High-throughput transcriptome sequencing and preliminary functional analysis in four Neotropical tree species

BMC Genomics

Ivan Scotti³  Pauline Garnier-Gere⁵  Tiange Lang²  Caroline Duret³  Alexandra Tinaut⁴  Louise Brousseau¹ 

[1] INRA, UMR 1137 EEF, allée de l’Arboretum, 54280 Champenoux, French Guiana;Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China;INRA, UMR 0745 EcoFoG, Campus agronomique BP 709, F-97387 Cedex, France;University of French West Indies and French Guiana, UMR EcoFoG, Campus agronomique BP 709, F-97387 KOUROU, Cedex, French Guiana;BIOGECO, UMR 1202, University of Bordeaux, F-33400 Talence, France

关键词: Polymorphism discovery;    Tropical rainforest tree species;    454-Pyrosequencing;   

Others  :  1217624
DOI  :  10.1186/1471-2164-15-238

 received in 2014-02-12, accepted in 2014-03-13,  发布年份 2014

【 摘 要 】

Background

The Amazonian rainforest is predicted to suffer from ongoing environmental changes. Despite the need to evaluate the impact of such changes on tree genetic diversity, we almost entirely lack genomic resources.

Results

In this study, we analysed the transcriptome of four tropical tree species (Carapa guianensis, Eperua falcata, Symphonia globulifera and Virola michelii) with contrasting ecological features, belonging to four widespread botanical families (respectively Meliaceae, Fabaceae, Clusiaceae and Myristicaceae). We sequenced cDNA libraries from three organs (leaves, stems, and roots) using 454 pyrosequencing. We have developed an R and bioperl-based bioinformatic procedure for de novo assembly, gene functional annotation and marker discovery. Mismatch identification takes into account single-base quality values as well as the likelihood of false variants as a function of contig depth and number of sequenced chromosomes. Between 17103 (for Symphonia globulifera) and 23390 (for Eperua falcata) contigs were assembled. Organs varied in the numbers of unigenes they apparently express, with higher number in roots. Patterns of gene expression were similar across species, with metabolism of aromatic compounds standing out as an overrepresented gene function. Transcripts corresponding to several gene functions were found to be over- or underrepresented in each organ. We identified between 4434 (for Symphonia globulifera) and 9076 (for Virola surinamensis) well-supported mismatches. The resulting overall mismatch density was comprised between 0.89 (S. globulifera) and 1.05 (V. surinamensis) mismatches/100 bp in variation-containing contigs.

Conclusion

The relative representation of gene functions in the four transcriptomes suggests that secondary metabolism may be particularly important in tropical trees. The differential representation of transcripts among tissues suggests differential gene expression, which opens the way to functional studies in these non-model, ecologically important species. We found substantial amounts of mismatches in the four species. These newly identified putative variants are a first step towards acquiring much needed genomic resources for tropical tree species.

