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Melton AE, Moran K, Martinez P, Ellestad P, Milliken E, Morales W, Child AW, Richardson BA, Serpe M, Novak SJ, Buerki S. A genotype × environment experiment reveals contrasting response strategies to drought between populations of a keystone species ( Artemisia tridentata; Asteraceae). PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2023; 4:201-214. [PMID: 37583876 PMCID: PMC10423975 DOI: 10.1002/pei3.10119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/18/2023] [Accepted: 07/11/2023] [Indexed: 08/17/2023]
Abstract
Western North America has been experiencing persistent drought exacerbated by climate change for over two decades. This extreme climate event is a clear threat to native plant communities. Artemisia tridentata is a keystone shrub species in western North America and is threatened by climate change, urbanization, and wildfire. A drought Genotype × Environment (G × E) experiment was conducted to assess phenotypic plasticity and differential gene expression in A. tridentata. The G × E experiment was performed on diploid A. tridentata seedlings from two populations (one from Idaho, USA and one from Utah, USA), which experience differing levels of drought stress during the summer months. Photosynthetic data, leaf temperature, and gene expression levels were compared between treatments and populations. The Utah population maintained higher photosynthetic rates and photosynthetic efficiency than the Idaho population under drought stress. The Utah population also exhibited far greater transcriptional plasticity than the Idaho population and expressed genes of response pathways distinct from those of the Idaho population. Populations of A. tridentata differ greatly in their drought response pathways, likely due to differences in response pathways that have evolved under distinct climatic regimes. Epigenetic processes likely contribute to the observed differences between the populations.
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Affiliation(s)
- Anthony E. Melton
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Kara Moran
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Peggy Martinez
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Paige Ellestad
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Erin Milliken
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Walker Morales
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Andrew W. Child
- Research Computing and Data ServicesUniversity of IdahoMoscowIdahoUSA
| | | | - Marcelo Serpe
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Stephen J. Novak
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Sven Buerki
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
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2
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Robb BC, Olsoy PJ, Mitchell JJ, Caughlin TT, Delparte DM, Galla SJ, Fremgen‐Tarantino MR, Nobler JD, Rachlow JL, Shipley LA, Forbey JS. Near‐infrared spectroscopy aids ecological restoration by classifying variation of taxonomy and phenology of a native shrub. Restor Ecol 2021. [DOI: 10.1111/rec.13584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Brecken C. Robb
- Department of Biological Sciences Boise State University 1910 W University Drive Boise ID 83725 U.S.A
| | - Peter J. Olsoy
- Department of Biological Sciences Boise State University 1910 W University Drive Boise ID 83725 U.S.A
| | - Jessica J. Mitchell
- Department of Ecosystem and Conservation Science University of Montana 32 Campus Drive Missoula MT 59812 U.S.A
| | - T. Trevor Caughlin
- Department of Biological Sciences Boise State University 1910 W University Drive Boise ID 83725 U.S.A
| | - Donna M. Delparte
- Department of Geosciences Idaho State University 921 S 8th Avenue Pocatello ID 83209 U.S.A
| | - Stephanie J. Galla
- Department of Biological Sciences Boise State University 1910 W University Drive Boise ID 83725 U.S.A
| | | | - Jordan D. Nobler
- Department of Biological Sciences Boise State University 1910 W University Drive Boise ID 83725 U.S.A
| | - Janet L. Rachlow
- Department of Fish and Wildlife Sciences University of Idaho 875 Perimeter Drive Moscow ID 83844 U.S.A
| | - Lisa A. Shipley
- School of the Environment Washington State University 100 Dairy Road/1228 Webster Pullman WA 99164 U.S.A
| | - Jennifer S. Forbey
- Department of Biological Sciences Boise State University 1910 W University Drive Boise ID 83725 U.S.A
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Wang L, Zhang R, Geng M, Qin Y, Liu H, Li L, Li M. De novo transcriptome assembly and EST-SSR markers development for Zelkova schneideriana Hand.-Mazz. (Ulmaceae). 3 Biotech 2021; 11:420. [PMID: 34603920 DOI: 10.1007/s13205-021-02968-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 08/19/2021] [Indexed: 11/25/2022] Open
Abstract
Zelkova schneideriana Hand.-Mazz. of the Ulmaceae family is a Tertiary relict and economically deciduous tree species endemic to Central and Southern China. In this study, we performed a transcriptome sequencing of Z. schneideriana using high-throughput sequencing approach to detect polymorphic expressed sequence tag-simple sequence repeats (EST-SSR) markers. A total of 3,235 microsatellite loci were detected from 53,517 unigenes. A set of 30 microsatellite markers were randomly selected to validate in 41 individuals from three populations, of which 10 were polymorphic. The number of alleles per locus ranged from 3 to 11. The observed heterozygosity and expected heterozygosity ranged from 0.366 to 0.829 and 0.439 to 0.848, respectively. These polymorphic SSR primers showed good transferability across different Zelkova species, and are valuable for future studies on genetic diversity, conservation, phylogeography, and species delimitation in Z. schneideriana, as well as other Zelkova species. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02968-5.
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Affiliation(s)
- Lingdan Wang
- Central South University of Forestry and Technology, Changsha, 410004 China
| | - Riqing Zhang
- Central South University of Forestry and Technology, Changsha, 410004 China
| | - Maolin Geng
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014 China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014 China
| | - Yufeng Qin
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning, 530002 China
| | - Hailong Liu
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning, 530002 China
| | - Lingli Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014 China
| | - Mimi Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014 China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014 China
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4
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Siniscalchi CM, Hidalgo O, Palazzesi L, Pellicer J, Pokorny L, Maurin O, Leitch IJ, Forest F, Baker WJ, Mandel JR. Lineage-specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family. APPLICATIONS IN PLANT SCIENCES 2021; 9:APS311422. [PMID: 34336403 PMCID: PMC8312747 DOI: 10.1002/aps3.11422] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/15/2021] [Indexed: 05/10/2023]
Abstract
PREMISE Phylogenetic studies in the Compositae are challenging due to the sheer size of the family and the challenges they pose for molecular tools, ranging from the genomic impact of polyploid events to their very conserved plastid genomes. The search for better molecular tools for phylogenetic studies led to the development of the family-specific Compositae1061 probe set, as well as the universal Angiosperms353 probe set designed for all flowering plants. In this study, we evaluate the extent to which data generated using the family-specific kit and those obtained with the universal kit can be merged for downstream analyses. METHODS We used comparative methods to verify the presence of shared loci between probe sets. Using two sets of eight samples sequenced with Compositae1061 and Angiosperms353, we ran phylogenetic analyses with and without loci flagged as paralogs, a gene tree discordance analysis, and a complementary phylogenetic analysis mixing samples from both sample sets. RESULTS Our results show that the Compositae1061 kit provides an average of 721 loci, with 9-46% of them presenting paralogs, while the Angiosperms353 set yields an average of 287 loci, which are less affected by paralogy. Analyses mixing samples from both sets showed that the presence of 30 shared loci in the probe sets allows the combination of data generated in different ways. DISCUSSION Combining data generated using different probe sets opens up the possibility of collaborative efforts and shared data within the synantherological community.
