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Xiao JH, Yue Z, Jia LY, Yang XH, Niu LH, Wang Z, Zhang P, Sun BF, He SM, Li Z, Xiong TL, Xin W, Gu HF, Wang B, Werren JH, Murphy RW, Wheeler D, Niu LM, Ma GC, Tang T, Bian SN, Wang NX, Yang CY, Wang N, Fu YG, Li WZ, Yi SV, Yang XY, Zhou Q, Lu CX, Xu CY, He LJ, Yu LL, Chen M, Zheng Y, Wang SW, Zhao S, Li YH, Yu YY, Qian XJ, Cai Y, Bian LL, Zhang S, Wang JY, Yin Y, Xiao H, Wang GH, Yu H, Wu WS, Cook JM, Wang J, Huang DW. Obligate mutualism within a host drives the extreme specialization of a fig wasp genome. Genome Biol 2013; 14:R141. [PMID: 24359812 PMCID: PMC4053974 DOI: 10.1186/gb-2013-14-12-r141] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 12/20/2013] [Indexed: 12/23/2022] Open
Abstract
Background Fig pollinating wasps form obligate symbioses with their fig hosts. This mutualism arose approximately 75 million years ago. Unlike many other intimate symbioses, which involve vertical transmission of symbionts to host offspring, female fig wasps fly great distances to transfer horizontally between hosts. In contrast, male wasps are wingless and cannot disperse. Symbionts that keep intimate contact with their hosts often show genome reduction, but it is not clear if the wide dispersal of female fig wasps will counteract this general tendency. We sequenced the genome of the fig wasp Ceratosolen solmsi to address this question. Results The genome size of the fig wasp C. solmsi is typical of insects, but has undergone dramatic reductions of gene families involved in environmental sensing and detoxification. The streamlined chemosensory ability reflects the overwhelming importance of females finding trees of their only host species, Ficus hispida, during their fleeting adult lives. Despite long-distance dispersal, little need exists for detoxification or environmental protection because fig wasps spend nearly all of their lives inside a largely benign host. Analyses of transcriptomes in females and males at four key life stages reveal that the extreme anatomical sexual dimorphism of fig wasps may result from a strong bias in sex-differential gene expression. Conclusions Our comparison of the C. solmsi genome with other insects provides new insights into the evolution of obligate mutualism. The draft genome of the fig wasp, and transcriptomic comparisons between both sexes at four different life stages, provide insights into the molecular basis for the extreme anatomical sexual dimorphism of this species.
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Steijger T, Abril JF, Engström PG, Kokocinski F, Hubbard TJ, Guigó R, Harrow J, Bertone P. Assessment of transcript reconstruction methods for RNA-seq. Nat Methods 2013; 10:1177-84. [PMID: 24185837 PMCID: PMC3851240 DOI: 10.1038/nmeth.2714] [Citation(s) in RCA: 462] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Accepted: 09/23/2013] [Indexed: 11/09/2022]
Abstract
We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are able to identify discrete transcript components with high success rates but that assembly of complete isoform structures poses a major challenge even when all constituent elements are identified. Expression-level estimates also varied widely across methods, even when based on similar transcript models. Consequently, the complexity of higher eukaryotic genomes imposes severe limitations on transcript recall and splice product discrimination that are likely to remain limiting factors for the analysis of current-generation RNA-seq data.
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Affiliation(s)
- Tamara Steijger
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Josep F Abril
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Pär G Engström
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | | | | | - Roderic Guigó
- Center for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Paul Bertone
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
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1453
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Yim HS, Cho YS, Guang X, Kang SG, Jeong JY, Cha SS, Oh HM, Lee JH, Yang EC, Kwon KK, Kim YJ, Kim TW, Kim W, Jeon JH, Kim SJ, Choi DH, Jho S, Kim HM, Ko J, Kim H, Shin YA, Jung HJ, Zheng Y, Wang Z, Chen Y, Chen M, Jiang A, Li E, Zhang S, Hou H, Kim TH, Yu L, Liu S, Ahn K, Cooper J, Park SG, Hong CP, Jin W, Kim HS, Park C, Lee K, Chun S, Morin PA, O'Brien SJ, Lee H, Kimura J, Moon DY, Manica A, Edwards J, Kim BC, Kim S, Wang J, Bhak J, Lee HS, Lee JH. Minke whale genome and aquatic adaptation in cetaceans. Nat Genet 2013; 46:88-92. [PMID: 24270359 DOI: 10.1038/ng.2835] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 11/01/2013] [Indexed: 01/14/2023]
Abstract
The shift from terrestrial to aquatic life by whales was a substantial evolutionary event. Here we report the whole-genome sequencing and de novo assembly of the minke whale genome, as well as the whole-genome sequences of three minke whales, a fin whale, a bottlenose dolphin and a finless porpoise. Our comparative genomic analysis identified an expansion in the whale lineage of gene families associated with stress-responsive proteins and anaerobic metabolism, whereas gene families related to body hair and sensory receptors were contracted. Our analysis also identified whale-specific mutations in genes encoding antioxidants and enzymes controlling blood pressure and salt concentration. Overall the whale-genome sequences exhibited distinct features that are associated with the physiological and morphological changes needed for life in an aquatic environment, marked by resistance to physiological stresses caused by a lack of oxygen, increased amounts of reactive oxygen species and high salt levels.
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Affiliation(s)
- Hyung-Soon Yim
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2]
| | - Yun Sung Cho
- 1] Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea. [2]
| | - Xuanmin Guang
- 1] Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China. [2]
| | - Sung Gyun Kang
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2] Department of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Jae-Yeon Jeong
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2] Department of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Sun-Shin Cha
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2] Department of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea. [3] Ocean Science and Technology School, Korea Maritime University, Busan, Republic of Korea
| | - Hyun-Myung Oh
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Jae-Hak Lee
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Eun Chan Yang
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Kae Kyoung Kwon
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2] Department of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Yun Jae Kim
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Tae Wan Kim
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Wonduck Kim
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Jeong Ho Jeon
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Sang-Jin Kim
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2] Department of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Dong Han Choi
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Sungwoong Jho
- Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea
| | - Hak-Min Kim
- Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea
| | - Junsu Ko
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Hyunmin Kim
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Young-Ah Shin
- Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea
| | - Hyun-Ju Jung
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Yuan Zheng
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Zhuo Wang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Yan Chen
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Ming Chen
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Awei Jiang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Erli Li
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Shu Zhang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Haolong Hou
- Shaanxi Yulin Energy Group Co. Ltd., Yulin, Shaanxi, China
| | - Tae Hyung Kim
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Lili Yu
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Sha Liu
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Kung Ahn
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Jesse Cooper
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Sin-Gi Park
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Chang Pyo Hong
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Wook Jin
- Department of Molecular Medicine, School of Medicine, Gachon University, Incheon, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, Republic of Korea
| | - Chankyu Park
- Laboratory of Genome Biology, Department of Animal Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Kyooyeol Lee
- Laboratory of Genome Biology, Department of Animal Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Sung Chun
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Phillip A Morin
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, California, USA
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | - Hang Lee
- College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jumpei Kimura
- Department of Anatomy and Cell Biology, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Dae Yeon Moon
- Marine Biodiversity Institute of Korea (MABIK), Ministry of Ocean and Fisheries, Sejong, Republic of Korea
| | - Andrea Manica
- Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Jeremy Edwards
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Byung Chul Kim
- Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea
| | - Sangsoo Kim
- School of Systems Biomedical Science, Soongsil University, Seoul, Republic of Korea
| | - Jun Wang
- 1] Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China. [2] Department of Biology, University of Copenhagen, Copenhagen, Denmark. [3] King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jong Bhak
- 1] Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea. [2] Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea. [3] Program in Nano Science and Technology, Department of Transdisciplinary Studies, Seoul National University, Suwon, Republic of Korea. [4] Advanced Institutes of Convergence Technology Nano Science and Technology, Suwon, Republic of Korea
| | - Hyun Sook Lee
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2] Department of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Jung-Hyun Lee
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2] Department of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
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Genomic insights into salt adaptation in a desert poplar. Nat Commun 2013; 4:2797. [DOI: 10.1038/ncomms3797] [Citation(s) in RCA: 203] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 10/21/2013] [Indexed: 01/27/2023] Open
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1455
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Wang Y, Fan G, Liu Y, Sun F, Shi C, Liu X, Peng J, Chen W, Huang X, Cheng S, Liu Y, Liang X, Zhu H, Bian C, Zhong L, Lv T, Dong H, Liu W, Zhong X, Chen J, Quan Z, Wang Z, Tan B, Lin C, Mu F, Xu X, Ding Y, Guo AY, Wang J, Ke W. The sacred lotus genome provides insights into the evolution of flowering plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:557-67. [PMID: 23952714 DOI: 10.1111/tpj.12313] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 08/04/2013] [Accepted: 08/12/2013] [Indexed: 05/07/2023]
Abstract
Sacred lotus (Nelumbo nucifera) is an ornamental plant that is also used for food and medicine. This basal eudicot species is especially important from an evolutionary perspective, as it occupies a critical phylogenetic position in flowering plants. Here we report the draft genome of a wild strain of sacred lotus. The assembled genome is 792 Mb, which is approximately 85-90% of genome size estimates. We annotated 392 Mb of repeat sequences and 36,385 protein-coding genes within the genome. Using these sequence data, we constructed a phylogenetic tree and confirmed the basal location of sacred lotus within eudicots. Importantly, we found evidence for a relatively recent whole-genome duplication event; any indication of the ancient paleo-hexaploid event was, however, absent. Genomic analysis revealed evidence of positive selection within 28 embryo-defective genes and one annexin gene that may be related to the long-term viability of sacred lotus seed. We also identified a significant expansion of starch synthase genes, which probably elevated starch levels within the rhizome of sacred lotus. Sequencing this strain of sacred lotus thus provided important insights into the evolution of flowering plant and revealed genetic mechanisms that influence seed dormancy and starch synthesis.
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Affiliation(s)
- Yun Wang
- Wuhan Vegetable Research Institute, Wuhan, 430065, China
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Gabaldón T, Martin T, Marcet-Houben M, Durrens P, Bolotin-Fukuhara M, Lespinet O, Arnaise S, Boisnard S, Aguileta G, Atanasova R, Bouchier C, Couloux A, Creno S, Almeida Cruz J, Devillers H, Enache-Angoulvant A, Guitard J, Jaouen L, Ma L, Marck C, Neuvéglise C, Pelletier E, Pinard A, Poulain J, Recoquillay J, Westhof E, Wincker P, Dujon B, Hennequin C, Fairhead C. Comparative genomics of emerging pathogens in the Candida glabrata clade. BMC Genomics 2013; 14:623. [PMID: 24034898 PMCID: PMC3847288 DOI: 10.1186/1471-2164-14-623] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 07/31/2013] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Candida glabrata follows C. albicans as the second or third most prevalent cause of candidemia worldwide. These two pathogenic yeasts are distantly related, C. glabrata being part of the Nakaseomyces, a group more closely related to Saccharomyces cerevisiae. Although C. glabrata was thought to be the only pathogenic Nakaseomyces, two new pathogens have recently been described within this group: C. nivariensis and C. bracarensis. To gain insight into the genomic changes underlying the emergence of virulence, we sequenced the genomes of these two, and three other non-pathogenic Nakaseomyces, and compared them to other sequenced yeasts. RESULTS Our results indicate that the two new pathogens are more closely related to the non-pathogenic N. delphensis than to C. glabrata. We uncover duplications and accelerated evolution that specifically affected genes in the lineage preceding the group containing N. delphensis and the three pathogens, which may provide clues to the higher propensity of this group to infect humans. Finally, the number of Epa-like adhesins is specifically enriched in the pathogens, particularly in C. glabrata. CONCLUSIONS Remarkably, some features thought to be the result of adaptation of C. glabrata to a pathogenic lifestyle, are present throughout the Nakaseomyces, indicating these are rather ancient adaptations to other environments. Phylogeny suggests that human pathogenesis evolved several times, independently within the clade. The expansion of the EPA gene family in pathogens establishes an evolutionary link between adhesion and virulence phenotypes. Our analyses thus shed light onto the relationships between virulence and the recent genomic changes that occurred within the Nakaseomyces. SEQUENCE ACCESSION NUMBERS Nakaseomyces delphensis: CAPT01000001 to CAPT01000179Candida bracarensis: CAPU01000001 to CAPU01000251Candida nivariensis: CAPV01000001 to CAPV01000123Candida castellii: CAPW01000001 to CAPW01000101Nakaseomyces bacillisporus: CAPX01000001 to CAPX01000186.