【 授权许可】

   
2014 Brousseau et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

【 参考文献 】

• [1]Hoorn C, Wesselingh FP, ter Steege H, Bermudez MA, Mora A, Sevink J, Sanmartín I, Sanchez-Meseguer A, Anderson CL, Figueiredo JP, Jaramillo C, Riff D, Negri FR, Hooghiemstra H, Lundberg J, Stadler T, Särkinen T, Antonelli A: Amazonia through time: andean uplift, climate change, landscape evolution, and biodiversity. Science 2010, 330(6006):927-931.
• [2]Hubbell SP, He F, Condit R, Borda-de-Água L, Kellner J, ter Steege H: How many tree species are there in the Amazon and how many of them will go extinct? Proc Natl Acad Sci 2008, 105(Supplement 1):11498-11504.
• [3]Hawkins BA, Rodríguez MÁ, Weller SG: Global angiosperm family richness revisited: linking ecology and evolution to climate. J Biogeogr 2011, 38(7):1253-1266.
• [4]Phillips OL, Aragao LEOC, Lewis SL, Fisher JB, Lloyd J, Lopez-Gonzalez G, Malhi Y, Monteagudo A, Peacock J, Quesada CA, van der Heijden G, Almeida S, Amaral I, Arroyo L, Aymard G, Baker TR, Banki O, Blanc L, Bonal D, Brando P, Chave J, de Oliveira ACA, Cardozo ND, Czimczik CI, Feldpausch TR, Freitas MA, Gloor E, Higuchi N, Jimenez E, Lloyd G, et al.: Drought Sensitivity of the Amazon Rainforest. Science 2009, 323(5919):1344-1347.
• [5]Savolainen O, Pyhäjärvi T, Knürr T: Gene Flow and Local Adaptation in Trees. Annu Rev Ecol Evol Syst 2007, 38(1):595-619.
• [6]Audigeos D, Brousseau L, Traissac S, Scotti-Saintagne C, Scotti I: Molecular divergence in tropical tree populations occupying environmental mosaics. J Evol Biol 2013, 26:529-544.
• [7]Audigeos D: Relations entre diversité génétique et environnement: quels sont les processus évolutifs mis en jeu ? Cas d’une espèce d’arbre tropical: Eperua falcata Aublet. Ph. D. thesis. . Kourou, French Guiana: University of French West Indes and French Guiana; 2010.
• [8]Argout X, Salse J, Aury J-M, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN, Abrouk M, Murat F, Fouet O, Poulain J, Ruiz M, Roguet Y, Rodier-Goud M, Barbosa-Neto JF, Sabot F, Kudrna D, Ammiraju JSS, Schuster SC, Carlson JE, Sallet E, Schiex T, Dievart A, Kramer M, Gelley L, Shi Z, Berard A, et al.: The genome of Theobroma cacao. Nat Genet 2010, 43(2):101-108.
• [9]Scotti I: Adaptive potential in forest tree populations: what is it, and how can we measure it? Ann For Sci 2010, 67(8):801-801.
• [10]Jump AS, Marchant R, Peñuelas J: Environmental change and the option value of genetic diversity. Trends Plant Sci 2008, 14(1):51-58.
• [11]Aitken SN, Yeaman S, Holliday JA, Wang T, Curtis-McLane S: Adaptation, migration or extirpation: climate change outcomes for tree populations. Evol Appl 2008, 1(1):95-111.
• [12]Stapley J, Reger J, Feulner PGD, Smadja C, Galindo J, Ekblom R, Bennison C, Ball AD, Beckerman AP, Slate J: Adaptation genomics: the next generation. Trends Ecol Evol 2010, 25(12):705-712.
• [13]Helyar SJ, Hemmer-Hansen J, Bekkevold D, Taylor MI, Ogden R, Limborg MT, Cariani A, Maes GE, Diopere E, Carvalho GR, Nielsen EE: Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges. Mol Ecol Resour 2011, 11:123-136.
• [14]Seeb JE, Carvalho G, Hauser L, Naish K, Roberts S, Seeb LW: Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms. Mol Ecol Resour 2011, 11:1-8.
• [15]Schlötterer C: Towards a molecular characterization of adaptation in local populations. Curr Opin Genet Dev 2002, 12(6):683-687.
• [16]Eckert AJ, van Heerwaarden J, Wegrzyn JL, Nelson CD, Ross-Ibarra J, Gonzalez-Martinez SC, Neale DB: Patterns of Population Structure and Environmental Associations to Aridity Across the Range of Loblolly Pine (Pinus taeda L., Pinaceae). Genetics 2010, 185(3):969-982.
• [17]Eveno E, Collada C, Guevara MA, Leger V, Soto A, Diaz L, Leger P, Gonzalez-Martinez SC, Cervera MT, Plomion C, Garnier-Gere PH: Contrasting Patterns of Selection at Pinus pinaster Ait. Drought Stress Candidate Genes as Revealed by Genetic Differentiation Analyses. Mol Biol Evol 2008, 25(2):417-437.