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Affiliation(s)
- Carolina M. Siniscalchi
- Department of Biological SciencesMississippi State UniversityMississippi StateMississippi39762USA
- Department of Biological SciencesUniversity of MemphisMemphisTennessee38152USA
| | - Oriane Hidalgo
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
- Institut Botànic de Barcelona (IBB, CSIC‐Ajuntament de Barcelona)Passeig del Migdia s.n.BarcelonaCatalonia08038Spain
| | - Luis Palazzesi
- División PaleobotánicaMuseo Argentino de Ciencias NaturalesCONICETBuenos AiresC1405DJRArgentina
| | - Jaume Pellicer
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
- Institut Botànic de Barcelona (IBB, CSIC‐Ajuntament de Barcelona)Passeig del Migdia s.n.BarcelonaCatalonia08038Spain
| | - Lisa Pokorny
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
- Present address:
Centre for Plant Biotechnology and Genomics (CBGP) UPM‐INIAPozuelo de Alarcón (Madrid)28223Spain
| | - Olivier Maurin
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
| | - Ilia J. Leitch
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
| | - Felix Forest
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
| | | | - Jennifer R. Mandel
- Department of Biological SciencesUniversity of MemphisMemphisTennessee38152USA
- Center for BiodiversityUniversity of MemphisMemphisTennessee38152USA
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Li X, Li Z, Shen Q, Pan Y, Dong X, Xu Z, Duan S, Li Y, Du Y, Chen S, Ma Z, Dong Y. HGFDB: a collective database of helmeted guinea fowl genomics. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6070151. [PMID: 33417691 PMCID: PMC7792568 DOI: 10.1093/database/baaa116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/21/2020] [Accepted: 12/22/2020] [Indexed: 11/12/2022]
Abstract
As a vigorous and hardy and an almost disease-free game bird, the domestic helmeted guinea fowl (Numida meleagris, hereafter HGF) has attracted considerable attention in a large number of genetic study projects. However, none of the current/recent avian databases are related to this agriculturally and commercially important poultry species. To address this data gap, we developed Helmeted Guinea Fowl Database (HGFDB), which manages and shares HGF genomic and genetic data. By processing the data of genome assembly, sequencing reads and genetic variations, we organized them into eight modules, which correspond to ‘Home’, ‘Genome’, ‘Re-sequence’, ‘Gene’, ‘Variation’, ‘Download’, ‘Tools’ and ‘Help’, HGFDB provides the most comprehensive view of the HGF genome to date and will be relevant for future studies on HGF structural and functional genomics and genetic improvement. Database URL:http://hgfdb.ynau.edu.cn/
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Affiliation(s)
- Xuzhen Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan 650201, China.,Nowbio Biotechnology Company, No. 168 Yunjing Road, Kunming, Yunnan 650201, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Zhi Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650093, China
| | - Quankuan Shen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi 999070, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yunbin Pan
- Nowbio Biotechnology Company, No. 168 Yunjing Road, Kunming, Yunnan 650201, China
| | - Xiao Dong
- Nowbio Biotechnology Company, No. 168 Yunjing Road, Kunming, Yunnan 650201, China
| | - Zetan Xu
- Nowbio Biotechnology Company, No. 168 Yunjing Road, Kunming, Yunnan 650201, China
| | - Shengchang Duan
- Nowbio Biotechnology Company, No. 168 Yunjing Road, Kunming, Yunnan 650201, China
| | - Yunfei Li
- Nowbio Biotechnology Company, No. 168 Yunjing Road, Kunming, Yunnan 650201, China
| | - Yuan Du
- Nowbio Biotechnology Company, No. 168 Yunjing Road, Kunming, Yunnan 650201, China
| | - Shanshan Chen
- College of Biological Big Data, Yunnan Agriculture University, Kunming, Yunnan 650201, China
| | - Zhaocheng Ma
- Shanghai Yangjing-Juyuan Experimental School, No 333 Pucheng Road, Pudong, Shanghai 200120, China
| | - Yang Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan 650201, China.,College of Biological Big Data, Yunnan Agriculture University, Kunming, Yunnan 650201, China.,Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan 650201, China
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6
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Jaiswal S, Antala TJ, Mandavia MK, Chopra M, Jasrotia RS, Tomar RS, Kheni J, Angadi UB, Iquebal MA, Golakia BA, Rai A, Kumar D. Transcriptomic signature of drought response in pearl millet (Pennisetum glaucum (L.) and development of web-genomic resources. Sci Rep 2018; 8:3382. [PMID: 29467369 PMCID: PMC5821703 DOI: 10.1038/s41598-018-21560-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 02/04/2018] [Indexed: 01/12/2023] Open
Abstract
Pearl millet, (Pennisetum glaucum L.), an efficient (C4) crop of arid/semi-arid regions is known for hardiness. Crop is valuable for bio-fortification combating malnutrition and diabetes, higher caloric value and wider climatic resilience. Limited studies are done in pot-based experiments for drought response at gene-expression level, but field-based experiment mimicking drought by withdrawal of irrigation is still warranted. We report de novo assembly-based transcriptomic signature of drought response induced by irrigation withdrawal in pearl millet. We found 19983 differentially expressed genes, 7595 transcription factors, gene regulatory network having 45 hub genes controlling drought response. We report 34652 putative markers (4192 simple sequence repeats, 12111 SNPs and 6249 InDels). Study reveals role of purine and tryptophan metabolism in ABA accumulation mediating abiotic response in which MAPK acts as major intracellular signal sensing drought. Results were validated by qPCR of 13 randomly selected genes. We report the first web-based genomic resource ( http://webtom.cabgrid.res.in/pmdtdb/ ) which can be used for candidate genes-based SNP discovery programs and trait-based association studies. Looking at climatic change, nutritional and pharmaceutical importance of this crop, present investigation has immense value in understanding drought response in field condition. This is important in germplasm management and improvement in endeavour of pearl millet productivity.
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Affiliation(s)
- Sarika Jaiswal
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Tushar J Antala
- Department of Biochemistry and Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - M K Mandavia
- Department of Biochemistry and Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Meenu Chopra
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Rahul Singh Jasrotia
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Rukam S Tomar
- Department of Biochemistry and Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Jashminkumar Kheni
- Department of Biochemistry and Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - U B Angadi
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - M A Iquebal
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - B A Golakia
- Department of Biochemistry and Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India.
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7
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Huang Y, Xiong JL, Gao XC, Sun XH. Transcriptome analysis of the Chinese giant salamander ( Andrias davidianus) using RNA-sequencing. GENOMICS DATA 2017; 14:126-131. [PMID: 29159068 PMCID: PMC5675895 DOI: 10.1016/j.gdata.2017.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/21/2017] [Accepted: 10/21/2017] [Indexed: 12/21/2022]
Abstract
The Chinese giant salamander (Andrias davidianus) is an economically important animal on academic value. However, the genomic information of this species has been less studied. In our study, the transcripts of A. davidianus were obtained by RNA-seq to conduct a transcriptomic analysis. In total 132,912 unigenes were generated with an average length of 690 bp and N50 of 1263 bp by de novo assembly using Trinity software. Using a sequence similarity search against the nine public databases (CDD, KOG, NR, NT, PFAM, Swiss-prot, TrEMBL, GO and KEGG databases), a total of 24,049, 18,406, 36,711, 15,858, 20,500, 27,515, 36,705, 28,879 and 10,958 unigenes were annotated in databases, respectively. Of these, 6323 unigenes were annotated in all database and 39,672 unigenes were annotated in at least one database. Blasted with KEGG pathway, 10,958 unigenes were annotated, and it was divided into 343 categories according to different pathways. In addition, we also identified 29,790 SSRs. This study provided a valuable resource for understanding transcriptomic information of A. davidianus and laid a foundation for further research on functional gene cloning, genomics, genetic diversity analysis and molecular marker exploitation in A. davidianus.
