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Montenegro JD, Golicz AA, Bayer PE, Hurgobin B, Lee H, Chan CKK, Visendi P, Lai K, Doležel J, Batley J, Edwards D. The pangenome of hexaploid bread wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:1007-1013. [PMID: 28231383 DOI: 10.1111/tpj.13515] [Citation(s) in RCA: 215] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/06/2017] [Indexed: 05/19/2023]
Abstract
There is an increasing understanding that variation in gene presence-absence plays an important role in the heritability of agronomic traits; however, there have been relatively few studies on variation in gene presence-absence in crop species. Hexaploid wheat is one of the most important food crops in the world and intensive breeding has reduced the genetic diversity of elite cultivars. Major efforts have produced draft genome assemblies for the cultivar Chinese Spring, but it is unknown how well this represents the genome diversity found in current modern elite cultivars. In this study we build an improved reference for Chinese Spring and explore gene diversity across 18 wheat cultivars. We predict a pangenome size of 140 500 ± 102 genes, a core genome of 81 070 ± 1631 genes and an average of 128 656 genes in each cultivar. Functional annotation of the variable gene set suggests that it is enriched for genes that may be associated with important agronomic traits. In addition to variation in gene presence, more than 36 million intervarietal single nucleotide polymorphisms were identified across the pangenome. This study of the wheat pangenome provides insight into genome diversity in elite wheat as a basis for genomics-based improvement of this important crop. A wheat pangenome, GBrowse, is available at http://appliedbioinformatics.com.au/cgi-bin/gb2/gbrowse/WheatPan/, and data are available to download from http://wheatgenome.info/wheat_genome_databases.php.
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Affiliation(s)
- Juan D Montenegro
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia
| | - Agnieszka A Golicz
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia
- School of Plant Biology, University of Western Australia, Crawley, WA, 6009, Australia
| | - Philipp E Bayer
- School of Plant Biology, University of Western Australia, Crawley, WA, 6009, Australia
| | - Bhavna Hurgobin
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia
- School of Plant Biology, University of Western Australia, Crawley, WA, 6009, Australia
| | - HueyTyng Lee
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia
- School of Plant Biology, University of Western Australia, Crawley, WA, 6009, Australia
| | - Chon-Kit Kenneth Chan
- School of Plant Biology, University of Western Australia, Crawley, WA, 6009, Australia
| | - Paul Visendi
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia
| | | | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-783 71, Olomouc, Czech Republic
| | - Jacqueline Batley
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia
- School of Plant Biology, University of Western Australia, Crawley, WA, 6009, Australia
- Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia
| | - David Edwards
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia
- School of Plant Biology, University of Western Australia, Crawley, WA, 6009, Australia
- Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia
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302
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Deng CH, Plummer KM, Jones DAB, Mesarich CH, Shiller J, Taranto AP, Robinson AJ, Kastner P, Hall NE, Templeton MD, Bowen JK. Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range. BMC Genomics 2017; 18:339. [PMID: 28464870 PMCID: PMC5412055 DOI: 10.1186/s12864-017-3699-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/11/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Fungal plant pathogens belonging to the genus Venturia cause damaging scab diseases of members of the Rosaceae. In terms of economic impact, the most important of these are V. inaequalis, which infects apple, and V. pirina, which is a pathogen of European pear. Given that Venturia fungi colonise the sub-cuticular space without penetrating plant cells, it is assumed that effectors that contribute to virulence and determination of host range will be secreted into this plant-pathogen interface. Thus the predicted secretomes of a range of isolates of Venturia with distinct host-ranges were interrogated to reveal putative proteins involved in virulence and pathogenicity. RESULTS Genomes of Venturia pirina (one European pear scab isolate) and Venturia inaequalis (three apple scab, and one loquat scab, isolates) were sequenced and the predicted secretomes of each isolate identified. RNA-Seq was conducted on the apple-specific V. inaequalis isolate Vi1 (in vitro and infected apple leaves) to highlight virulence and pathogenicity components of the secretome. Genes encoding over 600 small secreted proteins (candidate effectors) were identified, most of which are novel to Venturia, with expansion of putative effector families a feature of the genus. Numerous genes with similarity to Leptosphaeria maculans AvrLm6 and the Verticillium spp. Ave1 were identified. Candidates for avirulence effectors with cognate resistance genes involved in race-cultivar specificity were identified, as were putative proteins involved in host-species determination. Candidate effectors were found, on average, to be in regions of relatively low gene-density and in closer proximity to repeats (e.g. transposable elements), compared with core eukaryotic genes. CONCLUSIONS Comparative secretomics has revealed candidate effectors from Venturia fungal plant pathogens that attack pome fruit. Effectors that are putative determinants of host range were identified; both those that may be involved in race-cultivar and host-species specificity. Since many of the effector candidates are in close proximity to repetitive sequences this may point to a possible mechanism for the effector gene family expansion observed and a route to diversification via transposition and repeat-induced point mutation.
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Affiliation(s)
- Cecilia H. Deng
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
| | - Kim M. Plummer
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Plant Biosecurity Cooperative Research Centre, Bruce, ACT Australia
| | - Darcy A. B. Jones
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Present Address: The Centre for Crop and Disease Management, Curtin University, Bentley, Australia
| | - Carl H. Mesarich
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
- The School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Present Address: Institute of Agriculture & Environment, Massey University, Palmerston North, New Zealand
| | - Jason Shiller
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Present Address: INRA-Angers, Beaucouzé, Cedex, France
| | - Adam P. Taranto
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, Australia
| | - Andrew J. Robinson
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative (VLSCI), Victoria, Australia
| | - Patrick Kastner
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
| | - Nathan E. Hall
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative (VLSCI), Victoria, Australia
| | - Matthew D. Templeton
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
- The School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Joanna K. Bowen
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
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303
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Kushanov FN, Buriev ZT, Shermatov SE, Turaev OS, Norov TM, Pepper AE, Saha S, Ulloa M, Yu JZ, Jenkins JN, Abdukarimov A, Abdurakhmonov IY. QTL mapping for flowering-time and photoperiod insensitivity of cotton Gossypium darwinii Watt. PLoS One 2017; 12:e0186240. [PMID: 29016665 PMCID: PMC5633191 DOI: 10.1371/journal.pone.0186240] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/27/2017] [Indexed: 02/05/2023] Open
Abstract
Most wild and semi-wild species of the genus Gossypium are exhibit photoperiod-sensitive flowering. The wild germplasm cotton is a valuable source of genes for genetic improvement of modern cotton cultivars. A bi-parental cotton population segregating for photoperiodic flowering was developed by crossing a photoperiod insensitive irradiation mutant line with its pre-mutagenesis photoperiodic wild-type G. darwinii Watt genotype. Individuals from the F2 and F3 generations were grown with their parental lines and F1 hybrid progeny in the long day and short night summer condition (natural day-length) of Uzbekistan to evaluate photoperiod sensitivity, i.e., flowering-time during the seasons 2008-2009. Through genotyping the individuals of this bi-parental population segregating for flowering-time, linkage maps were constructed using 212 simple-sequence repeat (SSR) and three cleaved amplified polymorphic sequence (CAPS) markers. Six QTLs directly associated with flowering-time and photoperiodic flowering were discovered in the F2 population, whereas eight QTLs were identified in the F3 population. Two QTLs controlling photoperiodic flowering and duration of flowering were common in both populations. In silico annotations of the flanking DNA sequences of mapped SSRs from sequenced cotton (G. hirsutum L.) genome database has identified several potential 'candidate' genes that are known to be associated with regulation of flowering characteristics of plants. The outcome of this research will expand our understanding of the genetic and molecular mechanisms of photoperiodic flowering. Identified markers should be useful for marker-assisted selection in cotton breeding to improve early flowering characteristics.
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Affiliation(s)
- Fakhriddin N. Kushanov
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Zabardast T. Buriev
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Shukhrat E. Shermatov
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Ozod S. Turaev
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Tokhir M. Norov
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Alan E. Pepper
- Department of Biology, Texas A&M University, Colleges Station, Texas, United States of America
| | - Sukumar Saha
- Crop Science Research Laboratory, United States Department of Agriculture-Agricultural Research Services, Starkville, Mississippi, United States of America
| | - Mauricio Ulloa
- Plant Stress and Germplasm Development Research, United States Department of Agriculture-Agricultural Research Services, Lubbock, Texas, United States of America
| | - John Z. Yu
- Southern Plains Agricultural Research Center, United States Department of Agriculture-Agricultural Research Services, College Station, Texas, United States of America
| | - Johnie N. Jenkins
- Crop Science Research Laboratory, United States Department of Agriculture-Agricultural Research Services, Starkville, Mississippi, United States of America
| | - Abdusattor Abdukarimov
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Ibrokhim Y. Abdurakhmonov
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- * E-mail:
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304
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Identification and characterization of protein coding genes in monsonia (Monsonia burkeana Planch. ex harv) using a combination of approaches. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0499-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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305
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Hannula SE, van Veen JA. Primer Sets Developed for Functional Genes Reveal Shifts in Functionality of Fungal Community in Soils. Front Microbiol 2016; 7:1897. [PMID: 27965632 PMCID: PMC5126076 DOI: 10.3389/fmicb.2016.01897] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 11/11/2016] [Indexed: 12/16/2022] Open
Abstract
Phylogenetic diversity of soil microbes is a hot topic at the moment. However, the molecular tools for the assessment of functional diversity in the fungal community are less developed than tools based on genes encoding the ribosomal operon. Here 20 sets of primers targeting genes involved mainly in carbon cycling were designed and/or validated and the functioning of soil fungal communities along a chronosequence of land abandonment from agriculture was evaluated using them. We hypothesized that changes in fungal community structure during secondary succession would lead to difference in the types of genes present in soils and that these changes would be directional. We expected an increase in genes involved in degradation of recalcitrant organic matter in time since agriculture. Out of the investigated genes, the richness of the genes related to carbon cycling was significantly higher in fields abandoned for longer time. The composition of six of the genes analyzed revealed significant differences between fields abandoned for shorter and longer time. However, all genes revealed significant variance over the fields studied, and this could be related to other parameters than the time since agriculture such as pH, organic matter, and the amount of available nitrogen. Contrary to our initial hypothesis, the genes significantly different between fields were not related to the decomposition of more recalcitrant matter but rather involved in degradation of cellulose and hemicellulose.
