Cited by 714Genomics and Phylogenetic StudiesLepidoptera: Biology and TaxonomyChromosomal and Genetic Variations

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Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing

VERA, J. CRISTOBAL, WHEAT, CHRISTOPHER W., FESCEMYER, HOWARD W., FRILANDER, MIKKO J., CRAWFORD, DOUGLAS L., HANSKI, ILKKA, MARDEN, JAMES H.·2008·Molecular Ecology

DOI 10.1111/j.1365-294x.2008.03666.x

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Abstract

We present a de novo assembly of a eukaryote transcriptome using 454 pyrosequencing data. The Glanville fritillary butterfly ( Melitaea cinxia ; Lepidoptera: Nymphalidae) is a prominent species in population biology but had no previous genomic data. Sequencing runs using two normalized complementary DNA collections from a genetically diverse pool of larvae, pupae, and adults yielded 608 053 expressed sequence tags (mean length = 110 nucleotides), which assembled into 48 354 contigs (sets of overlapping DNA segments) and 59 943 singletons. blast comparisons confirmed the accuracy of the sequencing and assembly, and indicated the presence of c . 9000 unique genes, along with > 6000 additional microarray‐confirmed unannotated contigs. Average depth of coverage was 6.5‐fold for the longest 4800 contigs (348–2849 bp in length), sufficient for detecting large numbers of single nucleotide polymorphisms. Oligonucleotide microarray probes designed from the assembled sequences showed highly repeatable hybridization intensity and revealed biological differences among individuals. We conclude that 454 sequencing, when performed to provide sufficient coverage depth, allows de novo transcriptome assembly and a fast, cost‐effective, and reliable method for development of functional genomic tools for nonmodel species. This development narrows the gap between approaches based on model organisms with rich genetic resources vs. species that are most tractable for ecological and evolutionary studies.

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Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
Genealogical trees, coalescent theory and the analysis of genetic polymorphisms
Rosenberg, N. A., & Nordborg, M. (2002) · Nature Reviews Genetics · doi:10.1038/nrg795 · Cited by 750
SNP discovery via 454 transcriptome sequencing
Barbazuk, W. B., Emrich, S. J., Chen, H. D., Li, L., & Schnable, P. S. (2007) · The Plant Journal · doi:10.1111/j.1365-313x.2007.03193.x · Cited by 405
Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach
Bainbridge, M. N., Warren, R. L., Hirst, M., Romanuik, T., Zeng, T., Go, A., Delaney, A., Griffith, M., Hickenbotham, M., Magrini, V., et al. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-246 · Cited by 222

Show all 0 references

Research works printed but not linked: 51

10.1126/science.287.5461.2185 · DOI
10.1016/j.tem.2007.02.003 · DOI
10.1038/nrg1916 · DOI
10.1186/1471-2164-7-130 · DOI
10.1093/nar/gkg095 · DOI
10.1111/j.1365-294X.2006.03195.x · DOI
10.1186/1471-2164-7-272 · DOI
Ehrlich PR, 2004, On the Wings of Checkerspots: A Model System For Population Biology, 10.1093/oso/9780195158274.001.0001 · DOI
10.1101/gr.5145806 · DOI
10.1073/pnas.0604351103 · DOI
10.1098/rspb.2005.3235 · DOI
10.2307/3546736 · DOI
10.1371/journal.pbio.0040129 · DOI
10.1111/j.1461-0248.2004.00654.x · DOI
10.1111/j.1365-2656.2005.01024.x · DOI
10.1111/j.1471-8286.2007.02019.x · DOI
10.1038/86730 · DOI
10.1186/gb-2007-8-7-r143 · DOI
10.1371/journal.pbio.0040303 · DOI
10.1093/bioinformatics/16.11.1048 · DOI
10.1093/nar/gkl924 · DOI
10.1890/0012-9658(2001)082[2294:PRIAAI]2.0.CO;2 · DOI
10.2307/3545561 · DOI
10.1016/j.tree.2006.08.001 · DOI
10.1002/jez.1401940115 · DOI
MardenJH(2006)Quantitative and evolutionary biology of alternative splicing: how changing the mix of alternative transcripts affects phenotypic plasticity and reaction norms.Heredity 2006 September 27; [Epub ahead of print]. · DOI
10.1038/nature03959 · DOI · Paper page
10.1073/pnas.2234984100 · DOI
10.1186/1471-2229-6-17 · DOI
10.1093/bib/bbl015 · DOI
10.1093/nar/gkm070 · DOI
10.1016/S1470-2045(07)70104-3 · DOI
10.1111/j.1365-294X.2005.02609.x · DOI
10.1186/1471-2164-5-96 · DOI
10.1126/science.1123360 · DOI
10.1016/S1360-1385(03)00131-6 · DOI
10.1111/j.1365-2311.2007.00865.x · DOI
SaastamoinenM(2007b)Heritability of dispersal rate and other life history traits in the Glanville fritillary butterfly.Heredity. September 5; [Epub ahead of print]. · DOI
10.1101/gr.547002 · DOI
10.1186/1471-2105-8-S1-S22 · DOI
10.1093/nar/gki116 · DOI
10.2307/1312950 · DOI
10.1104/pp.107.096677 · DOI
10.1101/gr.5302 · DOI
10.1186/1471-2164-7-275 · DOI
10.1186/1471-2164-8-5 · DOI
10.1126/science.1102210 · DOI
10.1534/genetics.106.055541 · DOI
10.2144/01304pf02 · DOI
10.1093/nar/gnh031 · DOI
10.1007/s11171-005-0023-7 · DOI

