Publications by authors named "C Voelckel"

14 Publications

Evolutionary Transcriptomics and Proteomics: Insight into Plant Adaptation.

Trends Plant Sci 2017 06 30;22(6):462-471. Epub 2017 Mar 30.

Institute for Fundamental Sciences, Massey University, Palmerston North, New Zealand.

Comparative transcriptomics and proteomics (T&P) have brought biological insight into development, gene function, and physiological stress responses. However, RNA-seq and high-throughput proteomics remain underutilised in studies of plant adaptation. These methodologies have created discovery tools with the potential to significantly advance our understanding of adaptive diversification. We outline experimental recommendations for their application. We discuss analysis models and approaches that accelerate the identification of adaptive gene sets and integrate transcriptome, proteome, phenotypic, and environmental data. Finally, we encourage widespread uptake and future developments in T&P that will advance our understanding of evolution and adaptation.
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http://dx.doi.org/10.1016/j.tplants.2017.03.001DOI Listing
June 2017

De novo sequence assembly and characterisation of a partial transcriptome for an evolutionarily distinct reptile, the tuatara (Sphenodon punctatus).

BMC Genomics 2012 Aug 31;13:439. Epub 2012 Aug 31.

Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand.

Background: The tuatara (Sphenodon punctatus) is a species of extraordinary zoological interest, being the only surviving member of an entire order of reptiles which diverged early in amniote evolution. In addition to their unique phylogenetic placement, many aspects of tuatara biology, including temperature-dependent sex determination, cold adaptation and extreme longevity have the potential to inform studies of genome evolution and development. Despite increasing interest in the tuatara genome, genomic resources for the species are still very limited. We aimed to address this by assembling a transcriptome for tuatara from an early-stage embryo, which will provide a resource for genome annotation, molecular marker development and studies of development and adaptation in tuatara.

Results: We obtained 30 million paired-end 50 bp reads from an Illumina Genome Analyzer and assembled them with Velvet and Oases using a range of kmers. After removing redundancy and filtering out low quality transcripts, our transcriptome dataset contained 32911 transcripts, with an N50 of 675 and a mean length of 451 bp. Almost 50% (15965) of these transcripts could be annotated by comparison with the NCBI non-redundant (NR) protein database or the chicken, green anole and zebrafish UniGene sets. A scan of candidate genes and repetitive elements revealed genes involved in immune function, sex differentiation and temperature-sensitivity, as well as over 200 microsatellite markers.

Conclusions: This dataset represents a major increase in genomic resources for the tuatara, increasing the number of annotated gene sequences from just 60 to almost 16,000. This will facilitate future research in sex determination, genome evolution, local adaptation and population genetics of tuatara, as well as inform studies on amniote evolution.
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http://dx.doi.org/10.1186/1471-2164-13-439DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3478169PMC
August 2012

Chips and tags suggest plant-environment interactions differ for two alpine Pachycladon species.

BMC Genomics 2012 Jul 19;13:322. Epub 2012 Jul 19.

Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand.

Background: Expression profiling has been proposed as a means for screening non-model organisms in their natural environments to identify genes potentially important in adaptive diversification. Tag profiling using high throughput sequencing is a relatively low cost means of expression profiling with deep coverage. However the extent to which very short cDNA sequences can be effectively used in screening for candidate genes is unclear. Here we investigate this question using an evolutionarily distant as well as a closely related transcriptome for referencing tags. We do this by comparing differentially expressed genes and processes between two closely related allopolyploid species of Pachycladon which have distinct altitudinal preferences in the New Zealand Southern Alps. We validate biological inferences against earlier microarray analyses.

Results: Statistical and gene annotation enrichment analyses of tag profiles identified more differentially expressed genes of potential adaptive significance than previous analyses of array-based expression profiles. These include genes involved in glucosinolate metabolism, flowering time, and response to cold, desiccation, fungi and oxidation. In addition, despite the short length of 20mer tags, we were able to infer patterns of homeologous gene expression for 700 genes in our reference library of 7,128 full-length Pachycladon ESTs. We also demonstrate that there is significant information loss when mapping tags to the non-conspecific reference transcriptome of A. thaliana as opposed to P. fastigiatum ESTs but also describe mapping strategies by which the larger collection of A. thaliana ESTs can be used as a reference.

Conclusion: When coupled with a reference transcriptome generated using RNA-seq, tag sequencing offers a promising approach for screening natural populations and identifying candidate genes of potential adaptive significance. We identify computational issues important for the successful application of tag profiling in a non-model allopolyploid plant species.
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http://dx.doi.org/10.1186/1471-2164-13-322DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3460751PMC
July 2012

Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants.

BMC Genomics 2012 Mar 14;13:92. Epub 2012 Mar 14.

Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand.

Background: Transcriptome analysis is increasingly being used to study the evolutionary origins and ecology of non-model plants. One issue for both transcriptome assembly and differential gene expression analyses is the common occurrence in plants of hybridisation and whole genome duplication (WGD) and hybridization resulting in allopolyploidy. The divergence of duplicated genes following WGD creates near identical homeologues that can be problematic for de novo assembly and also reference based assembly protocols that use short reads (35 - 100 bp).

Results: Here we report a successful strategy for the assembly of two transcriptomes made using 75 bp Illumina reads from Pachycladon fastigiatum and Pachycladon cheesemanii. Both are allopolyploid plant species (2n = 20) that originated in the New Zealand Alps about 0.8 million years ago. In a systematic analysis of 19 different coverage cutoffs and 20 different k-mer sizes we showed that i) none of the genes could be assembled across all of the parameter space ii) assembly of each gene required an optimal set of parameter values and iii) these parameter values could be explained in part by different gene expression levels and different degrees of similarity between genes.

Conclusions: To obtain optimal transcriptome assemblies for allopolyploid plants, k-mer size and k-mer coverage need to be considered simultaneously across a broad parameter space. This is important for assembling a maximum number of full length ESTs and for avoiding chimeric assemblies of homeologous and paralogous gene copies.
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http://dx.doi.org/10.1186/1471-2164-13-92DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3378427PMC
March 2012

Shotgun proteomic profiling of five species of New Zealand Pachycladon.

Proteomics 2011 Jan 6;11(1):166-71. Epub 2010 Dec 6.

Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia.

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http://dx.doi.org/10.1002/pmic.200900816DOI Listing
January 2011