Transcriptome analysis reveals the genetic basis underlying the seasonal development of keratinized nuptial spines in Leptobrachium boringii

Zhang, Wei; Guo, Yue; Li, Jun; Huang, Li; Kazitsa, Eric Gilbert; Wu, Hua

doi:10.1186/s12864-016-3295-9

Cited by 14 publications

(16 citation statements)

References 81 publications

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“…Blast2GO identified more transcripts than Trinotate, and the taxonomic distribution of the BLAST hits differed between the two approaches, reflecting the inherent bias of species' representation in the Swiss-Prot database (which contains more than 20,200 H. sapiens sequences and approximately 6300 anuran sequences, but the latter representing few genera other than Xenopus). Approximately 34% of transcripts in the present assembly were annotated, within the range of values (32-57%) reported in similar studies [27,[35][36][37]. In D. chrysoscelis, the most common Metabolic Function category in the transcriptome was Catalytic, as also was observed in the transcriptome of the green-striped burrowing frog (Cyclorana alboguttata) [26].…”

Section: The Hepatic Transcriptome Of D Chrysoscelissupporting

confidence: 81%

“…As in other studies reporting amphibian transcriptomes [27,35,36], Cellular and Metabolic Processes were the most abundant Biological Process categories in the hepatic transcriptome of D. chrysoscelis. The present study focused on the hepatic transcriptome, whereas other studies have analyzed and reported a merged gene ontology classification of multiple tissues [27,35,36]; despite the distinct approaches and evolutionary histories of the species analyzed, the overall composition of the transcriptomes of D. chrysoscelis and these anurans is similar.…”

Section: The Hepatic Transcriptome Of D Chrysoscelissupporting

confidence: 76%

“…The RNA-Seq analysis undertaken in this study relied on a de novo transcriptome assembly, generating a high number of transcripts and an N50 on par with those in other RNA-Seq studies that involved a de novo assembly in amphibians (anurans or urodeles) [27,35,36]. Two different approaches were used for transcriptome annotation: one approach used Trinotate, which relies on Swiss-Prot as the main database for BLASTX searches; the other relied on Blast2GO to BLASTX sequences on NCBI's nr protein database, as well as Xenopus sp.…”

Section: The Hepatic Transcriptome Of D Chrysoscelismentioning

confidence: 99%

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Hepatic transcriptome of the freeze-tolerant Cope’s gray treefrog, Dryophytes chrysoscelis: responses to cold acclimation and freezing

et al. 2020

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Background: Cope's gray treefrog, Dryophytes chrysoscelis, withstands the physiological challenges of corporeal freezing, partly by accumulating cryoprotective compounds of hepatic origin, including glycerol, urea, and glucose. We hypothesized that expression of genes related to cryoprotectant mobilization and stress tolerance would be differentially regulated in response to cold. Using high-throughput RNA sequencing (RNA-Seq), a hepatic transcriptome was generated for D. chrysoscelis, and gene expression was compared among frogs that were warmacclimated, cold-acclimated, and frozen. Results: A total of 159,556 transcripts were generated; 39% showed homology with known transcripts, and 34% of all transcripts were annotated. Gene-level analyses identified 34,936 genes, 85% of which were annotated. Cold acclimation induced differential expression both of genes and non-coding transcripts; freezing induced few additional changes. Transcript-level analysis followed by gene-level aggregation revealed 3582 differentially expressed genes, whereas analysis at the gene level revealed 1324 differentially regulated genes. Approximately 3.6% of differentially expressed sequences were non-coding and of no identifiable homology. Expression of several genes associated with cryoprotectant accumulation was altered during cold acclimation. Of note, glycerol kinase expression decreased with cold exposure, possibly promoting accumulation of glycerol, whereas glucose export was transcriptionally promoted by upregulation of glucose-6-phosphatase and downregulation of genes of various glycolytic enzymes. Several genes related to heat shock protein response, DNA repair, and the ubiquitin proteasome pathway were upregulated in cold and frozen frogs, whereas genes involved in responses to oxidative stress and anoxia, both potential sources of cellular damage during freezing, were downregulated or unchanged.

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Section: The Hepatic Transcriptome Of D Chrysoscelissupporting

confidence: 81%

Section: The Hepatic Transcriptome Of D Chrysoscelissupporting

confidence: 76%

Section: The Hepatic Transcriptome Of D Chrysoscelismentioning

confidence: 99%

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Hepatic transcriptome of the freeze-tolerant Cope’s gray treefrog, Dryophytes chrysoscelis: responses to cold acclimation and freezing

et al. 2020

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“…Although no response in tau was observed, we found increased genetic differentiation between the selection lines in the allele frequencies of genes related to a circadian entrainment KEGG pathways (Table S5). Interestingly, in another study, we did not find a difference in onset of activity (as a measure of entrainment) in a L:D cycle between the selection lines nor a clear genomic signal underlying the variation in the circadian traits studied (Laine, Atema, et al, 2019; (Audet et al, 2018), behaviour and in the HPGL axis especially during reproduction (Maffucci & Gore, 2009;Neal-Perry & Santoro, 2006;Zhang et al, 2016).…”