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Affiliation(s)
- Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, Barcelona, 08003, Spain
- Comparative Genomics Group, CRG-Centre for Genomic Regulation, Doctor Aiguader, 88, Barcelona, 08003, Spain
| | - Tiphaine Martin
- Université de Bordeaux 1, LaBRI, INRIA Bordeaux Sud-Ouest (MAGNOME), Talence, F-33405, France
| | - Marina Marcet-Houben
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, Barcelona, 08003, Spain
| | - Pascal Durrens
- Université de Bordeaux 1, LaBRI, INRIA Bordeaux Sud-Ouest (MAGNOME), Talence, F-33405, France
| | - Monique Bolotin-Fukuhara
- Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris Sud, Bât 400, UFR des Sciences, Orsay Cedex, F 91405, France
| | - Olivier Lespinet
- Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris Sud, Bât 400, UFR des Sciences, Orsay Cedex, F 91405, France
| | - Sylvie Arnaise
- Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris Sud, Bât 400, UFR des Sciences, Orsay Cedex, F 91405, France
| | - Stéphanie Boisnard
- Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris Sud, Bât 400, UFR des Sciences, Orsay Cedex, F 91405, France
| | - Gabriela Aguileta
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, Barcelona, 08003, Spain
| | - Ralitsa Atanasova
- APHP, Hôpital St Antoine, Service de Parasitologie-Mycologie, and UMR S945, Inserm, Université P. M. Curie, Paris, France
| | - Christiane Bouchier
- Département Génomes et Génétique, Institut Pasteur, Plate-forme Génomique, rue du Dr. Roux, Paris, F-75015, France
| | - Arnaud Couloux
- CEA, IG, DSV, Genoscope, 2 rue Gaston Crémieux, Evry Cedex, 91057, France
| | - Sophie Creno
- Département Génomes et Génétique, Institut Pasteur, Plate-forme Génomique, rue du Dr. Roux, Paris, F-75015, France
| | - Jose Almeida Cruz
- Architecture et Réactivité de l‘ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg Cedex, F-67084, France
- Present adress: Champalimaud Foundation, Av. Brasília, Lisboa, 1400-038, Portugal
| | - Hugo Devillers
- Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris Sud, Bât 400, UFR des Sciences, Orsay Cedex, F 91405, France
| | - Adela Enache-Angoulvant
- Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris Sud, Bât 400, UFR des Sciences, Orsay Cedex, F 91405, France
- APHP, Hôpital Bicêtre, Service de Microbiologie, Paris, France
| | - Juliette Guitard
- APHP, Hôpital St Antoine, Service de Parasitologie-Mycologie, and UMR S945, Inserm, Université P. M. Curie, Paris, France
| | - Laure Jaouen
- Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris Sud, Bât 400, UFR des Sciences, Orsay Cedex, F 91405, France
| | - Laurence Ma
- Département Génomes et Génétique, Institut Pasteur, Plate-forme Génomique, rue du Dr. Roux, Paris, F-75015, France
| | - Christian Marck
- Institut de biologie et technologies de Saclay (iBiTec-S), Gif-sur-Yvette cedex, 91191, France
| | | | - Eric Pelletier
- CEA, IG, DSV, Genoscope, 2 rue Gaston Crémieux, Evry Cedex, 91057, France
| | - Amélie Pinard
- Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris Sud, Bât 400, UFR des Sciences, Orsay Cedex, F 91405, France
| | - Julie Poulain
- CEA, IG, DSV, Genoscope, 2 rue Gaston Crémieux, Evry Cedex, 91057, France
| | - Julien Recoquillay
- Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris Sud, Bât 400, UFR des Sciences, Orsay Cedex, F 91405, France
| | - Eric Westhof
- Architecture et Réactivité de l‘ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg Cedex, F-67084, France
| | - Patrick Wincker
- CEA, IG, DSV, Genoscope, 2 rue Gaston Crémieux, Evry Cedex, 91057, France
| | - Bernard Dujon
- Institut Pasteur, Unité de Génétique moléculaires des levures, UMR3525 CNRS, UFR927, Université P. M. Curie, 25 rue du Docteur Roux, Paris Cedex15, F75724, France
| | - Christophe Hennequin
- APHP, Hôpital St Antoine, Service de Parasitologie-Mycologie, and UMR S945, Inserm, Université P. M. Curie, Paris, France
| | - Cécile Fairhead
- Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris Sud, Bât 400, UFR des Sciences, Orsay Cedex, F 91405, France
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Wegrzyn JL, Lin BY, Zieve JJ, Dougherty WM, Martínez-García PJ, Koriabine M, Holtz-Morris A, deJong P, Crepeau M, Langley CH, Puiu D, Salzberg SL, Neale DB, Stevens KA. Insights into the loblolly pine genome: characterization of BAC and fosmid sequences. PLoS One 2013; 8:e72439. [PMID: 24023741 PMCID: PMC3762812 DOI: 10.1371/journal.pone.0072439] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 07/10/2013] [Indexed: 12/22/2022] Open
Abstract
Despite their prevalence and importance, the genome sequences of loblolly pine, Norway spruce, and white spruce, three ecologically and economically important conifer species, are just becoming available to the research community. Following the completion of these large assemblies, annotation efforts will be undertaken to characterize the reference sequences. Accurate annotation of these ancient genomes would be aided by a comprehensive repeat library; however, few studies have generated enough sequence to fully evaluate and catalog their non-genic content. In this paper, two sets of loblolly pine genomic sequence, 103 previously assembled BACs and 90,954 newly sequenced and assembled fosmid scaffolds, were analyzed. Together, this sequence represents 280 Mbp (roughly 1% of the loblolly pine genome) and one of the most comprehensive studies of repetitive elements and genes in a gymnosperm species. A combination of homology and de novo methodologies were applied to identify both conserved and novel repeats. Similarity analysis estimated a repetitive content of 27% that included both full and partial elements. When combined with the de novo investigation, the estimate increased to almost 86%. Over 60% of the repetitive sequence consists of full or partial LTR (long terminal repeat) retrotransposons. Through de novo approaches, 6,270 novel, full-length transposable element families and 9,415 sub-families were identified. Among those 6,270 families, 82% were annotated as single-copy. Several of the novel, high-copy families are described here, with the largest, PtPiedmont, comprising 133 full-length copies. In addition to repeats, analysis of the coding region reported 23 full-length eukaryotic orthologous proteins (KOGS) and another 29 novel or orthologous genes. These discoveries, along with other genomic resources, will be used to annotate conifer genomes and address long-standing questions about gymnosperm evolution.
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Affiliation(s)
- Jill L. Wegrzyn
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
- * E-mail: (JLW); (KAS)
| | - Brian Y. Lin
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Jacob J. Zieve
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - William M. Dougherty
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
| | - Pedro J. Martínez-García
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Maxim Koriabine
- Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Ann Holtz-Morris
- Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Pieter deJong
- Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Marc Crepeau
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
| | - Charles H. Langley
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
| | - Daniela Puiu
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Steven L. Salzberg
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - David B. Neale
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Kristian A. Stevens
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
- * E-mail: (JLW); (KAS)
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1458
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Laing R, Kikuchi T, Martinelli A, Tsai IJ, Beech RN, Redman E, Holroyd N, Bartley DJ, Beasley H, Britton C, Curran D, Devaney E, Gilabert A, Hunt M, Jackson F, Johnston SL, Kryukov I, Li K, Morrison AA, Reid AJ, Sargison N, Saunders GI, Wasmuth JD, Wolstenholme A, Berriman M, Gilleard JS, Cotton JA. The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery. Genome Biol 2013; 14:R88. [PMID: 23985316 PMCID: PMC4054779 DOI: 10.1186/gb-2013-14-8-r88] [Citation(s) in RCA: 263] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 06/27/2013] [Accepted: 08/28/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The small ruminant parasite Haemonchus contortus is the most widely used parasitic nematode in drug discovery, vaccine development and anthelmintic resistance research. Its remarkable propensity to develop resistance threatens the viability of the sheep industry in many regions of the world and provides a cautionary example of the effect of mass drug administration to control parasitic nematodes. Its phylogenetic position makes it particularly well placed for comparison with the free-living nematode Caenorhabditis elegans and the most economically important parasites of livestock and humans. RESULTS Here we report the detailed analysis of a draft genome assembly and extensive transcriptomic dataset for H. contortus. This represents the first genome to be published for a strongylid nematode and the most extensive transcriptomic dataset for any parasitic nematode reported to date. We show a general pattern of conservation of genome structure and gene content between H. contortus and C. elegans, but also a dramatic expansion of important parasite gene families. We identify genes involved in parasite-specific pathways such as blood feeding, neurological function, and drug metabolism. In particular, we describe complete gene repertoires for known drug target families, providing the most comprehensive understanding yet of the action of several important anthelmintics. Also, we identify a set of genes enriched in the parasitic stages of the lifecycle and the parasite gut that provide a rich source of vaccine and drug target candidates. CONCLUSIONS The H. contortus genome and transcriptome provide an essential platform for postgenomic research in this and other important strongylid parasites.
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Affiliation(s)
- Roz Laing
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow, Scotland, G61 1QH, UK
| | - Taisei Kikuchi
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Division of Parasitology, Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692 Japan
| | - Axel Martinelli
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Isheng J Tsai
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Division of Parasitology, Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692 Japan
| | - Robin N Beech
- Institute of Parasitology, Macdonald Campus, McGill University, 21,111 Lakeshore Road, Ste. Anne de Bellevue, Québec, Canada H9X 3V9
| | - Elizabeth Redman
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, Faculty of Veterinary Medicine, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Nancy Holroyd
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - David J Bartley
- Disease Control, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK
| | - Helen Beasley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Collette Britton
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow, Scotland, G61 1QH, UK
| | - David Curran
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, Faculty of Veterinary Medicine, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Eileen Devaney
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow, Scotland, G61 1QH, UK
| | - Aude Gilabert
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, Faculty of Veterinary Medicine, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Martin Hunt
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Frank Jackson
- Disease Control, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK
| | - Stephanie L Johnston
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow, Scotland, G61 1QH, UK
| | - Ivan Kryukov
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, Faculty of Veterinary Medicine, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Keyu Li
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, Faculty of Veterinary Medicine, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Alison A Morrison
- Disease Control, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK
| | - Adam J Reid
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Neil Sargison
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Veterinary Centre, Roslin, Midlothian EH25 9RG, Scotland, UK
| | - Gary I Saunders
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow, Scotland, G61 1QH, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - James D Wasmuth
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, Faculty of Veterinary Medicine, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Adrian Wolstenholme
- Department of Infectious Diseases and Center for Tropical and Emerging Global Disease, University of Georgia, Athens, Georgia 30602, USA
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - John S Gilleard
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, Faculty of Veterinary Medicine, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - James A Cotton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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1459
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Gardiner J. The evolution and diversification of plant microtubule-associated proteins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:219-29. [PMID: 23551562 DOI: 10.1111/tpj.12189] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 03/11/2013] [Accepted: 03/22/2013] [Indexed: 05/07/2023]
Abstract
Plant evolution is marked by major advances in structural characteristics that facilitated the highly successful colonization of dry land. Underlying these advances is the evolution of genes encoding specialized proteins that form novel microtubular arrays of the cytoskeleton. This review investigates the evolution of plant families of microtubule-associated proteins (MAPs) through the recently sequenced genomes of Arabidopsis thaliana, Oryza sativa, Selaginella moellendorffii, Physcomitrella patens, Volvox carteri and Chlamydomonas reinhardtii. The families of MAPs examined are AIR9, CLASP, CRIPT, MAP18, MOR1, TON, EB1, AtMAP70, SPR2, SPR1, WVD2 and MAP65 families (abbreviations are defined in the footnote to Table 1). Conjectures are made regarding the evolution of MAPs in plants in relation to the evolution of multicellularity, oriented cell division and vasculature. Angiosperms in particular have high numbers of proteins that are involved in promotion of helical growth or its suppression, and novel plant microtubular structures may have acted as a catalyst for the development of novel plant MAPs. Comparisons of plant MAP gene families with those of animals show that animals may have more flexibility in the structure of their microtubule cytoskeletons than plants, but with both plants and animals possessing many MAP splice variants.