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Affiliation(s)
- S. Emilia Hannula
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Wageningen, Netherlands
| | - Johannes A. van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Wageningen, Netherlands
- Insititute of Biology, Leiden UniversityLeiden, Netherlands
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306
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König S, Romoth LW, Gerischer L, Stanke M. Simultaneous gene finding in multiple genomes. Bioinformatics 2016; 32:3388-3395. [PMID: 27466621 PMCID: PMC5860283 DOI: 10.1093/bioinformatics/btw494] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 06/10/2016] [Accepted: 07/16/2016] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION As the tree of life is populated with sequenced genomes ever more densely, the new challenge is the accurate and consistent annotation of entire clades of genomes. We address this problem with a new approach to comparative gene finding that takes a multiple genome alignment of closely related species and simultaneously predicts the location and structure of protein-coding genes in all input genomes, thereby exploiting negative selection and sequence conservation. The model prefers potential gene structures in the different genomes that are in agreement with each other, or-if not-where the exon gains and losses are plausible given the species tree. We formulate the multi-species gene finding problem as a binary labeling problem on a graph. The resulting optimization problem is NP hard, but can be efficiently approximated using a subgradient-based dual decomposition approach. RESULTS The proposed method was tested on whole-genome alignments of 12 vertebrate and 12 Drosophila species. The accuracy was evaluated for human, mouse and Drosophila melanogaster and compared to competing methods. Results suggest that our method is well-suited for annotation of (a large number of) genomes of closely related species within a clade, in particular, when RNA-Seq data are available for many of the genomes. The transfer of existing annotations from one genome to another via the genome alignment is more accurate than previous approaches that are based on protein-spliced alignments, when the genomes are at close to medium distances. AVAILABILITY AND IMPLEMENTATION The method is implemented in C ++ as part of Augustus and available open source at http://bioinf.uni-greifswald.de/augustus/ CONTACT: stefaniekoenig@ymail.com or mario.stanke@uni-greifswald.deSupplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Stefanie König
- Institute of Mathematics and Computer Science, University of Greifswald, Greifswald, 17487, Germany
| | - Lars W Romoth
- Institute of Mathematics and Computer Science, University of Greifswald, Greifswald, 17487, Germany
| | - Lizzy Gerischer
- Institute of Mathematics and Computer Science, University of Greifswald, Greifswald, 17487, Germany
| | - Mario Stanke
- Institute of Mathematics and Computer Science, University of Greifswald, Greifswald, 17487, Germany
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307
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Xiong Z, Li F, Li Q, Zhou L, Gamble T, Zheng J, Kui L, Li C, Li S, Yang H, Zhang G. Draft genome of the leopard gecko, Eublepharis macularius. Gigascience 2016; 5:47. [PMID: 27784328 PMCID: PMC5080775 DOI: 10.1186/s13742-016-0151-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 10/11/2016] [Indexed: 01/21/2023] Open
Abstract
Background Geckos are among the most species-rich reptile groups and the sister clade to all other lizards and snakes. Geckos possess a suite of distinctive characteristics, including adhesive digits, nocturnal activity, hard, calcareous eggshells, and a lack of eyelids. However, one gecko clade, the Eublepharidae, appears to be the exception to most of these ‘rules’ and lacks adhesive toe pads, has eyelids, and lays eggs with soft, leathery eggshells. These differences make eublepharids an important component of any investigation into the underlying genomic innovations contributing to the distinctive phenotypes in ‘typical’ geckos. Findings We report high-depth genome sequencing, assembly, and annotation for a male leopard gecko, Eublepharis macularius (Eublepharidae). Illumina sequence data were generated from seven insert libraries (ranging from 170 to 20 kb), representing a raw sequencing depth of 136X from 303 Gb of data, reduced to 84X and 187 Gb after filtering. The assembled genome of 2.02 Gb was close to the 2.23 Gb estimated by k-mer analysis. Scaffold and contig N50 sizes of 664 and 20 kb, respectively, were comparable to the previously published Gekko japonicus genome. Repetitive elements accounted for 42 % of the genome. Gene annotation yielded 24,755 protein-coding genes, of which 93 % were functionally annotated. CEGMA and BUSCO assessment showed that our assembly captured 91 % (225 of 248) of the core eukaryotic genes, and 76 % of vertebrate universal single-copy orthologs. Conclusions Assembly of the leopard gecko genome provides a valuable resource for future comparative genomic studies of geckos and other squamate reptiles. Electronic supplementary material The online version of this article (doi:10.1186/s13742-016-0151-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zijun Xiong
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China
| | - Fang Li
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
| | - Qiye Li
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Long Zhou
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI, 53201, USA
| | - Jiao Zheng
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
| | - Ling Kui
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China
| | - Cai Li
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
| | - Shengbin Li
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China. .,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China. .,Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark.
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308
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Xu N, Ye C, Chen X, Liu J, Liu L, Chen J. Genome Sequencing of the Pyruvate-producing Strain Candida glabrata CCTCC M202019 and Genomic Comparison with Strain CBS138. Sci Rep 2016; 6:34893. [PMID: 27713500 PMCID: PMC5054605 DOI: 10.1038/srep34893] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/21/2016] [Indexed: 11/22/2022] Open
Abstract
Candida glabrata CCTCC M202019 as an industrial yeast strain that is widely used to produce α-oxocarboxylic acid. Strain M202019 has been proven to have a higher pyruvate-producing capacity than the reference strain CBS138. To characterize the genotype of the M202019 strain, we generated a draft sequence of its genome, which has a size of 12.1 Mbp and a GC content of 38.47%. Evidence accumulated during genome annotation suggests that strain M202019 has strong capacities for glucose transport and pyruvate biosynthesis, defects in pyruvate catabolism, as well as variations in genes involved in nutrient and dicarboxylic acid transport, oxidative phosphorylation, and other relevant aspects of carbon metabolism, which might promote pyruvate accumulation. In addition to differences in its central carbon metabolism, a genomic analysis revealed genetic differences in adhesion metabolism. Forty-nine adhesin-like proteins of strain M202019 were identified classified into seven subfamilies. Decreased amounts of adhesive proteins, and deletions or changes of low-complexity repeats and functional domains might lead to lower adhesion and reduced pathogenicity. Further virulence experiments validated the biological safety of strain M202019. Analysis of the C. glabrata CCTCC M202019 genome sequence provides useful insights into its genetic context, physical characteristics, and potential metabolic capacity.
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Affiliation(s)
- Nan Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Chao Ye
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jian Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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309
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Pucker B, Holtgräwe D, Rosleff Sörensen T, Stracke R, Viehöver P, Weisshaar B. A De Novo Genome Sequence Assembly of the Arabidopsis thaliana Accession Niederzenz-1 Displays Presence/Absence Variation and Strong Synteny. PLoS One 2016; 11:e0164321. [PMID: 27711162 PMCID: PMC5053417 DOI: 10.1371/journal.pone.0164321] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 09/22/2016] [Indexed: 11/23/2022] Open
Abstract
Arabidopsis thaliana is the most important model organism for fundamental plant biology. The genome diversity of different accessions of this species has been intensively studied, for example in the 1001 genome project which led to the identification of many small nucleotide polymorphisms (SNPs) and small insertions and deletions (InDels). In addition, presence/absence variation (PAV), copy number variation (CNV) and mobile genetic elements contribute to genomic differences between A. thaliana accessions. To address larger genome rearrangements between the A. thaliana reference accession Columbia-0 (Col-0) and another accession of about average distance to Col-0, we created a de novo next generation sequencing (NGS)-based assembly from the accession Niederzenz-1 (Nd-1). The result was evaluated with respect to assembly strategy and synteny to Col-0. We provide a high quality genome sequence of the A. thaliana accession (Nd-1, LXSY01000000). The assembly displays an N50 of 0.590 Mbp and covers 99% of the Col-0 reference sequence. Scaffolds from the de novo assembly were positioned on the basis of sequence similarity to the reference. Errors in this automatic scaffold anchoring were manually corrected based on analyzing reciprocal best BLAST hits (RBHs) of genes. Comparison of the final Nd-1 assembly to the reference revealed duplications and deletions (PAV). We identified 826 insertions and 746 deletions in Nd-1. Randomly selected candidates of PAV were experimentally validated. Our Nd-1 de novo assembly allowed reliable identification of larger genic and intergenic variants, which was difficult or error-prone by short read mapping approaches alone. While overall sequence similarity as well as synteny is very high, we detected short and larger (affecting more than 100 bp) differences between Col-0 and Nd-1 based on bi-directional comparisons. The de novo assembly provided here and additional assemblies that will certainly be published in the future will allow to describe the pan-genome of A. thaliana.
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Affiliation(s)
- Boas Pucker
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Daniela Holtgräwe
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Thomas Rosleff Sörensen
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Ralf Stracke
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Prisca Viehöver
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Bernd Weisshaar
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- * E-mail:
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310
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Taylor A, Vágány V, Jackson AC, Harrison RJ, Rainoni A, Clarkson JP. Identification of pathogenicity-related genes in Fusarium oxysporum f. sp. cepae. MOLECULAR PLANT PATHOLOGY 2016; 17:1032-47. [PMID: 26609905 PMCID: PMC4982077 DOI: 10.1111/mpp.12346] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 11/13/2015] [Accepted: 11/15/2015] [Indexed: 05/06/2023]
Abstract
Pathogenic isolates of Fusarium oxysporum, distinguished as formae speciales (f. spp.) on the basis of their host specificity, cause crown rots, root rots and vascular wilts on many important crops worldwide. Fusarium oxysporum f. sp. cepae (FOC) is particularly problematic to onion growers worldwide and is increasing in prevalence in the UK. We characterized 31 F. oxysporum isolates collected from UK onions using pathogenicity tests, sequencing of housekeeping genes and identification of effectors. In onion seedling and bulb tests, 21 isolates were pathogenic and 10 were non-pathogenic. The molecular characterization of these isolates, and 21 additional isolates comprising other f. spp. and different Fusarium species, was carried out by sequencing three housekeeping genes. A concatenated tree separated the F. oxysporum isolates into six clades, but did not distinguish between pathogenic and non-pathogenic isolates. Ten putative effectors were identified within FOC, including seven Secreted In Xylem (SIX) genes first reported in F. oxysporum f. sp. lycopersici. Two highly homologous proteins with signal peptides and RxLR motifs (CRX1/CRX2) and a gene with no previously characterized domains (C5) were also identified. The presence/absence of nine of these genes was strongly related to pathogenicity against onion and all were shown to be expressed in planta. Different SIX gene complements were identified in other f. spp., but none were identified in three other Fusarium species from onion. Although the FOC SIX genes had a high level of homology with other f. spp., there were clear differences in sequences which were unique to FOC, whereas CRX1 and C5 genes appear to be largely FOC specific.
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Affiliation(s)
- Andrew Taylor
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK
| | - Viktória Vágány
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK
| | - Alison C Jackson
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK
| | | | - Alessandro Rainoni
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK
| | - John P Clarkson
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK
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311
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Derelle R, López-García P, Timpano H, Moreira D. A Phylogenomic Framework to Study the Diversity and Evolution of Stramenopiles (=Heterokonts). Mol Biol Evol 2016; 33:2890-2898. [PMID: 27512113 DOI: 10.1093/molbev/msw168] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Stramenopiles or heterokonts constitute one of the most speciose and diverse clades of protists. It includes ecologically important algae (such as diatoms or large multicellular brown seaweeds), as well as heterotrophic (e.g., bicosoecids, MAST groups) and parasitic (e.g., Blastocystis, oomycetes) species. Despite their evolutionary and ecological relevance, deep phylogenetic relationships among stramenopile groups, inferred mostly from small-subunit rDNA phylogenies, remain unresolved, especially for the heterotrophic taxa. Taking advantage of recently released stramenopile transcriptome and genome sequences, as well as data from the genomic assembly of the MAST-3 species Incisomonas marina generated in our laboratory, we have carried out the first extensive phylogenomic analysis of stramenopiles, including representatives of most major lineages. Our analyses, based on a large data set of 339 widely distributed proteins, strongly support a root of stramenopiles lying between two clades, Bigyra and Gyrista (Pseudofungi plus Ochrophyta). Additionally, our analyses challenge the Phaeista-Khakista dichotomy of photosynthetic stramenopiles (ochrophytes) as two groups previously considered to be part of the Phaeista (Pelagophyceae and Dictyochophyceae), branch with strong support with the Khakista (Bolidophyceae and Diatomeae). We propose a new classification of ochrophytes within the two groups Chrysista and Diatomista to reflect the new phylogenomic results. Our stramenopile phylogeny provides a robust phylogenetic framework to investigate the evolution and diversification of this group of ecologically relevant protists.
