Temporal pattern of loss/persistence of duplicate genes involved in signal transduction and metabolic pathways after teleost-specific genome duplication

<p>Abstract</p> <p>Background</p> <p>Recent genomic studies have revealed a teleost-specific third-round whole genome duplication (3R-WGD) event occurred in a common ancestor of teleost fishes. However, it is unclear how the genes duplicated in this event were lost or persisted during the diversification of teleosts, and therefore, how many of the duplicated genes contribute to the genetic differences among teleosts. This subject is also important for understanding the process of vertebrate evolution through WGD events. We applied a comparative evolutionary approach to this question by focusing on the genes involved in long-term potentiation, taste and olfactory transduction, and the tricarboxylic acid cycle, based on the whole genome sequences of four teleosts; zebrafish, medaka, stickleback, and green spotted puffer fish.</p> <p>Results</p> <p>We applied a state-of-the-art method of maximum-likelihood phylogenetic inference and conserved synteny analyses to each of 130 genes involved in the above biological systems of human. These analyses identified 116 orthologous gene groups between teleosts and tetrapods, and 45 pairs of 3R-WGD-derived duplicate genes among them. This suggests that more than half [(45×2)/(116+45)] = 56.5%) of the loci, probably more than ten thousand genes, present in a common ancestor of the four teleosts were still duplicated after the 3R-WGD. The estimated temporal pattern of gene loss suggested that, after the 3R-WGD, many (71/116) of the duplicated genes were rapidly lost during the initial 75 million years (MY), whereas on average more than half (27.3/45) of the duplicated genes remaining in the ancestor of the four teleosts (45/116) have persisted for about 275 MY. The 3R-WGD-derived duplicates that have persisted for a long evolutionary periods of time had significantly larger number of interacting partners and longer length of protein coding sequence, implying that they tend to be more multifunctional than the singletons after the 3R-WGD.</p> <p>Conclusion</p> <p>We have shown firstly the temporal pattern of gene loss process after 3R-WGD on the basis of teleost phylogeny and divergence time frameworks. The 3R-WGD-derived duplicates have not undergone constant exponential decay, suggesting that selection favoured the long-term persistence of a subset of duplicates that tend to be multi-functional. On the basis of these results obtained from the analysis of 116 orthologous gene groups, we propose that more than ten thousand of 3R-WGD-derived duplicates have experienced lineage-specific evolution, that is, the differential sub-/neo-functionalization or secondary loss between lineages, and contributed to teleost diversity.</p

PACAP system evolution and its role in melanophore function in teleost fish skin

Pituitary adenylate cyclase-activating polypeptide (PACAP) administered to tilapia melanophores ex-vivo causes significant pigment aggregation and this is a newly identified function for this peptide in fish. The G-protein coupled receptors (GPCRs), adcyap1r1a (encoding Pac1a) and vipr2a (encoding Vpac2a), are the only receptors in melanophores with appreciable levels of expression and are significantly (p < 0.05) down-regulated in the absence of light. Vpac2a is activated exclusively by peptide histidine isoleucine (PHI), which suggests that Pac1a mediates the melanin aggregating effect of PACAP on melanophores. Paradoxically activation of Pac1a with PACAP caused a rise in cAMP, which in fish melanophores is associated with melanin dispersion. We hypothesise that the duplicate adcyap1ra and vipr2a genes in teleosts have acquired a specific role in skin and that the melanin aggregating effect of PACAP results from the interaction of Pac1a with Ramp that attenuates cAMP-dependent PKA activity and favours the Ca(2+)/Calmodulin dependent pathway.info:eu-repo/semantics/publishedVersio

Seahorse Brood Pouch Transcriptome Reveals Common Genes Associated with Vertebrate Pregnancy

Viviparity (live birth) has evolved more than 150 times in vertebrates, and represents an excellent model system for studying the evolution of complex traits. There are at least 23 independent origins of viviparity in fishes, with syngnathid fishes (seahorses and pipefish) unique in exhibiting male pregnancy. Male seahorses and pipefish have evolved specialized brooding pouches that provide protection, gas exchange, osmoregulation, and limited nutrient provisioning to developing embryos. Pouch structures differ widely across the Syngnathidae, offering an ideal opportunity to study the evolution of reproductive complexity. However, the physiological and genetic changes facilitating male pregnancy are largely unknown. We used transcriptome profiling to examine pouch gene expression at successive gestational stages in a syngnathid with the most complex brood pouch morphology, the seahorse Hippocampus abdominalis. Using a unique time-calibrated RNA-seq data set including brood pouch at key stages of embryonic development, we identified transcriptional changes associated with brood pouch remodeling, nutrient and waste transport, gas exchange, osmoregulation, and immunological protection of developing embryos at conception, development and parturition. Key seahorse transcripts share homology with genes of reproductive function in pregnant mammals, reptiles, and other live-bearing fish, suggesting a common toolkit of genes regulating pregnancy in divergent evolutionary lineage

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics

Computational analysis of expressed sequence tags for understanding gene regulation.