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Affiliation(s)
- John Gardiner
- School of Biological Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
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1460
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Vamathevan JJ, Hall MD, Hasan S, Woollard PM, Xu M, Yang Y, Li X, Wang X, Kenny S, Brown JR, Huxley-Jones J, Lyon J, Haselden J, Min J, Sanseau P. Minipig and beagle animal model genomes aid species selection in pharmaceutical discovery and development. Toxicol Appl Pharmacol 2013; 270:149-57. [DOI: 10.1016/j.taap.2013.04.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 04/07/2013] [Accepted: 04/08/2013] [Indexed: 10/26/2022]
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1461
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Wiemann P, Sieber CMK, von Bargen KW, Studt L, Niehaus EM, Espino JJ, Huß K, Michielse CB, Albermann S, Wagner D, Bergner SV, Connolly LR, Fischer A, Reuter G, Kleigrewe K, Bald T, Wingfield BD, Ophir R, Freeman S, Hippler M, Smith KM, Brown DW, Proctor RH, Münsterkötter M, Freitag M, Humpf HU, Güldener U, Tudzynski B. Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites. PLoS Pathog 2013; 9:e1003475. [PMID: 23825955 PMCID: PMC3694855 DOI: 10.1371/journal.ppat.1003475] [Citation(s) in RCA: 321] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 05/18/2013] [Indexed: 12/17/2022] Open
Abstract
The fungus Fusarium fujikuroi causes "bakanae" disease of rice due to its ability to produce gibberellins (GAs), but it is also known for producing harmful mycotoxins. However, the genetic capacity for the whole arsenal of natural compounds and their role in the fungus' interaction with rice remained unknown. Here, we present a high-quality genome sequence of F. fujikuroi that was assembled into 12 scaffolds corresponding to the 12 chromosomes described for the fungus. We used the genome sequence along with ChIP-seq, transcriptome, proteome, and HPLC-FTMS-based metabolome analyses to identify the potential secondary metabolite biosynthetic gene clusters and to examine their regulation in response to nitrogen availability and plant signals. The results indicate that expression of most but not all gene clusters correlate with proteome and ChIP-seq data. Comparison of the F. fujikuroi genome to those of six other fusaria revealed that only a small number of gene clusters are conserved among these species, thus providing new insights into the divergence of secondary metabolism in the genus Fusarium. Noteworthy, GA biosynthetic genes are present in some related species, but GA biosynthesis is limited to F. fujikuroi, suggesting that this provides a selective advantage during infection of the preferred host plant rice. Among the genome sequences analyzed, one cluster that includes a polyketide synthase gene (PKS19) and another that includes a non-ribosomal peptide synthetase gene (NRPS31) are unique to F. fujikuroi. The metabolites derived from these clusters were identified by HPLC-FTMS-based analyses of engineered F. fujikuroi strains overexpressing cluster genes. In planta expression studies suggest a specific role for the PKS19-derived product during rice infection. Thus, our results indicate that combined comparative genomics and genome-wide experimental analyses identified novel genes and secondary metabolites that contribute to the evolutionary success of F. fujikuroi as a rice pathogen.
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Affiliation(s)
- Philipp Wiemann
- Institut für Biologie und Biotechnologie der Pflanzen, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Christian M. K. Sieber
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Katharina W. von Bargen
- Institute for Food Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, Münster, Germany
| | - Lena Studt
- Institut für Biologie und Biotechnologie der Pflanzen, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-Universität Münster, Münster, Germany
- Institute for Food Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, Münster, Germany
| | - Eva-Maria Niehaus
- Institut für Biologie und Biotechnologie der Pflanzen, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Jose J. Espino
- Institut für Biologie und Biotechnologie der Pflanzen, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Kathleen Huß
- Institut für Biologie und Biotechnologie der Pflanzen, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Caroline B. Michielse
- Institut für Biologie und Biotechnologie der Pflanzen, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Sabine Albermann
- Institut für Biologie und Biotechnologie der Pflanzen, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Dominik Wagner
- Institut für Biologie und Biotechnologie der Pflanzen, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Sonja V. Bergner
- Institut für Biologie und Biotechnologie der Pflanzen, Plant Biochemistry and Biotechnology, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Lanelle R. Connolly
- Department of Biochemistry and Biophysics, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Andreas Fischer
- Institut of Genetics/Developmental Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
| | - Gunter Reuter
- Institut of Genetics/Developmental Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
| | - Karin Kleigrewe
- Institute for Food Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, Münster, Germany
| | - Till Bald
- Institut für Biologie und Biotechnologie der Pflanzen, Plant Biochemistry and Biotechnology, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Brenda D. Wingfield
- Department of Genetics, University of Pretoria, Hatfield, Pretoria, South Africa
| | - Ron Ophir
- Institute of Plant Sciences, Genomics, Agricultural Research Organization (ARO), The Volcani Center, Bet-Dagan, Israel
| | - Stanley Freeman
- Department of Plant Pathology, Agricultural Research Organization (ARO), The Volcani Center, Bet-Dagan, Israel
| | - Michael Hippler
- Institut für Biologie und Biotechnologie der Pflanzen, Plant Biochemistry and Biotechnology, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Kristina M. Smith
- Department of Biochemistry and Biophysics, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Daren W. Brown
- National Center for Agricultural Utilization Research, United States Department of Agriculture, Peoria, Illinois, United States of America
| | - Robert H. Proctor
- National Center for Agricultural Utilization Research, United States Department of Agriculture, Peoria, Illinois, United States of America
| | - Martin Münsterkötter
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Hans-Ulrich Humpf
- Institute for Food Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, Münster, Germany
| | - Ulrich Güldener
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Bettina Tudzynski
- Institut für Biologie und Biotechnologie der Pflanzen, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-Universität Münster, Münster, Germany
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1462
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Hacquard S, Kracher B, Maekawa T, Vernaldi S, Schulze-Lefert P, Ver Loren van Themaat E. Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts. Proc Natl Acad Sci U S A 2013; 110:E2219-28. [PMID: 23696672 PMCID: PMC3683789 DOI: 10.1073/pnas.1306807110] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Barley powdery mildew, Blumeria graminis f. sp. hordei (Bgh), is an obligate biotrophic ascomycete fungal pathogen that can grow and reproduce only on living cells of wild or domesticated barley (Hordeum sp.). Domestication and deployment of resistant barley cultivars by humans selected for amplification of Bgh isolates with different virulence combinations. We sequenced the genomes of two European Bgh isolates, A6 and K1, for comparative analysis with the reference genome of isolate DH14. This revealed a mosaic genome structure consisting of large isolate-specific DNA blocks with either high or low SNP densities. Some of the highly polymorphic blocks likely accumulated SNPs for over 10,000 years, well before the domestication of barley. These isolate-specific blocks of alternating monomorphic and polymorphic regions imply an exceptionally large standing genetic variation in the Bgh population and might be generated and maintained by rare outbreeding and frequent clonal reproduction. RNA-sequencing experiments with isolates A6 and K1 during four early stages of compatible and incompatible interactions on leaves of partially immunocompromised Arabidopsis mutants revealed a conserved Bgh transcriptional program during pathogenesis compared with the natural host barley despite ~200 million years of reproductive isolation of these hosts. Transcripts encoding candidate-secreted effector proteins are massively induced in successive waves. A specific decrease in candidate-secreted effector protein transcript abundance in the incompatible interaction follows extensive transcriptional reprogramming of the host transcriptome and coincides with the onset of localized host cell death, suggesting a host-inducible defense mechanism that targets fungal effector secretion or production.
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Affiliation(s)
| | | | - Takaki Maekawa
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Saskia Vernaldi
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Paul Schulze-Lefert
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Emiel Ver Loren van Themaat
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
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1463
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Supple MA, Hines HM, Dasmahapatra KK, Lewis JJ, Nielsen DM, Lavoie C, Ray DA, Salazar C, McMillan WO, Counterman BA. Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies. Genome Res 2013; 23:1248-57. [PMID: 23674305 PMCID: PMC3730099 DOI: 10.1101/gr.150615.112] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Identifying the genetic changes driving adaptive variation in natural populations is key to understanding the origins of biodiversity. The mosaic of mimetic wing patterns in Heliconius butterflies makes an excellent system for exploring adaptive variation using next-generation sequencing. In this study, we use a combination of techniques to annotate the genomic interval modulating red color pattern variation, identify a narrow region responsible for adaptive divergence and convergence in Heliconius wing color patterns, and explore the evolutionary history of these adaptive alleles. We use whole genome resequencing from four hybrid zones between divergent color pattern races of Heliconius erato and two hybrid zones of the co-mimic Heliconius melpomene to examine genetic variation across 2.2 Mb of a partial reference sequence. In the intergenic region near optix, the gene previously shown to be responsible for the complex red pattern variation in Heliconius, population genetic analyses identify a shared 65-kb region of divergence that includes several sites perfectly associated with phenotype within each species. This region likely contains multiple cis-regulatory elements that control discrete expression domains of optix. The parallel signatures of genetic differentiation in H. erato and H. melpomene support a shared genetic architecture between the two distantly related co-mimics; however, phylogenetic analysis suggests mimetic patterns in each species evolved independently. Using a combination of next-generation sequencing analyses, we have refined our understanding of the genetic architecture of wing pattern variation in Heliconius and gained important insights into the evolution of novel adaptive phenotypes in natural populations.
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Affiliation(s)
- Megan A Supple
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
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1464
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Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A, Bloom OE, Morgan JR, Buxbaum JD, Sachidanandam R, Sims C, Garruss AS, Cook M, Krumlauf R, Wiedemann LM, Sower SA, Decatur WA, Hall JA, Amemiya CT, Saha NR, Buckley KM, Rast JP, Das S, Hirano M, McCurley N, Guo P, Rohner N, Tabin CJ, Piccinelli P, Elgar G, Ruffier M, Aken BL, Searle SMJ, Muffato M, Pignatelli M, Herrero J, Jones M, Brown CT, Chung-Davidson YW, Nanlohy KG, Libants SV, Yeh CY, McCauley DW, Langeland JA, Pancer Z, Fritzsch B, de Jong PJ, Zhu B, Fulton LL, Theising B, Flicek P, Bronner ME, Warren WC, Clifton SW, Wilson RK, Li W. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet 2013; 45:415-21, 421e1-2. [PMID: 23435085 PMCID: PMC3709584 DOI: 10.1038/ng.2568] [Citation(s) in RCA: 437] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 01/31/2013] [Indexed: 12/19/2022]
Abstract
Lampreys are representatives of an ancient vertebrate lineage that diverged from our own ∼500 million years ago. By virtue of this deeply shared ancestry, the sea lamprey (P. marinus) genome is uniquely poised to provide insight into the ancestry of vertebrate genomes and the underlying principles of vertebrate biology. Here, we present the first lamprey whole-genome sequence and assembly. We note challenges faced owing to its high content of repetitive elements and GC bases, as well as the absence of broad-scale sequence information from closely related species. Analyses of the assembly indicate that two whole-genome duplications likely occurred before the divergence of ancestral lamprey and gnathostome lineages. Moreover, the results help define key evolutionary events within vertebrate lineages, including the origin of myelin-associated proteins and the development of appendages. The lamprey genome provides an important resource for reconstructing vertebrate origins and the evolutionary events that have shaped the genomes of extant organisms.
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Affiliation(s)
- Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA.
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1465
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Schardl CL, Young CA, Hesse U, Amyotte SG, Andreeva K, Calie PJ, Fleetwood DJ, Haws DC, Moore N, Oeser B, Panaccione DG, Schweri KK, Voisey CR, Farman ML, Jaromczyk JW, Roe BA, O'Sullivan DM, Scott B, Tudzynski P, An Z, Arnaoudova EG, Bullock CT, Charlton ND, Chen L, Cox M, Dinkins RD, Florea S, Glenn AE, Gordon A, Güldener U, Harris DR, Hollin W, Jaromczyk J, Johnson RD, Khan AK, Leistner E, Leuchtmann A, Li C, Liu J, Liu J, Liu M, Mace W, Machado C, Nagabhyru P, Pan J, Schmid J, Sugawara K, Steiner U, Takach JE, Tanaka E, Webb JS, Wilson EV, Wiseman JL, Yoshida R, Zeng Z. Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci. PLoS Genet 2013; 9:e1003323. [PMID: 23468653 PMCID: PMC3585121 DOI: 10.1371/journal.pgen.1003323] [Citation(s) in RCA: 271] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 12/31/2012] [Indexed: 01/01/2023] Open
Abstract
The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some-including the infamous ergot alkaloids-have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses.