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Affiliation(s)
- Romain Derelle
- Unité d'Ecologie, Systématique et Evolution, Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud/Paris-Saclay, AgroParisTech, Orsay, France
| | - Purificación López-García
- Unité d'Ecologie, Systématique et Evolution, Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud/Paris-Saclay, AgroParisTech, Orsay, France
| | - Hélène Timpano
- Unité d'Ecologie, Systématique et Evolution, Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud/Paris-Saclay, AgroParisTech, Orsay, France
| | - David Moreira
- Unité d'Ecologie, Systématique et Evolution, Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud/Paris-Saclay, AgroParisTech, Orsay, France
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312
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Draft Genome Sequence of Capniomyces stellatus, the Obligate Gut Fungal Symbiont of Stonefly. GENOME ANNOUNCEMENTS 2016; 4:4/4/e00761-16. [PMID: 27491991 PMCID: PMC4974312 DOI: 10.1128/genomea.00761-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Capniomyces stellatus is a host-specific endosymbiotic fungus, living in the hindgut of stoneflies (especially in Allocapnia). Here, we present the first draft genome sequence of the fungus, as well as the ab initio gene prediction and function analyses, which will facilitate the study and comparative analyses of insect-associated fungi.
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313
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Lu H, Quan H, Ren Z, Wang S, Xue R, Zhao B. The Genome of Undifilum oxytropis Provides Insights into Swainsonine Biosynthesis and Locoism. Sci Rep 2016; 6:30760. [PMID: 27477109 PMCID: PMC4967851 DOI: 10.1038/srep30760] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/08/2016] [Indexed: 01/15/2023] Open
Abstract
Undifilum oxytropis is a fungal endophyte of locoweeds. It produces swainsonine, which is the principal toxic ingredient of locoweeds. However, the genes, pathways and mechanisms of swainsonine biosynthesis are not known. In this study, the genome of U. oxytropis was firstly sequenced and assembled into a 70.05 megabases (Mb) draft genome, which encoded 11,057 protein-coding genes, and 54% of them were similar to current publicly available sequences. U. oxytropis genes were annotated and 164 putative genes were annotated into enzymes, such as Saccharopine dehydrogenase, Saccharopine oxidase, and Pyrroline-5-carboxylate reductase, hypothesized to be involved in the biosynthesis pathway of swainsonine. The genome sequence and gene annotation of U. oxytropis will provide new insights into functional analyses. The characterization of genes in swainsonine biosynthesis will greatly facilitate locoweed poisoning research and help direct locoism management.
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Affiliation(s)
- Hao Lu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Haiyun Quan
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhenhui Ren
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shuai Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ruixu Xue
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Baoyu Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
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314
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Qiu Z, Liu F, Lu H, Yuan H, Zhang Q, Huang Y. De Novo Assembly and Characterization of the Transcriptome of Grasshopper Shirakiacris shirakii. Int J Mol Sci 2016; 17:ijms17071110. [PMID: 27455245 PMCID: PMC4964485 DOI: 10.3390/ijms17071110] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 06/28/2016] [Accepted: 07/07/2016] [Indexed: 11/30/2022] Open
Abstract
Background: The grasshopper Shirakiacris shirakii is an important agricultural pest and feeds mainly on gramineous plants, thereby causing economic damage to a wide range of crops. However, genomic information on this species is extremely limited thus far, and transcriptome data relevant to insecticide resistance and pest control are also not available. Methods: The transcriptome of S. shirakii was sequenced using the Illumina HiSeq platform, and we de novo assembled the transcriptome. Results: Its sequencing produced a total of 105,408,878 clean reads, and the de novo assembly revealed 74,657 unigenes with an average length of 680 bp and N50 of 1057 bp. A total of 28,173 unigenes were annotated for the NCBI non-redundant protein sequences (Nr), NCBI non-redundant nucleotide sequences (Nt), a manually-annotated and reviewed protein sequence database (Swiss-Prot), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Based on the Nr annotation results, we manually identified 79 unigenes encoding cytochrome P450 monooxygenases (P450s), 36 unigenes encoding carboxylesterases (CarEs) and 36 unigenes encoding glutathione S-transferases (GSTs) in S. shirakii. Core RNAi components relevant to miroRNA, siRNA and piRNA pathways, including Pasha, Loquacious, Argonaute-1, Argonaute-2, Argonaute-3, Zucchini, Aubergine, enhanced RNAi-1 and Piwi, were expressed in S. shirakii. We also identified five unigenes that were homologous to the Sid-1 gene. In addition, the analysis of differential gene expressions revealed that a total of 19,764 unigenes were up-regulated and 4185 unigenes were down-regulated in larvae. In total, we predicted 7504 simple sequence repeats (SSRs) from 74,657 unigenes. Conclusions: The comprehensive de novo transcriptomic data of S. shirakii will offer a series of valuable molecular resources for better studying insecticide resistance, RNAi and molecular marker discovery in the transcriptome.
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Affiliation(s)
- Zhongying Qiu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China.
| | - Fei Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China.
- College of Life Sciences and Food Engineering, Shaanxi Xueqian Normal University, Xi'an 710061, China.
| | - Huimeng Lu
- Key Laboratory for Space Bioscience & Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China.
| | - Hao Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China.
| | - Qin Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China.
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China.
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315
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Xie J, Li S, Mo C, Xiao X, Peng D, Wang G, Xiao Y. Genome and Transcriptome Sequences Reveal the Specific Parasitism of the Nematophagous Purpureocillium lilacinum 36-1. Front Microbiol 2016; 7:1084. [PMID: 27486440 PMCID: PMC4949223 DOI: 10.3389/fmicb.2016.01084] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 06/28/2016] [Indexed: 01/12/2023] Open
Abstract
Purpureocillium lilacinum is a promising nematophagous ascomycete able to adapt diverse environments and it is also an opportunistic fungus that infects humans. A microbial inoculant of P. lilacinum has been registered to control plant parasitic nematodes. However, the molecular mechanism of the toxicological processes is still unclear because of the relatively few reports on the subject. In this study, using Illumina paired-end sequencing, the draft genome sequence and the transcriptome of P. lilacinum strain 36-1 infecting nematode-eggs were determined. Whole genome alignment indicated that P. lilacinum 36-1 possessed a more dynamic genome in comparison with P. lilacinum India strain. Moreover, a phylogenetic analysis showed that the P. lilacinum 36-1 had a closer relation to entomophagous fungi. The protein-coding genes in P. lilacinum 36-1 occurred much more frequently than they did in other fungi, which was a result of the depletion of repeat-induced point mutations (RIP). Comparative genome and transcriptome analyses revealed the genes that were involved in pathogenicity, particularly in the recognition, adhesion of nematode-eggs, downstream signal transduction pathways and hydrolase genes. By contrast, certain numbers of cellulose and xylan degradation genes and a lack of polysaccharide lyase genes showed the potential of P. lilacinum 36-1 as an endophyte. Notably, the expression of appressorium-formation and antioxidants-related genes exhibited similar infection patterns in P. lilacinum strain 36-1 to those of the model entomophagous fungi Metarhizium spp. These results uncovered the specific parasitism of P. lilacinum and presented the genes responsible for the infection of nematode-eggs.
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Affiliation(s)
- Jialian Xie
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University Wuhan, China
| | - Shaojun Li
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University Wuhan, China
| | - Chenmi Mo
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University Wuhan, China
| | - Xueqiong Xiao
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University Wuhan, China
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing, China
| | - Gaofeng Wang
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University Wuhan, China
| | - Yannong Xiao
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University Wuhan, China
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316
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Chang HX, Yendrek CR, Caetano-Anolles G, Hartman GL. Genomic characterization of plant cell wall degrading enzymes and in silico analysis of xylanases and polygalacturonases of Fusarium virguliforme. BMC Microbiol 2016; 16:147. [PMID: 27405320 PMCID: PMC4941037 DOI: 10.1186/s12866-016-0761-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 07/02/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Plant cell wall degrading enzymes (PCWDEs) are a subset of carbohydrate-active enzymes (CAZy) produced by plant pathogens to degrade plant cell walls. To counteract PCWDEs, plants release PCWDEs inhibitor proteins (PIPs) to reduce their impact. Several transgenic plants expressing exogenous PIPs that interact with fungal glycoside hydrolase (GH)11-type xylanases or GH28-type polygalacturonase (PG) have been shown to enhance disease resistance. However, many plant pathogenic Fusarium species were reported to escape PIPs inhibition. Fusarium virguliforme is a soilborne pathogen that causes soybean sudden death syndrome (SDS). Although the genome of F. virguliforme was sequenced, there were limited studies focused on the PCWDEs of F. virguliforme. Our goal was to understand the genomic CAZy structure of F. viguliforme, and determine if exogenous PIPs could be theoretically used in soybean to enhance resistance against F. virguliforme. RESULTS F. virguliforme produces diverse CAZy to degrade cellulose and pectin, similar to other necrotorphic and hemibiotrophic plant pathogenic fungi. However, some common CAZy of plant pathogenic fungi that catalyze hemicellulose, such as GH29, GH30, GH44, GH54, GH62, and GH67, were deficient in F. virguliforme. While the absence of these CAZy families might be complemented by other hemicellulases, F. virguliforme contained unique families including GH131, polysaccharide lyase (PL) 9, PL20, and PL22 that were not reported in other plant pathogenic fungi or oomycetes. Sequence analysis revealed two GH11 xylanases of F. virguliforme, FvXyn11A and FvXyn11B, have conserved residues that allow xylanase inhibitor protein I (XIP-I) binding. Structural modeling suggested that FvXyn11A and FvXyn11B could be blocked by XIP-I that serves as good candidate for developing transgenic soybeans. In contrast, one GH28 PG, FvPG2, contains an amino acid substitution that is potentially incompatible with the bean polygalacturonase-inhibitor protein II (PvPGIP2). CONCLUSIONS Identification and annotation of CAZy provided advanced understanding of genomic composition of PCWDEs in F. virguliforme. Sequence and structural analyses of FvXyn11A and FvXyn11B suggested both xylanases were conserved in residues that allow XIP-I inhibition, and expression of both xylanases were detected during soybean roots infection. We postulate that a transgenic soybean expressing wheat XIP-I may be useful for developing root rot resistance to F. virguliforme.
