Non‐canonical expression patterns and evolutionary rates of sex‐biased genes in a seasonal fish

Machado, Miguel P.; Matos, Isa; Grosso, Ana Rita; Schartl, Manfred; Coelho, M. M.

doi:10.1002/mrd.22752

Cited by 10 publications

(10 citation statements)

References 78 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The male-biased expression tendency in gonads, applies in all studied sparids and it seems to be a common pattern in fish (Tao et al, 2013; Böhne et al, 2014; Manousaki et al, 2014; Liu et al, 2015; Casas et al, 2016; Machado et al, 2016; Xu et al, 2016; Tsakogiannis et al, 2018). Important signaling pathways such as WNT (wingless-type MMTV integration site family), NOTCH, TGFβ (transforming growth factor beta), nuclear receptors, for example the retinoic acid receptor (RAR), and RTKs (receptor tyrosine kinases) such as FGFR (fibroblast growth factor receptor), EGFR (epidermal growth factor receptor), and IR (insulin receptor) were all found to be among the significantly overrepresented terms of common dentex and gilthead seabream as well as in the rest of the species (Manousaki et al, 2014; Tsakogiannis et al, 2018).…”

Section: Discussionmentioning

confidence: 91%

The Gene Toolkit Implicated in Functional Sex in Sparidae Hermaphrodites: Inferences From Comparative Transcriptomics

et al. 2019

View full text Add to dashboard Cite

Sex-biased gene expression is the mode through which sex dimorphism arises from a nearly identical genome, especially in organisms without genetic sex determination. Teleost fishes show great variations in the way the sex phenotype forms. Among them, Sparidae, that might be considered as a model family displays a remarkable diversity of reproductive modes. In this study, we sequenced and analyzed the sex-biased transcriptome in gonads and brain (the tissues with the most profound role in sexual development and reproduction) of two sparids with different reproductive modes: the gonochoristic common dentex, Dentex dentex, and the protandrous hermaphrodite gilthead seabream, Sparus aurata. Through comparative analysis with other protogynous and rudimentary protandrous sparid transcriptomes already available, we put forward common male and female-specific genes and pathways that are probably implicated in sex-maintenance in this fish family. Our results contribute to the understanding of the complex processes behind the establishment of the functional sex, especially in hermaphrodite species and set the groundwork for future experiments by providing a gene toolkit that can improve efforts to control phenotypic sex in finfish in the ever-increasingly important field of aquaculture.

show abstract

Section: Discussionmentioning

confidence: 91%

The Gene Toolkit Implicated in Functional Sex in Sparidae Hermaphrodites: Inferences From Comparative Transcriptomics

et al. 2019

View full text Add to dashboard Cite

show abstract

“…In summary:From juvenile samples: Three barcoded RNA libraries had been previously constructed and paired-end sequenced using Illumina HiSeq 2000, producing 12 Gb clean data in 3 data sets (juv-AA; juv-PA; and juv-PAA, ~4 Gb per library) of paired-end sequence reads (around 91 bp) 21 .From adult liver samples: Four barcoded RNA libraries had been previously constructed, one for S. pyrenaicus (liver- PP) and three for S. alburnoides (liver- AA, liver-PA and liver-PAA) 21 . The four libraries were paired-end sequenced using Illumina HiSeq 2000, producing 4 Gb of clean data in 4 data sets (Liv-AA; Liv-PA; Liv-PP and Liv-PAA, ~1 Gb per library) of short paired-end sequence reads (around 50 bp) 21 .From adult brain and gonad samples: Six barcoded RNA libraries were constructed, two for S. pyrenaicus brain and two for gonads 69 , one for S. alburnoides nuclear non-hybrid AA male brain and one for its gonad (this study). For the construction of the six libraries, total RNA was purified from individual gonads and brains of two S. pyrenaicus (PP) individuals, and from a pool of brains and gonads (separated by tissue type) of a AA S. alburnoides and a rare occurring AAA S. alburnoides .…”

Section: Methodsmentioning

confidence: 99%

“…From adult brain and gonad samples: Six barcoded RNA libraries were constructed, two for S. pyrenaicus brain and two for gonads 69 , one for S. alburnoides nuclear non-hybrid AA male brain and one for its gonad (this study). For the construction of the six libraries, total RNA was purified from individual gonads and brains of two S. pyrenaicus (PP) individuals, and from a pool of brains and gonads (separated by tissue type) of a AA S. alburnoides and a rare occurring AAA S. alburnoides .…”

