BMC Bioinformatics 2018; 19:166. [PMID: 29724166 PMCID: PMC5934817 DOI: 10.1186/s12859-018-2148-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/04/2018] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The development of new ortholog detection algorithms and the improvement of existing ones are of major importance in functional genomics. We have previously introduced a successful supervised pairwise ortholog classification approach implemented in a big data platform that considered several pairwise protein features and the low ortholog pair ratios found between two annotated proteomes (Galpert, D et al., BioMed Research International, 2015). The supervised models were built and tested using a Saccharomycete yeast benchmark dataset proposed by Salichos and Rokas (2011). Despite several pairwise protein features being combined in a supervised big data approach; they all, to some extent were alignment-based features and the proposed algorithms were evaluated on a unique test set. Here, we aim to evaluate the impact of alignment-free features on the performance of supervised models implemented in the Spark big data platform for pairwise ortholog detection in several related yeast proteomes. RESULTS The Spark Random Forest and Decision Trees with oversampling and undersampling techniques, and built with only alignment-based similarity measures or combined with several alignment-free pairwise protein features showed the highest classification performance for ortholog detection in three yeast proteome pairs. Although such supervised approaches outperformed traditional methods, there were no significant differences between the exclusive use of alignment-based similarity measures and their combination with alignment-free features, even within the twilight zone of the studied proteomes. Just when alignment-based and alignment-free features were combined in Spark Decision Trees with imbalance management, a higher success rate (98.71%) within the twilight zone could be achieved for a yeast proteome pair that underwent a whole genome duplication. The feature selection study showed that alignment-based features were top-ranked for the best classifiers while the runners-up were alignment-free features related to amino acid composition. CONCLUSIONS The incorporation of alignment-free features in supervised big data models did not significantly improve ortholog detection in yeast proteomes regarding the classification qualities achieved with just alignment-based similarity measures. However, the similarity of their classification performance to that of traditional ortholog detection methods encourages the evaluation of other alignment-free protein pair descriptors in future research.
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Affiliation(s)
- Deborah Galpert
- Departamento de Ciencia de la Computación, Universidad Central ¨Marta Abreu¨ de Las Villas (UCLV), 54830, Santa Clara, Cuba
| | - Alberto Fernández
- Department of Computer Science and Artificial Intelligence, Research Center on Information and Communications Technology (CITIC-UGR), University of Granada, 18071, Granada, Spain
| | - Francisco Herrera
- Department of Computer Science and Artificial Intelligence, Research Center on Information and Communications Technology (CITIC-UGR), University of Granada, 18071, Granada, Spain
| | - Agostinho Antunes
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n 4450-208 Matosinhos, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Reinaldo Molina-Ruiz
- Centro de Bioactivos Químicos (CBQ), Universidad Central ¨Marta Abreu¨ de Las Villas (UCLV), 54830, Santa Clara, Cuba
| | - Guillermin Agüero-Chapin
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n 4450-208 Matosinhos, Porto, Portugal. .,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal. .,Centro de Bioactivos Químicos (CBQ), Universidad Central ¨Marta Abreu¨ de Las Villas (UCLV), 54830, Santa Clara, Cuba.
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24
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Abstract
Advancements in MS-based phospho-proteomics techniques have helped uncover hundred thousands of protein phosphorylation sites in human and various model organisms. The majority of these sites are uncharacterized. The sheer number of uncharacterized sites necessitates systematic approaches to prioritize sites for more in-depth annotation. Analyzing the phosphorylation and sequence conservation of uncharacterized sites across species can help reveal a subset of the functionally important phosphorylation events. Here, we outline the workflow and provide an overview of publicly available computational resources for conservation analysis of novel phosphorylation sites.
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A multi-omics study of the grapevine-downy mildew (Plasmopara viticola) pathosystem unveils a complex protein coding- and noncoding-based arms race during infection. Sci Rep 2018; 8:757. [PMID: 29335535 PMCID: PMC5768699 DOI: 10.1038/s41598-018-19158-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 12/15/2017] [Indexed: 12/16/2022] Open
Abstract
Fungicides are applied intensively to prevent downy mildew infections of grapevines (Vitis vinifera) with high impact on the environment. In order to develop alternative strategies we sequenced the genome of the oomycete pathogen Plasmopara viticola causing this disease. We show that it derives from a Phytophthora-like ancestor that switched to obligate biotrophy by losing genes involved in nitrogen metabolism and γ-Aminobutyric acid catabolism. By combining multiple omics approaches we characterized the pathosystem and identified a RxLR effector that trigger an immune response in the wild species V. riparia. This effector is an ideal marker to screen novel grape resistant varieties. Our study reveals an unprecedented bidirectional noncoding RNA-based mechanism that, in one direction might be fundamental for P. viticola to proficiently infect its host, and in the other might reduce the effects of the infection on the plant.
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Chen J, Liu C, Gui Y, Si K, Zhang D, Wang J, Short DPG, Huang J, Li N, Liang Y, Zhang W, Yang L, Ma X, Li T, Zhou L, Wang B, Bao Y, Subbarao KV, Zhang G, Dai X. Comparative genomics reveals cotton-specific virulence factors in flexible genomic regions in Verticillium dahliae and evidence of horizontal gene transfer from Fusarium. THE NEW PHYTOLOGIST 2018; 217:756-770. [PMID: 29084346 PMCID: PMC5765495 DOI: 10.1111/nph.14861] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/21/2017] [Indexed: 05/20/2023]
Abstract
Verticillium dahliae isolates are most virulent on the host from which they were originally isolated. Mechanisms underlying these dominant host adaptations are currently unknown. We sequenced the genome of V. dahliae Vd991, which is highly virulent on its original host, cotton, and performed comparisons with the reference genomes of JR2 (from tomato) and VdLs.17 (from lettuce). Pathogenicity-related factor prediction, orthology and multigene family classification, transcriptome analyses, phylogenetic analyses, and pathogenicity experiments were performed. The Vd991 genome harbored several exclusive, lineage-specific (LS) genes within LS regions (LSRs). Deletion mutants of the seven genes within one LSR (G-LSR2) in Vd991 were less virulent only on cotton. Integration of G-LSR2 genes individually into JR2 and VdLs.17 resulted in significantly enhanced virulence on cotton but did not affect virulence on tomato or lettuce. Transcription levels of the seven LS genes in Vd991 were higher during the early stages of cotton infection, as compared with other hosts. Phylogenetic analyses suggested that G-LSR2 was acquired from Fusarium oxysporum f. sp. vasinfectum through horizontal gene transfer. Our results provide evidence that horizontal gene transfer from Fusarium to Vd991 contributed significantly to its adaptation to cotton and may represent a significant mechanism in the evolution of an asexual plant pathogen.