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Affiliation(s)
- Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Jian Li Xiong
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Xiao Chan Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Xi Hong Sun
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
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8
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Hannigan GD, Zheng Q, Meisel JS, Minot SS, Bushman FD, Grice EA. Evolutionary and functional implications of hypervariable loci within the skin virome. PeerJ 2017; 5:e2959. [PMID: 28194314 PMCID: PMC5299996 DOI: 10.7717/peerj.2959] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/05/2017] [Indexed: 01/04/2023] Open
Abstract
Localized genomic variability is crucial for the ongoing conflicts between infectious microbes and their hosts. An understanding of evolutionary and adaptive patterns associated with genomic variability will help guide development of vaccines and antimicrobial agents. While most analyses of the human microbiome have focused on taxonomic classification and gene annotation, we investigated genomic variation of skin-associated viral communities. We evaluated patterns of viral genomic variation across 16 healthy human volunteers. Human papillomavirus (HPV) and Staphylococcus phages contained 106 and 465 regions of diversification, or hypervariable loci, respectively. Propionibacterium phage genomes were minimally divergent and contained no hypervariable loci. Genes containing hypervariable loci were involved in functions including host tropism and immune evasion. HPV and Staphylococcus phage hypervariable loci were associated with purifying selection. Amino acid substitution patterns were virus dependent, as were predictions of their phenotypic effects. We identified diversity generating retroelements as one likely mechanism driving hypervariability. We validated these findings in an independently collected skin metagenomic sequence dataset, suggesting that these features of skin virome genomic variability are widespread. Our results highlight the genomic variation landscape of the skin virome and provide a foundation for better understanding community viral evolution and the functional implications of genomic diversification of skin viruses.
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Affiliation(s)
- Geoffrey D Hannigan
- Department of Dermatology, University of Pennsylvania , Philadelphia, PA , USA
| | - Qi Zheng
- Department of Dermatology, University of Pennsylvania , Philadelphia, PA , USA
| | - Jacquelyn S Meisel
- Department of Dermatology, University of Pennsylvania , Philadelphia, PA , USA
| | | | - Frederick D Bushman
- Department of Microbiology, University of Pennsylvania , Philadelphia, PA , USA
| | - Elizabeth A Grice
- Department of Dermatology, University of Pennsylvania, Philadelphia, PA, USA; Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
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9
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Expressed Sequence Tags Analysis and Design of Simple Sequence Repeats Markers from a Full-Length cDNA Library in Perilla frutescens (L.). Int J Genomics 2015; 2015:679548. [PMID: 26664999 PMCID: PMC4668317 DOI: 10.1155/2015/679548] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/21/2015] [Indexed: 11/17/2022] Open
Abstract
Perilla frutescens is valuable as a medicinal plant as well as a natural medicine and functional food. However, comparative genomics analyses of P. frutescens are limited due to a lack of gene annotations and characterization. A full-length cDNA library from P. frutescens leaves was constructed to identify functional gene clusters and probable EST-SSR markers via analysis of 1,056 expressed sequence tags. Unigene assembly was performed using basic local alignment search tool (BLAST) homology searches and annotated Gene Ontology (GO). A total of 18 simple sequence repeats (SSRs) were designed as primer pairs. This study is the first to report comparative genomics and EST-SSR markers from P. frutescens will help gene discovery and provide an important source for functional genomics and molecular genetic research in this interesting medicinal plant.
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10
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Christmas MJ, Biffin E, Lowe AJ. Transcriptome sequencing, annotation and polymorphism detection in the hop bush, Dodonaea viscosa. BMC Genomics 2015; 16:803. [PMID: 26474753 PMCID: PMC4609105 DOI: 10.1186/s12864-015-1987-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 10/06/2015] [Indexed: 01/09/2023] Open
Abstract
Background The hop bush, Dodonaea viscosa, is a trans-oceanic species distributed oversix continents. It evolved in Australia where it is found over a wide range of habitat types and is an ecologically important species. Limited genomic resources are currently available for this species, thus our understanding of its evolutionary history and ecological adaptation is restricted. Here, we present a comprehensive transcriptome dataset for future genomic studies into this species. Methods We performed Illumina sequencing of cDNA prepared from leaf tissue collected from seven populations of D. viscosa ssp. angustissima and spatulata distributed along an environmental gradient in South Australia. Sequenced reads were assembled to provide a transcriptome resource. Contiguous sequences (contigs) were annotated using BLAST searches against the NCBI non-redundant database and gene ontology definitions were assigned. Single nucleotide polymorphisms were detected for the establishment of a genetic marker set. A comparison between the two subspecies was also carried out. Results Illumina sequencing returned 268,672,818 sequence reads, which were de novoassembled into 105,125 contigs. Contigs with significant BLAST alignments (E value < 1e-5)numbered at 44,191, with 38,311 of these having their most significant hits to sequences from land plant species. Gene Ontology terms were assigned to 28,440 contigs and KEGG analysis identified 146 pathways that the gene products from 5,070 contigs are potentially involved in. The subspecies comparison identified 8,494 fixed SNP differences across 3,979 contiguous sequences, indicating a level of genetic differentiation between them. Across all samples, 248,235 SNPs were detected. Conclusions We have established a significant genomic data resource for D. viscosa,providing a comprehensive transcriptomic reference. Genetic differences among morphologically distinct subspecies were found. A wide range of putative gene regions were identified along with a large set of variable SNP markers, providing a basis for studies into the evolution and ecological adaptation of D. viscosa. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1987-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew J Christmas
- Environment Institute and School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, 5005, SA, Australia.
| | - Ed Biffin
- Environment Institute and School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, 5005, SA, Australia.
| | - Andrew J Lowe
- Environment Institute and School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, 5005, SA, Australia.
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11
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Wang L, Wang Z, Chen J, Liu C, Zhu W, Wang L, Meng L. De Novo Transcriptome Assembly and Development of Novel Microsatellite Markers for the Traditional Chinese Medicinal Herb, Veratrilla baillonii Franch (Gentianaceae). Evol Bioinform Online 2015; 11:39-45. [PMID: 26244005 PMCID: PMC4498661 DOI: 10.4137/ebo.s20942] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 06/02/2015] [Accepted: 06/08/2015] [Indexed: 02/02/2023] Open
Abstract
Veratrilla baillonii Franch is an important Chinese medicinal herb for treating liver-related diseases, which has been over-collected in the recent decades. However, the effective conservation and related population genetic study has been hindered because of the lack of genome sequences and genetic markers in the natural population. We have conducted RNA-seq on V. baillonii. We performed de novo assembly of these data to characterize the V. baillonii transcriptome, resulting in 133,019 contigs with size >200 bp. These contigs were annotated using the NCBI nonredundant database and Gene Ontology (GO) terms. From these contigs, we developed novel microsatellite simple sequence repeat (SSR) markers, identifying a total of 40,885 SSRs. SSRs with repeat motifs of 1–4 bp (mono-, di-, tri-, and tetranucleotides) accounted for 99.8% of all SSRs, with mononucleotide repeats most common, followed by dinucleotide (16.2%) and trinucleotide repeats (14.7%). We selected 151 SSRs for experimental validation, of which 74 were confirmed by polymerase chain reaction. Fourteen SSRs were determined to be polymorphic by screening 40 individuals from six distant populations. The number of alleles per locus ranged from two to four, and the expected heterozygosity varied from 0.2637 to 0.8571, suggesting that these SSR markers are highly polymorphic and effective for further genetic analysis in the nature population. In addition, we explored the genetic structure of V. baillonii using five SSRs in four geographic populations and found that the identified genotypes were clustered into two phylogenetic clades: the Mekong River clade and Jinsha River clade. This result indicates that these two regions may harbor highly divergent genetic lineages and enriched genetic diversity. The de novo transcriptome sequences and new SSR markers discovered by this study provide an initial step for understanding the population genetics of V. baillonii, and a valuable resource for effective conservation management.