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de Oliveira, P. N., Matias, F., Galeano, E., & Carrer, H. (2021) · Compendium of plant genomes · doi:10.1007/978-3-030-79311-1_16 · Cited by 2
Understanding Adaptations and Responses to Change in Antarctica: Recent Physiological and Genomic Advances in Marine Environments
Peck, L., & Clark, M. (2012) · doi:10.1007/978-3-642-27352-0_9 · Cited by 3
PERSPECTIVES Transcriptome sequencing: next generation approach to RNA functional analysis
Żmieńko, A., Jackowiak, P., & Figlerowicz, M. (2014) · Biotechnologia · doi:10.5114/bta.2011.46548 · Cited by 3
Construction of microarrays and their application to virus analysis
Allen, M. J., Tiwari, B., Futschik, M., & Lindell, D. (2009) · doi:10.4319/mave.2010.978-0-9845591-0-7.34 · Cited by 3
“High-throughput sequencing methods have already been used to provide sequence for use in designing transcriptomic arrays (Vera et al. 2008), and this is likely to become a popular avenue in the future.”
Method
Omics in Oxidative Stress Tolerance in Crops
Kayıhan, C., & Eyidoğan, F. (2019) · Reactive Oxygen, Nitrogen and Sulfur Species in Plants · doi:10.1002/9781119468677.ch9 · Cited by 2
De novo assembly of Chinese forest musk deer (Moschus berezovskii) transcriptome from Next-Generation mRNA Sequencing
Xu, Z., Jie, H., Chen, B.-L., Gaur, U., Yang, M.-Y., Wu, N., Gao, J., Li, P.-W., Zhao, G.-J., Zeng, D.-J., et al. (2016) · doi:10.7287/peerj.preprints.2252v1 · Cited by 2
Transcriptic analysis of Huanghai No. 1 strain of Chinese shrimp Fenneropenaeus chinensis using 454 pyrosequencing
He, Y., Li, Z., Liu, P., Wang, Q., & Li, J. (2016) · Fisheries Science · doi:10.1007/s12562-015-0961-9 · Cited by 2
Elucidation of Terpenoid Biosynthesis in Non-model Plants Utilizing Transcriptomic Data
Simonsen, H. T. (2015) · Journal of Next Generation Sequencing & Applications · doi:10.4172/2469-9853.1000111 · Cited by 2
“This is a general trend seen in nonmodel plants and not only for terpenoid biosynthesis [43].”
Background
Identificação e Caracterização de Microssatélites de Coffea arabica a partir de dados de sequenciamento de RNA e de BACs
Silvestre, B., Cação, S. B., Ivamoto, S. T., Silva, J. C., Domingues, S., Filipe, L., & Pereira, P. (2013) · doi:10.5433/2316-5200.2013v2n3espp186 · Cited by 2
Plasticité phénotypique et moléculaire de deux clones d'eucalyptus sous contrainte hydrique au champ
Villar, É. (2011) · theses.fr (ABES) · doi:10.70675/52657987zfd09z428dz9e36z619c173798ea · Cited by 2
“Figure 4 – Evolution of water reserve was modeled using soil volumetric water content measured with TDR trases installed on P6 for the two genotypes (1-41; 18-50) subjected to the two treatments (NIR; IR).”
Method
A Preliminary Transcriptomic Study of Galaxiid Fishes Reveals a Larval Glycoprotein Gene Under Strong Positive Selection
Wallis, G. P., & Wallis, L. J. (2014) · Springer eBooks · doi:10.1007/978-3-319-07623-2_3 · Cited by 2
The scope of things to come
Dassanayake, M., Oh, D., Yun, D., Bressan, R. A., Cheeseman, J. M., & Bohnert, J. H. (2011) · Elsevier eBooks · doi:10.1016/b978-0-12-381466-1.00002-x · Cited by 2
Identification and Characterization of Biomineralization-Related Genes
Zhang, R.-Q., Xie, L.-P., & Yan, Z.-G. (2018) · Biomineralization Mechanism of the Pearl Oyster, Pinctada fucata · doi:10.1007/978-981-13-1459-9_2 · Cited by 1
De Novo Assembly and Characterization of the Transcriptome and Molecular Discovery in Capsicum Annuum L. R597
Xu, X., Li, T., Li, Y., Wang, H., & Xu, X. (2015) · International Journal of Control and Automation · doi:10.14257/ijca.2015.8.2.11 · Cited by 1
Next‐Generation Sequencing and Functional Genomic Analysis in Rainbow Trout
Salem, M. (2012) · doi:10.1002/9781118350041.ch11 · Cited by 1
Analyse bioinformatique du transcriptome des champignons mycorhiziens Tuber melanosporum et Glomus intraradices
Tisserant, É. (2011) · theses.fr (ABES) · doi:10.70675/79abe9fcza8e3z42bdz86c2zba051d687e1e
Perspective: from molecular endocrinology of mouse to genomic endocrinology of animals.
Robinson-Rechavi, M. (2008) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2008.06.005 · Cited by 1