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Affiliation(s)
- Jie‐Yin Chen
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Chun Liu
- BGI‐ShenzhenShenzhenGuangdong518083China
| | - Yue‐Jing Gui
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Kai‐Wei Si
- BGI‐ShenzhenShenzhenGuangdong518083China
| | - Dan‐Dan Zhang
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Jie Wang
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Dylan P. G. Short
- Department of Plant PathologyUniversity of CaliforniaDavisCA95616USA
| | | | - Nan‐Yang Li
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Yong Liang
- BGI‐ShenzhenShenzhenGuangdong518083China
| | - Wen‐Qi Zhang
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Lin Yang
- BGI‐ShenzhenShenzhenGuangdong518083China
| | - Xue‐Feng Ma
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Ting‐Gang Li
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Lei Zhou
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Bao‐Li Wang
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Yu‐Ming Bao
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | | | | | - Xiao‐Feng Dai
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
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Panda A, Sen D, Ghosh A, Gupta A, C. MM, Prakash Mishra G, Singh D, Ye W, Tyler BM, Tripathy S. EumicrobeDBLite: a lightweight genomic resource and analytic platform for draft oomycete genomes. MOLECULAR PLANT PATHOLOGY 2018; 19:227-237. [PMID: 27785876 PMCID: PMC6638084 DOI: 10.1111/mpp.12505] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 09/09/2016] [Accepted: 10/22/2016] [Indexed: 05/13/2023]
Abstract
We have developed EumicrobeDBLite-a lightweight comprehensive genome resource and sequence analysis platform for oomycete organisms. EumicrobeDBLite is a successor of the VBI Microbial Database (VMD) that was built using the Genome Unified Schema (GUS). In this version, GUS has been greatly simplified with the removal of many obsolete modules and the redesign of others to incorporate contemporary data. Several dependences, such as perl object layers used for data loading in VMD, have been replaced with independent lightweight scripts. EumicrobeDBLite now runs on a powerful annotation engine developed at our laboratory, called 'Genome Annotator Lite'. Currently, this database has 26 publicly available genomes and 10 expressed sequence tag (EST) datasets of oomycete organisms. The browser page has dynamic tracks presenting comparative genomics analyses, coding and non-coding data, tRNA genes, repeats and EST alignments. In addition, we have defined 44 777 core conserved proteins from 12 oomycete organisms which form 2974 clusters. Synteny viewing is enabled by the incorporation of the Genome Synteny Viewer (GSV) tool. The user interface has undergone major changes for ease of browsing. Queryable comparative genomics information, conserved orthologous genes and pathways are among the new key features updated in this database. The browser has been upgraded to enable user upload of GFF files for quick view of genome annotation comparisons. The toolkit page integrates the EMBOSS package and has a gene prediction tool. Annotations for the organisms are updated once every 6 months to ensure quality. The database resource is available at www.eumicrobedb.org.
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Affiliation(s)
- Arijit Panda
- Computational Genomics Laboratory, Structural Biology and Bioinformatics DivisionCouncil of Scientific and Industrial Research –Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, JadavpurKolkata700032India
| | - Diya Sen
- Computational Genomics Laboratory, Structural Biology and Bioinformatics DivisionCouncil of Scientific and Industrial Research –Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, JadavpurKolkata700032India
| | - Arup Ghosh
- Computational Genomics Laboratory, Structural Biology and Bioinformatics DivisionCouncil of Scientific and Industrial Research –Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, JadavpurKolkata700032India
| | - Akash Gupta
- Computational Genomics Laboratory, Structural Biology and Bioinformatics DivisionCouncil of Scientific and Industrial Research –Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, JadavpurKolkata700032India
| | - Mathu Malar C.
- Computational Genomics Laboratory, Structural Biology and Bioinformatics DivisionCouncil of Scientific and Industrial Research –Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, JadavpurKolkata700032India
| | - Gyan Prakash Mishra
- Computational Genomics Laboratory, Structural Biology and Bioinformatics DivisionCouncil of Scientific and Industrial Research –Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, JadavpurKolkata700032India
| | - Deeksha Singh
- Computational Genomics Laboratory, Structural Biology and Bioinformatics DivisionCouncil of Scientific and Industrial Research –Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, JadavpurKolkata700032India
| | - Wenwu Ye
- Center for Genome Research and Biocomputing and Department of Botany and Plant PathologyOregon State UniversityCorvallisOR97331‐7303, USA
- Department of Plant PathologyNanjing Agricultural UniversityNanjing210095China
| | - Brett M. Tyler
- Center for Genome Research and Biocomputing and Department of Botany and Plant PathologyOregon State UniversityCorvallisOR97331‐7303, USA
| | - Sucheta Tripathy
- Computational Genomics Laboratory, Structural Biology and Bioinformatics DivisionCouncil of Scientific and Industrial Research –Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, JadavpurKolkata700032India
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Abstract
Computational pan-genome analysis has emerged from the rapid increase of available genome sequencing data. Starting from a microbial pan-genome, the concept has spread to a variety of species, such as plants or viruses. Characterizing a pan-genome provides insights into intra-species evolution, functions, and diversity. However, researchers face challenges such as processing and maintaining large datasets while providing accurate and efficient analysis approaches. Comparative genomics methods are required for detecting conserved and unique regions between a set of genomes. This chapter gives an overview of tools available for indexing pan-genomes, identifying the sub-regions of a pan-genome and offering a variety of downstream analysis methods. These tools are categorized into two groups, gene-based and sequence-based, according to the pan-genome identification method. We highlight the differences, advantages, and disadvantages between the tools, and provide information about the general workflow, methodology of pan-genome identification, covered functionalities, usability and availability of the tools.
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Affiliation(s)
- Tina Zekic
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
- International Research Training Group 1906, Bielefeld University, Bielefeld, Germany
| | - Guillaume Holley
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
- International Research Training Group 1906, Bielefeld University, Bielefeld, Germany
| | - Jens Stoye
- Faculty of Technology, Bielefeld University, Bielefeld, Germany.
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
- International Research Training Group 1906, Bielefeld University, Bielefeld, Germany.