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Affiliation(s)
- Lei Wang
- School of Life Sciences, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy Ministry of Education, Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals-Plants in Southwest Mountain Ecosystem of University in Yunnan Province, Yunnan Normal University, Kunming, Yunnan, People's Republic of China
| | - Zhengkun Wang
- School of Life Sciences, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy Ministry of Education, Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals-Plants in Southwest Mountain Ecosystem of University in Yunnan Province, Yunnan Normal University, Kunming, Yunnan, People's Republic of China
| | - Jianbing Chen
- Department of Information Management, Yunnan Normal University, Kunming, Yunnan, People's Republic of China
| | - Chunyan Liu
- School of Life Sciences, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy Ministry of Education, Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals-Plants in Southwest Mountain Ecosystem of University in Yunnan Province, Yunnan Normal University, Kunming, Yunnan, People's Republic of China
| | - Wanlong Zhu
- School of Life Sciences, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy Ministry of Education, Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals-Plants in Southwest Mountain Ecosystem of University in Yunnan Province, Yunnan Normal University, Kunming, Yunnan, People's Republic of China
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Lihua Meng
- School of Life Sciences, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy Ministry of Education, Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals-Plants in Southwest Mountain Ecosystem of University in Yunnan Province, Yunnan Normal University, Kunming, Yunnan, People's Republic of China
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Huynh MD, Page JT, Richardson BA, Udall JA. Insights into transcriptomes of big and low sagebrush. PLoS One 2015; 10:e0127593. [PMID: 26020526 PMCID: PMC4447352 DOI: 10.1371/journal.pone.0127593] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 04/16/2015] [Indexed: 01/25/2023] Open
Abstract
We report the sequencing and assembly of three transcriptomes from Big (Artemisia tridentata ssp. wyomingensis and A. tridentata ssp. tridentata) and Low (A. arbuscula ssp. arbuscula) sagebrush. The sequence reads are available in the Sequence Read Archive of NCBI. We demonstrate the utilities of these transcriptomes for gene discovery and phylogenomic analysis. An assembly of 61,883 transcripts followed by transcript identification by the program TRAPID revealed 16 transcripts directly related to terpene synthases, proteins critical to the production of multiple secondary metabolites in sagebrush. A putative terpene synthase was identified in two of our sagebrush samples. Using paralogs with synonymous mutations we reconstructed an evolutionary time line of ancient genome duplications. By applying a constant mutation rate to the data we estimate that these three ancient duplications occurred about 18, 34 and 60 million years ago. These transcriptomes offer a foundation for future studies of sagebrush, including inferences in chemical defense and the identification of species and subspecies of sagebrush for restoration and preservation of the threatened sage-grouse.
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Affiliation(s)
- Mark D. Huynh
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, United States of America
| | - Justin T. Page
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, United States of America
| | - Bryce A. Richardson
- Rocky Mountain Research Station, USDA Forest Service, Provo, UT, 84606, United States of America
| | - Joshua A. Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, United States of America
- * E-mail:
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13
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Yuan Y, Long P, Jiang C, Li M, Huang L. Development and characterization of simple sequence repeat (SSR) markers based on a full-length cDNA library of Scutellaria baicalensis. Genomics 2015; 105:61-7. [DOI: 10.1016/j.ygeno.2014.10.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 10/13/2014] [Accepted: 10/21/2014] [Indexed: 12/17/2022]
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De novo transcriptome assembly and the identification of gene-associated single-nucleotide polymorphism markers in Asian and American ginseng roots. Mol Genet Genomics 2014; 290:1055-65. [PMID: 25527477 DOI: 10.1007/s00438-014-0974-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 12/05/2014] [Indexed: 10/24/2022]
Abstract
We performed de novo transcriptome sequencing for Panax ginseng and Panax quinquefolius accessions using the 454 GS FLX Titanium System and discovered annotation-based genome-wide single-nucleotide polymorphism (SNPs) using next-generation ginseng transcriptome data without reference genome sequence. The comprehensive transcriptome characterization with the mature roots of four ginseng accessions generated 297,170 reads for 'Cheonryang' cultivar, 305,673 reads for 'Yunpoong' cultivar, 311,861 reads for the G03080 breeding line, and 308,313 reads for P. quinquefolius. In transcriptome assembly, the lengths of the sample read were 156.42 Mb for 'Cheonryang', 161.95 Mb for 'Yunpoong', 165.07 Mb for G03080 breeding line, and 166.48 Mb for P. quinquefolius. A total of 97 primer pairs were designed with the homozygous SNP presented in all four accessions. SNP genotyping using high-resolution melting (HRM) analysis was performed to validate the putative SNP markers of 97 primer pairs. Out of the 73 primer pairs, 73 primer pairs amplified the target sequence and 34 primer pairs showed polymorphic melting curves in samples from 11 P. ginseng cultivars and one P. quinquefolius accession. Among the 34 polymorphic HRM-SNP primers, four primers were useful to distinguish ginseng cultivars. In the present study, we demonstrated that de novo transcriptome assembly and mapping analyses are useful in providing four HRM-SNP primer pairs that reliably show a high degree of polymorphism among ginseng cultivars.
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Angelis K, Dos Reis M, Yang Z. Bayesian estimation of nonsynonymous/synonymous rate ratios for pairwise sequence comparisons. Mol Biol Evol 2014; 31:1902-13. [PMID: 24748652 PMCID: PMC4069626 DOI: 10.1093/molbev/msu142] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The nonsynonymous/synonymous rate ratio (ω = dN/dS) is an important measure of the mode and strength of natural selection acting on nonsynonymous mutations in protein-coding genes. The simplest such analysis is the estimation of the dN/dS ratio using two sequences. Both heuristic counting methods and the maximum-likelihood (ML) method based on a codon substitution model are widely used for such analysis. However, these methods do not have nice statistical properties, as the estimates can be zero or infinity in some data sets, so that their means and variances are infinite. In large genome-scale comparisons, such extreme estimates (either 0 or ∞) of ω and sequence distance (t) are common. Here, we implement a Bayesian method to estimate ω and t in pairwise sequence comparisons. Using a combination of computer simulation and real data analysis, we show that the Bayesian estimates have better statistical properties than the ML estimates, because the prior on ω and t shrinks the posterior of those parameters away from extreme values. We also calculate the posterior probability for ω > 1 as a Bayesian alternative to the likelihood ratio test. The new method is computationally efficient and may be useful for genome-scale comparisons of protein-coding gene sequences.
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Affiliation(s)
- Konstantinos Angelis
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Mario Dos Reis
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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Che R, Sun Y, Sun D, Xu T. Characterization of the miiuy croaker (Miichthys miiuy) transcriptome and development of immune-relevant genes and molecular markers. PLoS One 2014; 9:e94046. [PMID: 24714210 PMCID: PMC3979730 DOI: 10.1371/journal.pone.0094046] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 03/10/2014] [Indexed: 12/04/2022] Open
Abstract
Background The miiuy croaker (Miichthys miiuy) is an important species of marine fish that supports capture fisheries and aquaculture. At present commercial scale aquaculture of this species is limited due to diseases caused by pathogens and parasites which restrict production and limit commercial value. The lack of transcriptomic and genomic information for the miiuy croaker limits the ability of researchers to study the pathogenesis and immune system of this species. In this study we constructed a cDNA library from liver, spleen and kidney which was sequenced using Illumina paired-end sequencing to enable gene discovery and molecular marker development. Principal Findings In our study, a total of 69,071 unigenes with an average length of 572 bp were obtained. Of these, 45,676 (66.13%) were successfully annotated in public databases. The unigenes were also annotated with Gene Ontology, Clusters of Orthologous Groups and KEGG pathways. Additionally, 498 immune-relevant genes were identified and classified. Furthermore, 14,885 putative simple sequence repeats (cSSRs) and 8,510 putative single nucleotide polymorphisms (SNPs) were identified from the 69,071 unigenes. Conclusion The miiuy croaker (Miichthys miiuy) transcriptome data provides a large resource to identify new genes involved in many processes including those involved in the response to pathogens and diseases. Furthermore, the thousands of potential cSSR and SNP markers found in this study are important resources with respect to future development of molecular marker assisted breeding programs for the miiuy croaker.