Applications of Genomic Methods to Studies of Wild Primate Populations
Kelaita, M. A. (2015) · Springer eBooks · doi:10.1007/978-3-662-46306-2_7 · Cited by 14
Updating Genomic Data of Lepidoptera
Pozo, C., Prado, B. R., & Castañeda-Sortibrán, A. (2015) · doi:10.1007/978-3-319-24235-4_3 · Cited by 1
Expressed sequence tag analysis of the emu (Dromaius novaehollandiae) pituitary by 454 GS Junior pyrosequencing.
Kim, J. E., Leung, F., Jiang, J.-W., Kwok, A. H. Y., Bennett, D. C., & Cheng, K. M. (2013) · Poultry Science · doi:10.3382/ps.2012-02594 · Cited by 1
“become a relatively rapid and cost-effective method for de novo EST sequencing in non-model avian and fish species (Vera et al., 2008; Salem et al., 2010; Künstner et al., 2010; Jiang et al., 2012).”
Method
Investigation and development of statistical method for gene expression data analysis
Larson, N. B. (2011) · doi:10.31274/etd-180810-4311
Genome-based technologies useful for aquaculture research and genetic improvement of aquaculture species.
Liu, Z.-J. (2009) · doi:10.1533/9781845696474.1.3 · Cited by 1
Bivalve transcriptomics reveal pathogen sequences and a powerful immune response of the Mediterranean mussel (Mytilus galloprovincialis)
Moreira, R., Balseiro, P., Forn‐Cuní, G., Milan, M., Bargelloni, L., Novoa, B., & Figueras, A. J. (2018) · Marine Biology · doi:10.1007/s00227-018-3308-0 · Cited by 29
“…discovery rate (FDR) < 0.01, and a reduction was performed to 251 find the most specific terms with the same FDR. 252 253 254 Genomic research in non-model species has taken advantage of next-generation 256 sequencing methods (NGSs) (Carlsson et al. 2013; Riesgo et al. 2012; Vera et al. 2008).”
BackgroundInfluential
What, if anything, is Galaxias vulgaris?
Wallis, G., Wallis, L. J., & Waters, J. (2024) · New Zealand Science Review · doi:10.26686/nzsr.v66.9438
“New technologies are giving us the ability to look at both DNA sequence and gene expression across the entire genome, even in non-model organisms (Vera et al. 2008).”
Background
Curry tree, Murraya koenigii (L.) (Spreng): A review and future prospects using applications of next generation sequencing technology
Deshpande, P. K., Dubey, A., & Gothalwal, R. (2023) · World Journal of Biology Pharmacy and Health Sciences · doi:10.30574/wjbphs.2023.14.2.0214
“Previously, combinatorial strategy involving cDNA normalization and FLX-454 deep sequencing platform has been employed in transcriptome characterization studies in Medicago 26 , Coral 27 , Melitaea cinxia (Glanville fritillary butterfly) 28 and many other non-model organisms.”
Method
De novo assembly, transcriptome characterization and marker discovery in Indian major carp, Labeo rohita through pyrosequencing
Sahoo, L., Das, S. P., Bit, A., Patnaik, S., Mohanty, M., Das, G., & Das, P. (2021) · Genetica · doi:10.1007/s10709-021-00141-7 · Cited by 6
“…of development, found in all eukaryotic organisms and involved in a wide range of functions such as growth and development, metabolism, circadian rhythm, learning, memory, response to stress and development and differentiation of skeletal muscle and neural tissues etc. (Wagner 2001; Deppmann et al.”
Background
Ilkka Aulis Hanski. 14 February 1953—10 May 2016
Simberloff, D., & Ovaskainen, O. (2020) · Biographical Memoirs of Fellows of the Royal Society · doi:10.1098/rsbm.2019.0033
Développement du séquençage ARN ciblé sur cellules uniques en microfluidique de gouttes et applications
Foulon, S. (2019) · theses.fr (ABES) · doi:10.70675/7fffe149z4261z4e0fzb9a4z6c3a50265345
“…ou de variations génétiques, telles que de SNPs (Chen, Zhou, Wang, & Ning, 2016)(Y. Zhao et al., 2019) (Polymorphisme d’un Seul Nucléotide) ou encore pour la construction de novo de transcriptome (VERA et al., 2008), grâce à la capacité de pouvoir séquencer les transcrits sur toute leur longueur.”
Background
From gene expression to genetic adaptation : insights into the spatio-temporal dynamics of Alexandrium minutum cryptic species complex
Metegnier, G. (2018) · doi:10.70675/ed174668zb804z4d03z86dbz753c857790a1
Hormone responsive genes involved in osteoporosis in post-menopausal women
Dera, A. (2017) · doi:10.17638/03016126