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1466
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Kelemen O, Convertini P, Zhang Z, Wen Y, Shen M, Falaleeva M, Stamm S. Function of alternative splicing. Gene 2013; 514:1-30. [PMID: 22909801 PMCID: PMC5632952 DOI: 10.1016/j.gene.2012.07.083] [Citation(s) in RCA: 515] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 07/21/2012] [Accepted: 07/30/2012] [Indexed: 12/15/2022]
Abstract
Almost all polymerase II transcripts undergo alternative pre-mRNA splicing. Here, we review the functions of alternative splicing events that have been experimentally determined. The overall function of alternative splicing is to increase the diversity of mRNAs expressed from the genome. Alternative splicing changes proteins encoded by mRNAs, which has profound functional effects. Experimental analysis of these protein isoforms showed that alternative splicing regulates binding between proteins, between proteins and nucleic acids as well as between proteins and membranes. Alternative splicing regulates the localization of proteins, their enzymatic properties and their interaction with ligands. In most cases, changes caused by individual splicing isoforms are small. However, cells typically coordinate numerous changes in 'splicing programs', which can have strong effects on cell proliferation, cell survival and properties of the nervous system. Due to its widespread usage and molecular versatility, alternative splicing emerges as a central element in gene regulation that interferes with almost every biological function analyzed.
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Affiliation(s)
- Olga Kelemen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Paolo Convertini
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Zhaiyi Zhang
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Yuan Wen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Manli Shen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Marina Falaleeva
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Stefan Stamm
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
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1467
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Zhang H, Miao H, Wang L, Qu L, Liu H, Wang Q, Yue M. Genome sequencing of the important oilseed crop Sesamum indicum L. Genome Biol 2013; 14:401. [PMID: 23369264 PMCID: PMC3663098 DOI: 10.1186/gb-2013-14-1-401] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The Sesame Genome Working Group (SGWG) has been formed to sequence and assemble the sesame (Sesamum indicum L.) genome. The status of this project and our planned analyses are described.
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Affiliation(s)
- Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, People's Republic of China
| | - Hongmei Miao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, People's Republic of China
| | - Lei Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, People's Republic of China
| | - Lingbo Qu
- Department of Bioengineering, Henan Technology University, Zhengzhou 450001, People's Republic of China
| | - Hongyan Liu
- Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Zhengzhou 450002, People's Republic of China
| | - Qiang Wang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, People's Republic of China
| | - Meiwang Yue
- Crops Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, People's Republic of China
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1468
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Zheng A, Lin R, Zhang D, Qin P, Xu L, Ai P, Ding L, Wang Y, Chen Y, Liu Y, Sun Z, Feng H, Liang X, Fu R, Tang C, Li Q, Zhang J, Xie Z, Deng Q, Li S, Wang S, Zhu J, Wang L, Liu H, Li P. The evolution and pathogenic mechanisms of the rice sheath blight pathogen. Nat Commun 2013; 4:1424. [PMID: 23361014 PMCID: PMC3562461 DOI: 10.1038/ncomms2427] [Citation(s) in RCA: 173] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 12/31/2012] [Indexed: 11/09/2022] Open
Abstract
Rhizoctonia solani is a major fungal pathogen of rice (Oryza sativa L.) that causes great yield losses in all rice-growing regions of the world. Here we report the draft genome sequence of the rice sheath blight disease pathogen, R. solani AG1 IA, assembled using next-generation Illumina Genome Analyser sequencing technologies. The genome encodes a large and diverse set of secreted proteins, enzymes of primary and secondary metabolism, carbohydrate-active enzymes, and transporters, which probably reflect an exclusive necrotrophic lifestyle. We find few repetitive elements, a closer relationship to Agaricomycotina among Basidiomycetes, and expand protein domains and families. Among the 25 candidate pathogen effectors identified according to their functionality and evolution, we validate 3 that trigger crop defence responses; hence we reveal the exclusive expression patterns of the pathogenic determinants during host infection.
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Affiliation(s)
- Aiping Zheng
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu 611130, China
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’an 625014, China
- These authors contributed equally to this work
| | - Runmao Lin
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu 611130, China
- These authors contributed equally to this work
| | - Danhua Zhang
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu 611130, China
| | - Peigang Qin
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu 611130, China
| | - Lizhi Xu
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu 611130, China
| | - Peng Ai
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu 611130, China
| | - Lei Ding
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’an 625014, China
| | - Yanran Wang
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu 611130, China
| | - Yao Chen
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu 611130, China
| | - Yao Liu
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhigang Sun
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu 611130, China
| | - Haitao Feng
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoxing Liang
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu 611130, China
| | - Rongtao Fu
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu 611130, China
| | - Changqing Tang
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiao Li
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Zhang
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu 611130, China
| | - Zelin Xie
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’an 625014, China
| | - Qiming Deng
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu 611130, China
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’an 625014, China
| | - Shuangcheng Li
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu 611130, China
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’an 625014, China
| | - Shiquan Wang
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu 611130, China
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’an 625014, China
| | - Jun Zhu
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu 611130, China
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’an 625014, China
| | - Lingxia Wang
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Huainian Liu
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Ping Li
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu 611130, China
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’an 625014, China
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1469
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Liu C, Shi L, Zhu Y, Chen H, Zhang J, Lin X, Guan X. CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences. BMC Genomics 2012. [PMID: 23256920 DOI: 10.1063/1.2745082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND The complete sequences of chloroplast genomes provide wealthy information regarding the evolutionary history of species. With the advance of next-generation sequencing technology, the number of completely sequenced chloroplast genomes is expected to increase exponentially, powerful computational tools annotating the genome sequences are in urgent need. RESULTS We have developed a web server CPGAVAS. The server accepts a complete chloroplast genome sequence as input. First, it predicts protein-coding and rRNA genes based on the identification and mapping of the most similar, full-length protein, cDNA and rRNA sequences by integrating results from Blastx, Blastn, protein2genome and est2genome programs. Second, tRNA genes and inverted repeats (IR) are identified using tRNAscan, ARAGORN and vmatch respectively. Third, it calculates the summary statistics for the annotated genome. Fourth, it generates a circular map ready for publication. Fifth, it can create a Sequin file for GenBank submission. Last, it allows the extractions of protein and mRNA sequences for given list of genes and species. The annotation results in GFF3 format can be edited using any compatible annotation editing tools. The edited annotations can then be uploaded to CPGAVAS for update and re-analyses repeatedly. Using known chloroplast genome sequences as test set, we show that CPGAVAS performs comparably to another application DOGMA, while having several superior functionalities. CONCLUSIONS CPGAVAS allows the semi-automatic and complete annotation of a chloroplast genome sequence, and the visualization, editing and analysis of the annotation results. It will become an indispensible tool for researchers studying chloroplast genomes. The software is freely accessible from http://www.herbalgenomics.org/cpgavas.
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Affiliation(s)
- Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, 151 MaLianWa North Road, Haidian District, Beijing 100191, People's Republic of China.
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1470
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CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences. BMC Genomics 2012; 13:715. [PMID: 23256920 PMCID: PMC3543216 DOI: 10.1186/1471-2164-13-715] [Citation(s) in RCA: 467] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 12/15/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The complete sequences of chloroplast genomes provide wealthy information regarding the evolutionary history of species. With the advance of next-generation sequencing technology, the number of completely sequenced chloroplast genomes is expected to increase exponentially, powerful computational tools annotating the genome sequences are in urgent need. RESULTS We have developed a web server CPGAVAS. The server accepts a complete chloroplast genome sequence as input. First, it predicts protein-coding and rRNA genes based on the identification and mapping of the most similar, full-length protein, cDNA and rRNA sequences by integrating results from Blastx, Blastn, protein2genome and est2genome programs. Second, tRNA genes and inverted repeats (IR) are identified using tRNAscan, ARAGORN and vmatch respectively. Third, it calculates the summary statistics for the annotated genome. Fourth, it generates a circular map ready for publication. Fifth, it can create a Sequin file for GenBank submission. Last, it allows the extractions of protein and mRNA sequences for given list of genes and species. The annotation results in GFF3 format can be edited using any compatible annotation editing tools. The edited annotations can then be uploaded to CPGAVAS for update and re-analyses repeatedly. Using known chloroplast genome sequences as test set, we show that CPGAVAS performs comparably to another application DOGMA, while having several superior functionalities. CONCLUSIONS CPGAVAS allows the semi-automatic and complete annotation of a chloroplast genome sequence, and the visualization, editing and analysis of the annotation results. It will become an indispensible tool for researchers studying chloroplast genomes. The software is freely accessible from http://www.herbalgenomics.org/cpgavas.
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1471
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Ohm RA, Feau N, Henrissat B, Schoch CL, Horwitz BA, Barry KW, Condon BJ, Copeland AC, Dhillon B, Glaser F, Hesse CN, Kosti I, LaButti K, Lindquist EA, Lucas S, Salamov AA, Bradshaw RE, Ciuffetti L, Hamelin RC, Kema GHJ, Lawrence C, Scott JA, Spatafora JW, Turgeon BG, de Wit PJGM, Zhong S, Goodwin SB, Grigoriev IV. Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathog 2012; 8:e1003037. [PMID: 23236275 PMCID: PMC3516569 DOI: 10.1371/journal.ppat.1003037] [Citation(s) in RCA: 374] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 09/30/2012] [Indexed: 12/21/2022] Open
Abstract
The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress. Dothideomycetes is the largest and most ecologically diverse class of fungi that includes many plant pathogens with high economic impact. Currently 18 genome sequences of Dothideomycetes are available, 14 of which are newly described in this paper and in several companion papers, allowing unprecedented resolution in comparative analyses. These 18 organisms have diverse lifestyles and strategies of plant pathogenesis. Three feed on dead organic matter only, six are necrotrophs (killing the host plant cells), one is a biotroph (forming an association with and thus feeding on the living cells of the host plant cells) and 8 are hemibiotrophs (having an initial biotrophic stage, and killing the host plant at a later stage). These various lifestyles are also reflected in the gene sets present in each group. For example, sets of genes involved in carbohydrate degradation and secondary metabolism are expanded in necrotrophs. Many genes involved in pathogenesis are located near repetitive sequences, which are believed to speed up their evolution. Blocks of genes with conserved gene order were identified. In addition to this we deduce that the mechanism for mesosynteny, a type of genome evolution particular to Dothideomycetes, is by intra-chromosomal inversions.
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Affiliation(s)
- Robin A. Ohm
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
- * E-mail: (RAO); (IVG)
| | - Nicolas Feau
- Faculty of Forestry, Forest Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, CNRS, Marseille, France
| | | | | | - Kerrie W. Barry
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Bradford J. Condon
- Department of Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Alex C. Copeland
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Braham Dhillon
- Faculty of Forestry, Forest Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Fabian Glaser
- Bioinformatics Knowledge Unit, Technion - IIT, Haifa, Israel
| | - Cedar N. Hesse
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Idit Kosti
- Department of Biology, Technion - IIT, Haifa, Israel
| | - Kurt LaButti
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Erika A. Lindquist
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Susan Lucas
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Asaf A. Salamov
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Rosie E. Bradshaw
- Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand
| | - Lynda Ciuffetti
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Richard C. Hamelin
- Faculty of Forestry, Forest Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Natural Resources Canada, Ste-Foy, Quebec, Canada
| | | | - Christopher Lawrence
- Virginia Bioinformatics Institute & Department of Biological Sciences, Blacksburg, Virginia, United States of America
| | - James A. Scott
- Division of Occupational & Environmental Health, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Joseph W. Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - B. Gillian Turgeon
- Department of Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | | | - Shaobin Zhong
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Stephen B. Goodwin
- United States Department of Agriculture, Agricultural Research Service, Purdue University, West Lafayette, Indiana, United States of America
| | - Igor V. Grigoriev
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
- * E-mail: (RAO); (IVG)
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1472
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Pan B, Sheng J, Sun W, Zhao Y, Hao P, Li X. OrysPSSP: a comparative platform for small secreted proteins from rice and other plants. Nucleic Acids Res 2012. [PMID: 23203890 PMCID: PMC3531210 DOI: 10.1093/nar/gks1090] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Plants have large diverse families of small secreted proteins (SSPs) that play critical roles in the processes of development, differentiation, defense, flowering, stress response, symbiosis, etc. Oryza sativa is one of the major crops worldwide and an excellent model for monocotyledonous plants. However, there had not been any effort to systematically analyze rice SSPs. Here, we constructed a comparative platform, OrysPSSP (http://www.genoportal.org/PSSP/index.do), involving >100 000 SSPs from rice and 25 plant species. OrysPSSP is composed of a core SSP database and a dynamic web interface that integrates a variety of user tools and resources. The current release (v0530) of core SSP database contains a total of 101 048 predicted SSPs, which were generated through a rigid computation/curation pipeline. The web interface consists of eight different modules, providing users with rich resources/functions, e.g. browsing SSP by chromosome, searching and filtering SSP, validating SSP with omics data, comparing SSP among multiple species and querying core SSP database with BLAST. Some cases of application are discussed to demonstrate the utility of OrysPSSP. OrysPSSP serves as a comprehensive resource to explore SSP on the genome scale and across the phylogeny of plant species.