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Affiliation(s)
- Hao-Xun Chang
- />Department of Crop Sciences, University of Illinois, Urbana, IL 61801 USA
| | | | | | - Glen L. Hartman
- />Department of Crop Sciences, University of Illinois, Urbana, IL 61801 USA
- />USDA–Agricultural Research Services, Urbana, IL 61801 USA
- />National Soybean Research Center, University of Illinois, 1101 W. Peabody Dr., Urbana, IL 61801 USA
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317
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Wang Y, White MM, Kvist S, Moncalvo JM. Genome-Wide Survey of Gut Fungi (Harpellales) Reveals the First Horizontally Transferred Ubiquitin Gene from a Mosquito Host. Mol Biol Evol 2016; 33:2544-54. [PMID: 27343289 PMCID: PMC5026252 DOI: 10.1093/molbev/msw126] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Harpellales, an early-diverging fungal lineage, is associated with the digestive tracts of aquatic arthropod hosts. Concurrent with the production and annotation of the first four Harpellales genomes, we discovered that Zancudomyces culisetae, one of the most widely distributed Harpellales species, encodes an insect-like polyubiquitin chain. Ubiquitin and ubiquitin-like proteins are universally involved in protein degradation and regulation of immune response in eukaryotic organisms. Phylogenetic analyses inferred that this polyubiquitin variant has a mosquito origin. In addition, its amino acid composition, animal-like secondary structure, as well as the fungal nature of flanking genes all further support this as a horizontal gene transfer event. The single-copy polyubiquitin gene from Z. culisetae has lower GC ratio compared with homologs of insect taxa, which implies homogenization of the gene since its putatively ancient transfer. The acquired polyubiquitin gene may have served to improve important functions within Z. culisetae, by perhaps exploiting the insect hosts' ubiquitin-proteasome systems in the gut environment. Preliminary comparisons among the four Harpellales genomes highlight the reduced genome size of Z. culisetae, which corroborates its distinguishable symbiotic lifestyle. This is the first record of a horizontally transferred ubiquitin gene from disease-bearing insects to the gut-dwelling fungal endobiont and should invite further exploration in an evolutionary context.
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Affiliation(s)
- Yan Wang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Merlin M White
- Department of Biological Sciences, Boise State University
| | - Sebastian Kvist
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Jean-Marc Moncalvo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
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318
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Seemann SE, Anthon C, Palasca O, Gorodkin J. Quality Assessment of Domesticated Animal Genome Assemblies. Bioinform Biol Insights 2016; 9:49-58. [PMID: 27279738 PMCID: PMC4898645 DOI: 10.4137/bbi.s29333] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 05/02/2016] [Accepted: 05/03/2016] [Indexed: 11/07/2022] Open
Abstract
The era of high-throughput sequencing has made it relatively simple to sequence genomes and transcriptomes of individuals from many species. In order to analyze the resulting sequencing data, high-quality reference genome assemblies are required. However, this is still a major challenge, and many domesticated animal genomes still need to be sequenced deeper in order to produce high-quality assemblies. In the meanwhile, ironically, the extent to which RNAseq and other next-generation data is produced frequently far exceeds that of the genomic sequence. Furthermore, basic comparative analysis is often affected by the lack of genomic sequence. Herein, we quantify the quality of the genome assemblies of 20 domesticated animals and related species by assessing a range of measurable parameters, and we show that there is a positive correlation between the fraction of mappable reads from RNAseq data and genome assembly quality. We rank the genomes by their assembly quality and discuss the implications for genotype analyses.
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Affiliation(s)
- Stefan E Seemann
- Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, København, Denmark
| | - Christian Anthon
- Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, København, Denmark
| | - Oana Palasca
- Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, København, Denmark
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, København, Denmark
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319
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Wingfield BD, Ambler JM, Coetzee MP, de Beer ZW, Duong TA, Joubert F, Hammerbacher A, McTaggart AR, Naidoo K, Nguyen HD, Ponomareva E, Santana QS, Seifert KA, Steenkamp ET, Trollip C, van der Nest MA, Visagie CM, Wilken PM, Wingfield MJ, Yilmaz N. IMA Genome-F 6: Draft genome sequences of Armillaria fuscipes, Ceratocystiopsis minuta, Ceratocystis adiposa, Endoconidiophora laricicola, E. polonica and Penicillium freii DAOMC 242723. IMA Fungus 2016; 7:217-27. [PMID: 27433447 PMCID: PMC4941685 DOI: 10.5598/imafungus.2016.07.01.11] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 06/15/2016] [Indexed: 10/25/2022] Open
Abstract
The genomes of Armillaria fuscipes, Ceratocystiopsis minuta, Ceratocystis adiposa, Endoconidiophora laricicola, E. polonica, and Penicillium freii DAOMC 242723 are presented in this genome announcement. These six genomes are from plant pathogens and otherwise economically important fungal species. The genome sizes range from 21 Mb in the case of Ceratocystiopsis minuta to 58 Mb for the basidiomycete Armillaria fuscipes. These genomes include the first reports of genomes for the genus Endoconidiophora. The availability of these genome data will provide opportunities to resolve longstanding questions regarding the taxonomy of species in these genera. In addition these genome sequences through comparative studies with closely related organisms will increase our understanding of how these pathogens cause disease.
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Affiliation(s)
- Brenda D. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Jon M. Ambler
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Martin P.A. Coetzee
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Z. Wilhelm de Beer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Tuan A. Duong
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Fourie Joubert
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry and Genomics Research Institute, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Almuth Hammerbacher
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Alistair R. McTaggart
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Kershney Naidoo
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Hai D.T. Nguyen
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
- Department of Biology, University of Ottawa, 30 Marie-Curie, Ottawa, Ontario, K1N6N5, Canada
| | - Ekaterina Ponomareva
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
| | - Quentin S. Santana
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Keith A. Seifert
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
| | - Emma T. Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Conrad Trollip
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Magriet A. van der Nest
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Cobus M. Visagie
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
| | - P. Markus Wilken
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Michael J. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Neriman Yilmaz
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
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Drăgan MA, Moghul I, Priyam A, Bustos C, Wurm Y. GeneValidator: identify problems with protein-coding gene predictions. Bioinformatics 2016; 32:1559-61. [PMID: 26787666 PMCID: PMC4866521 DOI: 10.1093/bioinformatics/btw015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/08/2015] [Accepted: 12/18/2015] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED : Genomes of emerging model organisms are now being sequenced at very low cost. However, obtaining accurate gene predictions remains challenging: even the best gene prediction algorithms make substantial errors and can jeopardize subsequent analyses. Therefore, many predicted genes must be time-consumingly visually inspected and manually curated. We developed GeneValidator (GV) to automatically identify problematic gene predictions and to aid manual curation. For each gene, GV performs multiple analyses based on comparisons to gene sequences from large databases. The resulting report identifies problematic gene predictions and includes extensive statistics and graphs for each prediction to guide manual curation efforts. GV thus accelerates and enhances the work of biocurators and researchers who need accurate gene predictions from newly sequenced genomes. AVAILABILITY AND IMPLEMENTATION GV can be used through a web interface or in the command-line. GV is open-source (AGPL), available at https://wurmlab.github.io/tools/genevalidator CONTACT : y.wurm@qmul.ac.uk SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Ismail Moghul
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK and
| | - Anurag Priyam
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK and
| | - Claudio Bustos
- Departamento de Psiquiatría y Salud Mental, University of Concepción, Concepción, Chile
| | - Yannick Wurm
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK and
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321
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Liu X, Gao F, Ma Y, Liu S, Cui Y, Yuan Z, Kang X. Crystal structure and molecular mechanism of an aspartate/glutamate racemase from Escherichia coli O157. FEBS Lett 2016; 590:1262-9. [PMID: 27001440 DOI: 10.1002/1873-3468.12148] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 03/13/2016] [Accepted: 03/16/2016] [Indexed: 02/02/2023]
Abstract
EcL-DER, the aspartate/glutamate racemase from the pathogen Escherichia coli O157, exhibits racemase activity for l-aspartate and l-glutamate. This study reports the crystal structures of apo-EcL-DER, the EcL-DER-l-aspartate and the EcL-DER-d-aspartate complexes. The EcL-DER structure contains two domains, forming pseudo-mirror symmetry in the active site. A unique catalytic pair consisting of Thr(83) and Cys(197) exists in the active site. The characteristic conformations of l-Asp and d-Asp in the active site provide a straight structural evidence for the racemization mechanism of EcL-DER. In addition, the diversity of catalytic pairs implies that PLP-independent amino acid racemases adopt various catalytic mechanisms and are classified into different subgroups.
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Affiliation(s)
- Xiuhua Liu
- College of Life Sciences, Hebei University, Baoding, China
| | - Fei Gao
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Yinliang Ma
- College of Life Sciences, Hebei University, Baoding, China
| | - Shuang Liu
- College of Life Sciences, Hebei University, Baoding, China
| | - Yaqi Cui
- College of Life Sciences, Hebei University, Baoding, China
| | - Zenglin Yuan
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Xianjiang Kang
- College of Life Sciences, Hebei University, Baoding, China
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322
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Cho YB, Lee EJ, Cho S, Kim TY, Park JH, Cho BK. Functional elucidation of the non-coding RNAs of Kluyveromyces marxianus in the exponential growth phase. BMC Genomics 2016; 17:154. [PMID: 26923790 PMCID: PMC4770515 DOI: 10.1186/s12864-016-2474-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 02/15/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Non-coding RNAs (ncRNAs), which perform diverse regulatory roles, have been found in organisms from all superkingdoms of life. However, there have been limited numbers of studies on the functions of ncRNAs, especially in nonmodel organisms such as Kluyveromyces marxianus that is widely used in the field of industrial biotechnology. RESULTS In this study, we measured changes in transcriptome at three time points during the exponential growth phase of K. marxianus by using strand-specific RNA-seq. We found that approximately 60% of the transcriptome consists of ncRNAs transcribed from antisense and intergenic regions of the genome that were transcribed at lower levels than mRNA. In the transcriptome, a substantial number of long antisense ncRNAs (lancRNAs) are differentially expressed and enriched in carbohydrate and energy metabolism pathways. Furthermore, this enrichment is evolutionarily conserved, at least in yeast. Particularly, the mode of regulation of mRNA/lancRNA pairs is associated with mRNA transcription levels; the correlation between the pairs is positive at high mRNA transcriptional levels and negative at low levels. In addition, significant induction of mRNA and coverage of more than half of the mRNA sequence by a lancRNA strengthens the positive correlation between mRNA/lancRNA pairs. CONCLUSIONS Transcriptome sequencing of K. marxianus in the exponential growth phase reveals pervasive transcription of ncRNAs with evolutionarily conserved functions. Studies of the mode of regulation of mRNA/lancRNA pairs suggest that induction of lancRNA may be associated with switch-like behavior of mRNA/lancRNA pairs and efficient regulation of the carbohydrate and energy metabolism pathways in the exponential growth phase of K. marxianus being used in industrial applications.
