Comparative transcriptomics and gene expression in larval tiger salamander (Ambystoma tigrinum) gill and lung tissues as revealed by pyrosequencing

Eo, Soo Hyung; Doyle, Jacqueline; Hale, Matthew C.; Marra, Nicholas J.; Ruhl, Joseph D.; DeWoody, J. Andrew

doi:10.1016/j.gene.2011.11.018

Cited by 24 publications

(20 citation statements)

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“…The transcriptome is one of the best places to look for functional genetic differences because it represents expressed genes and varies with changing conditions [11]. The transcriptomes of different tissues of the same individual are qualitatively and quantitatively different [12], as is the transcriptome of the same tissue from different individuals (of the same species) in similar conditions [13]. Despite this, comparative approaches have succeeded in measuring the response of gene expression to specific changes in the environment, such as drought or salinity stress [13,14].…”

Section: Introductionmentioning

confidence: 99%

Differences in gene expression within a striking phenotypic mosaic Eucalyptus tree that varies in susceptibility to herbivory

et al. 2013

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BackgroundLong-lived trees can accumulate mutations throughout their lifetimes that may influence biotic and abiotic interactions. For example, some Eucalyptus trees display marked variation in herbivore defence within a single canopy. These “mosaic” trees support foliage with distinct chemotypes which are differentially favoured by insect and vertebrate herbivores, resulting in susceptible and resistant branches within a single canopy. These mosaic trees provide a unique opportunity to explore the biosynthesis and genetic regulation of chemical defences in the foliage. The biosynthesis of the principal defence compounds, terpenoid-dominated essential oils, is well understood. However, the regulation of the genes involved and thus the control of phenotypic variation within a single tree canopy remains a mystery.ResultsWe sequenced the transcriptomes of the leaves of the two different chemotypes of a chemically mosaic Eucalyptus melliodora tree using 454 pyrosequencing technology. We used gene set enrichment analysis to identify differentially expressed transcripts and found the proportion of differentially expressed genes in the resistant and susceptible foliage similar to the transcript difference between functionally distinct tissues of the same organism, for example roots and leaves. We also investigated sequence differences in the form of single nucleotide polymorphisms and found 10 nucleotides that were different between the two branches. These are likely true SNPs and several occur in regulatory genes.ConclusionWe found three lines of evidence that suggest changes to a ‘master switch’ can result in large scale phenotypic changes: 1. We found differential expression of terpene biosynthetic genes between the two chemotypes that could contribute to chemical variation within this plant. 2. We identified many genes that are differentially expressed between the two chemotypes, including some unique genes in each branch. These genes are involved in a variety of processes within the plant and many could contribute to the regulation of secondary metabolism, thus contributing to the chemical variation. 3. We identified 10 SNPs, some of which occur in regulatory genes that could influence secondary metabolism and thus contribute to chemical variation. Whilst this research is inherently limited by sample size, the patterns we describe could be indicative of other plant genetic mosaics.

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Section: Introductionmentioning

confidence: 99%

Differences in gene expression within a striking phenotypic mosaic Eucalyptus tree that varies in susceptibility to herbivory

et al. 2013

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“…Increases in amphibian genome sizes mainly depend on the increase in repetitive DNA, especially in the moderately repetitive C 0 t analysis fraction [Morescalchi and Olmo, 1982] and on a lengthening of the introns, which in Ambystoma mexicanum and in other salamanders are longer than in humans, chickens, and frogs [Smith et al, 2009;Eo et al, 2012;Sun et al, 2012a;Voss et al, 2013]. The presence of transposons has been studied only in 2 frog species and in 7 species of salamanders: the primitive Cryptobranchus and 6 species of plethodontids, one of the most advanced family of the suborder.…”