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Affiliation(s)
- Bohu Pan
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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1473
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Wu J, Wang Z, Shi Z, Zhang S, Ming R, Zhu S, Khan MA, Tao S, Korban SS, Wang H, Chen NJ, Nishio T, Xu X, Cong L, Qi K, Huang X, Wang Y, Zhao X, Wu J, Deng C, Gou C, Zhou W, Yin H, Qin G, Sha Y, Tao Y, Chen H, Yang Y, Song Y, Zhan D, Wang J, Li L, Dai M, Gu C, Wang Y, Shi D, Wang X, Zhang H, Zeng L, Zheng D, Wang C, Chen M, Wang G, Xie L, Sovero V, Sha S, Huang W, Zhang S, Zhang M, Sun J, Xu L, Li Y, Liu X, Li Q, Shen J, Wang J, Paull RE, Bennetzen JL, Wang J, Zhang S. The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res 2012; 23:396-408. [PMID: 23149293 PMCID: PMC3561880 DOI: 10.1101/gr.144311.112] [Citation(s) in RCA: 510] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The draft genome of the pear (Pyrus bretschneideri) using a combination of BAC-by-BAC and next-generation sequencing is reported. A 512.0-Mb sequence corresponding to 97.1% of the estimated genome size of this highly heterozygous species is assembled with 194× coverage. High-density genetic maps comprising 2005 SNP markers anchored 75.5% of the sequence to all 17 chromosomes. The pear genome encodes 42,812 protein-coding genes, and of these, ∼28.5% encode multiple isoforms. Repetitive sequences of 271.9 Mb in length, accounting for 53.1% of the pear genome, are identified. Simulation of eudicots to the ancestor of Rosaceae has reconstructed nine ancestral chromosomes. Pear and apple diverged from each other ∼5.4–21.5 million years ago, and a recent whole-genome duplication (WGD) event must have occurred 30–45 MYA prior to their divergence, but following divergence from strawberry. When compared with the apple genome sequence, size differences between the apple and pear genomes are confirmed mainly due to the presence of repetitive sequences predominantly contributed by transposable elements (TEs), while genic regions are similar in both species. Genes critical for self-incompatibility, lignified stone cells (a unique feature of pear fruit), sorbitol metabolism, and volatile compounds of fruit have also been identified. Multiple candidate SFB genes appear as tandem repeats in the S-locus region of pear; while lignin synthesis-related gene family expansion and highly expressed gene families of HCT, C3′H, and CCOMT contribute to high accumulation of both G-lignin and S-lignin. Moreover, alpha-linolenic acid metabolism is a key pathway for aroma in pear fruit.
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Affiliation(s)
- Jun Wu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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1474
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Abstract
The monarch butterfly (Danaus plexippus) is emerging as a model organism to study the mechanisms of circadian clocks and animal navigation, and the genetic underpinnings of long-distance migration. The initial assembly of the monarch genome was released in 2011, and the biological interpretation of the genome focused on the butterfly’s migration biology. To make the extensive data associated with the genome accessible to the general biological and lepidopteran communities, we established MonarchBase (available at http://monarchbase.umassmed.edu). The database is an open-access, web-available portal that integrates all available data associated with the monarch butterfly genome. Moreover, MonarchBase provides access to an updated version of genome assembly (v3) upon which all data integration is based. These include genes with systematic annotation, as well as other molecular resources, such as brain expressed sequence tags, migration expression profiles and microRNAs. MonarchBase utilizes a variety of retrieving methods to access data conveniently and for integrating biological interpretations.
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Affiliation(s)
- Shuai Zhan
- Department of Neurobiology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
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1475
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Müller S, Baldin C, Groth M, Guthke R, Kniemeyer O, Brakhage AA, Valiante V. Comparison of transcriptome technologies in the pathogenic fungus Aspergillus fumigatus reveals novel insights into the genome and MpkA dependent gene expression. BMC Genomics 2012; 13:519. [PMID: 23031507 PMCID: PMC3505472 DOI: 10.1186/1471-2164-13-519] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 09/21/2012] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The filamentous fungus Aspergillus fumigatus has become the most important airborne fungal pathogen causing life-threatening infections in immuno-compromised patients. Recently developed high-throughput transcriptome and proteome technologies, such as microarrays, RNA deep-sequencing, and LC-MS/MS of peptide mixtures, are of enormous value for systematically investigating pathogenic organisms. In the field of infection biology, one of the priorities is to collect and standardise data, in order to generate datasets that can be used to investigate and compare pathways and gene responses involved in pathogenicity. The "omics" era provides a multitude of inputs that need to be integrated and assessed. We therefore evaluated the potential of paired-end mRNA-Seq for investigating the regulatory role of the central mitogen activated protein kinase (MpkA). This kinase is involved in the cell wall integrity signalling pathway of A. fumigatus and essential for maintaining an intact cell wall in response to stress. RESULTS The comparison of the transcriptome and proteome of an A. fumigatus wild-type strain with an mpkA null mutant strain revealed that 70.4% of the genome was found to be expressed and that MpkA plays a significant role in the regulation of many genes involved in cell wall remodelling, oxidative stress and iron starvation response, and secondary metabolite biosynthesis. Moreover, absence of the mpkA gene also strongly affects the expression of genes involved in primary metabolism. The data were further processed to evaluate the potential of the mRNA-Seq technique. We comprehensively matched up our data to published transcriptome studies and were able to show an improved data comparability of mRNA-Seq experiments independently of the technique used. Analysis of transcriptome and proteome data revealed only a weak correlation between mRNA and protein abundance. CONCLUSIONS High-throughput analysis of MpkA-dependent gene expression confirmed many previous findings that this kinase is important for regulating many genes involved in metabolic pathways. Our analysis showed more than 2000 differentially regulated genes. RNA deep-sequencing is less error-prone than established microarray-based technologies. It also provides additional information in A. fumigatus studies and as a result is more suitable for the creation of extensive datasets.
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Affiliation(s)
- Sebastian Müller
- Department of Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Beutenbergstr. 11a, Jena 07745, Germany
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1476
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Yang E, Xu L, Yang Y, Zhang X, Xiang M, Wang C, An Z, Liu X. Origin and evolution of carnivorism in the Ascomycota (fungi). Proc Natl Acad Sci U S A 2012; 109:10960-5. [PMID: 22715289 PMCID: PMC3390824 DOI: 10.1073/pnas.1120915109] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Carnivorism is one of the basic life strategies of fungi. Carnivorous fungi possess the ability to trap and digest their preys by sophisticated trapping devices. However, the origin and development of fungal carnivorism remains a gap in evolution biology. In this study, five protein-encoding genes were used to construct the phylogeny of the carnivorous fungi in the phylum Ascomycota; these fungi prey on nematodes by means of specialized trapping structures such as constricting rings and adhesive traps. Our analysis revealed a definitive pattern of evolutionary development for these trapping structures. Molecular clock calibration based on two fossil records revealed that fungal carnivorism diverged from saprophytism about 419 Mya, which was after the origin of nematodes about 550-600 Mya. Active carnivorism (fungi with constricting rings) and passive carnivorism (fungi with adhesive traps) diverged from each other around 246 Mya, shortly after the occurrence of the Permian-Triassic extinction event about 251.4 Mya. The major adhesive traps evolved around 198-208 Mya, which was within the time frame of the Triassic-Jurassic extinction event about 201.4 Mya. However, no major carnivorous ascomycetes divergence was correlated to the Cretaceous-Tertiary extinction event, which occurred more recently (about 65.5 Mya). Therefore, a causal relationship between mass extinction events and fungal carnivorism evolution is not validated in this study. More evidence including additional fossil records is needed to establish if fungal carnivorism evolution was a response to mass extinction events.
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Affiliation(s)
- Ence Yang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lingling Xu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Biotechnology, Xi'an University of Arts and Science, Xi'an 710065, China
| | - Ying Yang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xinyu Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Meichun Xiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengshu Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; and
| | - Zhiqiang An
- Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030
| | - Xingzhong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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1477
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Torruella G, Derelle R, Paps J, Lang BF, Roger AJ, Shalchian-Tabrizi K, Ruiz-Trillo I. Phylogenetic relationships within the Opisthokonta based on phylogenomic analyses of conserved single-copy protein domains. Mol Biol Evol 2012; 29:531-44. [PMID: 21771718 PMCID: PMC3350318 DOI: 10.1093/molbev/msr185] [Citation(s) in RCA: 138] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Many of the eukaryotic phylogenomic analyses published to date were based on alignments of hundreds to thousands of genes. Frequently, in such analyses, the most realistic evolutionary models currently available are often used to minimize the impact of systematic error. However, controversy remains over whether or not idiosyncratic gene family dynamics (i.e., gene duplications and losses) and incorrect orthology assignments are always appropriately taken into account. In this paper, we present an innovative strategy for overcoming orthology assignment problems. Rather than identifying and eliminating genes with paralogy problems, we have constructed a data set comprised exclusively of conserved single-copy protein domains that, unlike most of the commonly used phylogenomic data sets, should be less confounded by orthology miss-assignments. To evaluate the power of this approach, we performed maximum likelihood and Bayesian analyses to infer the evolutionary relationships within the opisthokonts (which includes Metazoa, Fungi, and related unicellular lineages). We used this approach to test 1) whether Filasterea and Ichthyosporea form a clade, 2) the interrelationships of early-branching metazoans, and 3) the relationships among early-branching fungi. We also assessed the impact of some methods that are known to minimize systematic error, including reducing the distance between the outgroup and ingroup taxa or using the CAT evolutionary model. Overall, our analyses support the Filozoa hypothesis in which Ichthyosporea are the first holozoan lineage to emerge followed by Filasterea, Choanoflagellata, and Metazoa. Blastocladiomycota appears as a lineage separate from Chytridiomycota, although this result is not strongly supported. These results represent independent tests of previous phylogenetic hypotheses, highlighting the importance of sophisticated approaches for orthology assignment in phylogenomic analyses.