COMPUTATIONAL APPROACHES IN THE ESTIMATION AND ANALYSIS OF TRANSCRIPTS DIFFERENTIAL EXPRESSION AND SPLICING: APPLICATION TO SPINAL MUSCULAR ATROPHY
Vashisht, S. (2017) · doi:10.13130/s-vashisht_phd2017-03-02
Marine Genomics: Recent Advancement and Wide-Area Applications
You, X.-X., Bian, C., Fang, X.-D., Sun, Y., Bai, J., Peng, C., Zhang, X.-H., & Shi, Q. (2016) · doi:10.1201/9781315372303-16
The role of next generation sequencing technologies in shaping the future of insect molecular systematics
Hughes, J., & Longhorn, S. J. (2016) · Cambridge University Press eBooks · doi:10.1017/cbo9781139236355.003
Characterization of Root Transcriptome among Korean Ginseng Cultivars and American Ginseng using Next Generation Sequencing
Jo, I.-H., Kim, Y.-C., Seung, H.-L., Kim, J., Kim, S., Hyun, D., Kim, D. H., Kim, K.-H., Kim, H., Chung, J., et al. (2014) · Korean Journal of Medicinal Crop Science · doi:10.7783/kjmcs.2014.22.5.339
“This has great significance for non-model organisms, which are of interest to respective scientific communities, as development of non-model species has lagged relative to model species (Ellegren, 2008; Meyer et al., 2008; Vera et al., 2008).”
Background
Transcriptome Characterization and Single Nucleotide Polymorphism (SNP) Identification in Vicia amurensis Oett. Using Next-Generation Sequencing Technology
Sundan, S., Kim, T. S., Raveendar, S., Cho, G., Sung, J.-S., Cho, Y., Lee, S., Ma, K., & Chung, J. (2014) · Plant Breeding and Biotechnology · doi:10.9787/pbb.2014.2.3.213
“For the deep and redundant coverage produced over many genes, pyrosequencing of cDNA is ideal for SNP discovery and characterization (Barbazuk et al. 2007; Vera et al. 2008; Meyer et al. 2009).”
Background
Diversity and Evolution in tropical rainforest trees : example of Eperua falcata in French Guiana
Brousseau, L. (2013) · theses.fr (ABES) · doi:10.70675/42c2967ez366az47a4z9150z54d710d80d7f
Patterns of population genetic structure among Australian and South Pacific humpback whales (Megaptera novaeangliae)
Schmitt, N. (2013) · doi:10.25911/5d78d989ba47e
De novo assembly and annotation of the grey reindeer lichen (Cladonia rangiferina) transcriptome
Junttila, S., & Rudd, S. A. (2013) · EMBnet journal · doi:10.14806/ej.19.a.644 · Cited by 1
Omics: Potential Role in Early Phase Drug Development
Grallert, H., Marzi, C., Hauck, S. M., & Gieger, C. (2019) · Springer eBooks · doi:10.1007/978-3-030-11748-1_12
Emerging Concepts and Techniques
Nañez, A., McBride, H. J., Long, T., Steffen, J. M., & Steffen, M. C. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-801238-3.95618-6
Omics: Potential Role in Early-Phase Drug Development
Grallert, H., Marzi, C., Hauck, S. M., & Gieger, C. (2014) · Springer eBooks · doi:10.1007/978-1-4471-4920-0_8
“For example, Illumina IG [ 104 – 108 ], Applied Biosystems SOLiD [ 109 ], and Roche 454 Life Science [ 111 , 112 ] systems have already been applied for this purpose.”
Method
Proteomics of Toxoplasma gondii
Wastling, J. M., & Xia, D. (2013) · Elsevier eBooks · doi:10.1016/b978-0-12-396481-6.00022-2 · Cited by 5
“RNA-Seq can be done on a variety of high-throughput sequencing platforms including Illumina IG [230], Applied Biosystems SOLiD [231] and Roche 454 Life Science systems [232].”
Silene latifolia (Caryophyllaceae) sex chromosome evolution
Blavet, N. (2012) · doi:10.3929/ethz-a-007575940
Omics Era in Stem Cell Research: Data Integration of Multi-regulatory Layers
Sevilla, A., Trinité, B., & Lemischka, I. R. (2012) · Springer eBooks · doi:10.1007/978-94-007-4330-4_7 · Cited by 1
“Those include the Illumina IG [8, 9, 11, 12, 16] Applied Biosystems SOLiD [10] and Roche 454 Life Science [17–19].”
Method
Insect Genomics
Palli, S. R., Bai, H., & Wigginton, J. (2011) · Elsevier eBooks · doi:10.1016/b978-0-12-384747-8.10001-7
Generation of a large catalog of unique transcripts for whole-genome expression analysis in nonmodel species.
Bellin, D., Ferrarini, A., & Delledonne, M. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-065-2_17
Emerging Concepts and Techniques
Steffen, J. M., & Steffen, M. C. (2010) · Elsevier eBooks · doi:10.1016/b978-0-08-046884-6.00242-6