Section: Deuterostomesmentioning

confidence: 99%

Transposons, Genome Size, and Evolutionary Insights in Animals

Canapa¹,

Barucca

Biscotti³

et al. 2015

Cytogenet Genome Res

133

124

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The relationship between genome size and the percentage of transposons in 161 animal species evidenced that variations in genome size are linked to the amplification or the contraction of transposable elements. The activity of transposable elements could represent a response to environmental stressors. Indeed, although with different trends in protostomes and deuterostomes, comprehensive changes in genome size were recorded in concomitance with particular periods of evolutionary history or adaptations to specific environments. During evolution, genome size and the presence of transposable elements have influenced structural and functional parameters of genomes and cells. Changes of these parameters have had an impact on morphological and functional characteristics of the organism on which natural selection directly acts. Therefore, the current situation represents a balance between insertion and amplification of transposons and the mechanisms responsible for their deletion or for decreasing their activity. Among the latter, methylation and the silencing action of small RNAs likely represent the most frequent mechanisms.

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“…For the D. spectabilis and H. desmarestianus samples, ½ plate of 454 sequencing was conducted using cDNA synthesized from our initial RNA extractions with the ClonTech SMART cDNA synthesis kit [44] with a modified CDS III/3’ primer (see [43, 45, 46]). For Illumina sequencing, fresh RNA extractions were used to obtain total RNA for all 12 samples, which were then purified using RNA Clean and Concentrator columns (Zymo Research).…”

Section: Methodsmentioning

confidence: 99%

“…After filtering out all contigs that were ≤100 bp, we annotated the three resulting de novo transcriptomes with BLASTx [55] using the Swiss-Prot database and an e-value threshold of e ≤1 × 10 -6 [46] to obtain annotated transcriptomes from the pool of four individuals per species. Using Blast2GO [56], we obtained gene ontology (GO) terms for our annotated contigs and conducted a Fisher’s exact test to identify gene ontologies that were consistently overrepresented or underrepresented in the H. desmarestianus dataset at p ≤ 0.05 relative to the other two species.…”

Section: Methodsmentioning

confidence: 99%

Transcriptomic characterization of the immunogenetic repertoires of heteromyid rodents

Marra

DeWoody

2014

BMC Genomics

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BackgroundWhen populations evolve under disparate environmental conditions, they experience different selective pressures that shape patterns of sequence evolution and gene expression. These may be manifested in genetic and phenotypic differences such as a diverse immunogenetic repertoire in species from tropical latitudes that have greater and/or different parasite burdens than more temperate species. To test this idea, we compared the transcriptomes of one tropical species (Heteromys desmarestianus) and two species from temperate latitudes (Dipodomys spectabilis and Chaetodipus baileyi) from the Heteromyidae. We did so in a search for positive selection on sequences and/or differential expression, while controlling for phylogenetic history in our choice of species.ResultsWe identified 127,812 contigs and annotated 34,878 of these, identifying immune genes associated with interleukins, cytokines, and the production of mast cells. We identified 632 genes that were upregulated in H. desmarestianus (8.7% of genes tested) and 492 (6.7%) that were downregulated. Gene ontology terms including “immune response” were associated with 31 (4.9%) of the 632 upregulated genes. We found preliminary evidence for positive selection on three genes (Palmitoyltransferase ZDHHC5 Ubiquitin-conjugating enzyme E2 N, Krueppel-like factor 10, and Spindle and kinetochore-associated protein 1) along the H. desmarestianus lineage.ConclusionsOverall our findings pinpoint genes in species from disparate environments that are on different evolutionary trajectories in terms of expression levels and/or nucleotide sequence. Our data indicate there are significant differences in the expression of genes among the spleen transcriptomes of these species and that a number of these differentially expressed genes do not show the same pattern of differential expression in another tissue type. This points to the possibility of expression differences between these species specific to the spleen transcriptome.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-929) contains supplementary material, which is available to authorized users.

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Comparative transcriptomics and gene expression in larval tiger salamander (Ambystoma tigrinum) gill and lung tissues as revealed by pyrosequencing

Cited by 24 publications

References 61 publications

Differences in gene expression within a striking phenotypic mosaic Eucalyptus tree that varies in susceptibility to herbivory

Differences in gene expression within a striking phenotypic mosaic Eucalyptus tree that varies in susceptibility to herbivory

Transposons, Genome Size, and Evolutionary Insights in Animals

Transcriptomic characterization of the immunogenetic repertoires of heteromyid rodents

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