Section: Methodsmentioning

confidence: 99%

Allele-specific expression variation at different ploidy levels in Squalius alburnoides

Matos

Machado

Schartl

et al. 2019

Sci Rep

Self Cite

View full text Add to dashboard Cite

Allopolyploid plants are long known to be subject to a homoeolog expression bias of varying degree. The same phenomenon was only much later suspected to occur also in animals based on studies of single selected genes in an allopolyploid vertebrate, the Iberian fish Squalius alburnoides . Consequently, this species became a good model for understanding the evolution of gene expression regulation in polyploid vertebrates. Here, we analyzed for the first time genome-wide allele-specific expression data from diploid and triploid hybrids of S. alburnoides and compared homoeolog expression profiles of adult livers and of juveniles. Co-expression of alleles from both parental genomic types was observed for the majority of genes, but with marked homoeolog expression bias, suggesting homoeolog specific reshaping of expression level patterns in hybrids. Complete silencing of one allele was also observed irrespective of ploidy level, but not transcriptome wide as previously speculated. Instead, it was found only in a restricted number of genes, particularly ones with functions related to mitochondria and ribosomes. This leads us to hypothesize that allelic silencing may be a way to overcome intergenomic gene expression interaction conflicts, and that homoeolog expression bias may be an important mechanism in the achievement of sustainable genomic interactions, mandatory to the success of allopolyploid systems, as in S. alburnoides .

show abstract

“…Samples of S. pyrenaicus were also stored at -80ºC from previous projects. This work includes two sampling sites: Almargem (37°09'50.7"N; 7°37'13.2"W) [60] and Tagus…”

Section: Samplingmentioning

confidence: 99%

Adaptation and convergence in circadian-related genes in Iberian freshwater fish

Moreno

Jesus

Sousa³

et al. 2020

Preprint

View full text Add to dashboard Cite

BackgroundThe circadian clock is a biological timing system that improves the ability of organisms to deal with environmental fluctuations. At the molecular level it consists of a network of transcription-translation feedback loops, involving genes that activate (bmal and clock – positive loop) and repress expression (cryptochrome (cry) and period (per) – negative loop). This is regulated by daily alternations of light but can also be affected by temperature. Fish, as ectothermic, depend on the environmental temperature and thus are good models to study its integration within the circadian system. Here, we studied the molecular evolution of circadian genes in four Squalius freshwater fish species, distributed across Western Iberian rivers affected by two climatic types with different environmental conditions (e.g. light and temperature). S. carolitertii and S. pyrenaicus inhabit the colder northern region under Atlantic climate type, while S. torgalensis, S. aradensis and some populations of S. pyrenaicus inhabit the warmer southern region affected by summer droughts, under Mediterranean climate type. ResultsWe identified 16 circadian-core genes in the Squalius species using a comparative transcriptomics approach. We detected evidence of positive selection in nine of these genes using methods based on dN/dS. Positive selection was mainly found in cry and per genes of the negative loop of the cycle, with 11 putatively adaptive substitutions mostly located on protein domains. Evidence for positive selection is predominant in southern populations affected by the Mediterranean climate type. By predicting protein features we found that changes at sites under positive selection can impact protein thermostability by changing their aliphatic index and isoelectric point. Additionally, in nine genes, the phylogenetic clustering of species that belong to different clades but inhabit southern basins with similar environmental conditions indicated evolutionary convergence.ConclusionsOur results support that temperature may be a strong selective pressure driving the evolution of genes involved in the circadian system. By integrating sequence-based functional protein prediction with dN/dS-based methods to detect selection we also uncovered adaptive convergence in the southern populations, probably related to their similar thermal conditions.

show abstract

Non‐canonical expression patterns and evolutionary rates of sex‐biased genes in a seasonal fish

Cited by 10 publications

References 78 publications

The Gene Toolkit Implicated in Functional Sex in Sparidae Hermaphrodites: Inferences From Comparative Transcriptomics

The Gene Toolkit Implicated in Functional Sex in Sparidae Hermaphrodites: Inferences From Comparative Transcriptomics

Allele-specific expression variation at different ploidy levels in Squalius alburnoides

Adaptation and convergence in circadian-related genes in Iberian freshwater fish

Contact Info

Product

Resources

About