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Affiliation(s)
- Rongbo Che
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
| | - Yueyan Sun
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
| | - Dianqiao Sun
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
| | - Tianjun Xu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
- * E-mail:
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Che R, Sun Y, Wang R, Xu T. Transcriptomic analysis of endangered Chinese salamander: identification of immune, sex and reproduction-related genes and genetic markers. PLoS One 2014; 9:e87940. [PMID: 24498226 PMCID: PMC3909259 DOI: 10.1371/journal.pone.0087940] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 01/01/2014] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The Chinese salamander (Hynobius chinensis), an endangered amphibian species of salamander endemic to China, has attracted much attention because of its value of studying paleontology evolutionary history and decreasing population size. Despite increasing interest in the Hynobius chinensis genome, genomic resources for the species are still very limited. A comprehensive transcriptome of Hynobius chinensis, which will provide a resource for genome annotation, candidate genes identification and molecular marker development should be generated to supplement it. PRINCIPAL FINDINGS We performed a de novo assembly of Hynobius chinensis transcriptome by Illumina sequencing. A total of 148,510 nonredundant unigenes with an average length of approximately 580 bp were obtained. In all, 60,388 (40.66%) unigenes showed homologous matches in at least one database and 33,537 (22.58%) unigenes were annotated by all four databases. In total, 41,553 unigenes were categorized into 62 sub-categories by BLAST2GO search, and 19,468 transcripts were assigned to 140 KEGG pathways. A large number of unigenes involved in immune system, local adaptation, reproduction and sex determination were identified, as well as 31,982 simple sequence repeats (SSRs) and 460,923 putative single nucleotide polymorphisms (SNPs). CONCLUSION This dataset represents the first transcriptome analysis of the Chinese salamander (Hynobius chinensis), an endangered species, to be also the first time of hynobiidae. The transcriptome will provide valuable resource for further research in discovery of new genes, protection of population, adaptive evolution and survey of various pathways, as well as development of molecule markers in Chinese salamander; and reference information for closely related species.
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Affiliation(s)
- Rongbo Che
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
| | - Yuena Sun
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
| | - Rixin Wang
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
| | - Tianjun Xu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
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Pellino M, Hojsgaard D, Schmutzer T, Scholz U, Hörandl E, Vogel H, Sharbel TF. Asexual genome evolution in the apomicticRanunculus auricomuscomplex: examining the effects of hybridization and mutation accumulation. Mol Ecol 2013; 22:5908-21. [DOI: 10.1111/mec.12533] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 08/21/2013] [Accepted: 08/26/2013] [Indexed: 10/26/2022]
Affiliation(s)
- Marco Pellino
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK); D-06466 Gatersleben Germany
| | - Diego Hojsgaard
- Department of Systematic Botany; Albrecht-von-Haller Institute for Plant Sciences; Georg-August-University of Goettingen; Untere Karspuele 2 D-37073 Goettingen Germany
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK); D-06466 Gatersleben Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK); D-06466 Gatersleben Germany
| | - Elvira Hörandl
- Department of Systematic Botany; Albrecht-von-Haller Institute for Plant Sciences; Georg-August-University of Goettingen; Untere Karspuele 2 D-37073 Goettingen Germany
| | - Heiko Vogel
- Department of Entomology; Max Planck Institute for Chemical Ecology; D-07745 Jena Germany
| | - Timothy F. Sharbel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK); D-06466 Gatersleben Germany
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Livaja M, Wang Y, Wieckhorst S, Haseneyer G, Seidel M, Hahn V, Knapp SJ, Taudien S, Schön CC, Bauer E. BSTA: a targeted approach combines bulked segregant analysis with next- generation sequencing and de novo transcriptome assembly for SNP discovery in sunflower. BMC Genomics 2013; 14:628. [PMID: 24330545 PMCID: PMC3848877 DOI: 10.1186/1471-2164-14-628] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 09/16/2013] [Indexed: 01/31/2023] Open
Abstract
Background Sunflower belongs to the largest plant family on earth, the genomically poorly explored Compositae. Downy mildew Plasmopara halstedii (Farlow) Berlese & de Toni is one of the major diseases of cultivated sunflower (Helianthus annuus L.). In the search for new sources of downy mildew resistance, the locus PlARG on linkage group 1 (LG1) originating from H. argophyllus is promising since it confers resistance against all known races of the pathogen. However, the mapping resolution in the PlARG region is hampered by significantly suppressed recombination and by limited availability of polymorphic markers. Here we examined a strategy developed for the enrichment of molecular markers linked to this specific genomic region. We combined bulked segregant analysis (BSA) with next-generation sequencing (NGS) and de novo assembly of the sunflower transcriptome for single nucleotide polymorphism (SNP) discovery in a sequence resource combining reads originating from two sunflower species, H. annuus and H. argophyllus. Results A computational pipeline developed for SNP calling and pattern detection identified 219 candidate genes. For a proof of concept, 42 resistance gene-like sequences were subjected to experimental SNP validation. Using a high-resolution mapping population, 12 SNP markers were mapped to LG1. We successfully verified candidate sequences either co-segregating with or closely flanking PlARG. Conclusions This study is the first successful example to improve bulked segregant analysis with de novo transcriptome assembly using next generation sequencing. The BSTA pipeline we developed provides a useful guide for similar studies in other non-model organisms. Our results demonstrate this method is an efficient way to enrich molecular markers and to identify candidate genes in a specific mapping interval.
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Badouin H, Belkhir K, Gregson E, Galindo J, Sundström L, Martin SJ, Butlin RK, Smadja CM. Transcriptome characterisation of the ant Formica exsecta with new insights into the evolution of desaturase genes in social hymenoptera. PLoS One 2013; 8:e68200. [PMID: 23874539 PMCID: PMC3709892 DOI: 10.1371/journal.pone.0068200] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 05/28/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Despite the recent sequencing of seven ant genomes, no genomic data are available for the genus Formica, an important group for the study of eusocial traits. We sequenced the transcriptome of the ant Formica exsecta with the 454 FLX Titanium technology from a pooled sample of workers from 70 Finnish colonies. RESULTS About 1,000,000 reads were obtained from a normalised cDNA library. We compared the assemblers MIRA3.0 and Newbler2.6 and showed that the latter performed better on this dataset due to a new option which is dedicated to improve contig formation in low depth portions of the assemblies. The 29,579 contigs represent 27 Mb. 50% showed similarity with known proteins and 25% could be assigned a category of gene ontology. We found more than 13,000 high-quality single nucleotide polymorphisms. The Δ9 desaturase gene family is an important multigene family involved in chemical communication in insects. We found six Δ9 desaturases in this Formica exsecta transcriptome dataset that were used to reconstruct a maximum-likelihood phylogeny of insect desaturases and to test for signatures of positive selection in this multigene family in ant lineages. We found differences with previous phylogenies of this gene family in ants, and found two clades potentially under positive selection. CONCLUSION This first transcriptome reference sequence of Formica exsecta provided sequence and polymorphism data that will allow researchers working on Formica ants to develop studies to tackle the genetic basis of eusocial phenotypes. In addition, this study provided some general guidelines for de novo transcriptome assembly that should be useful for future transcriptome sequencing projects. Finally, we found potential signatures of positive selection in some clades of the Δ9 desaturase gene family in ants, which suggest the potential role of sequence divergence and adaptive evolution in shaping the large diversity of chemical cues in social insects.