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Takashima M, Sriswasdi S, Manabe RI, Ohkuma M, Sugita T, Iwasaki W. A Trichosporonales genome tree based on 27 haploid and three evolutionarily conserved 'natural' hybrid genomes. Yeast 2017; 35:99-111. [PMID: 29027707 DOI: 10.1002/yea.3284] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 09/27/2017] [Accepted: 09/28/2017] [Indexed: 01/08/2023] Open
Abstract
To construct a backbone tree consisting of basidiomycetous yeasts, draft genome sequences from 25 species of Trichosporonales (Tremellomycetes, Basidiomycota) were generated. In addition to the hybrid genomes of Trichosporon coremiiforme and Trichosporon ovoides that we described previously, we identified an interspecies hybrid genome in Cutaneotrichosporon mucoides (formerly Trichosporon mucoides). This hybrid genome had a gene retention rate of ~55%, and its closest haploid relative was Cutaneotrichosporon dermatis. After constructing the C. mucoides subgenomes, we generated a phylogenetic tree using genome data from the 27 haploid species and the subgenome data from the three hybrid genome species. It was a high-quality tree with 100% bootstrap support for all of the branches. The genome-based tree provided superior resolution compared with previous multi-gene analyses. Although our backbone tree does not include all Trichosporonales genera (e.g. Cryptotrichosporon), it will be valuable for future analyses of genome data. Interest in interspecies hybrid fungal genomes has recently increased because they may provide a basis for new technologies. The three Trichosporonales hybrid genomes described in this study are different from well-characterized hybrid genomes (e.g. those of Saccharomyces pastorianus and Saccharomyces bayanus) because these hybridization events probably occurred in the distant evolutionary past. Hence, they will be useful for studying genome stability following hybridization and speciation events. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Masako Takashima
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Sira Sriswasdi
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.,Research Affairs, Faculty of Medicine, Chulalongkorn University, Pathum Wan, Bangkok, 10330, Thailand
| | - Ri-Ichiroh Manabe
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Takashi Sugita
- Department of Microbiology, Meiji Pharmaceutical University, Kiyose, Tokyo, 204-8588, Japan
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-8568, Japan.,Atmosphere and Ocean Research Institute, the University of Tokyo, Kashiwa, Chiba, 277-8564, Japan
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30
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Evolutionary recruitment of flexible Esrp-dependent splicing programs into diverse embryonic morphogenetic processes. Nat Commun 2017; 8:1799. [PMID: 29180615 PMCID: PMC5703972 DOI: 10.1038/s41467-017-01961-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 10/29/2017] [Indexed: 01/16/2023] Open
Abstract
Epithelial-mesenchymal interactions are crucial for the development of numerous animal structures. Thus, unraveling how molecular tools are recruited in different lineages to control interplays between these tissues is key to understanding morphogenetic evolution. Here, we study Esrp genes, which regulate extensive splicing programs and are essential for mammalian organogenesis. We find that Esrp homologs have been independently recruited for the development of multiple structures across deuterostomes. Although Esrp is involved in a wide variety of ontogenetic processes, our results suggest ancient roles in non-neural ectoderm and regulating specific mesenchymal-to-epithelial transitions in deuterostome ancestors. However, consistent with the extensive rewiring of Esrp-dependent splicing programs between phyla, most developmental defects observed in vertebrate mutants are related to other types of morphogenetic processes. This is likely connected to the origin of an event in Fgfr, which was recruited as an Esrp target in stem chordates and subsequently co-opted into the development of many novel traits in vertebrates.
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31
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Ke HM, Yu CP, Liu YC, Tsai IJ. Popmarker: Identifying Phylogenetic Markers at the Population Level. Evol Bioinform Online 2017; 13:1176934317724404. [PMID: 29104426 PMCID: PMC5562387 DOI: 10.1177/1176934317724404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 07/05/2017] [Indexed: 11/17/2022] Open
Abstract
As phylogenomic approach becomes a common practice for constructing true bacterial phylogenies, it has become apparent that single molecular markers such as 16S ribosomal DNA often lead to misclassification of species. In this study, we present a program called Popmarker that uses the true species phylogeny and identifies a minimum set of molecular markers reflecting the bacterial evolution history and phylogenetic relationship at the resolution of populations. Popmarker ranks the proteome according to the correlation of whole species tree or subtree branch length against orthologous sequence distances. We demonstrate that 5 proteins of 2 top ranks achieve the same resolution as concatenation of 2203 single-copy orthologous genes and the right species classification as well as correct split of the 2 groups of Vibrio campbellii . The top-ranking genes selected by Popmarker are candidates that lead to speciation and are useful in distinguishing close related species in microbiome study.
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Affiliation(s)
- Huei-Mien Ke
- Biodiversity Research Center, Academia Sinica (BRCAS), Taipei, Taiwan
| | - Chun-Ping Yu
- Biodiversity Research Center, Academia Sinica (BRCAS), Taipei, Taiwan
| | - Yu-Ching Liu
- Biodiversity Research Center, Academia Sinica (BRCAS), Taipei, Taiwan
| | - Isheng J Tsai
- Biodiversity Research Center, Academia Sinica (BRCAS), Taipei, Taiwan
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32
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Tamiru M, Natsume S, Takagi H, White B, Yaegashi H, Shimizu M, Yoshida K, Uemura A, Oikawa K, Abe A, Urasaki N, Matsumura H, Babil P, Yamanaka S, Matsumoto R, Muranaka S, Girma G, Lopez-Montes A, Gedil M, Bhattacharjee R, Abberton M, Kumar PL, Rabbi I, Tsujimura M, Terachi T, Haerty W, Corpas M, Kamoun S, Kahl G, Takagi H, Asiedu R, Terauchi R. Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination. BMC Biol 2017; 15:86. [PMID: 28927400 PMCID: PMC5604175 DOI: 10.1186/s12915-017-0419-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/10/2017] [Indexed: 11/10/2022] Open
Abstract
Background Root and tuber crops are a major food source in tropical Africa. Among these crops are several species in the monocotyledonous genus Dioscorea collectively known as yam, a staple tuber crop that contributes enormously to the subsistence and socio-cultural lives of millions of people, principally in West and Central Africa. Yam cultivation is constrained by several factors, and yam can be considered a neglected “orphan” crop that would benefit from crop improvement efforts. However, the lack of genetic and genomic tools has impeded the improvement of this staple crop. Results To accelerate marker-assisted breeding of yam, we performed genome analysis of white Guinea yam (Dioscorea rotundata) and assembled a 594-Mb genome, 76.4% of which was distributed among 21 linkage groups. In total, we predicted 26,198 genes. Phylogenetic analyses with 2381 conserved genes revealed that Dioscorea is a unique lineage of monocotyledons distinct from the Poales (rice), Arecales (palm), and Zingiberales (banana). The entire Dioscorea genus is characterized by the occurrence of separate male and female plants (dioecy), a feature that has limited efficient yam breeding. To infer the genetics of sex determination, we performed whole-genome resequencing of bulked segregants (quantitative trait locus sequencing [QTL-seq]) in F1 progeny segregating for male and female plants and identified a genomic region associated with female heterogametic (male = ZZ, female = ZW) sex determination. We further delineated the W locus and used it to develop a molecular marker for sex identification of Guinea yam plants at the seedling stage. Conclusions Guinea yam belongs to a unique and highly differentiated clade of monocotyledons. The genome analyses and sex-linked marker development performed in this study should greatly accelerate marker-assisted breeding of Guinea yam. In addition, our QTL-seq approach can be utilized in genetic studies of other outcrossing crops and organisms with highly heterozygous genomes. Genomic analysis of orphan crops such as yam promotes efforts to improve food security and the sustainability of tropical agriculture. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0419-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Hiroki Takagi
- Iwate Biotechnology Research Center, Kitakami, Japan
| | | | | | | | | | - Aiko Uemura
- Iwate Biotechnology Research Center, Kitakami, Japan
| | - Kaori Oikawa
- Iwate Biotechnology Research Center, Kitakami, Japan
| | - Akira Abe
- Iwate Biotechnology Research Center, Kitakami, Japan
| | | | | | | | - Shinsuke Yamanaka
- Japan International Research Center for Agricultural Sciences, Tsukuba, Japan
| | - Ryo Matsumoto
- Japan International Research Center for Agricultural Sciences, Tsukuba, Japan
| | - Satoru Muranaka
- Japan International Research Center for Agricultural Sciences, Tsukuba, Japan
| | - Gezahegn Girma
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | | | - Melaku Gedil
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | | | - Michael Abberton
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - P Lava Kumar
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Ismail Rabbi
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | | | | | | | | | | | | | - Hiroko Takagi
- Japan International Research Center for Agricultural Sciences, Tsukuba, Japan.