• [18]Allendorf FW, Hohenlohe PA, Luikart G: Genomics and the future of conservation genetics. Nat Rev Genet 2010, 11(10):697-709.
• [19]Ellegren H: Sequencing goes 454 and takes large-scale genomics into the wild. Mol Ecol 2008, 17(7):1629-1631.
• [20]Egan AN, Schlueter J, Spooner DM: Applications of next-generation sequencing in plant biology. Am J Bot 2012, 99(2):175-185.
• [21]Pop M, Salzberg SL: Bioinformatics challenges of new sequencing technology. Trends Genet 2008, 24(3):142-149.
• [22]Bouck AMY, Vision T: The molecular ecologist's guide to expressed sequence tags. Mol Ecol 2007, 16(5):907-924.
• [23]Emrich SJ, Barbazuk WB, Li L, Schnable PS: Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res 2007, 17(1):69-73.
• [24]Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH: Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol 2008, 17(7):1636-1647.
• [25]Novaes E, Drost D, Farmerie W, Pappas G, Grattapaglia D, Sederoff R, Kirst M: High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 2008, 9(1):312. BioMed Central Full Text
• [26]Namroud M-C, Beaulieu J, Juge N, Laroche J, Bousquet J: Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce. Mol Ecol 2008, 17:3599-3613.
• [27]Mutz K-O, Heilkenbrinker A, Lönne M, Walter J-G, Stahl F: Transcriptome analysis using next-generation sequencing. Curr Opin Biotechnol 2013, 24(1):22-30.
• [28]Weber APM, Weber KL, Carr K, Wilkerson C, Ohlrogge JB: Sampling the Arabidopsis Transcriptome with Massively Parallel Pyrosequencing. Plant physiology 2007, 144(1):32-42.
• [29]Wicker T, Schlagenhauf E, Graner A, Close T, Keller B, Stein N: 454 sequencing put to the test using the complex genome of barley. BMC Genomics 2006, 7(1):275. BioMed Central Full Text
• [30]Blanca J, Pascual L, Ziarsolo P, Nuez F, Canizares J: ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence. BMC Genomics 2011, 12(1):285. BioMed Central Full Text
• [31]Margam VM, Coates BS, Bayles DO, Hellmich RL, Agunbiade T, Seufferheld MJ, Sun W, Kroemer JA, Ba MN, Binso-Dabire CL, Baoua I, Ishiyaku MF, Covas FG, Srinivasan R, Armstrong J, Murdock LL, Pittendrigh BR: Transcriptome Sequencing, and Rapid Development and Application of SNP Markers for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae). PLOS One 2011, 6(7):e21388.
• [32]Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS: SNP discovery via 454 transcriptome sequencing. Plant J 2007, 51(5):910-918.
• [33]Morozova O, Marra MA: Applications of next-generation sequencing technologies in functional genomics. Genomics 2008, 92(5):255-264.
• [34]Kenfack D: A Synoptic Revision of Carapa (Meliaceae). Harv Pap Bot 2011, 16(2):171-231.
• [35]Vincent G, Molino J-F, Marescot L, Barkaoui K, Sabatier D, Freycon V, Roelens J: The relative importance of dispersal limitation and habitat preference in shaping spatial distribution of saplings in a tropical moist forest: a case study along a combination of hydromorphic and canopy disturbance gradients. Ann For Sci 2011, 68(2):357-370.
• [36]Degen B, Caron H, Bandou E, Maggia L, Chevallier MH, Leveau A, Kremer A: Fine-scale spatial genetic structure of eight tropical tree species as analysed by RAPDs. Heredity 2001, 87:497-507.
• [37]Forget P-M, Cuijpers L: Survival and Scatterhoarding of Frugivores-Dispersed Seeds as a Function of Forest Disturbance. Biotropica 2008, 40(3):380-385.
• [38]Cowan RS: A monograph of the genus Eperua (Leguminosae: Caesalpinioideae). Smithsonian Contr Bot 1975, 28:26-28.
• [39]Ter Steege H, Zondervan G, ter Steege H: A preliminary analysis of large-scale forest inventory data of the Guiana Shield. In Plant Diversity in Guyana. 18th edition. Wageningen, NL: Tropenbos Foundation; 2000.
• [40]Dick Christopher W, Abdulah Salim K, Bermingham E: Molecular systematic analysis reveals cryptic tertiary diversification of a widespread tropical rain forest tree. Am Nat 2003, 162(6):691-703.