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Affiliation(s)
- Hélène Badouin
- Centre National de la Recherche Scientifique CNRS - Institut des Sciences de l'Evolution UMR 5554, Université Montpellier 2, Montpellier, France.
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Zhang L, Yan HF, Wu W, Yu H, Ge XJ. Comparative transcriptome analysis and marker development of two closely related Primrose species (Primula poissonii and Primula wilsonii). BMC Genomics 2013; 14:329. [PMID: 23672467 PMCID: PMC3658987 DOI: 10.1186/1471-2164-14-329] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 05/11/2013] [Indexed: 01/28/2023] Open
Abstract
Background Primula species are important early spring garden plants with a centre of diversity and speciation in the East Himalaya-Hengduan Mountains in Western China. Studies on population genetics, speciation and phylogeny of Primula have been impeded by a lack of genomic resources. In the present study, we sequenced the transcriptomes of two closely related primrose species, Primula poissonii and Primula wilsonii, using short reads on the Illumina Genome Analyzer platform. Results We obtained 55,284 and 55,011 contigs with N50 values of 938 and 1,085 for P. poissonii and P. wilsonii, respectively, and 6,654 pairs of putative orthologs were identified between the two species. Estimations of non-synonymous/synonymous substitution rate ratios for these orthologs indicated that 877 of the pairs may be under positive selection (Ka/Ks > 0.5), and functional enrichment analysis revealed that significant proportions of the orthologs were in the categories DNA repair, stress resistance, which may provide some hints as to how the two closely related Primula species adapted differentially to extreme environments, such as habitats characterized by aridity, high altitude and high levels of ionizing radiation. It was possible for the first time to estimate the divergence time between the radiated species pair, P. poissonii and P. wilsonii; this was found to be approximately 0.90 ± 0.57 Mya, which falls between the Donau and Gunz glaciation in the Middle Pleistocene. Primers based on 54 pairs of orthologous SSR-containing sequences between the two Primula species were designed and verified. About half of these pairs successfully amplified for both species. Of the 959 single copy nuclear genes shared by four model plants (known as APVO genes), 111 single copy nuclear genes were verified as being present in both Primula species and exon-anchored and intron-spanned primers were designed for use. Conclusion We characterized the transcriptomes for the two Primula species, and produced an unprecedented amount of genomic resources for these important garden plants. Evolutionary analysis of these two Primula species not only revealed a more precise divergence time, but also provided some novel insights into how differential adaptations occurred in extreme habitats. Furthermore, we developed two sets of genetic markers, single copy nuclear genes and nuclear microsatellites (EST-SSR). Both these sets of markers will facilitate studies on the genetic improvement, population genetics and phylogenetics of this rapidly adapting taxon.
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Affiliation(s)
- Lu Zhang
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Science, Guangzhou 510650, China
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Joy N, Asha S, Mallika V, Soniya EV. De novo transcriptome sequencing reveals a considerable bias in the incidence of simple sequence repeats towards the downstream of 'Pre-miRNAs' of black pepper. PLoS One 2013; 8:e56694. [PMID: 23469176 PMCID: PMC3587635 DOI: 10.1371/journal.pone.0056694] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 01/13/2013] [Indexed: 12/18/2022] Open
Abstract
Next generation sequencing has an advantageon transformational development of species with limited available sequence data as it helps to decode the genome and transcriptome. We carried out the de novo sequencing using illuminaHiSeq™ 2000 to generate the first leaf transcriptome of black pepper (Piper nigrum L.), an important spice variety native to South India and also grown in other tropical regions. Despite the economic and biochemical importance of pepper, a scientifically rigorous study at the molecular level is far from complete due to lack of sufficient sequence information and cytological complexity of its genome. The 55 million raw reads obtained, when assembled using Trinity program generated 2,23,386 contigs and 1,28,157 unigenes. Reports suggest that the repeat-rich genomic regions give rise to small non-coding functional RNAs. MicroRNAs (miRNAs) are the most abundant type of non-coding regulatory RNAs. In spite of the widespread research on miRNAs, little is known about the hair-pin precursors of miRNAs bearing Simple Sequence Repeats (SSRs). We used the array of transcripts generated, for the in silico prediction and detection of ‘43 pre-miRNA candidates bearing different types of SSR motifs’. The analysis identified 3913 different types of SSR motifs with an average of one SSR per 3.04 MB of thetranscriptome. About 0.033% of the transcriptome constituted ‘pre-miRNA candidates bearing SSRs’. The abundance, type and distribution of SSR motifs studied across the hair-pin miRNA precursors, showed a significant bias in the position of SSRs towards the downstream of predicted ‘pre-miRNA candidates’. The catalogue of transcripts identified, together with the demonstration of reliable existence of SSRs in the miRNA precursors, permits future opportunities for understanding the genetic mechanism of black pepper and likely functions of ‘tandem repeats’ in miRNAs.
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Affiliation(s)
- Nisha Joy
- Plant Molecular Biology, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Srinivasan Asha
- Plant Molecular Biology, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Vijayan Mallika
- Plant Molecular Biology, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Eppurathu Vasudevan Soniya
- Plant Molecular Biology, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala, India
- * E-mail:
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Howe GT, Yu J, Knaus B, Cronn R, Kolpak S, Dolan P, Lorenz WW, Dean JFD. A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation. BMC Genomics 2013; 14:137. [PMID: 23445355 PMCID: PMC3673906 DOI: 10.1186/1471-2164-14-137] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Accepted: 01/31/2013] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Douglas-fir (Pseudotsuga menziesii), one of the most economically and ecologically important tree species in the world, also has one of the largest tree breeding programs. Although the coastal and interior varieties of Douglas-fir (vars. menziesii and glauca) are native to North America, the coastal variety is also widely planted for timber production in Europe, New Zealand, Australia, and Chile. Our main goal was to develop a SNP resource large enough to facilitate genomic selection in Douglas-fir breeding programs. To accomplish this, we developed a 454-based reference transcriptome for coastal Douglas-fir, annotated and evaluated the quality of the reference, identified putative SNPs, and then validated a sample of those SNPs using the Illumina Infinium genotyping platform. RESULTS We assembled a reference transcriptome consisting of 25,002 isogroups (unique gene models) and 102,623 singletons from 2.76 million 454 and Sanger cDNA sequences from coastal Douglas-fir. We identified 278,979 unique SNPs by mapping the 454 and Sanger sequences to the reference, and by mapping four datasets of Illumina cDNA sequences from multiple seed sources, genotypes, and tissues. The Illumina datasets represented coastal Douglas-fir (64.00 and 13.41 million reads), interior Douglas-fir (80.45 million reads), and a Yakima population similar to interior Douglas-fir (8.99 million reads). We assayed 8067 SNPs on 260 trees using an Illumina Infinium SNP genotyping array. Of these SNPs, 5847 (72.5%) were called successfully and were polymorphic. CONCLUSIONS Based on our validation efficiency, our SNP database may contain as many as ~200,000 true SNPs, and as many as ~69,000 SNPs that could be genotyped at ~20,000 gene loci using an Infinium II array-more SNPs than are needed to use genomic selection in tree breeding programs. Ultimately, these genomic resources will enhance Douglas-fir breeding and allow us to better understand landscape-scale patterns of genetic variation and potential responses to climate change.