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Affiliation(s)
- Yoo-Bok Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Republic of Korea.
| | - Eun Ju Lee
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Republic of Korea.
| | - Suhyung Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Republic of Korea.
| | - Tae Yong Kim
- Biomaterials Lab., Samsung Advanced Institute of Technology (SAIT), 130 Samsung-ro, Yeongtong-gu, Suwon, 443-803, Republic of Korea.
| | - Jin Hwan Park
- Biomaterials Lab., Samsung Advanced Institute of Technology (SAIT), 130 Samsung-ro, Yeongtong-gu, Suwon, 443-803, Republic of Korea.
| | - Byung-Kwan Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Republic of Korea. .,Intelligent Synthetic Biology Center, Daejeon, 305-701, Republic of Korea.
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323
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Chang HX, Domier LL, Radwan O, Yendrek CR, Hudson ME, Hartman GL. Identification of Multiple Phytotoxins Produced by Fusarium virguliforme Including a Phytotoxic Effector (FvNIS1) Associated With Sudden Death Syndrome Foliar Symptoms. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:96-108. [PMID: 26646532 DOI: 10.1094/mpmi-09-15-0219-r] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Sudden death syndrome (SDS) of soybean is caused by a soilborne pathogen, Fusarium virguliforme. Phytotoxins produced by F. virguliforme are translocated from infected roots to leaves, in which they cause SDS foliar symptoms. In this study, additional putative phytotoxins of F. virguliforme were identified, including three secondary metabolites and 11 effectors. While citrinin, fusaric acid, and radicicol induced foliar chlorosis and wilting, Soybean mosaic virus (SMV)-mediated overexpression of F. virguliforme necrosis-inducing secreted protein 1 (FvNIS1) induced SDS foliar symptoms that mimicked the development of foliar symptoms in the field. The expression level of fvnis1 remained steady over time, although foliar symptoms were delayed compared with the expression levels. SMV::FvNIS1 also displayed genotype-specific toxicity to which 75 of 80 soybean cultivars were susceptible. Genome-wide association mapping further identified three single nucleotide polymorphisms at two loci, where three leucine-rich repeat receptor-like protein kinase (LRR-RLK) genes were found. Culture filtrates of fvnis1 knockout mutants displayed a mild reduction in phytotoxicity, indicating that FvNIS1 is one of the phytotoxins responsible for SDS foliar symptoms and may contribute to the quantitative susceptibility of soybean by interacting with the LRR-RLK genes.
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Affiliation(s)
| | - Leslie L Domier
- 1 University of Illinois
- 2 USDA-Agricultural Research Service; and
| | | | - Craig R Yendrek
- 1 University of Illinois
- 3 Institute for Genomic Biology, Urbana, IL, U.S.A
| | | | - Glen L Hartman
- 1 University of Illinois
- 2 USDA-Agricultural Research Service; and
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324
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A Comprehensive Review of Emerging Computational Methods for Gene Identification. JOURNAL OF INFORMATION PROCESSING SYSTEMS 2016. [DOI: 10.3745/jips.04.0023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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325
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Hara Y, Tatsumi K, Yoshida M, Kajikawa E, Kiyonari H, Kuraku S. Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation. BMC Genomics 2015; 16:977. [PMID: 26581708 PMCID: PMC4652379 DOI: 10.1186/s12864-015-2007-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 10/03/2015] [Indexed: 01/07/2023] Open
Abstract
Background RNA-seq enables gene expression profiling in selected spatiotemporal windows and yields massive sequence information with relatively low cost and time investment, even for non-model species. However, there remains a large room for optimizing its workflow, in order to take full advantage of continuously developing sequencing capacity. Method Transcriptome sequencing for three embryonic stages of Madagascar ground gecko (Paroedura picta) was performed with the Illumina platform. The output reads were assembled de novo for reconstructing transcript sequences. In order to evaluate the completeness of transcriptome assemblies, we prepared a reference gene set consisting of vertebrate one-to-one orthologs. Result To take advantage of increased read length of >150 nt, we demonstrated shortened RNA fragmentation time, which resulted in a dramatic shift of insert size distribution. To evaluate products of multiple de novo assembly runs incorporating reads with different RNA sources, read lengths, and insert sizes, we introduce a new reference gene set, core vertebrate genes (CVG), consisting of 233 genes that are shared as one-to-one orthologs by all vertebrate genomes examined (29 species)., The completeness assessment performed by the computational pipelines CEGMA and BUSCO referring to CVG, demonstrated higher accuracy and resolution than with the gene set previously established for this purpose. As a result of the assessment with CVG, we have derived the most comprehensive transcript sequence set of the Madagascar ground gecko by means of assembling individual libraries followed by clustering the assembled sequences based on their overall similarities. Conclusion Our results provide several insights into optimizing de novo RNA-seq workflow, including the coordination between library insert size and read length, which manifested in improved connectivity of assemblies. The approach and assembly assessment with CVG demonstrated here would be applicable to transcriptome analysis of other species as well as whole genome analyses. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2007-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuichiro Hara
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
| | - Kaori Tatsumi
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
| | - Michio Yoshida
- Laboratory for Vertebrate Body Plan, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
| | - Eriko Kajikawa
- Laboratory for Vertebrate Body Plan, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
| | - Hiroshi Kiyonari
- Animal Resource Development Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo, 650-0047, Japan. .,Genetic Engineering Team, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
| | - Shigehiro Kuraku
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
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326
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AlMomin S, Kumar V, Al-Amad S, Al-Hussaini M, Dashti T, Al-Enezi K, Akbar A. Draft genome sequence of the silver pomfret fish, Pampus argenteus. Genome 2015; 59:51-8. [PMID: 26692342 DOI: 10.1139/gen-2015-0056] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Silver pomfret, Pampus argenteus, is a fish species from coastal waters. Despite its high commercial value, this edible fish has not been sequenced. Hence, its genetic and genomic studies have been limited. We report the first draft genome sequence of the silver pomfret obtained using a Next Generation Sequencing (NGS) technology. We assembled 38.7 Gb of nucleotides into scaffolds of 350 Mb with N50 of about 1.5 kb, using high quality paired end reads. These scaffolds represent 63.7% of the estimated silver pomfret genome length. The newly sequenced and assembled genome has 11.06% repetitive DNA regions, and this percentage is comparable to that of the tilapia genome. The genome analysis predicted 16 322 genes. About 91% of these genes showed homology with known proteins. Many gene clusters were annotated to protein and fatty-acid metabolism pathways that may be important in the context of the meat texture and immune system developmental processes. The reference genome can pave the way for the identification of many other genomic features that could improve breeding and population-management strategies, and it can also help characterize the genetic diversity of P. argenteus.
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Affiliation(s)
- Sabah AlMomin
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Vinod Kumar
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Sami Al-Amad
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Mohsen Al-Hussaini
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Talal Dashti
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Khaznah Al-Enezi
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Abrar Akbar
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
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327
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Wang J, Zhang Y, Xu Y, Fang W, Wang X, Fang Z, Xiao Y. Genome sequence of a laccase producing fungus Trametes sp. AH28-2. J Biotechnol 2015; 216:167-8. [PMID: 26548723 DOI: 10.1016/j.jbiotec.2015.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/02/2015] [Indexed: 11/24/2022]
Abstract
Trametes sp. AH28-2 (CCTCC AF 2015027) is a white rot fungus isolated from rotting wood in China. Primary study indicated that this strain can be induced by kraft lignin to secrete high levels of extracellular laccase, and differentially express laccase genes upon addition of different phenolic compounds. Here we report the complete genome sequence of Trametes sp. AH28-2 and its genetic basis for lignin degradation and phenolic xenobiotics metabolism.
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Affiliation(s)
- Jingjing Wang
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China; Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui 230601, China
| | - Yinliang Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yong Xu
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China; Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui 230601, China
| | - Wei Fang
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China; Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui 230601, China
| | - Xiaotang Wang
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, United States
| | - Zemin Fang
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China; Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui 230601, China.
| | - Yazhong Xiao
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China; Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui 230601, China.
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328
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Cock PJA, Chilton JM, Grüning B, Johnson JE, Soranzo N. NCBI BLAST+ integrated into Galaxy. Gigascience 2015; 4:39. [PMID: 26336600 PMCID: PMC4557756 DOI: 10.1186/s13742-015-0080-7] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 08/18/2015] [Indexed: 01/29/2023] Open
Abstract
Background The NCBI BLAST suite has become ubiquitous in modern molecular biology and is used for small tasks such as checking capillary sequencing results of single PCR products, genome annotation or even larger scale pan-genome analyses. For early adopters of the Galaxy web-based biomedical data analysis platform, integrating BLAST into Galaxy was a natural step for sequence comparison workflows. Findings The command line NCBI BLAST+ tool suite was wrapped for use within Galaxy. Appropriate datatypes were defined as needed. The integration of the BLAST+ tool suite into Galaxy has the goal of making common BLAST tasks easy and advanced tasks possible. Conclusions This project is an informal international collaborative effort, and is deployed and used on Galaxy servers worldwide. Several examples of applications are described here.
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Affiliation(s)
- Peter J A Cock
- Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - John M Chilton
- Minnesota Supercomputing Institute, University of Minnesota, 599 Walter Library, 117 Pleasant St. SE, 55455 Minneapolis, MN USA
| | - Björn Grüning
- Department of Computer Science, Albert-Ludwigs-University of Freiburg, Georges-Köhler-Allee 106, Freiburg, 79110 Germany
| | - James E Johnson
- Minnesota Supercomputing Institute, University of Minnesota, 599 Walter Library, 117 Pleasant St. SE, 55455 Minneapolis, MN USA
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329
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Marcet-Houben M, Gabaldón T. Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage. PLoS Biol 2015; 13:e1002220. [PMID: 26252497 PMCID: PMC4529251 DOI: 10.1371/journal.pbio.1002220] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/01/2015] [Indexed: 11/21/2022] Open
Abstract
Whole-genome duplications have shaped the genomes of several vertebrate, plant, and fungal lineages. Earlier studies have focused on establishing when these events occurred and on elucidating their functional and evolutionary consequences, but we still lack sufficient understanding of how genome duplications first originated. We used phylogenomics to study the ancient genome duplication occurred in the yeast Saccharomyces cerevisiae lineage and found compelling evidence for the existence of a contemporaneous interspecies hybridization. We propose that the genome doubling was a direct consequence of this hybridization and that it served to provide stability to the recently formed allopolyploid. This scenario provides a mechanism for the origin of this ancient duplication and the lineage that originated from it and brings a new perspective to the interpretation of the origin and consequences of whole-genome duplications.