| | - Robert Asiedu
- International Institute of Tropical Agriculture, Ibadan, Nigeria.
| | - Ryohei Terauchi
- Iwate Biotechnology Research Center, Kitakami, Japan. .,Kyoto University, Kyoto, Japan.
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33
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Transcriptomes and expression profiling of deep-sea corals from the Red Sea provide insight into the biology of azooxanthellate corals. Sci Rep 2017; 7:6442. [PMID: 28743941 PMCID: PMC5526985 DOI: 10.1038/s41598-017-05572-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 05/31/2017] [Indexed: 12/15/2022] Open
Abstract
Despite the importance of deep-sea corals, our current understanding of their ecology and evolution is limited due to difficulties in sampling and studying deep-sea environments. Moreover, a recent re-evaluation of habitat limitations has been suggested after characterization of deep-sea corals in the Red Sea, where they live at temperatures of above 20 °C at low oxygen concentrations. To gain further insight into the biology of deep-sea corals, we produced reference transcriptomes and studied gene expression of three deep-sea coral species from the Red Sea, i.e. Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. Our analyses suggest that deep-sea coral employ mitochondrial hypometabolism and anaerobic glycolysis to manage low oxygen conditions present in the Red Sea. Notably, we found expression of genes related to surface cilia motion that presumably enhance small particle transport rates in the oligotrophic deep-sea environment. This is the first study to characterize transcriptomes and in situ gene expression for deep-sea corals. Our work offers several mechanisms by which deep-sea corals might cope with the distinct environmental conditions present in the Red Sea As such, our data provide direction for future research and further insight to organismal response of deep-sea coral to environmental change and ocean warming.
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Di Donato A, Andolfo G, Ferrarini A, Delledonne M, Ercolano MR. Investigation of orthologous pathogen recognition gene-rich regions in solanaceous species. Genome 2017; 60:850-859. [PMID: 28742982 DOI: 10.1139/gen-2016-0217] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pathogen receptor proteins such as receptor-like protein (RLP), receptor-like kinase (RLK), and nucleotide-binding leucine-rich repeat (NLR) play a leading role in plant immunity activation. The genome architecture of such genes has been extensively investigated in several plant species. However, we still know little about their elaborate reorganization that arose during the plant speciation process. Using recently released pepper and eggplant genome sequences, we were able to identify 1097 pathogen recognition genes (PRGs) in the cultivated pepper Zunla-1 and 775 in the eggplant line Nakate-Shinkuro. The retrieved genes were analysed for their tendency to cluster, using different methods to infer the means of grouping. Orthologous relationships among clustering loci were found, and interesting reshuffling within given loci was observed for each analysed species. The information obtained was integrated into a comparative map to highlight the evolutionary dynamics in which the PRG loci were involved. Diversification of 14 selected PRG-rich regions was also explored using a DNA target-enrichment approach. A large number of gene variants were found as well as rearrangements of sequences encoding single protein domain and changes in chromosome gene order among species. Gene duplication and transposition activity have clearly influenced plant genome R-gene architecture and diversification. Our findings contribute to addressing several biological questions concerning the parallel evolution that occurred between genomes of the family Solanaceae. Moreover, the integration of different methods proved a powerful approach to reconstruct the evolutionary history in plant families and to transfer important biology findings among plant genomes.
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Affiliation(s)
- A Di Donato
- a Dipartimento di Agraria, Università di Napoli 'Federico II', Via Università 100, 80055 Portici, Italy
| | - G Andolfo
- a Dipartimento di Agraria, Università di Napoli 'Federico II', Via Università 100, 80055 Portici, Italy
| | - A Ferrarini
- b Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada le Grazie, 15, 37134 Verona, Italy
| | - M Delledonne
- b Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada le Grazie, 15, 37134 Verona, Italy
| | - M R Ercolano
- a Dipartimento di Agraria, Università di Napoli 'Federico II', Via Università 100, 80055 Portici, Italy
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35
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Jeffrey B, Rose SJ, Gilbert K, Lewis M, Bermudez LE. Comparative analysis of the genomes of clinical isolates of Mycobacterium avium subsp. hominissuis regarding virulence-related genes. J Med Microbiol 2017; 66:1063-1075. [PMID: 28671535 DOI: 10.1099/jmm.0.000507] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
PURPOSE Mycobacterium avium subsp. hominissuis is a member of the M. avium complex, a heterogeneous group of bacteria that cause lung infection in immunocompetent patients or disseminated infection in patients with immunosuppression. The bacteria belonging to this complex have variable virulence, depending on the strain considered, and therefore a representative of the most common clinical phenotype was analysed. METHODOLOGY The genomic sequences of four M. avium subsp. hominissuis isolates obtained from clinical specimens were completed. Mav101, Mav100 and MavA5 were isolated from the blood of patients with AIDS. MavA5 was disseminated from the lung, while Mav3388 was isolated from the lungs of a patient with chronic lung disease. The sequences were annotated using the published Mav104 genome as a blueprint. Functional and virulence analyses of the sequences were carried out. Mice studies comparing the virulence of the strains were performed. RESULTS Findings showed that while Mav101 was very similar to Mav104, there were numerous differences between Mav104 and the remaining strains at nucleotide and predicted protein levels. The presence of genes associated with biofilm formation and several known virulence-related genes were sometimes differentially present among the isolates, suggesting overlapping functions by different genetic determinants. CONCLUSIONS The sequences provided important information about M. avium heterogenicity and evolution as a pathogen. The limitation is the lack of understanding on possible overlapping functions of genes/proteins.