• [41]Pr A, Hamrick JL, Chavarriaga P, Kochert G: Microsatellite analysis of demographic genetic structure in fragmented populations of the tropical tree Symphonia globulifera. Mol Ecol 1998, 7(8):933-944.
• [42]Wilson TK: Myristicaceae. In Flowering plants of the Neotropics. Edited by Smith N, Mori SA, Henderson DW, Heald SV. Princeton, NJ: New York Botanical garden & Princeton University Press; 2004.
• [43]Forget PM, Sabatier D: Dynamics of the seedling shadow of a frugivore-dispersed tree species in French Guiana. Journal of tropical ecology 1997, 13:767-773.
• [44]Baraloto C, Morneau F, Bonal D, Blanc L, Ferry B: Seasonal water stress tolerance and habitat associations within four neotropical tree genera. Ecology 2007, 88(2):478-489.
• [45]Le Provost G, Paiva J, Pot D, Brach J, Plomion C: Seasonal variation in transcript accumulation in wood-forming tissues of maritime pine (Pinus pinaster Ait.) with emphasis on a cell wall glycine-rich protein. Planta 2003, 217(5):820-830.
• [46]Meyer M, Stenzel U, Hofreiter M: Parallel tagged sequencing on the 454 platform. Nat Protocols 2008, 3(2):267-278.
• [47]Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WEG, Wetter T, Suhai S: Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs. Genome research 2004, 14(6):1147-1159.
• [48]Kumar S, Blaxter M: Comparing de novo assemblers for 454 transcriptome data. BMC Genomics 2010, 11(1):571. BioMed Central Full Text
• [49]Conesa A, Götz S: Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics 2008, 2008:1-13.
• [50]Scotti I, Montaigne W, Cseke K, Traissac S: RaBoT: a rarefaction-by-bootstrap method to compare genome-wide levels of genetic diversity. Ann For Sci 2013, 70(6):631-635.
• [51]Consortium TGO: The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res 2010, 38(suppl 1):D331-D335.
• [52]Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, Hub tA: AmiGO: online access to ontology and annotation data. Bioinformatics 2009, 25(2):288-289.
• [53]Consortium TGO: The Gene Ontology project in 2008. Nucleic Acids Res 2008, 36(suppl 1):D440-D444.
• [54]Torres TT, Metta M, Ottenwälder B, Schlötterer C: Gene expression profiling by massively parallel sequencing. Genome Res 2008, 18(1):172-177.
• [55]Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, Chisholm SW, DeLong EF: Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci 2008, 105(10):3805-3810.
• [56]Craft JA, Gilbert JA, Temperton B, Dempsey KE, Ashelford K, Tiwari B, Hutchinson TH, Chipman JK: Pyrosequencing of Mytilus galloprovincialis cDNAs: Tissue-Specific Expression Patterns. PLOS One 2010, 5(1):e8875.
• [57]You F, Huo N, Deal K, Gu Y, Luo M-C, McGuire P, Dvorak J, Anderson O: Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence. BMC Genomics 2011, 12(1):59. BioMed Central Full Text
• [58]Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU: A gene expression map of Arabidopsis thaliana development. Nat Genet 2005, 37(5):501-506.
• [59]Sloan DB, Keller SR, Berardi AE, Sanderson BJ, Karpovich JF, Taylor DR: De novo transcriptome assembly and polymorphism detection in the flowering plant Silene vulgaris (Caryophyllaceae). Mol Ecol Resour 2012, 12(2):333-343.
• [60]Blanca J, Canizares J, Roig C, Ziarsolo P, Nuez F, Pico B: Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics 2011, 12(1):104. BioMed Central Full Text
• [61]Parchman T, Geist K, Grahnen J, Benkman C, Buerkle CA: Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics 2010, 11(1):180. BioMed Central Full Text
• [62]Cottet K, Genta-Jouve G, Fromentin Y, Duplais C, Laprévote O, Michel S, Lallemand M-C: Comparative LC-MS-based metabolite profiling of the ancient tropical rainforest tree Symphonia globulifera. Phytochemistry 2014. in press