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Affiliation(s)
- Marina Marcet-Houben
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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330
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Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 2015; 31:3210-2. [PMID: 26059717 DOI: 10.1093/bioinformatics/btv351] [Citation(s) in RCA: 7408] [Impact Index Per Article: 823.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/21/2015] [Indexed: 01/27/2023] Open
Abstract
MOTIVATION Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly limited to technical measures like N50. RESULTS We propose a measure for quantitative assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content. We implemented the assessment procedure in open-source software, with sets of Benchmarking Universal Single-Copy Orthologs, named BUSCO. AVAILABILITY AND IMPLEMENTATION Software implemented in Python and datasets available for download from http://busco.ezlab.org. CONTACT evgeny.zdobnov@unige.ch SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Felipe A Simão
- Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Robert M Waterhouse
- Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Evgenia V Kriventseva
- Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
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331
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Chu PY, Tyan YC, Chen YS, Chen HL, Lu PL, Chen YH, Chen BC, Huang TS, Wang CF, Su HJ, Shi YY, Sanno-Duanda B, Lin KH, Motomura K. Transmission and Demographic Dynamics of Coxsackievirus B1. PLoS One 2015; 10:e0129272. [PMID: 26053872 PMCID: PMC4460132 DOI: 10.1371/journal.pone.0129272] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 05/06/2015] [Indexed: 11/19/2022] Open
Abstract
The infectious activity of coxsackievirus B1 (CV-B1) in Taiwan was high from 2008 to 2010, following an alarming increase in severe neonate disease in the United States (US). To examine the relationship between CV-B1 strains isolated in Taiwan and those from other parts of the world, we performed a phylodynamic study using VP1 and partial 3Dpol (414 nt) sequences from 22 strains of CV-B1 isolated in Taiwan (1989-2010) and compared them to sequences from strains isolated worldwide. Phylogenetic trees were constructed by neighbor-joining, maximum likelihood, and Bayesian Monte Carlo Markov Chain methods. Four genotypes (GI-IV) in the VP1 region of CV-B1 and three genotypes (GA-C) in the 3Dpol region of enterovirus B were identified and had high support values. The phylogenetic analysis indicates that the GI and GIII strains in VP1 were geographically distributed in Taiwan (1993-1994) and in India (2007-2009). On the other hand, the GII and GIV strains appear to have a wider spatiotemporal distribution and ladder-like topology A stair-like phylogeny was observed in the VP1 region indicating that the phylogeny of the virus may be affected by different selection pressures in the specified regions. Further, most of the GI and GII strains in the VP1 tree were clustered together in GA in the 3D tree, while the GIV strains diverged into GB and GC. Taken together, these data provide important insights into the population dynamics of CV-B1 and indicate that incongruencies in specific gene regions may contribute to spatiotemporal patterns of epidemicity for this virus.
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Affiliation(s)
- Pei-Yu Chu
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan, ROC
- * E-mail: (PYC); (KM)
| | - Yu-Chang Tyan
- Department of Medical Imaging and Radiological Sciences, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Translational Research Center, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- National Sun Yat-Sen University-Kaohsiung Medical University Joint Research Center, Kaohsiung 804, Taiwan
- Institute of Medical Science and Technology, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - Yao-Shen Chen
- Division of Infectious Diseases, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, ROC
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, ROC
- Department of Internal Medicine, National Yang-Ming Medical University, Taipei, Taiwan, ROC
| | - Hsiu-Lin Chen
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Respiratory Therapy, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Po-Liang Lu
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan, ROC
- Department of Laboratory Medicine, School of Medicine, College of Medicine, Kaohsiung Medical University, Taiwan
| | - Yu-Hsien Chen
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC
| | - Bao-Chen Chen
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, ROC
| | - Tsi-Shu Huang
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, ROC
| | - Chu-Feng Wang
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan, ROC
| | - Hui-Ju Su
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan, ROC
| | - Yong-Ying Shi
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC
| | - Bintou Sanno-Duanda
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC
- Edward Francis Small Teaching Hospital, Banjul, Gambia
| | - Kuei-Hsiang Lin
- Department of Laboratory Medicine, School of Medicine, College of Medicine, Kaohsiung Medical University, Taiwan
| | - Kazushi Motomura
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute of Microbial Diseases, Osaka University, Nonthaburi, Thailand
- * E-mail: (PYC); (KM)
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Suárez-Vega A, Gutiérrez-Gil B, Benavides J, Perez V, Tosser-Klopp G, Klopp C, Keennel SJ, Arranz JJ. Combining GWAS and RNA-Seq Approaches for Detection of the Causal Mutation for Hereditary Junctional Epidermolysis Bullosa in Sheep. PLoS One 2015; 10:e0126416. [PMID: 25955497 PMCID: PMC4425408 DOI: 10.1371/journal.pone.0126416] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 04/01/2015] [Indexed: 12/18/2022] Open
Abstract
In this study, we demonstrate the use of a genome-wide association mapping together with RNA-seq in a reduced number of samples, as an efficient approach to detect the causal mutation for a Mendelian disease. Junctional epidermolysis bullosa is a recessive genodermatosis that manifests with neonatal mechanical fragility of the skin, blistering confined to the lamina lucida of the basement membrane and severe alteration of the hemidesmosomal junctions. In Spanish Churra sheep, junctional epidermolysis bullosa (JEB) has been detected in two commercial flocks. The JEB locus was mapped to Ovis aries chromosome 11 by GWAS and subsequently fine-mapped to an 868-kb homozygous segment using the identical-by-descent method. The ITGB4, which is located within this region, was identified as the best positional and functional candidate gene. The RNA-seq variant analysis enabled us to discover a 4-bp deletion within exon 33 of the ITGB4 gene (c.4412_4415del). The c.4412_4415del mutation causes a frameshift resulting in a premature stop codon at position 1472 of the integrin β4 protein. A functional analysis of this deletion revealed decreased levels of mRNA in JEB skin samples and the absence of integrin β4 labeling in immunohistochemical assays. Genotyping of c.4412_4415del showed perfect concordance with the recessive mode of the disease phenotype. Selection against this causal mutation will now be used to solve the problem of JEB in flocks of Churra sheep. Furthermore, the identification of the ITGB4 mutation means that affected sheep can be used as a large mammal animal model for the human form of epidermolysis bullosa with aplasia cutis. Our approach evidences that RNA-seq offers cost-effective alternative to identify variants in the species in which high resolution exome-sequencing is not straightforward.
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Affiliation(s)
- Aroa Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
| | - Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
| | - Julio Benavides
- Departamento de Sanidad Animal (Anatomía Patológica), Instituto de Ganadería de Montaña (CSIC-ULE), Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
| | - Valentín Perez
- Departamento de Sanidad Animal (Anatomía Patológica), Instituto de Ganadería de Montaña (CSIC-ULE), Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
| | - Gwenola Tosser-Klopp
- INRA, UMR1388 GenPhySE (Génétique, Physiologie et Systèmes d’Elevage), F-31326, Castanet-Tolosan, France
- Université de Toulouse, INP, ENSAT, GenPhySE (Génétique, Physiologie et Systèmes d’Elevage), F-31326, Castanet-Tolosan, France
- Université de Toulouse, INP, ENVT, GenPhySE (Génétique, Physiologie et Systèmes d’Elevage), F-31076, Toulouse, France
| | - Christophe Klopp
- INRA, Plateforme bioinformatique Toulouse Midi-Pyrénées, UR875 Biométrie et Intelligence Artificielle, BP 52627, 31326, Castanet-Tolosan Cedex, France
| | - Stephen J. Keennel
- Graduate School of Medicine, University of Tennessee, Knoxville, 37920, Tennessee, United States of America
| | - Juan José Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
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333
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Lin YL, Ma LT, Lee YR, Lin SS, Wang SY, Chang TT, Shaw JF, Li WH, Chu FH. MicroRNA-like small RNAs prediction in the development of Antrodia cinnamomea. PLoS One 2015; 10:e0123245. [PMID: 25860872 PMCID: PMC4393119 DOI: 10.1371/journal.pone.0123245] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 03/02/2015] [Indexed: 01/19/2023] Open
Abstract
Antrodia cinnamomea, a precious, host-specific brown-rot fungus that has been used as a folk medicine in Taiwan for centuries is known to have diverse bioactive compounds with potent pharmaceutical activity. In this study, different fermentation states of A. cinnamomea (wild-type fruiting bodies and liquid cultured mycelium) were sequenced using the next-generation sequencing (NGS) technique. A 45.58 Mb genome encoding 6,522 predicted genes was obtained. High quality reads were assembled into a total of 13,109 unigenes. Using a previously constructed pipeline to search for microRNAs (miRNAs), we then identified 4 predicted conserved miRNA and 63 novel predicted miRNA-like small RNA (milRNA) candidates. Target prediction revealed several interesting proteins involved in tri-terpenoid synthesis, mating type recognition, chemical or physical sensory protein and transporters predicted to be regulated by the miRNAs and milRNAs.
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Affiliation(s)
- Yan-Liang Lin
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
| | - Li-Ting Ma
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
| | - Yi-Ru Lee
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Sheng-Yang Wang
- Department of Forestry, National Chung-Hsing University, Taichun, Taiwan
- Agricultural, Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Agricultural Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan
| | - Tun-Tschu Chang
- Division on Forest Protection, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Jei-Fu Shaw
- Department of Biological Science & Technology, I-Shou University, Kaohsiung, Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Fang-Hua Chu
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
- Experimental Forest, National Taiwan University, Nan-Tou, Taiwan
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334
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Hoff KJ, Stanke M. Current methods for automated annotation of protein-coding genes. CURRENT OPINION IN INSECT SCIENCE 2015; 7:8-14. [PMID: 32846689 DOI: 10.1016/j.cois.2015.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 12/08/2014] [Accepted: 02/18/2015] [Indexed: 06/11/2023]
Abstract
We review software tools for gene prediction - the identification of protein-coding genes and their structure in genome sequences. The discussed approaches include methods based on RNA-Seq and current methods based on homology - comparative gene prediction and protein spliced alignments. Many methods require that their parameters are adjusted to the target species or its broader clade. These include ab initio gene finders, integrated approaches with ab initio components and some aligners. We also review current automatic methods for training for the common case that a bona fide training set of gene structures is not available before annotation.
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Affiliation(s)
- K J Hoff
- Institut für Mathematik und Informatik, Universität Greifswald, Walther-Rathenau-Str. 47, 17487 Greifswald, Germany
| | - M Stanke
- Institut für Mathematik und Informatik, Universität Greifswald, Walther-Rathenau-Str. 47, 17487 Greifswald, Germany
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335
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An update to polyketide synthase and non-ribosomal synthetase genes and nomenclature in Fusarium. Fungal Genet Biol 2015; 75:20-9. [DOI: 10.1016/j.fgb.2014.12.004] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 12/15/2014] [Accepted: 12/17/2014] [Indexed: 12/21/2022]
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336
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Junne T, Wong J, Studer C, Aust T, Bauer BW, Beibel M, Bhullar B, Bruccoleri R, Eichenberger J, Estoppey D, Hartmann N, Knapp B, Krastel P, Melin N, Oakeley EJ, Oberer L, Riedl R, Roma G, Schuierer S, Petersen F, Tallarico JA, Rapoport TA, Spiess M, Hoepfner D. Decatransin, a new natural product inhibiting protein translocation at the Sec61/SecYEG translocon. J Cell Sci 2015; 128:1217-29. [PMID: 25616894 DOI: 10.1242/jcs.165746] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A new cyclic decadepsipeptide was isolated from Chaetosphaeria tulasneorum with potent bioactivity on mammalian and yeast cells. Chemogenomic profiling in S. cerevisiae indicated that the Sec61 translocon complex, the machinery for protein translocation and membrane insertion at the endoplasmic reticulum, is the target. The profiles were similar to those of cyclic heptadepsipeptides of a distinct chemotype (including HUN-7293 and cotransin) that had previously been shown to inhibit cotranslational translocation at the mammalian Sec61 translocon. Unbiased, genome-wide mutagenesis followed by full-genome sequencing in both fungal and mammalian cells identified dominant mutations in Sec61p (yeast) or Sec61α1 (mammals) that conferred resistance. Most, but not all, of these mutations affected inhibition by both chemotypes, despite an absence of structural similarity. Biochemical analysis confirmed inhibition of protein translocation into the endoplasmic reticulum of both co- and post-translationally translocated substrates by both chemotypes, demonstrating a mechanism independent of a translating ribosome. Most interestingly, both chemotypes were found to also inhibit SecYEG, the bacterial Sec61 translocon homolog. We suggest 'decatransin' as the name for this new decadepsipeptide translocation inhibitor.