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Affiliation(s)
- Brendan Jeffrey
- Department of Biomedical Sciences, College of Veterinary Medicine, Corvallis, Oregon, USA
| | - Sasha J Rose
- Department of Biomedical Sciences, College of Veterinary Medicine, Corvallis, Oregon, USA.,Department of Microbiology, College of Science, Oregon State University, Corvallis, Oregon, USA
| | - Kerrigan Gilbert
- Department of Biomedical Sciences, College of Veterinary Medicine, Corvallis, Oregon, USA
| | - Matthew Lewis
- Department of Biomedical Sciences, College of Veterinary Medicine, Corvallis, Oregon, USA.,Department of Microbiology, College of Science, Oregon State University, Corvallis, Oregon, USA
| | - Luiz E Bermudez
- Department of Microbiology, College of Science, Oregon State University, Corvallis, Oregon, USA.,Department of Biomedical Sciences, College of Veterinary Medicine, Corvallis, Oregon, USA
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Wu FY, Tang CY, Guo YM, Bian ZW, Fu JY, Lu GH, Qi JL, Pang YJ, Yang YH. Transcriptome analysis explores genes related to shikonin biosynthesis in Lithospermeae plants and provides insights into Boraginales' evolutionary history. Sci Rep 2017; 7:4477. [PMID: 28667265 PMCID: PMC5493674 DOI: 10.1038/s41598-017-04750-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 05/22/2017] [Indexed: 11/09/2022] Open
Abstract
Shikonin and its derivatives extracted from Lithospermeae plants' red roots have current applications in food and pharmaceutical industries. Previous studies have cloned some genes related to shikonin biosynthesis. However, most genes related to shikonin biosynthesis remain unclear, because the lack of the genome/transcriptome of the Lithospermeae plants. Therefore, in order to provide a new understanding of shikonin biosynthesis, we obtained transcriptome data and unigenes expression profiles in three shikonin-producing Lithospermeae plants, i.e., Lithospermum erythrorhizon, Arnebia euchroma and Echium plantagineum. As a result, two unigenes (i.e., G10H and 12OPR) that are involved in "shikonin downstream biosynthesis" and "methyl jasmonate biosynthesis" were deemed to relate to shikonin biosynthesis in this study. Furthermore, we conducted a Lamiids phylogenetic model and identified orthologous unigenes under positive selection in above three Lithospermeae plants. The results indicated Boraginales was more relative to Solanales/Gentianales than to Lamiales.
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Affiliation(s)
- Feng-Yao Wu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Cheng-Yi Tang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China.
| | - Yu-Min Guo
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Zhuo-Wu Bian
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Jiang-Yan Fu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Gui-Hua Lu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Jin-Liang Qi
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Yan-Jun Pang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China.
| | - Yong-Hua Yang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China.
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Abstract
With increased production of genomic data since the advent of next-generation sequencing (NGS), there has been a need to develop new bioinformatics tools and areas, such as comparative genomics. In comparative genomics, the genetic material of an organism is directly compared to that of another organism to better understand biological species. Moreover, the exponentially growing number of deposited prokaryote genomes has enabled the investigation of several genomic characteristics that are intrinsic to certain species. Thus, a new approach to comparative genomics, termed pan-genomics, was developed. In pan-genomics, various organisms of the same species or genus are compared. Currently, there are many tools that can perform pan-genomic analyses, such as PGAP (Pan-Genome Analysis Pipeline), Panseq (Pan-Genome Sequence Analysis Program) and PGAT (Prokaryotic Genome Analysis Tool). Among these software tools, PGAP was developed in the Perl scripting language and its reliance on UNIX platform terminals and its requirement for an extensive parameterized command line can become a problem for users without previous computational knowledge. Thus, the aim of this study was to develop a web application, known as PanWeb, that serves as a graphical interface for PGAP. In addition, using the output files of the PGAP pipeline, the application generates graphics using custom-developed scripts in the R programming language. PanWeb is freely available at http://www.computationalbiology.ufpa.br/panweb.
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Lan Y, Sun J, Tian R, Bartlett DH, Li R, Wong YH, Zhang W, Qiu JW, Xu T, He LS, Tabata HG, Qian PY. Molecular adaptation in the world's deepest-living animal: Insights from transcriptome sequencing of the hadal amphipod Hirondellea gigas. Mol Ecol 2017; 26:3732-3743. [PMID: 28429829 DOI: 10.1111/mec.14149] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 03/30/2017] [Accepted: 04/05/2017] [Indexed: 12/17/2022]
Abstract
The Challenger Deep in the Mariana Trench is the deepest point in the oceans of our planet. Understanding how animals adapt to this harsh environment characterized by high hydrostatic pressure, food limitation, dark and cold is of great scientific interest. Of the animals dwelling in the Challenger Deep, amphipods have been captured using baited traps. In this study, we sequenced the transcriptome of the amphipod Hirondellea gigas collected at a depth of 10,929 m from the East Pond of the Challenger Deep. Assembly of these sequences resulted in 133,041 contigs and 22,046 translated proteins. Functional annotation of these contigs was made using the go and kegg databases. Comparison of these translated proteins with those of four shallow-water amphipods revealed 10,731 gene families, of which 5659 were single-copy orthologs. Base substitution analysis on these single-copy orthologs showed that 62 genes are positively selected in H. gigas, including genes related to β-alanine biosynthesis, energy metabolism and genetic information processing. For multiple-copy orthologous genes, gene family expansion analysis revealed that cold-inducible proteins (i.e., transcription factors II A and transcription elongation factor 1) as well as zinc finger domains are expanded in H. gigas. Overall, our results indicate that genetic adaptation to the hadal environment by H. gigas may be mediated by both gene family expansion and amino acid substitutions of specific proteins.
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Affiliation(s)
- Yi Lan
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Jin Sun
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Renmao Tian
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Douglas H Bartlett
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Runsheng Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yue Him Wong
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Weipeng Zhang
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Ting Xu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Li-Sheng He
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Harry G Tabata
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
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Chi W, Ma X, Niu J, Zou M. Genome-wide identification of genes probably relevant to the adaptation of schizothoracins (Teleostei: Cypriniformes) to the uplift of the Qinghai-Tibet Plateau. BMC Genomics 2017; 18:310. [PMID: 28427344 PMCID: PMC5397779 DOI: 10.1186/s12864-017-3703-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 04/12/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Molecular adaptation to the severe environments present during the uplift of the Qinghai-Tibet Plateau has attracted the attention of researchers. The divergence of the three specialization groups of schizothoracins (Primitive, Specialized and Highly Specialized) may correspond to the three phases of plateau uplift. Based on the transcripts of representative species of the three specialized groups and an outgroup, genes in schizothoracins that may have played important roles during the adaptation to new environments were investigated. RESULTS The contigs of Gymnodiptychus dybowskii and Schizothorax pseudaksaiensis were compared with those of Gymnocypris przewalskii ganzihonensis and the outgroup Sinocyclocheilus angustiporus, and 5,894 ortholog groups with an alignment length longer than 90 nt after deleting gaps were retained. Evolutionary analyses indicated that the average evolutionary rate of the branch leading to the Specialized group was faster than that of the branch leading to the Highly Specialized group. Moreover, the numbers of gene categories in which more than half of the genes evolved faster than the average values of the genome were 117 and 15 along the branches leading to the Specialized and Highly Specialized groups, respectively. A total of 40, 36, and 55 genes were likely subject to positive selection along the branches leading to the Primitive, Specialized and Highly Specialized groups, respectively, and many of these genes are likely relevant to adaptation to the cold temperatures, low oxygen concentrations, and strong ultraviolet radiation that result from elevation. CONCLUSIONS By selecting representative species of the three groups of schizothoracins and applying next-generation sequencing technology, several candidate genes corresponding to adaptation to the three phases of plateau uplift were identified. Some of the genes identified in this report that were likely subject to positive selection are good candidates for subsequent evolutionary and functional analyses of adaptation to high altitude.