• [63]Lamarre GPA, Baraloto C, Fortunel C, Dávila N, Mesones I, Rios JG, Ríos M, Valderrama E, Pilco MV, Fine PVA: Herbivory, growth rates, and habitat specialization in tropical tree lineages: implications for Amazonian beta-diversity. Ecology 2012, 93(sp8):S195-S210.
• [64]Bagchi R, Gallery RE, Gripenberg S, Gurr SJ, Narayan L, Addis CE, Freckleton RP, Lewis OT: Pathogens and insect herbivores drive rainforest plant diversity and composition. Nature 2014. advance online publication
• [65]Burt A, Koufopanou V: Homing endonuclease genes: the rise and fall and rise again of a selfish element. Curr Opin Genet Dev 2004, 14(6):609-615.
• [66]Cho Y, Qiu Y-L, Kuhlman P, Palmer JD: Explosive invasion of plant mitochondria by a group I intron. Proc Natl Acad Sci 1998, 95(24):14244-14249.
• [67]Yahara K, Fukuyo M, Sasaki A, Kobayashi I: Evolutionary maintenance of selfish homing endonuclease genes in the absence of horizontal transfer. Proc Natl Acad Sci 2009, 106(44):18861-18866.
• [68]Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin Y-C, Scofield DG, Vezzi F, Delhomme N, Giacomello S, Alexeyenko A, Vicedomini R, Sahlin K, Sherwood E, Elfstrand M, Gramzow L, Holmberg K, Hallman J, Keech O, Klasson L, Koriabine M, Kucukoglu M, Kaller M, Luthman J, Lysholm F, Niittyla T, Olson A, Rilakovic N, Ritland C, Rossello JA, Sena J, et al.: The Norway spruce genome sequence and conifer genome evolution. Nature 2013. Advance online publication
• [69]Koufopanou V, Goddard MR, Burt A: Adaptation for Horizontal Transfer in a Homing Endonuclease. Mol Biol Evol 2002, 19(3):239-246.
• [70]Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM: Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 2007, 8(7):R143. BioMed Central Full Text
• [71]DePristo MA: A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genet 2011, 43(5):491-498.
• [72]Parchman TL, Gompert Z, Mudge J, Schilkey FD, Benkman CW, Buerkle CA: Genome-wide association genetics of an adaptive trait in lodgepole pine. Mol Ecol 2012, 21(12):2991-3005.
• [73]Nielsen R, Williamson S, Kim Y, Hubisz MJ, Clark AG, Bustamante C: Genomic scans for selective sweeps using SNP data. Genome Res 2005, 15(11):1566-1575.
• [74]Nielsen R, Hubisz MJ, Hellmann I, Torgerson D, Andrés AM, Albrechtsen A, Gutenkunst R, Adams MD, Cargill M, Boyko A, Indap A, Bustamante CD, Clark AG: Darwinian and demographic forces affecting human protein coding genes. Genome Res 2009, 19(5):838-849.
• [75]Li H, Stephan W: Inferring the Demographic History and Rate of Adaptive Substitution in Drosophila. PLoS Genet 2006, 2(10):e166.
• [76]Siol M, Wright SI, Barrett SCH: The population genomics of plant adaptation. New Phytol 2010, 188(2):313-332.
• [77]Turner TL, Bourne EC, Von Wettberg EJ, Hu TT, Nuzhdin SV: Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nat Genet 2010, 42(3):260-263.
• [78]Fournier-Level A, Korte A, Cooper MD, Nordborg M, Schmitt J, Wilczek AM: A Map of Local Adaptation in Arabidopsis thaliana. Science 2011, 334(6052):86-89.
• [79]Hancock AM, Brachi B, Faure N, Horton MW, Jarymowycz LB, Sperone FG, Toomajian C, Roux F, Bergelson J: Adaptation to Climate Across the Arabidopsis thaliana Genome. Science 2011, 334(6052):83-86.
• [80]Eckert AJ, Wegrzyn JL, Pande B, Jermstad KD, Lee JM, Liechty JD, Tearse BR, Krutovsky KV, Neale DB: Multilocus Patterns of Nucleotide Diversity and Divergence Reveal Positive Selection at Candidate Genes Related to Cold Hardiness in Coastal Douglas Fir (Pseudotsuga menziesii var. menziesii). Genetics 2009, 183(1):289-298.
• [81]Holliday JA, Suren H, Aitken SN: Divergent selection and heterogeneous migration rates across the range of Sitka spruce (Picea sitchensis). Proc R Soc B-Biol Sci 2012, 279(1734):1675-1683.
• [82]Lister R, Gregory BD, Ecker JR: Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. Curr Opin Plant Biol 2009, 12(2):107-118.
• [83]Morozova O, Hirst M, Marra MA: Applications of New Sequencing Technologies for Transcriptome Analysis. Annu Rev Genomics Hum Genet 2009, 10(1):135-151.