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Affiliation(s)
- Tina Junne
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Joanne Wong
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Christian Studer
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Thomas Aust
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Benedikt W Bauer
- Howard Hughes Medical Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Martin Beibel
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Bhupinder Bhullar
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | | | - Jürg Eichenberger
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - David Estoppey
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Nicole Hartmann
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Britta Knapp
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Philipp Krastel
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Nicolas Melin
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Edward J Oakeley
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Lukas Oberer
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Ralph Riedl
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Sven Schuierer
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Frank Petersen
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - John A Tallarico
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Tom A Rapoport
- Howard Hughes Medical Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Martin Spiess
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Dominic Hoepfner
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
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337
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338
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The complex task of choosing a de novo assembly: Lessons from fungal genomes. Comput Biol Chem 2014; 53 Pt A:97-107. [DOI: 10.1016/j.compbiolchem.2014.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2014] [Indexed: 12/21/2022]
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339
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Reijnders MJ, van Heck RG, Lam CM, Scaife MA, Santos VAMD, Smith AG, Schaap PJ. Green genes: bioinformatics and systems-biology innovations drive algal biotechnology. Trends Biotechnol 2014; 32:617-26. [DOI: 10.1016/j.tibtech.2014.10.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 09/30/2014] [Accepted: 10/01/2014] [Indexed: 01/18/2023]
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340
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Hulse-Kemp AM, Ashrafi H, Zheng X, Wang F, Hoegenauer KA, Maeda ABV, Yang SS, Stoffel K, Matvienko M, Clemons K, Udall JA, Van Deynze A, Jones DC, Stelly DM. Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts. BMC Genomics 2014. [PMID: 25359292 DOI: 10.1186/1471‐2164‐15‐945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cotton (Gossypium spp.) is the largest producer of natural fibers for textile and is an important crop worldwide. Crop production is comprised primarily of G. hirsutum L., an allotetraploid. However, elite cultivars express very small amounts of variation due to the species monophyletic origin, domestication and further bottlenecks due to selection. Conversely, wild cotton species harbor extensive genetic diversity of prospective utility to improve many beneficial agronomic traits, fiber characteristics, and resistance to disease and drought. Introgression of traits from wild species can provide a natural way to incorporate advantageous traits through breeding to generate higher-producing cotton cultivars and more sustainable production systems. Interspecific introgression efforts by conventional methods are very time-consuming and costly, but can be expedited using marker-assisted selection. RESULTS Using transcriptome sequencing we have developed the first gene-associated single nucleotide polymorphism (SNP) markers for wild cotton species G. tomentosum, G. mustelinum, G. armourianum and G. longicalyx. Markers were also developed for a secondary cultivated species G. barbadense cv. 3-79. A total of 62,832 non-redundant SNP markers were developed from the five wild species which can be utilized for interspecific germplasm introgression into cultivated G. hirsutum and are directly associated with genes. Over 500 of the G. barbadense markers have been validated by whole-genome radiation hybrid mapping. Overall 1,060 SNPs from the five different species have been screened and shown to produce acceptable genotyping assays. CONCLUSIONS This large set of 62,832 SNPs relative to cultivated G. hirsutum will allow for the first high-density mapping of genes from five wild species that affect traits of interest, including beneficial agronomic and fiber characteristics. Upon mapping, the markers can be utilized for marker-assisted introgression of new germplasm into cultivated cotton and in subsequent breeding of agronomically adapted types, including cultivar development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - David M Stelly
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, USA.
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341
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Hulse-Kemp AM, Ashrafi H, Zheng X, Wang F, Hoegenauer KA, Maeda ABV, Yang SS, Stoffel K, Matvienko M, Clemons K, Udall JA, Van Deynze A, Jones DC, Stelly DM. Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts. BMC Genomics 2014; 15:945. [PMID: 25359292 PMCID: PMC4298081 DOI: 10.1186/1471-2164-15-945] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 10/03/2014] [Indexed: 11/18/2022] Open
Abstract
Background Cotton (Gossypium spp.) is the largest producer of natural fibers for textile and is an important crop worldwide. Crop production is comprised primarily of G. hirsutum L., an allotetraploid. However, elite cultivars express very small amounts of variation due to the species monophyletic origin, domestication and further bottlenecks due to selection. Conversely, wild cotton species harbor extensive genetic diversity of prospective utility to improve many beneficial agronomic traits, fiber characteristics, and resistance to disease and drought. Introgression of traits from wild species can provide a natural way to incorporate advantageous traits through breeding to generate higher-producing cotton cultivars and more sustainable production systems. Interspecific introgression efforts by conventional methods are very time-consuming and costly, but can be expedited using marker-assisted selection. Results Using transcriptome sequencing we have developed the first gene-associated single nucleotide polymorphism (SNP) markers for wild cotton species G. tomentosum, G. mustelinum, G. armourianum and G. longicalyx. Markers were also developed for a secondary cultivated species G. barbadense cv. 3–79. A total of 62,832 non-redundant SNP markers were developed from the five wild species which can be utilized for interspecific germplasm introgression into cultivated G. hirsutum and are directly associated with genes. Over 500 of the G. barbadense markers have been validated by whole-genome radiation hybrid mapping. Overall 1,060 SNPs from the five different species have been screened and shown to produce acceptable genotyping assays. Conclusions This large set of 62,832 SNPs relative to cultivated G. hirsutum will allow for the first high-density mapping of genes from five wild species that affect traits of interest, including beneficial agronomic and fiber characteristics. Upon mapping, the markers can be utilized for marker-assisted introgression of new germplasm into cultivated cotton and in subsequent breeding of agronomically adapted types, including cultivar development. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-945) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - David M Stelly
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, USA.
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342
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Jagtap PD, Johnson JE, Onsongo G, Sadler FW, Murray K, Wang Y, Shenykman GM, Bandhakavi S, Smith LM, Griffin TJ. Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework. J Proteome Res 2014; 13:5898-908. [PMID: 25301683 PMCID: PMC4261978 DOI: 10.1021/pr500812t] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Proteogenomics combines large-scale
genomic and transcriptomic
data with mass-spectrometry-based proteomic data to discover novel
protein sequence variants and improve genome annotation. In contrast
with conventional proteomic applications, proteogenomic analysis requires
a number of additional data processing steps. Ideally, these required
steps would be integrated and automated via a single software platform
offering accessibility for wet-bench researchers as well as flexibility
for user-specific customization and integration of new software tools
as they emerge. Toward this end, we have extended the Galaxy bioinformatics
framework to facilitate proteogenomic analysis. Using analysis of
whole human saliva as an example, we demonstrate Galaxy’s flexibility
through the creation of a modular workflow incorporating both established
and customized software tools that improve depth and quality of proteogenomic
results. Our customized Galaxy-based software includes automated,
batch-mode BLASTP searching and a Peptide Sequence Match Evaluator
tool, both useful for evaluating the veracity of putative novel peptide
identifications. Our complex workflow (approximately 140 steps) can
be easily shared using built-in Galaxy functions, enabling their use
and customization by others. Our results provide a blueprint for the
establishment of the Galaxy framework as an ideal solution for the
emerging field of proteogenomics.
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Affiliation(s)
- Pratik D Jagtap
- Center for Mass Spectrometry and Proteomics, University of Minnesota , 43 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
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343
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Burke GR, Walden KKO, Whitfield JB, Robertson HM, Strand MR. Widespread genome reorganization of an obligate virus mutualist. PLoS Genet 2014; 10:e1004660. [PMID: 25232843 PMCID: PMC4169385 DOI: 10.1371/journal.pgen.1004660] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 08/11/2014] [Indexed: 11/18/2022] Open
Abstract
The family Polydnaviridae is of interest because it provides the best example of viruses that have evolved a mutualistic association with their animal hosts. Polydnaviruses in the genus Bracovirus are strictly associated with parasitoid wasps in the family Braconidae, and evolved ∼100 million years ago from a nudivirus. Each wasp species relies on its associated bracovirus to parasitize hosts, while each bracovirus relies on its wasp for vertical transmission. Prior studies establish that bracovirus genomes consist of proviral segments and nudivirus-like replication genes, but how these components are organized in the genomes of wasps is unknown. Here, we sequenced the genome of the wasp Microplitis demolitor to characterize the proviral genome of M. demolitor bracovirus (MdBV). Unlike nudiviruses, bracoviruses produce virions that package multiple circular, double-stranded DNAs. DNA segments packaged into MdBV virions resided in eight dispersed loci in the M. demolitor genome. Each proviral segment was bounded by homologous motifs that guide processing to form mature viral DNAs. Rapid evolution of proviral segments obscured homology between other bracovirus-carrying wasps and MdBV. However, some domains flanking MdBV proviral loci were shared with other species. All MdBV genes previously identified to encode proteins required for replication were identified. Some of these genes resided in a multigene cluster but others, including subunits of the RNA polymerase that transcribes structural genes and integrases that process proviral segments, were widely dispersed in the M. demolitor genome. Overall, our results indicate that genome dispersal is a key feature in the evolution of bracoviruses into mutualists.
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Affiliation(s)
- Gaelen R. Burke
- Department of Entomology, University of Georgia, Athens, Georgia, United States of America
- * E-mail: (GRB); (MRS)
| | - Kimberly K. O. Walden
- Department of Entomology, University of Illinois, Urbana-Champaign, Champaign, Illinois, United States of America
| | - James B. Whitfield
- Department of Entomology, University of Illinois, Urbana-Champaign, Champaign, Illinois, United States of America
| | - Hugh M. Robertson
- Department of Entomology, University of Illinois, Urbana-Champaign, Champaign, Illinois, United States of America
| | - Michael R. Strand
- Department of Entomology, University of Georgia, Athens, Georgia, United States of America
- * E-mail: (GRB); (MRS)
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344
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Kelly S, Ivens A, Manna PT, Gibson W, Field MC. A draft genome for the African crocodilian trypanosome Trypanosoma grayi. Sci Data 2014; 1:140024. [PMID: 25977781 PMCID: PMC4322581 DOI: 10.1038/sdata.2014.24] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 07/09/2014] [Indexed: 02/01/2023] Open
Abstract
The availability of genome sequence data has greatly enhanced our understanding of the adaptations of trypanosomatid parasites to their respective host environments. However, these studies remain somewhat restricted by modest taxon sampling, generally due to focus on the most important pathogens of humans. To address this problem, at least in part, we are releasing a draft genome sequence for the African crocodilian trypanosome, Trypanosoma grayi ANR4. This dataset comprises genomic DNA sequences assembled de novo into contigs, encompassing over 10,000 annotated putative open reading frames and predicted protein products. Using phylogenomic approaches we demonstrate that T. grayi is more closely related to Trypanosoma cruzi than it is to the African trypanosomes T. brucei, T. congolense and T. vivax, despite the fact T. grayi and the African trypanosomes are each transmitted by tsetse flies. The data are deposited in publicly accessible repositories where we hope they will prove useful to the community in evolutionary studies of the trypanosomatids.