Authors: VERA, J. C., WHEAT, C. W., FESCEMYER, H. W., FRILANDER, M. J., CRAWFORD, D. L., HANSKI, I., & MARDEN, J. H.
Affiliations: Pennsylvania State University (US)
University of Helsinki (FI)
University of Miami (US)
Corresponding author: VERA, J. CRISTOBAL
ORCID: WHEAT, CHRISTOPHER W.
FRILANDER, MIKKO J.
CRAWFORD, DOUGLAS L.
MARDEN, JAMES H.
Venue: Molecular Ecology
Publisher: Wiley
Published: 2008-03-25
Volume: 17
Issue: 7
Pages: 1636-1647
ISSN: 0962-1083 (ISSN-L)
1365-294X
DOI: 10.1111/j.1365-294x.2008.03666.x
OpenAlex: W1985484001
Cited by: 714
References: 0
Citations by year: 2026: 2 · 2025: 2 · 2024: 5 · 2023: 2 · 2022: 3 · 2021: 35 · 2020: 24 · 2019: 13 · 2018: 12 · 2017: 16 · 2016: 17 · 2015: 41 · 2014: 75 · 2013: 81 · 2012: 101
FWCI: 38.76
Type: journal article
Language: en
Open access: closed
Licence: onlinelibrary.wiley.com/termsAndConditions#vor (vor)
Locations: Molecular Ecology (publishedVersion)
PubMed (publishedVersion)
Funders: National Science Foundation
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Agricultural and Biological Sciences › Insect Science › Lepidoptera: Biology and Taxonomy
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
Keywords: Melitaea cinxia, transcriptome assembly, de novo assembly, 454 pyrosequencing, non-model organisms, expressed sequence tags, oligonucleotide microarrays, single nucleotide polymorphisms, functional genomics
MeSH terms: Animals, Base Sequence, Butterflies, Sequence Alignment, Alternative Splicing, Sequence Analysis, DNA, DNA, Complementary, Expressed Sequence Tags, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Gene Expression Profiling

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Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing

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