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Affiliation(s)
- Guifré Torruella
- Departament de Genètica and Institut de Recerca en Biodiversitat (Irbio), Universitat de Barcelona, Barcelona, Spain
| | - Romain Derelle
- Departament de Genètica and Institut de Recerca en Biodiversitat (Irbio), Universitat de Barcelona, Barcelona, Spain
- Present address: Centre de regulació genòmica (CRG), Parc de recerca biomèdica de Barcelona (PRBB), Barcelona, Spain
| | - Jordi Paps
- Departament de Genètica and Institut de Recerca en Biodiversitat (Irbio), Universitat de Barcelona, Barcelona, Spain
- Present address: Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - B. Franz Lang
- Département de Biochimie, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - Andrew J. Roger
- Department of Biochemistry and Molecular Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Faculty of Medicine, Dalhousie University, Halifax, Canada
| | | | - Iñaki Ruiz-Trillo
- Departament de Genètica and Institut de Recerca en Biodiversitat (Irbio), Universitat de Barcelona, Barcelona, Spain
- Institució Catalana per a la Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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1478
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Zhan S, Merlin C, Boore JL, Reppert SM. The monarch butterfly genome yields insights into long-distance migration. Cell 2012; 147:1171-85. [PMID: 22118469 DOI: 10.1016/j.cell.2011.09.052] [Citation(s) in RCA: 387] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 08/26/2011] [Accepted: 09/06/2011] [Indexed: 12/30/2022]
Abstract
We present the draft 273 Mb genome of the migratory monarch butterfly (Danaus plexippus) and a set of 16,866 protein-coding genes. Orthology properties suggest that the Lepidoptera are the fastest evolving insect order yet examined. Compared to the silkmoth Bombyx mori, the monarch genome shares prominent similarity in orthology content, microsynteny, and protein family sizes. The monarch genome reveals a vertebrate-like opsin whose existence in insects is widespread; a full repertoire of molecular components for the monarch circadian clockwork; all members of the juvenile hormone biosynthetic pathway whose regulation shows unexpected sexual dimorphism; additional molecular signatures of oriented flight behavior; microRNAs that are differentially expressed between summer and migratory butterflies; monarch-specific expansions of chemoreceptors potentially important for long-distance migration; and a variant of the sodium/potassium pump that underlies a valuable chemical defense mechanism. The monarch genome enhances our ability to better understand the genetic and molecular basis of long-distance migration.
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Affiliation(s)
- Shuai Zhan
- Department of Neurobiology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
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1479
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Abstract
Evolutionary genomics is a field that relies heavily upon comparing genomes, that is, the full complement of genes of one species with another. However, given a genome sequence and little else, as is now often the case, genes must first be found and annotated before downstream analyses can be done. Computational gene prediction techniques are brought to bear on the problem of constructing a genome annotation as manual annotation is extremely time-consuming and costly. This chapter reviews the methods by which the individual components of a typical gene structure are detected in genomic sequence and then discusses several popular statistical frameworks for integrated gene prediction on eukaryotic genome sequences.
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Affiliation(s)
- Tyler Alioto
- Centro Nacional de Análisis Genómico, Barcelona, Spain.
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1480
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Zhang Q, Chen W, Sun L, Zhao F, Huang B, Yang W, Tao Y, Wang J, Yuan Z, Fan G, Xing Z, Han C, Pan H, Zhong X, Shi W, Liang X, Du D, Sun F, Xu Z, Hao R, Lv T, Lv Y, Zheng Z, Sun M, Luo L, Cai M, Gao Y, Wang J, Yin Y, Xu X, Cheng T, Wang J. The genome of Prunus mume. Nat Commun 2012; 3:1318. [PMID: 23271652 PMCID: PMC3535359 DOI: 10.1038/ncomms2290] [Citation(s) in RCA: 274] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 11/14/2012] [Indexed: 11/21/2022] Open
Abstract
Prunus mume (mei), which was domesticated in China more than 3,000 years ago as ornamental plant and fruit, is one of the first genomes among Prunus subfamilies of Rosaceae been sequenced. Here, we assemble a 280M genome by combining 101-fold next-generation sequencing and optical mapping data. We further anchor 83.9% of scaffolds to eight chromosomes with genetic map constructed by restriction-site-associated DNA sequencing. Combining P. mume genome with available data, we succeed in reconstructing nine ancestral chromosomes of Rosaceae family, as well as depicting chromosome fusion, fission and duplication history in three major subfamilies. We sequence the transcriptome of various tissues and perform genome-wide analysis to reveal the characteristics of P. mume, including its regulation of early blooming in endodormancy, immune response against bacterial infection and biosynthesis of flower scent. The P. mume genome sequence adds to our understanding of Rosaceae evolution and provides important data for improvement of fruit trees.
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Affiliation(s)
- Qixiang Zhang
- College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
- These authors contributed equally to this work
| | - Wenbin Chen
- BGI-Shenzhen, Shenzhen 518083, China
- These authors contributed equally to this work
| | - Lidan Sun
- College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
- These authors contributed equally to this work
| | - Fangying Zhao
- Beijing Lin Fu Ke Yuan Flowers Co., Ltd, Beijing 101322, China
- These authors contributed equally to this work
| | - Bangqing Huang
- BGI-Shenzhen, Shenzhen 518083, China
- These authors contributed equally to this work
| | - Weiru Yang
- College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Ye Tao
- BGI-Shenzhen, Shenzhen 518083, China
| | - Jia Wang
- National Engineering Research Center for Floriculture, Beijing 100083, China
| | - Zhiqiong Yuan
- Beijing Lin Fu Ke Yuan Flowers Co., Ltd, Beijing 101322, China
| | | | - Zhen Xing
- College of Resources and Environment, Tibet Agriculture and Animal Husbandry University, Tibet 860000, China
| | | | - Huitang Pan
- College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | | | - Wenfang Shi
- College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | | | - Dongliang Du
- College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | | | - Zongda Xu
- College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Ruijie Hao
- College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Tian Lv
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yingmin Lv
- College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | | | - Ming Sun
- College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Le Luo
- College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Ming Cai
- College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Yike Gao
- College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | | | - Ye Yin
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Tangren Cheng
- National Engineering Research Center for Floriculture, Beijing 100083, China
| | - Jun Wang
- BGI-Shenzhen, Shenzhen 518083, China
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1481
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Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 2011; 40:D1202-10. [PMID: 22140109 PMCID: PMC3245047 DOI: 10.1093/nar/gkr1090] [Citation(s) in RCA: 1462] [Impact Index Per Article: 112.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The Arabidopsis Information Resource (TAIR, http://arabidopsis.org) is a genome database for Arabidopsis thaliana, an important reference organism for many fundamental aspects of biology as well as basic and applied plant biology research. TAIR serves as a central access point for Arabidopsis data, annotates gene function and expression patterns using controlled vocabulary terms, and maintains and updates the A. thaliana genome assembly and annotation. TAIR also provides researchers with an extensive set of visualization and analysis tools. Recent developments include several new genome releases (TAIR8, TAIR9 and TAIR10) in which the A. thaliana assembly was updated, pseudogenes and transposon genes were re-annotated, and new data from proteomics and next generation transcriptome sequencing were incorporated into gene models and splice variants. Other highlights include progress on functional annotation of the genome and the release of several new tools including Textpresso for Arabidopsis which provides the capability to carry out full text searches on a large body of research literature.
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Affiliation(s)
- Philippe Lamesch
- Department of Plant Biology, Carnegie Institution, 260 Panama St, Stanford, CA 94305, USA
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1482
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Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK, Schlueter JA, Donoghue MTA, Azam S, Fan G, Whaley AM, Farmer AD, Sheridan J, Iwata A, Tuteja R, Penmetsa RV, Wu W, Upadhyaya HD, Yang SP, Shah T, Saxena KB, Michael T, McCombie WR, Yang B, Zhang G, Yang H, Wang J, Spillane C, Cook DR, May GD, Xu X, Jackson SA. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol 2011; 30:83-9. [PMID: 22057054 DOI: 10.1038/nbt.2022] [Citation(s) in RCA: 432] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 10/03/2011] [Indexed: 11/08/2022]
Abstract
Pigeonpea is an important legume food crop grown primarily by smallholder farmers in many semi-arid tropical regions of the world. We used the Illumina next-generation sequencing platform to generate 237.2 Gb of sequence, which along with Sanger-based bacterial artificial chromosome end sequences and a genetic map, we assembled into scaffolds representing 72.7% (605.78 Mb) of the 833.07 Mb pigeonpea genome. Genome analysis predicted 48,680 genes for pigeonpea and also showed the potential role that certain gene families, for example, drought tolerance-related genes, have played throughout the domestication of pigeonpea and the evolution of its ancestors. Although we found a few segmental duplication events, we did not observe the recent genome-wide duplication events observed in soybean. This reference genome sequence will facilitate the identification of the genetic basis of agronomically important traits, and accelerate the development of improved pigeonpea varieties that could improve food security in many developing countries.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
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1483
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Raymond F, Boisvert S, Roy G, Ritt JF, Légaré D, Isnard A, Stanke M, Olivier M, Tremblay MJ, Papadopoulou B, Ouellette M, Corbeil J. Genome sequencing of the lizard parasite Leishmania tarentolae reveals loss of genes associated to the intracellular stage of human pathogenic species. Nucleic Acids Res 2011; 40:1131-47. [PMID: 21998295 PMCID: PMC3273817 DOI: 10.1093/nar/gkr834] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The Leishmania tarentolae Parrot-TarII strain genome sequence was resolved to an average 16-fold mean coverage by next-generation DNA sequencing technologies. This is the first non-pathogenic to humans kinetoplastid protozoan genome to be described thus providing an opportunity for comparison with the completed genomes of pathogenic Leishmania species. A high synteny was observed between all sequenced Leishmania species. A limited number of chromosomal regions diverged between L. tarentolae and L. infantum, while remaining syntenic to L. major. Globally, >90% of the L. tarentolae gene content was shared with the other Leishmania species. We identified 95 predicted coding sequences unique to L. tarentolae and 250 genes that were absent from L. tarentolae. Interestingly, many of the latter genes were expressed in the intracellular amastigote stage of pathogenic species. In addition, genes coding for products involved in antioxidant defence or participating in vesicular-mediated protein transport were underrepresented in L. tarentolae. In contrast to other Leishmania genomes, two gene families were expanded in L. tarentolae, namely the zinc metallo-peptidase surface glycoprotein GP63 and the promastigote surface antigen PSA31C. Overall, L. tarentolae's gene content appears better adapted to the promastigote insect stage rather than the amastigote mammalian stage.
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Affiliation(s)
- Frédéric Raymond
- Infectious Disease Research Centre, CHUL Research Centre (CHUQ), Quebec City,Quebec, Canada
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1484
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Zuccaro A, Lahrmann U, Güldener U, Langen G, Pfiffi S, Biedenkopf D, Wong P, Samans B, Grimm C, Basiewicz M, Murat C, Martin F, Kogel KH. Endophytic life strategies decoded by genome and transcriptome analyses of the mutualistic root symbiont Piriformospora indica. PLoS Pathog 2011; 7:e1002290. [PMID: 22022265 PMCID: PMC3192844 DOI: 10.1371/journal.ppat.1002290] [Citation(s) in RCA: 244] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 08/14/2011] [Indexed: 11/18/2022] Open
Abstract
Recent sequencing projects have provided deep insight into fungal lifestyle-associated genomic adaptations. Here we report on the 25 Mb genome of the mutualistic root symbiont Piriformospora indica (Sebacinales, Basidiomycota) and provide a global characterization of fungal transcriptional responses associated with the colonization of living and dead barley roots. Extensive comparative analysis of the P. indica genome with other Basidiomycota and Ascomycota fungi that have diverse lifestyle strategies identified features typically associated with both, biotrophism and saprotrophism. The tightly controlled expression of the lifestyle-associated gene sets during the onset of the symbiosis, revealed by microarray analysis, argues for a biphasic root colonization strategy of P. indica. This is supported by a cytological study that shows an early biotrophic growth followed by a cell death-associated phase. About 10% of the fungal genes induced during the biotrophic colonization encoded putative small secreted proteins (SSP), including several lectin-like proteins and members of a P. indica-specific gene family (DELD) with a conserved novel seven-amino acids motif at the C-terminus. Similar to effectors found in other filamentous organisms, the occurrence of the DELDs correlated with the presence of transposable elements in gene-poor repeat-rich regions of the genome. This is the first in depth genomic study describing a mutualistic symbiont with a biphasic lifestyle. Our findings provide a significant advance in understanding development of biotrophic plant symbionts and suggest a series of incremental shifts along the continuum from saprotrophy towards biotrophy in the evolution of mycorrhizal association from decomposer fungi.
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Affiliation(s)
- Alga Zuccaro
- Department of Organismic Interactions, Max-Planck Institute (MPI) for Terrestrial Microbiology, Marburg, Germany.