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Affiliation(s)
- Wei Chi
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Xufa Ma
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Jiangong Niu
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
- Fisheries Research Institute of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Ming Zou
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
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Luo X, Hu Q, Zhou P, Zhang D, Wang Q, Abbott RJ, Liu J. Chasing ghosts: allopolyploid origin ofOxyria sinensis(Polygonaceae) from its only diploid congener and an unknown ancestor. Mol Ecol 2017; 26:3037-3049. [DOI: 10.1111/mec.14097] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/02/2017] [Accepted: 03/02/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Xin Luo
- MOE Key Laboratory for Bio-resources and Eco-environment; College of Life Science; Sichuan University; Chengdu China
| | - Quanjun Hu
- MOE Key Laboratory for Bio-resources and Eco-environment; College of Life Science; Sichuan University; Chengdu China
- State Key Laboratory of Grassland Agro-Ecosystem; College of Life Science; Lanzhou University; Lanzhou China
| | - Pingping Zhou
- MOE Key Laboratory for Bio-resources and Eco-environment; College of Life Science; Sichuan University; Chengdu China
| | - Dan Zhang
- MOE Key Laboratory for Bio-resources and Eco-environment; College of Life Science; Sichuan University; Chengdu China
| | - Qian Wang
- MOE Key Laboratory for Bio-resources and Eco-environment; College of Life Science; Sichuan University; Chengdu China
- Research Center for Medicine and Biology; Zunyi Medical University; Zunyi China
| | - Richard J. Abbott
- School of Biology; University of St Andrews; St Andrews Fife KY16 9TH UK
| | - Jianquan Liu
- MOE Key Laboratory for Bio-resources and Eco-environment; College of Life Science; Sichuan University; Chengdu China
- State Key Laboratory of Grassland Agro-Ecosystem; College of Life Science; Lanzhou University; Lanzhou China
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Luo W, Zhang C, Zhang J, Jiang D, Guo W, Wan D. Transcriptome analysis of four poplars exposed to continuous salinity stress. BIOCHEM SYST ECOL 2017. [DOI: 10.1016/j.bse.2017.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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42
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McNulty SN, Tort JF, Rinaldi G, Fischer K, Rosa BA, Smircich P, Fontenla S, Choi YJ, Tyagi R, Hallsworth-Pepin K, Mann VH, Kammili L, Latham PS, Dell’Oca N, Dominguez F, Carmona C, Fischer PU, Brindley PJ, Mitreva M. Genomes of Fasciola hepatica from the Americas Reveal Colonization with Neorickettsia Endobacteria Related to the Agents of Potomac Horse and Human Sennetsu Fevers. PLoS Genet 2017; 13:e1006537. [PMID: 28060841 PMCID: PMC5257007 DOI: 10.1371/journal.pgen.1006537] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 01/23/2017] [Accepted: 12/15/2016] [Indexed: 12/30/2022] Open
Abstract
Food borne trematodes (FBTs) are an assemblage of platyhelminth parasites transmitted through the food chain, four of which are recognized as neglected tropical diseases (NTDs). Fascioliasis stands out among the other NTDs due to its broad and significant impact on both human and animal health, as Fasciola sp., are also considered major pathogens of domesticated ruminants. Here we present a reference genome sequence of the common liver fluke, Fasciola hepatica isolated from sheep, complementing previously reported isolate from cattle. A total of 14,642 genes were predicted from the 1.14 GB genome of the liver fluke. Comparative genomics indicated that F. hepatica Oregon and related food-borne trematodes are metabolically less constrained than schistosomes and cestodes, taking advantage of the richer millieux offered by the hepatobiliary organs. Protease families differentially expanded between diverse trematodes may facilitate migration and survival within the heterogeneous environments and niches within the mammalian host. Surprisingly, the sequencing of Oregon and Uruguay F. hepatica isolates led to the first discovery of an endobacteria in this species. Two contigs from the F. hepatica Oregon assembly were joined to complete the 859,205 bp genome of a novel Neorickettsia endobacterium (nFh) closely related to the etiological agents of human Sennetsu and Potomac horse fevers. Immunohistochemical studies targeting a Neorickettsia surface protein found nFh in specific organs and tissues of the adult trematode including the female reproductive tract, eggs, the Mehlis' gland, seminal vesicle, and oral suckers, suggesting putative routes for fluke-to-fluke and fluke-to-host transmission. The genomes of F. hepatica and nFh will serve as a resource for further exploration of the biology of F. hepatica, and specifically its newly discovered trans-kingdom interaction with nFh and the impact of both species on disease in ruminants and humans.