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Affiliation(s)
- Glenn T Howe
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Jianbin Yu
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, Oregon, 97331, USA
- Current address, DuPont Pioneer International, Willmar, Minnesota, 56201, USA
| | - Brian Knaus
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, Oregon, 97331, USA
| | - Richard Cronn
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, Oregon, 97331, USA
| | - Scott Kolpak
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Peter Dolan
- Department of Mathematics, University of Minnesota, Morris, MN, USA
| | - W Walter Lorenz
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, 30602, USA
| | - Jeffrey FD Dean
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, 30602, USA
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Howe GT, Yu J, Knaus B, Cronn R, Kolpak S, Dolan P, Lorenz WW, Dean JFD. A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation. BMC Genomics 2013. [PMID: 23445355 DOI: 10.1186/1471‐2164‐14‐137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Douglas-fir (Pseudotsuga menziesii), one of the most economically and ecologically important tree species in the world, also has one of the largest tree breeding programs. Although the coastal and interior varieties of Douglas-fir (vars. menziesii and glauca) are native to North America, the coastal variety is also widely planted for timber production in Europe, New Zealand, Australia, and Chile. Our main goal was to develop a SNP resource large enough to facilitate genomic selection in Douglas-fir breeding programs. To accomplish this, we developed a 454-based reference transcriptome for coastal Douglas-fir, annotated and evaluated the quality of the reference, identified putative SNPs, and then validated a sample of those SNPs using the Illumina Infinium genotyping platform. RESULTS We assembled a reference transcriptome consisting of 25,002 isogroups (unique gene models) and 102,623 singletons from 2.76 million 454 and Sanger cDNA sequences from coastal Douglas-fir. We identified 278,979 unique SNPs by mapping the 454 and Sanger sequences to the reference, and by mapping four datasets of Illumina cDNA sequences from multiple seed sources, genotypes, and tissues. The Illumina datasets represented coastal Douglas-fir (64.00 and 13.41 million reads), interior Douglas-fir (80.45 million reads), and a Yakima population similar to interior Douglas-fir (8.99 million reads). We assayed 8067 SNPs on 260 trees using an Illumina Infinium SNP genotyping array. Of these SNPs, 5847 (72.5%) were called successfully and were polymorphic. CONCLUSIONS Based on our validation efficiency, our SNP database may contain as many as ~200,000 true SNPs, and as many as ~69,000 SNPs that could be genotyped at ~20,000 gene loci using an Infinium II array-more SNPs than are needed to use genomic selection in tree breeding programs. Ultimately, these genomic resources will enhance Douglas-fir breeding and allow us to better understand landscape-scale patterns of genetic variation and potential responses to climate change.
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Affiliation(s)
- Glenn T Howe
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, Oregon 97331, USA.
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Hirsch CN, Buell CR. Tapping the promise of genomics in species with complex, nonmodel genomes. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:89-110. [PMID: 23451780 DOI: 10.1146/annurev-arplant-050312-120237] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Genomics is enabling a renaissance in all disciplines of plant biology. However, many plant genomes are complex and remain recalcitrant to current genomic technologies. The complexities of these nonmodel plant genomes are attributable to gene and genome duplication, heterozygosity, ploidy, and/or repetitive sequences. Methods are available to simplify the genome and reduce these barriers, including inbreeding and genome reduction, making these species amenable to current sequencing and assembly methods. Some, but not all, of the complexities in nonmodel genomes can be bypassed by sequencing the transcriptome rather than the genome. Additionally, comparative genomics approaches, which leverage phylogenetic relatedness, can aid in the interpretation of complex genomes. Although there are limitations in accessing complex nonmodel plant genomes using current sequencing technologies, genome manipulation and resourceful analyses can allow access to even the most recalcitrant plant genomes.
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Affiliation(s)
- Candice N Hirsch
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
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Zhou L, Holliday JA. Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture. BMC Genomics 2012; 13:703. [PMID: 23241106 PMCID: PMC3542275 DOI: 10.1186/1471-2164-13-703] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 12/05/2012] [Indexed: 01/04/2023] Open
Abstract
Background High-throughput re-sequencing is rapidly becoming the method of choice for studies of neutral and adaptive processes in natural populations across taxa. As re-sequencing the genome of large numbers of samples is still cost-prohibitive in many cases, methods for genome complexity reduction have been developed in attempts to capture most ecologically-relevant genetic variation. One of these approaches is sequence capture, in which oligonucleotide baits specific to genomic regions of interest are synthesized and used to retrieve and sequence those regions. Results We used sequence capture to re-sequence most predicted exons, their upstream regulatory regions, as well as numerous random genomic intervals in a panel of 48 genotypes of the angiosperm tree Populus trichocarpa (black cottonwood, or ‘poplar’). A total of 20.76Mb (5%) of the poplar genome was targeted, corresponding to 173,040 baits. With 12 indexed samples run in each of four lanes on an Illumina HiSeq instrument (2x100 paired-end), 86.8% of the bait regions were on average sequenced at a depth ≥10X. Few off-target regions (>250bp away from any bait) were present in the data, but on average ~80bp on either side of the baits were captured and sequenced to an acceptable depth (≥10X) to call heterozygous SNPs. Nucleotide diversity estimates within and adjacent to protein-coding genes were similar to those previously reported in Populus spp., while intergenic regions had higher values consistent with a relaxation of selection. Conclusions Our results illustrate the efficiency and utility of sequence capture for re-sequencing highly heterozygous tree genomes, and suggest design considerations to optimize the use of baits in future studies.
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Affiliation(s)
- Lecong Zhou
- Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University, 304 Cheatham Hall, Blacksburg, VA 24061, USA
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27
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Hao DC, Chen SL, Xiao PG, Liu M. Application of High-Throughput Sequencing in Medicinal Plant Transcriptome Studies. Drug Dev Res 2012. [DOI: 10.1002/ddr.21041] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Da-Cheng Hao
- Biotechnology Institute/School of Environment; Dalian Jiaotong University; Dalian; 116028; China
| | - Shi-Lin Chen
- Institute of Medicinal Plant Development; Chinese Academy of Medical sciences/Peking Union Medical College; Beijing; 100193; China
| | - Pei-Gen Xiao
- Institute of Medicinal Plant Development; Chinese Academy of Medical sciences/Peking Union Medical College; Beijing; 100193; China
| | - Ming Liu
- Biotechnology Institute/School of Environment; Dalian Jiaotong University; Dalian; 116028; China
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Mu HZ, Liu ZJ, Lin L, Li HY, Jiang J, Liu GF. Transcriptomic analysis of phenotypic changes in birch (Betula platyphylla) autotetraploids. Int J Mol Sci 2012. [PMID: 23202935 PMCID: PMC3497309 DOI: 10.3390/ijms131013012] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Plant breeders have focused much attention on polyploid trees because of their importance to forestry. To evaluate the impact of intraspecies genome duplication on the transcriptome, a series of Betula platyphylla autotetraploids and diploids were generated from four full-sib families. The phenotypes and transcriptomes of these autotetraploid individuals were compared with those of diploid trees. Autotetraploids were generally superior in breast-height diameter, volume, leaf, fruit and stoma and were generally inferior in height compared to diploids. Transcriptome data revealed numerous changes in gene expression attributable to autotetraploidization, which resulted in the upregulation of 7052 unigenes and the downregulation of 3658 unigenes. Pathway analysis revealed that the biosynthesis and signal transduction of indoleacetate (IAA) and ethylene were altered after genome duplication, which may have contributed to phenotypic changes. These results shed light on variations in birch autotetraploidization and help identify important genes for the genetic engineering of birch trees.