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Affiliation(s)
- Steven Kelly
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Alasdair Ivens
- Centre for Immunity, Infection and Evolution, Ashworth Laboratories, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Paul T. Manna
- Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Wendy Gibson
- School of Biological Sciences, University of Bristol, Bristol BS8 1UG, UK
| | - Mark C. Field
- Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, Scotland, UK
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345
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Gao Y, Gao Q, Zhang H, Wang L, Zhang F, Yang C, Song L. Draft sequencing and analysis of the genome of pufferfish Takifugu flavidus. DNA Res 2014; 21:627-37. [PMID: 25053628 PMCID: PMC4263296 DOI: 10.1093/dnares/dsu025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The pufferfish Takifugu flavidus is an important economic species due to its outstanding flavour and high market value. It has been regarded as an excellent model of genetic study for decades as well. In the present study, three mate-pair libraries of T. flavidus genome were sequenced by the SOLiD 4 next-generation sequencing platform, and the draft genome was constructed with the short reads using an assisted assembly strategy. The draft consists of 50,947 scaffolds with an N50 value of 305.7 kb, and the average GC content was 45.2%. The combined length of repetitive sequences was 26.5 Mb, which accounted for 6.87% of the genome, indicating that the compactness of T. flavidus genome was approximative with that of T. rubripes genome. A total of 1,253 non-coding RNA genes and 30,285 protein-encoding genes were assigned to the genome. There were 132,775 and 394 presumptive genes playing roles in the colour pattern variation, the relatively slow growth and the lipid metabolism, respectively. Among them, genes involved in the microtubule-dependent transport system, angiogenesis, decapentaplegic pathway and lipid mobilization were significantly expanded in the T. flavidus genome. This draft genome provides a valuable resource for understanding and improving both fundamental and applied research with pufferfish in the future.
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Affiliation(s)
- Yang Gao
- The Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, China University of Chinese Academy of Sciences, Shijingshan, Beijing 100049, China
| | - Qiang Gao
- The Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, China
| | - Huan Zhang
- The Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, China
| | - Lingling Wang
- The Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, China
| | - Fuchong Zhang
- Ocean and Fishery Sciences Research Institute of Hebei Province, Qinhuangdao, Hebei 066200, China
| | - Chuanyan Yang
- The Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, China
| | - Linsheng Song
- The Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, China
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Reid I, O’Toole N, Zabaneh O, Nourzadeh R, Dahdouli M, Abdellateef M, Gordon PMK, Soh J, Butler G, Sensen CW, Tsang A. SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models. BMC Bioinformatics 2014; 15:229. [PMID: 24980894 PMCID: PMC4084796 DOI: 10.1186/1471-2105-15-229] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 06/17/2014] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Locating the protein-coding genes in novel genomes is essential to understanding and exploiting the genomic information but it is still difficult to accurately predict all the genes. The recent availability of detailed information about transcript structure from high-throughput sequencing of messenger RNA (RNA-Seq) delineates many expressed genes and promises increased accuracy in gene prediction. Computational gene predictors have been intensively developed for and tested in well-studied animal genomes. Hundreds of fungal genomes are now or will soon be sequenced. The differences of fungal genomes from animal genomes and the phylogenetic sparsity of well-studied fungi call for gene-prediction tools tailored to them. RESULTS SnowyOwl is a new gene prediction pipeline that uses RNA-Seq data to train and provide hints for the generation of Hidden Markov Model (HMM)-based gene predictions and to evaluate the resulting models. The pipeline has been developed and streamlined by comparing its predictions to manually curated gene models in three fungal genomes and validated against the high-quality gene annotation of Neurospora crassa; SnowyOwl predicted N. crassa genes with 83% sensitivity and 65% specificity. SnowyOwl gains sensitivity by repeatedly running the HMM gene predictor Augustus with varied input parameters and selectivity by choosing the models with best homology to known proteins and best agreement with the RNA-Seq data. CONCLUSIONS SnowyOwl efficiently uses RNA-Seq data to produce accurate gene models in both well-studied and novel fungal genomes. The source code for the SnowyOwl pipeline (in Python) and a web interface (in PHP) is freely available from http://sourceforge.net/projects/snowyowl/.
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Affiliation(s)
- Ian Reid
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W, Montreal, QC H4B 1R6, Canada
| | - Nicholas O’Toole
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W, Montreal, QC H4B 1R6, Canada
| | - Omar Zabaneh
- Faculty of Medicine, Visual Genomics Centre, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Reza Nourzadeh
- Faculty of Medicine, Visual Genomics Centre, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Mahmoud Dahdouli
- Faculty of Medicine, Visual Genomics Centre, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Mostafa Abdellateef
- Faculty of Medicine, Visual Genomics Centre, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Paul MK Gordon
- Faculty of Medicine, Visual Genomics Centre, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Jung Soh
- Faculty of Medicine, Visual Genomics Centre, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Gregory Butler
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W, Montreal, QC H4B 1R6, Canada
| | - Christoph W Sensen
- Faculty of Medicine, Visual Genomics Centre, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W, Montreal, QC H4B 1R6, Canada
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de Setta N, Monteiro-Vitorello CB, Metcalfe CJ, Cruz GMQ, Del Bem LE, Vicentini R, Nogueira FTS, Campos RA, Nunes SL, Turrini PCG, Vieira AP, Ochoa Cruz EA, Corrêa TCS, Hotta CT, de Mello Varani A, Vautrin S, da Trindade AS, de Mendonça Vilela M, Lembke CG, Sato PM, de Andrade RF, Nishiyama MY, Cardoso-Silva CB, Scortecci KC, Garcia AAF, Carneiro MS, Kim C, Paterson AH, Bergès H, D'Hont A, de Souza AP, Souza GM, Vincentz M, Kitajima JP, Van Sluys MA. Building the sugarcane genome for biotechnology and identifying evolutionary trends. BMC Genomics 2014; 15:540. [PMID: 24984568 PMCID: PMC4122759 DOI: 10.1186/1471-2164-15-540] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 06/19/2014] [Indexed: 01/24/2023] Open
Abstract
Background Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome. Results Three hundred and seventeen chiefly euchromatic BACs were sequenced. A reference set of one thousand four hundred manually-annotated protein-coding genes was generated. A small RNA collection and a RNA-seq library were used to explore expression patterns and the sRNA landscape. In the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. One of the sucrose pathway genes, sucrose-6-phosphate phosphohydrolase, is duplicated in sugarcane and sorghum, but not in rice and maize. A diversity analysis of the s6pp duplication region revealed haplotype-structured sequence composition. Examination of hom(e)ologous loci indicate both sequence structural and sRNA landscape variation. A synteny analysis shows that the sugarcane genome has expanded relative to the sorghum genome, largely due to the presence of transposable elements and uncharacterized intergenic and intronic sequences. Conclusion This release of sugarcane genomic sequences will advance our understanding of sugarcane genetics and contribute to the development of molecular tools for breeding purposes and gene discovery. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-540) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Marie-Anne Van Sluys
- Departamento de Botânica - Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo 05508-090, SP, Brazil.
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Mühlhausen S, Kollmar M. Predicting the fungal CUG codon translation with Bagheera. BMC Genomics 2014; 15:411. [PMID: 24885275 PMCID: PMC4050208 DOI: 10.1186/1471-2164-15-411] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Accepted: 05/21/2014] [Indexed: 12/03/2022] Open
Abstract
Background Many eukaryotes have been shown to use alternative schemes to the universal genetic code. While most Saccharomycetes, including Saccharomyces cerevisiae, use the standard genetic code translating the CUG codon as leucine, some yeasts, including many but not all of the “Candida”, translate the same codon as serine. It has been proposed that the change in codon identity was accomplished by an almost complete loss of the original CUG codons, making the CUG positions within the extant species highly discriminative for the one or other translation scheme. Results In order to improve the prediction of genes in yeast species by providing the correct CUG decoding scheme we implemented a web server, called Bagheera, that allows determining the most probable CUG codon translation for a given transcriptome or genome assembly based on extensive reference data. As reference data we use 2071 manually assembled and annotated sequences from 38 cytoskeletal and motor proteins belonging to 79 yeast species. The web service includes a pipeline, which starts with predicting and aligning homologous genes to the reference data. CUG codon positions within the predicted genes are analysed with respect to amino acid similarity and CUG codon conservation in related species. In addition, the tRNACAG gene is predicted in genomic data and compared to known leu-tRNACAG and ser-tRNACAG genes. Bagheera can also be used to evaluate any mRNA and protein sequence data with the codon usage of the respective species. The usage of the system has been demonstrated by analysing six genomes not included in the reference data. Conclusions Gene prediction and consecutive comparison with reference data from other Saccharomycetes are sufficient to predict the most probable decoding scheme for CUG codons. This approach has been implemented into Bagheera (http://www.motorprotein.de/bagheera). Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-411) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Martin Kollmar
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.
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349
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Haitjema CH, Solomon KV, Henske JK, Theodorou MK, O'Malley MA. Anaerobic gut fungi: Advances in isolation, culture, and cellulolytic enzyme discovery for biofuel production. Biotechnol Bioeng 2014; 111:1471-82. [PMID: 24788404 DOI: 10.1002/bit.25264] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 04/09/2014] [Accepted: 04/10/2014] [Indexed: 12/12/2022]
Abstract
Anaerobic gut fungi are an early branching family of fungi that are commonly found in the digestive tract of ruminants and monogastric herbivores. It is becoming increasingly clear that they are the primary colonizers of ingested plant biomass, and that they significantly contribute to the decomposition of plant biomass into fermentable sugars. As such, anaerobic fungi harbor a rich reservoir of undiscovered cellulolytic enzymes and enzyme complexes that can potentially transform the conversion of lignocellulose into bioenergy products. Despite their unique evolutionary history and cellulolytic activity, few species have been isolated and studied in great detail. As a result, their life cycle, cellular physiology, genetics, and cellulolytic metabolism remain poorly understood compared to aerobic fungi. To help address this limitation, this review briefly summarizes the current body of knowledge pertaining to anaerobic fungal biology, and describes progress made in the isolation, cultivation, molecular characterization, and long-term preservation of these microbes. We also discuss recent cellulase- and cellulosome-discovery efforts from gut fungi, and how these interesting, non-model microbes could be further adapted for biotechnology applications.
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Affiliation(s)
- Charles H Haitjema
- Department of Chemical Engineering, University of California, Santa Barbara, California, 93106
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Ahuja A, Extavour CG. Patterns of molecular evolution of the germ line specification gene oskar suggest that a novel domain may contribute to functional divergence in Drosophila. Dev Genes Evol 2014; 224:65-77. [DOI: 10.1007/s00427-013-0463-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/07/2013] [Indexed: 01/04/2023]
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