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Affiliation(s)
- Samantha N. McNulty
- McDonnell Genome Institute at Washington University, St. Louis, Missouri, United States of America
| | - Jose F. Tort
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UDELAR), Montevideo, Uruguay
| | - Gabriel Rinaldi
- Department of Microbiology, Immunology and Tropical Medicine, and Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC, United States of America
| | - Kerstin Fischer
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Bruce A. Rosa
- McDonnell Genome Institute at Washington University, St. Louis, Missouri, United States of America
| | - Pablo Smircich
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UDELAR), Montevideo, Uruguay
| | - Santiago Fontenla
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UDELAR), Montevideo, Uruguay
| | - Young-Jun Choi
- McDonnell Genome Institute at Washington University, St. Louis, Missouri, United States of America
| | - Rahul Tyagi
- McDonnell Genome Institute at Washington University, St. Louis, Missouri, United States of America
| | | | - Victoria H. Mann
- Department of Microbiology, Immunology and Tropical Medicine, and Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC, United States of America
| | - Lakshmi Kammili
- Department of Pathology, School of Medicine & Health Sciences, George Washington University, Washington, DC, United States of America
| | - Patricia S. Latham
- Department of Pathology, School of Medicine & Health Sciences, George Washington University, Washington, DC, United States of America
| | - Nicolas Dell’Oca
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UDELAR), Montevideo, Uruguay
| | - Fernanda Dominguez
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UDELAR), Montevideo, Uruguay
| | - Carlos Carmona
- Unidad de Biología Parasitaria, Instituto de Biología, Facultad de Ciencias, Instituto de Higiene, Montevideo, Uruguay
| | - Peter U. Fischer
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Paul J. Brindley
- Department of Microbiology, Immunology and Tropical Medicine, and Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC, United States of America
| | - Makedonka Mitreva
- McDonnell Genome Institute at Washington University, St. Louis, Missouri, United States of America
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
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Deng X, Memari N, Teatero S, Athey T, Isabel M, Mazzulli T, Fittipaldi N, Gubbay JB. Whole-genome Sequencing for Surveillance of Invasive Pneumococcal Diseases in Ontario, Canada: Rapid Prediction of Genotype, Antibiotic Resistance and Characterization of Emerging Serotype 22F. Front Microbiol 2016; 7:2099. [PMID: 28082965 PMCID: PMC5187366 DOI: 10.3389/fmicb.2016.02099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 12/12/2016] [Indexed: 11/13/2022] Open
Abstract
Background: Molecular typing is essential for inferring genetic relatedness between bacterial pathogens. In this study, we applied whole genome sequencing (WGS) for rapid prediction of sequence type and antibiotic resistance for invasive pneumococcal isolates. Methods: 240 isolates from adults (≥50 years old) in Ontario, Canada during 2009 to 2013 were subjected to WGS. Sequence type, antibiotic susceptibility and resistance were predicted directly from short reads. Emerging non-vaccine serotype 22F was further characterized by WGS. Results: Sequence type was successfully determined for 98.3% of isolates. The overall sensitivity and specificity for antibiotic resistance prediction were 95 and 100% respectively, compared to standard susceptibility testing methods. WGS-based phylogeny divided emerging 22F (ST433) strains into two distinct clades: clade A harboring a 23 kb-prophage and anti-phage PhD/Doc system and clade B with virulence-related proteases. Five isolates in clade A developed macrolide resistance via 5.1 kb mega element recombination (encoding mefE and msrD), while one isolate in clade B displayed quinolone resistance via a gyrA mutation. Conclusions: WGS is valuable for routine surveillance of pneumococcal clinical isolates and facilitates prediction of genotype and antibiotic resistance. The emergence of 22F in Ontario in the post-vaccine era and evidence of evolution and divergence of the 22F population warrants heightened pneumococcal molecular surveillance.
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Affiliation(s)
- Xianding Deng
- Public Health Ontario LaboratoryToronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of TorontoToronto, ON, Canada
- Mount Sinai Hospital and University Health NetworkToronto, ON, Canada
| | - Nader Memari
- Public Health Ontario LaboratoryToronto, ON, Canada
| | | | - Taryn Athey
- Public Health Ontario LaboratoryToronto, ON, Canada
| | - Marc Isabel
- Department of Mathematics and Statistics, University of LavalQuebec, QC, Canada
| | - Tony Mazzulli
- Public Health Ontario LaboratoryToronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of TorontoToronto, ON, Canada
- Mount Sinai Hospital and University Health NetworkToronto, ON, Canada
| | - Nahuel Fittipaldi
- Public Health Ontario LaboratoryToronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of TorontoToronto, ON, Canada
| | - Jonathan B. Gubbay
- Public Health Ontario LaboratoryToronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of TorontoToronto, ON, Canada
- Mount Sinai Hospital and University Health NetworkToronto, ON, Canada
- The Hospital for Sick ChildrenToronto, ON, Canada
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Suvorov A, Jensen NO, Sharkey CR, Fujimoto MS, Bodily P, Wightman HMC, Ogden TH, Clement MJ, Bybee SM. Opsins have evolved under the permanent heterozygote model: insights from phylotranscriptomics of Odonata. Mol Ecol 2016; 26:1306-1322. [DOI: 10.1111/mec.13884] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 09/24/2016] [Accepted: 10/04/2016] [Indexed: 02/04/2023]
Affiliation(s)
- Anton Suvorov
- Department of Biology; Brigham Young University; Provo UT 84602 USA
| | | | | | | | - Paul Bodily
- Computer Science Department; Brigham Young University; Provo UT 84602 USA
| | | | - T. Heath Ogden
- Department of Biology; Utah Valley University; Orem UT 84058 USA
| | - Mark J. Clement
- Computer Science Department; Brigham Young University; Provo UT 84602 USA
| | - Seth M. Bybee
- Department of Biology; Brigham Young University; Provo UT 84602 USA
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Wang J, Lamer JT, Gaughan S, Wachholtz M, Wang C, Lu G. Transcriptomic comparison of invasive bigheaded carps ( Hypophthalmichthys nobilis and Hypophthalmichthys molitrix) and their hybrids. Ecol Evol 2016; 6:8452-8459. [PMID: 28031797 PMCID: PMC5167015 DOI: 10.1002/ece3.2574] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 09/30/2016] [Accepted: 10/05/2016] [Indexed: 11/15/2022] Open
Abstract
Bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix), collectively called bigheaded carps, are invasive species in the Mississippi River Basin (MRB). Interspecific hybridization between bigheaded carps has been considered rare within their native rivers in China; however, it is prevalent in the MRB. We conducted de novo transcriptome analysis of pure and hybrid bigheaded carps and obtained 40,759 to 51,706 transcripts for pure, F1 hybrid, and backcross bigheaded carps. The search against protein databases resulted in 20,336–28,133 annotated transcripts (over 50% of the transcriptome) with over 13,000 transcripts mapped to 23 Gene Ontology biological processes and 127 KEGG metabolic pathways. More transcripts were detected in silver carp than in bighead carp; however, comparable numbers of transcripts were annotated. Transcriptomic variation detected between two F1 hybrids may indicate a potential loss of fitness in hybrids. The neighbor‐joining distance tree constructed using over 2,500 one‐to‐one orthologous sequences suggests transcriptomes could be used to infer the history of introgression and hybridization. Moreover, we detected 24,792 candidate SNPs that can be used to identify different species. The transcriptomes, orthologous sequences, and candidate SNPs obtained in this study should provide further knowledge of interspecific hybridization and introgression.