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1485
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Kikuchi T, Cotton JA, Dalzell JJ, Hasegawa K, Kanzaki N, McVeigh P, Takanashi T, Tsai IJ, Assefa SA, Cock PJA, Otto TD, Hunt M, Reid AJ, Sanchez-Flores A, Tsuchihara K, Yokoi T, Larsson MC, Miwa J, Maule AG, Sahashi N, Jones JT, Berriman M. Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. PLoS Pathog 2011; 7:e1002219. [PMID: 21909270 PMCID: PMC3164644 DOI: 10.1371/journal.ppat.1002219] [Citation(s) in RCA: 272] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 06/28/2011] [Indexed: 01/17/2023] Open
Abstract
Bursaphelenchus xylophilus is the nematode responsible for a devastating epidemic of pine wilt disease in Asia and Europe, and represents a recent, independent origin of plant parasitism in nematodes, ecologically and taxonomically distinct from other nematodes for which genomic data is available. As well as being an important pathogen, the B. xylophilus genome thus provides a unique opportunity to study the evolution and mechanism of plant parasitism. Here, we present a high-quality draft genome sequence from an inbred line of B. xylophilus, and use this to investigate the biological basis of its complex ecology which combines fungal feeding, plant parasitic and insect-associated stages. We focus particularly on putative parasitism genes as well as those linked to other key biological processes and demonstrate that B. xylophilus is well endowed with RNA interference effectors, peptidergic neurotransmitters (including the first description of ins genes in a parasite) stress response and developmental genes and has a contracted set of chemosensory receptors. B. xylophilus has the largest number of digestive proteases known for any nematode and displays expanded families of lysosome pathway genes, ABC transporters and cytochrome P450 pathway genes. This expansion in digestive and detoxification proteins may reflect the unusual diversity in foods it exploits and environments it encounters during its life cycle. In addition, B. xylophilus possesses a unique complement of plant cell wall modifying proteins acquired by horizontal gene transfer, underscoring the impact of this process on the evolution of plant parasitism by nematodes. Together with the lack of proteins homologous to effectors from other plant parasitic nematodes, this confirms the distinctive molecular basis of plant parasitism in the Bursaphelenchus lineage. The genome sequence of B. xylophilus adds to the diversity of genomic data for nematodes, and will be an important resource in understanding the biology of this unusual parasite.
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Affiliation(s)
- Taisei Kikuchi
- Forestry and Forest Products Research Institute, Tsukuba, Japan.
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1486
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Xing XB, Li QR, Sun H, Fu X, Zhan F, Huang X, Li J, Chen CL, Shyr Y, Zeng R, Li YX, Xie L. The discovery of novel protein-coding features in mouse genome based on mass spectrometry data. Genomics 2011; 98:343-51. [PMID: 21840390 DOI: 10.1016/j.ygeno.2011.07.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 07/18/2011] [Accepted: 07/23/2011] [Indexed: 01/07/2023]
Abstract
Identifying protein-coding genes in eukaryotic genomes remains a challenge in post-genome era due to the complex gene models. We applied a proteogenomics strategy to detect un-annotated protein-coding regions in mouse genome. High-accuracy tandem mass spectrometry (MS/MS) data from diverse mouse samples were generated by LTQ-Orbitrap mass spectrometer in house. Two searchable diagnostic proteomic datasets were constructed, one with all possible encoding exon junctions, and the other with all putative encoding exons, for the discovery of novel exon splicing events and novel uninterrupted protein-coding regions. Altogether 29,586 unique peptides were identified. Aligning backwards to the mouse genome, the translation of 4471 annotated genes was validated by the known peptides; and 172 genic events were defined in mouse genome by the novel peptides. The approach in the current work can provide substantial evidences for eukaryote genome annotation in encoding genes.
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Affiliation(s)
- Xiao-Bin Xing
- Shanghai Center for Bioinformation Technology, PR China
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1487
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Nygaard S, Zhang G, Schiøtt M, Li C, Wurm Y, Hu H, Zhou J, Ji L, Qiu F, Rasmussen M, Pan H, Hauser F, Krogh A, Grimmelikhuijzen CJP, Wang J, Boomsma JJ. The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming. Genome Res 2011; 21:1339-48. [PMID: 21719571 DOI: 10.1101/gr.121392.111] [Citation(s) in RCA: 179] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We present a high-quality (>100× depth) Illumina genome sequence of the leaf-cutting ant Acromyrmex echinatior, a model species for symbiosis and reproductive conflict studies. We compare this genome with three previously sequenced genomes of ants from different subfamilies and focus our analyses on aspects of the genome likely to be associated with known evolutionary changes. The first is the specialized fungal diet of A. echinatior, where we find gene loss in the ant's arginine synthesis pathway, loss of detoxification genes, and expansion of a group of peptidase proteins. One of these is a unique ant-derived contribution to the fecal fluid, which otherwise consists of "garden manuring" fungal enzymes that are unaffected by ant digestion. The second is multiple mating of queens and ejaculate competition, which may be associated with a greatly expanded nardilysin-like peptidase gene family. The third is sex determination, where we could identify only a single homolog of the feminizer gene. As other ants and the honeybee have duplications of this gene, we hypothesize that this may partly explain the frequent production of diploid male larvae in A. echinatior. The fourth is the evolution of eusociality, where we find a highly conserved ant-specific profile of neuropeptide genes that may be related to caste determination. These first analyses of the A. echinatior genome indicate that considerable genetic changes are likely to have accompanied the transition from hunter-gathering to agricultural food production 50 million years ago, and the transition from single to multiple queen mating 10 million years ago.
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Affiliation(s)
- Sanne Nygaard
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark.
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1488
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Buerth C, Heilmann CJ, Klis FM, de Koster CG, Ernst JF, Tielker D. Growth-dependent secretome of Candida utilis. MICROBIOLOGY-SGM 2011; 157:2493-2503. [PMID: 21680638 DOI: 10.1099/mic.0.049320-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Recently, the food yeast Candida utilis has emerged as an excellent host for production of heterologous proteins. Since secretion of the recombinant product is advantageous for its purification, we characterized the secreted proteome of C. utilis. Cells were cultivated to the exponential or stationary growth phase, and the proteins in the medium were identified by MS. In parallel, a draft genome sequence of C. utilis strain DSM 2361 was determined by massively parallel sequencing. Comparisons of protein and coding sequences established that C. utilis is not a member of the CUG clade of Candida species. In total, we identified 37 proteins in the culture solution, 17 of which were exclusively present in the stationary phase, whereas three proteins were specific to the exponential growth phase. Identified proteins represented mostly carbohydrate-active enzymes associated with cell wall organization, while no proteolytic enzymes and only a few cytoplasmic proteins were detected. Remarkably, cultivation in xylose-based medium generated a protein pattern that diverged significantly from glucose-grown cells, containing the invertase Inv1 as the major extracellular protein, particularly in its highly glycosylated S-form (slow-migrating). Furthermore, cultivation without ammonium sulfate induced the secretion of the asparaginase Asp3. Comparisons of the secretome of C. utilis with those of Kluyveromyces lactis and Pichia pastoris, as well as with those of the human fungal pathogens Candida albicans and Candida glabrata, revealed a conserved set of 10 and six secretory proteins, respectively.
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Affiliation(s)
- Christoph Buerth
- Molecular Mycology, Heinrich-Heine-University, Duesseldorf, Universitaetsstraße 1, 40225 Duesseldorf, Germany
| | - Clemens J Heilmann
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Frans M Klis
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Chris G de Koster
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Joachim F Ernst
- Molecular Mycology, Heinrich-Heine-University, Duesseldorf, Universitaetsstraße 1, 40225 Duesseldorf, Germany
| | - Denis Tielker
- Molecular Mycology, Heinrich-Heine-University, Duesseldorf, Universitaetsstraße 1, 40225 Duesseldorf, Germany
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1489
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Truszkowski J, Brown DG. More accurate recombination prediction in HIV-1 using a robust decoding algorithm for HMMs. BMC Bioinformatics 2011; 12:168. [PMID: 21586147 PMCID: PMC3123234 DOI: 10.1186/1471-2105-12-168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Accepted: 05/17/2011] [Indexed: 11/13/2022] Open
Abstract
Background Identifying recombinations in HIV is important for studying the epidemiology of the virus and aids in the design of potential vaccines and treatments. The previous widely-used tool for this task uses the Viterbi algorithm in a hidden Markov model to model recombinant sequences. Results We apply a new decoding algorithm for this HMM that improves prediction accuracy. Exactly locating breakpoints is usually impossible, since different subtypes are highly conserved in some sequence regions. Our algorithm identifies these sites up to a certain error tolerance. Our new algorithm is more accurate in predicting the location of recombination breakpoints. Our implementation of the algorithm is available at http://www.cs.uwaterloo.ca/~jmtruszk/jphmm_balls.tar.gz. Conclusions By explicitly accounting for uncertainty in breakpoint positions, our algorithm offers more reliable predictions of recombination breakpoints in HIV-1. We also document a new domain of use for our new decoding approach in HMMs.
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Affiliation(s)
- Jakub Truszkowski
- David R Cheriton School of Computer Science, University of Waterloo, Waterloo, ON, Canada.
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1490
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Chan CX, Yang EC, Banerjee T, Yoon HS, Martone PT, Estevez JM, Bhattacharya D. Red and Green Algal Monophyly and Extensive Gene Sharing Found in a Rich Repertoire of Red Algal Genes. Curr Biol 2011; 21:328-33. [DOI: 10.1016/j.cub.2011.01.037] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 12/17/2010] [Accepted: 01/12/2011] [Indexed: 11/30/2022]
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1491
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Ancestral and derived attributes of the dlx gene repertoire, cluster structure and expression patterns in an African cichlid fish. EvoDevo 2011; 2:1. [PMID: 21205289 PMCID: PMC3024246 DOI: 10.1186/2041-9139-2-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Accepted: 01/04/2011] [Indexed: 01/03/2023] Open
Abstract
Background Cichlid fishes have undergone rapid, expansive evolutionary radiations that are manifested in the diversification of their trophic morphologies, tooth patterning and coloration. Understanding the molecular mechanisms that underlie the cichlids' unique patterns of evolution requires a thorough examination of genes that pattern the neural crest, from which these diverse phenotypes are derived. Among those genes, the homeobox-containing Dlx gene family is of particular interest since it is involved in the patterning of the brain, jaws and teeth. Results In this study, we characterized the dlx genes of an African cichlid fish, Astatotilapia burtoni, to provide a baseline to later allow cross-species comparison within Cichlidae. We identified seven dlx paralogs (dlx1a, -2a, -4a, -3b, -4b, -5a and -6a), whose orthologies were validated with molecular phylogenetic trees. The intergenic regions of three dlx gene clusters (dlx1a-2a, dlx3b-4b, and dlx5a-6a) were amplified with long PCR. Intensive cross-species comparison revealed a number of conserved non-coding elements (CNEs) that are shared with other percomorph fishes. This analysis highlighted additional lineage-specific gains/losses of CNEs in different teleost fish lineages and a novel CNE that had previously not been identified. Our gene expression analyses revealed overlapping but distinct expression of dlx orthologs in the developing brain and pharyngeal arches. Notably, four of the seven A. burtoni dlx genes, dlx2a, dlx3b, dlx4a and dlx5a, were expressed in the developing pharyngeal teeth. Conclusion This comparative study of the dlx genes of A. burtoni has deepened our knowledge of the diversity of the Dlx gene family, in terms of gene repertoire, expression patterns and non-coding elements. We have identified possible cichlid lineage-specific changes, including losses of a subset of dlx expression domains in the pharyngeal teeth, which will be the targets of future functional studies.
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1492
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Lam TY, Meyer IM. Efficient algorithms for training the parameters of hidden Markov models using stochastic expectation maximization (EM) training and Viterbi training. Algorithms Mol Biol 2010; 5:38. [PMID: 21143925 PMCID: PMC3019189 DOI: 10.1186/1748-7188-5-38] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 12/09/2010] [Indexed: 11/10/2022] Open
Abstract
Background Hidden Markov models are widely employed by numerous bioinformatics programs used today. Applications range widely from comparative gene prediction to time-series analyses of micro-array data. The parameters of the underlying models need to be adjusted for specific data sets, for example the genome of a particular species, in order to maximize the prediction accuracy. Computationally efficient algorithms for parameter training are thus key to maximizing the usability of a wide range of bioinformatics applications. Results We introduce two computationally efficient training algorithms, one for Viterbi training and one for stochastic expectation maximization (EM) training, which render the memory requirements independent of the sequence length. Unlike the existing algorithms for Viterbi and stochastic EM training which require a two-step procedure, our two new algorithms require only one step and scan the input sequence in only one direction. We also implement these two new algorithms and the already published linear-memory algorithm for EM training into the hidden Markov model compiler HMM-CONVERTER and examine their respective practical merits for three small example models. Conclusions Bioinformatics applications employing hidden Markov models can use the two algorithms in order to make Viterbi training and stochastic EM training more computationally efficient. Using these algorithms, parameter training can thus be attempted for more complex models and longer training sequences. The two new algorithms have the added advantage of being easier to implement than the corresponding default algorithms for Viterbi training and stochastic EM training.