Section: Underlying Genomic Changesmentioning

confidence: 54%

Genetic and phenotypic responses to genomic selection for timing of breeding in a wild songbird

et al. 2019

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The physiological mechanisms underlying avian seasonal timing of reproduction, a life‐history trait with major fitness consequences, are not well understood. Comparing individuals that have been selected to differ in their timing of breeding may prove to be a promising in studying these mechanisms, making selection lines a valuable tool. We created selection lines for early and late timing of breeding in great tits (Parus major) using genomic selection, that is selection based on multi‐marker genotypes rather than on the phenotype. We took in nestlings (F1 generation) from wild broods of which the mother was either an extremely early (“early line”) or extremely late (“late line”) breeder. These chicks were then genotyped and, based on their “genomic breeding values” (GEBVs), we selected individuals for early and late line breeding pairs to produce the F2 generation in captivity. The F2 offspring was hand‐reared, genotyped and selected to produce an F3 generation, which were then again genotyped and selected. This way we obtained laying dates in aviaries for F1, F2 and F3 birds. We studied the genetic response to the artificial selection and found increased genetic differentiation between the early and late reproducing selection lines over generations (F1–F3), indicated by both diverging GEBVs and increased fixation indices (FST). We studied the phenotypic response to selection for birds breeding in outdoor breeding aviaries. We found that early line birds laid earlier than late line birds, and this difference increased over the generations (F1–F3), with non‐significant line effects for the F1 and F2, but highly significant line differences for the F3. We also assessed whether there was correlated selection on two traits that are potentially part of the mechanisms underlying seasonal timing: the endogenous free‐running period of the day/night clock (tau) and basal metabolic rate, but found no correlated selection. We have successfully created selection lines on seasonal timing in a wild bird species and obtained an instrument for future studies to investigate the physiological mechanisms underlying timing of breeding, and the genetic variation in these mechanisms, an essential component for evolutionary change in timing of reproduction. A free Plain Language Summary can be found within the Supporting Information of this article.

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“…One should note, however, that the genes investigated in differ from the genes in the circadian entrainment KEGG pathway, where the latter may thus give potential insights in genetic variation underlying phenotypic variation in circadian traits. Furthermore, neuronal and especially glutamate related GO groups and KEGG pathways are known to be important in learning (Audet et al 2018), behaviour (X. and in the HPGL axis especially during reproduction (Maffucci & Gore 2009;Neal-Perry & Santoro 2006;Zhang et al 2016).…”

Section: Underlying Genomic Changesmentioning

confidence: 99%

The mechanisms underlying seasonal timing of breeding : a multi-level approach using bi-directional genomic selection on timing of egg-laying

Verhagen¹

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Table of contents Chapter 1 General introduction Chapter 2 Genetic and phenotypic responses to genomic selection for timing of breeding in a wild songbird Chapter 3 Temperature has a causal and plastic effect on timing of breeding in a small songbird Chapter 4 Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a songbird Chapter 5 Fine-tuning of seasonal timing of breeding is regulated downstream in the underlying neuro-endocrine system in a small songbird Chapter 6 Exploring temporal changes in DNA methylation and RNA expression in a small songbird-correlations within and between tissues Chapter 7 General discussion References Summary Samenvatting Curriculum vitae List of publications Acknowledgements WIAS Training and Education Statement CHAPTER 1 General introduction Chapter 1 10 Evolution and natural selection Evolution, the process that leads to the formation of and change in biological systems in response to their environment, has shaped life since its beginning and continues to do so. All organisms, simple and complex, evolve over different scales in both time and space. In general, evolution is described and studied as two distinct hierarchical processes; macroevolution and micro-evolution. Macro-evolution refers to the origin of new morphological forms, species and divisions of the taxonomic hierarchy above the species level, together with the origin of complex adaptations, such as the eye (Reznick & Ricklefs 2009), but on which I will not dwell further. In contrast, micro-evolution refers to the processes of adaptive modifications (i.e. through alteration in allele frequencies in gene pools) within and among populations, propelled by mutation, migration, genetic drift and natural selection. The latter, put first into words by, independently, both Charles Darwin (1859) and Alfred Russel Wallace (1858), is usually defined as the consequence of three organismal properties: (1) variation among organisms of a population, (2) differential reproduction, and (3) traits that are important for survival or reproduction show heritability (Darwin 1859; Wallace 1858).

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Transcriptome analysis reveals the genetic basis underlying the seasonal development of keratinized nuptial spines in Leptobrachium boringii

Cited by 14 publications

References 81 publications

Hepatic transcriptome of the freeze-tolerant Cope’s gray treefrog, Dryophytes chrysoscelis: responses to cold acclimation and freezing

Hepatic transcriptome of the freeze-tolerant Cope’s gray treefrog, Dryophytes chrysoscelis: responses to cold acclimation and freezing

Genetic and phenotypic responses to genomic selection for timing of breeding in a wild songbird

The mechanisms underlying seasonal timing of breeding : a multi-level approach using bi-directional genomic selection on timing of egg-laying

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