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Affiliation(s)
- Huai-Zhi Mu
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
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De novo characterization of the root transcriptome of a traditional Chinese medicinal plant Polygonum cuspidatum. SCIENCE CHINA-LIFE SCIENCES 2012; 55:452-66. [DOI: 10.1007/s11427-012-4319-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 04/09/2012] [Indexed: 12/31/2022]
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30
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Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B. RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res 2012; 40:W622-7. [PMID: 22684630 PMCID: PMC3394330 DOI: 10.1093/nar/gks540] [Citation(s) in RCA: 602] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Recent rapid advances in next generation RNA sequencing (RNA-Seq)-based provide researchers with unprecedentedly large data sets and open new perspectives in transcriptomics. Furthermore, RNA-Seq-based transcript profiling can be applied to non-model and newly discovered organisms because it does not require a predefined measuring platform (like e.g. microarrays). However, these novel technologies pose new challenges: the raw data need to be rigorously quality checked and filtered prior to analysis, and proper statistical methods have to be applied to extract biologically relevant information. Given the sheer volume of data, this is no trivial task and requires a combination of considerable technical resources along with bioinformatics expertise. To aid the individual researcher, we have developed RobiNA as an integrated solution that consolidates all steps of RNA-Seq-based differential gene-expression analysis in one user-friendly cross-platform application featuring a rich graphical user interface. RobiNA accepts raw FastQ files, SAM/BAM alignment files and counts tables as input. It supports quality checking, flexible filtering and statistical analysis of differential gene expression based on state-of-the art biostatistical methods developed in the R/Bioconductor projects. In-line help and a step-by-step manual guide users through the analysis. Installer packages for Mac OS X, Windows and Linux are available under the LGPL licence from http://mapman.gabipd.org/web/guest/robin.
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Affiliation(s)
- Marc Lohse
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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Yang F, Xu B, Zhao S, Li J, Yang Y, Tang X, Wang F, Peng M, Huang Z. De novo sequencing and analysis of the termite mushroom (Termitomyces albuminosus) transcriptome to discover putative genes involved in bioactive component biosynthesis. J Biosci Bioeng 2012; 114:228-31. [PMID: 22608552 DOI: 10.1016/j.jbiosc.2012.03.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Revised: 03/22/2012] [Accepted: 03/26/2012] [Indexed: 11/29/2022]
Abstract
A one-eighth 454 sequencing run produced 82,386 high-quality reads. De novo assembly generated 6494 unique sequences. Based on the bioinformatic analysis, we found many the known enzymes involved in the biosynthesis of triterpene saponin in Termitomyces albuminosus, including 6 cytochrome P450 and 22 glycosyltransferase unique genes.
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Affiliation(s)
- Fang Yang
- School of Life Science, Yunnan Normal University, Kunming 650500, China
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Hamilton JP, Buell CR. Advances in plant genome sequencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:177-90. [PMID: 22449051 DOI: 10.1111/j.1365-313x.2012.04894.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The study of plant biology in the 21st century is, and will continue to be, vastly different from that in the 20th century. One driver for this has been the use of genomics methods to reveal the genetic blueprints for not one but dozens of plant species, as well as resolving genome differences in thousands of individuals at the population level. Genomics technology has advanced substantially since publication of the first plant genome sequence, that of Arabidopsis thaliana, in 2000. Plant genomics researchers have readily embraced new algorithms, technologies and approaches to generate genome, transcriptome and epigenome datasets for model and crop species that have permitted deep inferences into plant biology. Challenges in sequencing any genome include ploidy, heterozygosity and paralogy, all which are amplified in plant genomes compared to animal genomes due to the large genome sizes, high repetitive sequence content, and rampant whole- or segmental genome duplication. The ability to generate de novo transcriptome assemblies provides an alternative approach to bypass these complex genomes and access the gene space of these recalcitrant species. The field of genomics is driven by technological improvements in sequencing platforms; however, software and algorithm development has lagged behind reductions in sequencing costs, improved throughput, and quality improvements. It is anticipated that sequencing platforms will continue to improve the length and quality of output, and that the complementary algorithms and bioinformatic software needed to handle large, repetitive genomes will improve. The future is bright for an exponential improvement in our understanding of plant biology.
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Affiliation(s)
- John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
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Cronn R, Knaus BJ, Liston A, Maughan PJ, Parks M, Syring JV, Udall J. Targeted enrichment strategies for next-generation plant biology. AMERICAN JOURNAL OF BOTANY 2012; 99:291-311. [PMID: 22312117 DOI: 10.3732/ajb.1100356] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
PREMISE OF THE STUDY The dramatic advances offered by modern DNA sequencers continue to redefine the limits of what can be accomplished in comparative plant biology. Even with recent achievements, however, plant genomes present obstacles that can make it difficult to execute large-scale population and phylogenetic studies on next-generation sequencing platforms. Factors like large genome size, extensive variation in the proportion of organellar DNA in total DNA, polyploidy, and gene number/redundancy contribute to these challenges, and they demand flexible targeted enrichment strategies to achieve the desired goals. METHODS In this article, we summarize the many available targeted enrichment strategies that can be used to target partial-to-complete organellar genomes, as well as known and anonymous nuclear targets. These methods fall under four categories: PCR-based enrichment, hybridization-based enrichment, restriction enzyme-based enrichment, and enrichment of expressed gene sequences. KEY RESULTS Examples of plant-specific applications exist for nearly all methods described. While some methods are well established (e.g., transcriptome sequencing), other promising methods are in their infancy (hybridization enrichment). A direct comparison of methods shows that PCR-based enrichment may be a reasonable strategy for accessing small genomic targets (e.g., ≤50 kbp), but that hybridization and transcriptome sequencing scale more efficiently if larger targets are desired. CONCLUSIONS While the benefits of targeted sequencing are greatest in plants with large genomes, nearly all comparative projects can benefit from the improved throughput offered by targeted multiplex DNA sequencing, particularly as the amount of data produced from a single instrument approaches a trillion bases per run.
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Affiliation(s)
- Richard Cronn
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, Oregon 97331, USA.
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Edwards CE, Parchman TL, Weekley CW. Assembly, gene annotation and marker development using 454 floral transcriptome sequences in Ziziphus celata (Rhamnaceae), a highly endangered, Florida endemic plant. DNA Res 2011; 19:1-9. [PMID: 22039173 PMCID: PMC3276261 DOI: 10.1093/dnares/dsr037] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Large-scale DNA sequence data may enable development of genetic resources in endangered species, thereby facilitating conservation efforts. Ziziphus celata, a federally endangered, self-incompatible plant species occurring in Florida, USA, is one species for which genetic resources are necessary to facilitate new introductions and augmentations essential for recovery of the species. We used 454 pyrosequencing of a Z. celata normalized floral cDNA library to create a genomic resource for gene and marker discovery. A half-plate GS-FLX Titanium run yielded 655 337 reads averaging 250 bp. A total of 474 025 reads were assembled de novo into 84 645 contigs averaging 408 bp, while 181 312 reads remained unassembled. Forty-seven and 43% of contig consensus sequences had BLAST matches to known proteins in the Uniref50 and TAIR9 annotated protein databases, respectively; many contigs fully represented orthologous proteins in TAIR9. A total of 22 707 unique genes were sequenced, indicating substantial coverage of the Z. celata transcriptome. We detected single-nucleotide polymorphisms and simple sequence repeats (SSRs) and developed thousands of SSR primers for use in future genetic studies. As a first step towards understanding self-incompatibility in Z. celata, we identified sequences belonging to the gene family encoding self-incompatibility. This study demonstrates the efficacy of 454 transcriptome sequencing for rapid gene and marker discovery in an endangered plant.
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Affiliation(s)
- Christine E Edwards
- USACE ERDC, Environmental Laboratory, 3909 Halls Ferry Road, Vicksburg, MS 39180, USA.
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