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1493
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Wong P, Walter M, Lee W, Mannhaupt G, Münsterkötter M, Mewes HW, Adam G, Güldener U. FGDB: revisiting the genome annotation of the plant pathogen Fusarium graminearum. Nucleic Acids Res 2010; 39:D637-9. [PMID: 21051345 PMCID: PMC3013644 DOI: 10.1093/nar/gkq1016] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The MIPS Fusarium graminearum Genome Database (FGDB) was established as a comprehensive genome database on one of the most devastating fungal plant pathogens of wheat, barley and maize. The current version of FGDB v3.1 provides information on the full manually revised gene set based on the Broad Institute assembly FG3 genome sequence. The results of gene prediction tools were integrated with the help of comparative data on related species to result in a set of 13.718 annotated protein coding genes. This rigorous approach involved adding or modifying gene models and represents a coding sequence gold standard for the genus Fusarium. The gene loci improvements results in 2461 genes which either are new or have different structures compared to the Broad Institute assembly 3 gene set. Moreover the database serves as a convenient entry point to explore expression data results and to obtain information on the Affymetrix GeneChip probe sets. The resource is accessible on http://mips.gsf.de/genre/proj/FGDB/.
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Affiliation(s)
- Philip Wong
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Bioinformatics and Systems Biology, Ingolstädter Landstrasse 1, D-85764 Neuherberg, Germany
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1494
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Bridges HR, Fearnley IM, Hirst J. The subunit composition of mitochondrial NADH:ubiquinone oxidoreductase (complex I) from Pichia pastoris. Mol Cell Proteomics 2010; 9:2318-26. [PMID: 20610779 PMCID: PMC2953923 DOI: 10.1074/mcp.m110.001255] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Respiratory complex I (NADH:quinone oxidoreductase) is an entry point to the electron transport chain in the mitochondria of many eukaryotes. It is a large, multisubunit enzyme with a hydrophilic domain in the matrix and a hydrophobic domain in the mitochondrial inner membrane. Here we present a comprehensive analysis of the protein composition and post-translational modifications of complex I from Pichia pastoris, using a combination of proteomic and bioinformatic approaches. Forty-one subunits were identified in P. pastoris complex I, comprising the 14 core (conserved) subunits and 27 supernumerary subunits; seven of the core subunits are mitochondrial encoded. Three of the supernumerary subunits (named NUSM, NUTM, and NUUM) have not been observed previously in any species of complex I. However, homologues to all three of them are present in either Yarrowia lipolytica or Pichia angusta complex I. P. pastoris complex I has 39 subunits in common with Y. lipolytica complex I, 37 in common with N. crassa complex I, and 35 in common with the bovine enzyme. The mitochondrial encoded subunits (translated by the mold mitochondrial genetic code) retain their N-α-formyl methionine residues. At least eight subunits are N-α-acetylated, but the N-terminal modifications of the nuclear encoded subunits are not well-conserved. A combination of two methods of protein separation (SDS-PAGE and HPLC) and three different mass spectrometry techniques (peptide mass fingerprinting, tandem MS and molecular mass measurements) were required to define the protein complement of P. pastoris complex I. This requirement highlights the need for inclusive and comprehensive strategies for the characterization of challenging membrane-bound protein complexes containing both hydrophilic and hydrophobic components.
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Affiliation(s)
- Hannah R Bridges
- Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK
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1495
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Kovach A, Wegrzyn JL, Parra G, Holt C, Bruening GE, Loopstra CA, Hartigan J, Yandell M, Langley CH, Korf I, Neale DB. The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics 2010; 11:420. [PMID: 20609256 PMCID: PMC2996948 DOI: 10.1186/1471-2164-11-420] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 07/07/2010] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND In today's age of genomic discovery, no attempt has been made to comprehensively sequence a gymnosperm genome. The largest genus in the coniferous family Pinaceae is Pinus, whose 110-120 species have extremely large genomes (c. 20-40 Gb, 2N = 24). The size and complexity of these genomes have prompted much speculation as to the feasibility of completing a conifer genome sequence. Conifer genomes are reputed to be highly repetitive, but there is little information available on the nature and identity of repetitive units in gymnosperms. The pines have extensive genetic resources, with approximately 329000 ESTs from eleven species and genetic maps in eight species, including a dense genetic map of the twelve linkage groups in Pinus taeda. RESULTS We present here the Sanger sequence and annotation of ten P. taeda BAC clones and Genome Analyzer II whole genome shotgun (WGS) sequences representing 7.5% of the genome. Computational annotation of ten BACs predicts three putative protein-coding genes and at least fifteen likely pseudogenes in nearly one megabase of sequence. We found three conifer-specific LTR retroelements in the BACs, and tentatively identified at least 15 others based on evidence from the distantly related angiosperms. Alignment of WGS sequences to the BACs indicates that 80% of BAC sequences have similar copies (> or = 75% nucleotide identity) elsewhere in the genome, but only 23% have identical copies (99% identity). The three most common repetitive elements in the genome were identified and, when combined, represent less than 5% of the genome. CONCLUSIONS This study indicates that the majority of repeats in the P. taeda genome are 'novel' and will therefore require additional BAC or genomic sequencing for accurate characterization. The pine genome contains a very large number of diverged and probably defunct repetitive elements. This study also provides new evidence that sequencing a pine genome using a WGS approach is a feasible goal.
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Affiliation(s)
- Allen Kovach
- Section of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Jill L Wegrzyn
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Genis Parra
- Genome Center, Division of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Carson Holt
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - George E Bruening
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Carol A Loopstra
- Department of Ecological Science and Management, Texas A&M University, College Station, TX 77843, USA
| | - James Hartigan
- Beckman Coulter Genomics (formerly Agencourt Biosciences), Danvers, MA 01923, USA
| | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Charles H Langley
- Section of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Ian Korf
- Genome Center, Division of Biological Sciences, University of California, Davis, CA 95616, USA
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- Institute of Forest Genetics, USDA Forest Service, Davis, CA, 95616, USA
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1496
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Ancient origin of the integrin-mediated adhesion and signaling machinery. Proc Natl Acad Sci U S A 2010; 107:10142-7. [PMID: 20479219 DOI: 10.1073/pnas.1002257107] [Citation(s) in RCA: 198] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The evolution of animals (metazoans) from their unicellular ancestors required the emergence of novel mechanisms for cell adhesion and cell-cell communication. One of the most important cell adhesion mechanisms for metazoan development is integrin-mediated adhesion and signaling. The integrin adhesion complex mediates critical interactions between cells and the extracellular matrix, modulating several aspects of cell physiology. To date this machinery has been considered strictly metazoan specific. Here we report the results of a comparative genomic analysis of the integrin adhesion machinery, using genomic data from several unicellular relatives of Metazoa and Fungi. Unexpectedly, we found that core components of the integrin adhesion complex are encoded in the genome of the apusozoan protist Amastigomonas sp., and therefore their origins predate the divergence of Opisthokonta, the clade that includes metazoans and fungi. Furthermore, our analyses suggest that key components of this apparatus have been lost independently in fungi and choanoflagellates. Our data highlight the fact that many of the key genes that had formerly been cited as crucial for metazoan origins have a much earlier origin. This underscores the importance of gene cooption in the unicellular-to-multicellular transition that led to the emergence of the Metazoa.
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1497
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Brown DG, Truszkowski J. New decoding algorithms for Hidden Markov Models using distance measures on labellings. BMC Bioinformatics 2010; 11 Suppl 1:S40. [PMID: 20122214 PMCID: PMC3009513 DOI: 10.1186/1471-2105-11-s1-s40] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Existing hidden Markov model decoding algorithms do not focus on approximately identifying the sequence feature boundaries. RESULTS We give a set of algorithms to compute the conditional probability of all labellings "near" a reference labelling lambda for a sequence y for a variety of definitions of "near". In addition, we give optimization algorithms to find the best labelling for a sequence in the robust sense of having all of its feature boundaries nearly correct. Natural problems in this domain are NP-hard to optimize. For membrane proteins, our algorithms find the approximate topology of such proteins with comparable success to existing programs, while being substantially more accurate in estimating the positions of transmembrane helix boundaries. CONCLUSION More robust HMM decoding may allow for better analysis of sequence features, in reasonable runtimes.
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Affiliation(s)
- Daniel G Brown
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
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1498
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Stanke M. Computational Gene Prediction in Eukaryotic Genomes. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2010:291-306. [DOI: 10.1007/978-90-481-3795-4_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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1499
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Estill JC, Bennetzen JL. The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes. PLANT METHODS 2009; 5:8. [PMID: 19545381 PMCID: PMC2705364 DOI: 10.1186/1746-4811-5-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Accepted: 06/19/2009] [Indexed: 05/09/2023]
Abstract
BACKGROUND High quality annotation of the genes and transposable elements in complex genomes requires a human-curated integration of multiple sources of computational evidence. These evidences include results from a diversity of ab initio prediction programs as well as homology-based searches. Most of these programs operate on a single contiguous sequence at a time, and the results are generated in a diverse array of readable formats that must be translated to a standardized file format. These translated results must then be concatenated into a single source, and then presented in an integrated form for human curation. RESULTS We have designed, implemented, and assessed a Perl-based workflow named DAWGPAWS for the generation of computational results for human curation of the genes and transposable elements in plant genomes. The use of DAWGPAWS was found to accelerate annotation of 80-200 kb wheat DNA inserts in bacterial artificial chromosome (BAC) vectors by approximately twenty-fold and to also significantly improve the quality of the annotation in terms of completeness and accuracy. CONCLUSION The DAWGPAWS genome annotation pipeline fills an important need in the annotation of plant genomes by generating computational evidences in a high throughput manner, translating these results to a common file format, and facilitating the human curation of these computational results. We have verified the value of DAWGPAWS by using this pipeline to annotate the genes and transposable elements in 220 BAC insertions from the hexaploid wheat genome (Triticum aestivum L.). DAWGPAWS can be applied to annotation efforts in other plant genomes with minor modifications of program-specific configuration files, and the modular design of the workflow facilitates integration into existing pipelines.
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Affiliation(s)
- James C Estill
- Department of Plant Biology, The University of Georgia, Athens, Georgia 30602-7271, USA
| | - Jeffrey L Bennetzen
- Department of Genetics, The University of Georgia, Athens, Georgia 30602-7223, USA
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1500
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Agger S, Lopez-Gallego F, Schmidt-Dannert C. Diversity of sesquiterpene synthases in the basidiomycete Coprinus cinereus. Mol Microbiol 2009; 72:1181-95. [PMID: 19400802 DOI: 10.1111/j.1365-2958.2009.06717.x] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fungi are a rich source of bioactive secondary metabolites, and mushroom-forming fungi (Agaricomycetes) are especially known for the synthesis of numerous bioactive and often cytotoxic sesquiterpenoid secondary metabolites. Compared with the large number of sesquiterpene synthases identified in plants, less than a handful of unique sesquiterpene synthases have been described from fungi. Here we describe the functional characterization of six sesquiterpene synthases (Cop1 to Cop6) and two terpene-oxidizing cytochrome P450 monooxygenases (Cox1 and Cox2) from Coprinus cinereus. The genes were cloned and, except for cop5, functionally expressed in Escherichia coli and/or Saccharomyces cerevisiae. Cop1 and Cop2 each synthesize germacrene A as the major product. Cop3 was identified as an alpha-muurolene synthase, an enzyme that has not been described previously, while Cop4 synthesizes delta-cadinene as its major product. Cop6 was originally annotated as a trichodiene synthase homologue but instead was found to catalyse the highly specific synthesis of alpha-cuprenene. Coexpression of cop6 and the two monooxygenase genes next to it yields oxygenated alpha-cuprenene derivatives, including cuparophenol, suggesting that these genes encode the enzymes for the biosynthesis of antimicrobial quinone sesquiterpenoids (known as lagopodins) that were previously isolated from C. cinereus and other Coprinus species.
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Affiliation(s)
- Sean Agger
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, St Paul, MN 55108, USA
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