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Affiliation(s)
- Jun Wang
- Department of Biology University of Nebraska at Omaha Omaha NE 68182 USA; Key Laboratory of Freshwater Fisheries Germplasm Resources Ministry of Agriculture Shanghai Ocean University Shanghai 201306 China
| | - James T Lamer
- Department of Biological Sciences Western Illinois University Macomb IL 61455 USA
| | - Sarah Gaughan
- Department of Biology University of Nebraska at Omaha Omaha NE 68182 USA
| | - Michael Wachholtz
- Department of Biology University of Nebraska at Omaha Omaha NE 68182 USA
| | - Chenghui Wang
- Key Laboratory of Freshwater Fisheries Germplasm Resources Ministry of Agriculture Shanghai Ocean University Shanghai 201306 China
| | - Guoqing Lu
- Department of Biology University of Nebraska at Omaha Omaha NE 68182 USA; School of Interdisciplinary Informatics University of Nebraska at Omaha Omaha NE 68182 USA
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Shin J, Song Y, Jeong Y, Cho BK. Analysis of the Core Genome and Pan-Genome of Autotrophic Acetogenic Bacteria. Front Microbiol 2016; 7:1531. [PMID: 27733845 PMCID: PMC5039349 DOI: 10.3389/fmicb.2016.01531] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 09/12/2016] [Indexed: 01/07/2023] Open
Abstract
Acetogens are obligate anaerobic bacteria capable of reducing carbon dioxide (CO2) to multicarbon compounds coupled to the oxidation of inorganic substrates, such as hydrogen (H2) or carbon monoxide (CO), via the Wood-Ljungdahl pathway. Owing to the metabolic capability of CO2 fixation, much attention has been focused on understanding the unique pathways associated with acetogens, particularly their metabolic coupling of CO2 fixation to energy conservation. Most known acetogens are phylogenetically and metabolically diverse bacteria present in 23 different bacterial genera. With the increased volume of available genome information, acetogenic bacterial genomes can be analyzed by comparative genome analysis. Even with the genetic diversity that exists among acetogens, the Wood-Ljungdahl pathway, a central metabolic pathway, and cofactor biosynthetic pathways are highly conserved for autotrophic growth. Additionally, comparative genome analysis revealed that most genes in the acetogen-specific core genome were associated with the Wood-Ljungdahl pathway. The conserved enzymes and those predicted as missing can provide insight into biological differences between acetogens and allow for the discovery of promising candidates for industrial applications.
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Affiliation(s)
- Jongoh Shin
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology Daejeon, South Korea
| | - Yoseb Song
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology Daejeon, South Korea
| | - Yujin Jeong
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology Daejeon, South Korea
| | - Byung-Kwan Cho
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and TechnologyDaejeon, South Korea; Intelligent Synthetic Biology CenterDaejeon, South Korea
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47
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Making sense of genomes of parasitic worms: Tackling bioinformatic challenges. Biotechnol Adv 2016; 34:663-686. [DOI: 10.1016/j.biotechadv.2016.03.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 02/25/2016] [Accepted: 03/01/2016] [Indexed: 01/25/2023]
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Koehorst JJ, Saccenti E, Schaap PJ, Martins Dos Santos VAP, Suarez-Diez M. Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics. F1000Res 2016; 5:1987. [PMID: 27703668 PMCID: PMC5031134 DOI: 10.12688/f1000research.9416.3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/26/2017] [Indexed: 11/20/2022] Open
Abstract
A functional comparative genome analysis is essential to understand the mechanisms underlying bacterial evolution and adaptation. Detection of functional orthologs using standard global sequence similarity methods faces several problems; the need for defining arbitrary acceptance thresholds for similarity and alignment length, lateral gene acquisition and the high computational cost for finding bi-directional best matches at a large scale. We investigated the use of protein domain architectures for large scale functional comparative analysis as an alternative method. The performance of both approaches was assessed through functional comparison of 446 bacterial genomes sampled at different taxonomic levels. We show that protein domain architectures provide a fast and efficient alternative to methods based on sequence similarity to identify groups of functionally equivalent proteins within and across taxonomic boundaries, and it is suitable for large scale comparative analysis. Running both methods in parallel pinpoints potential functional adaptations that may add to bacterial fitness.
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Affiliation(s)
- Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands.,LifeGlimmer GmBH, Berlin, Germany
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
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49
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Sriswasdi S, Takashima M, Manabe RI, Ohkuma M, Sugita T, Iwasaki W. Global deceleration of gene evolution following recent genome hybridizations in fungi. Genome Res 2016; 26:1081-90. [PMID: 27440871 PMCID: PMC4971771 DOI: 10.1101/gr.205948.116] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 06/17/2016] [Indexed: 11/27/2022]
Abstract
Polyploidization events such as whole-genome duplication and inter-species hybridization are major evolutionary forces that shape genomes. Although long-term effects of polyploidization have been well-characterized, early molecular evolutionary consequences of polyploidization remain largely unexplored. Here, we report the discovery of two recent and independent genome hybridizations within a single clade of a fungal genus, Trichosporon. Comparative genomic analyses revealed that redundant genes are experiencing decelerations, not accelerations, of evolutionary rates. We identified a relationship between gene conversion and decelerated evolution suggesting that gene conversion may improve the genome stability of young hybrids by restricting gene functional divergences. Furthermore, we detected large-scale gene losses from transcriptional and translational machineries that indicate a global compensatory mechanism against increased gene dosages. Overall, our findings illustrate counteracting mechanisms during an early phase of post-genome hybridization and fill a critical gap in existing theories on genome evolution.
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Affiliation(s)
- Sira Sriswasdi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Masako Takashima
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Ri-Ichiroh Manabe
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Takashi Sugita
- Department of Microbiology, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588, Japan
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8568, Japan; Atmosphere and Ocean Research Institute, University of Tokyo, Kashiwa, Chiba 277-8564, Japan
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50
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Mechanical cell competition kills cells via induction of lethal p53 levels. Nat Commun 2016; 7:11373. [PMID: 27109213 PMCID: PMC4848481 DOI: 10.1038/ncomms11373] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 03/18/2016] [Indexed: 02/07/2023] Open
Abstract
Cell competition is a quality control mechanism that eliminates unfit cells. How cells compete is poorly understood, but it is generally accepted that molecular exchange between cells signals elimination of unfit cells. Here we report an orthogonal mechanism of cell competition, whereby cells compete through mechanical insults. We show that MDCK cells silenced for the polarity gene scribble (scribKD) are hypersensitive to compaction, that interaction with wild-type cells causes their compaction and that crowding is sufficient for scribKD cell elimination. Importantly, we show that elevation of the tumour suppressor p53 is necessary and sufficient for crowding hypersensitivity. Compaction, via activation of Rho-associated kinase (ROCK) and the stress kinase p38, leads to further p53 elevation, causing cell death. Thus, in addition to molecules, cells use mechanical means to compete. Given the involvement of p53, compaction hypersensitivity may be widespread among damaged cells and offers an additional route to eliminate unfit cells. Cell competition is a quality control mechanism to eliminate unfit cells. Here the authors show that physical compaction of less fit cells surrounded by healthy neighbours leads to increased expression of tumour suppressor p53 in the compacted cells, causing cell death.
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