High-throughput sequencing has provided a myriad of genetic data for thousands of organisms. Computational analysis of one data type, expressed sequence tags (ESTs) yields insight into gene expression, alternative splicing, tissue specificity gene functionality and the detection and differentiation of pseudogenes. Two computational methods have been developed to analyze alternative splicing events and to detect and characterize pseudogenes using ESTs. A case study of rat phosphodiesterase 4 (PDE4) genes yielded more than twenty-five previously unreported isoforms. These were experimentally verified through wet lab collaboration and found to be tissue specific. In addition, thirteen cytochrome-like gene and pseudogene sequences from the human genome were analyzed for pseudogene properties. Of the thirteen sequences, one was identified as the actual cytochrome gene, two were found to be non-cytochrome-related sequences, and eight were determined to be pseudogenes. The remaining two sequences were identified to be duplicates. As a precursor to applying the two new methods, the efficiency of three BLAST algorithms (NCBI BLAST, WU BLAST and mpiBLAST) were examined for comparing large numbers of short sequences (ESTs) to fewer large sequences (genomic regions). In general, WU BLAST was found to be the most efficient sequence comparison tool. These approaches illustrate the power of ESTs in understanding gene expression. Efficient computational analysis of ESTs (such as the two tools described) will be vital to understanding the complexity of gene expression as more high-throughput EST data is made available via advances in molecular sequencing technologies, such as the current next-generation approaches

Chromosomal-level assembly of the Asian seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species’ native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics.Web of Scienc

The role of ryanodine receptors in development

PhDCalcium ions (Ca2+) are fundamental to the regulation of many cellular processes; however, the coordination of these signals during embryogenesis is not well understood. Ryanodine receptors (RyR) are a family of important intracellular ion channels that are responsible for the release of Ca2+ and they regulate the cytosolic Ca2+ concentration. Humans have three differentially expressed ryr genes (ryr1, ryr2 and ryr3) and mutations can cause both skeletal and cardiac diseases. Although the primary function of RyR is to mediate excitation-contraction coupling in muscle, they may also regulate Ca2+ signalling during developmental processes. The project has addressed the role of RyR during embryonic development, using the zebrafish as an in vivo vertebrate model. Five zebrafish RyR genes (ryr1a, ryr1b, ryr2a, ryr2b and ryr3) were characterised and a comprehensive overview of their spatial and temporal expression in the embryo was determined. At 24 hours post-fertilisation (hpf), ryr1a, ryr1b and ryr3 are expressed in the skeletal muscle, ryr2a in specific neuronal populations and ryr2b in the cardiac muscle. Semi-quantitative PCR data and wholemount in situ hybridisation revealed strong maternal expression of ryr3 during the cleavage and blastula periods and into adulthood. The early expression of the ryr3 gene suggests that this receptor functions during the initial stages of development; a role that has not been described previously. The functional significance of RyR3 during early embryogenesis was investigated in a loss-of- 3 function model using antisense morpholino oligonucleotides. The ryr3 specific knockdown experiments appeared to affect the establishment of embryonic axis prior to the segmentation periods (before 10 hpf). In addition, by 19 to 20 hpf ryr3 morphants failed to exhibit spontaneous muscle contractions and displayed a defect in neuromuscular development. In conclusion, this study has characterised the ryr genes and provided an overview on their temporal and spatial expression. The work provides evidence that ryr3 expression provides the Ca2+ vital for myofibrils organisation and that is required for the spontaneous movements during zebrafish embryonic development. The knowledge of RyR tissue distribution in zebrafish has provided a strong foundation for loss-of-function studies aimed at addressing their role in development. In the long term, the work will also facilitate more focused studies on disease.School of Biological and Chemical Sciences Queen Mary University of London. Central Research Fund and Physiological Society Travel Grant

Neurogenomic dynamics following social interactions in male threespined sticklebacks

Social interactions provoke changes in brain and behavior, however molecular changes associated with social interactions remain obscure. This thesis explored the neurogenomic responses to aggressive and affiliative social interactions in male threespined sticklebacks (Gasterosteus aculeatus), a small fish famous for their rich behavioral repertoire. In chapter one I provided the detailed overview of the research included in this dissertation. The second chapter tested the hypothesis that there are conserved transcriptional responses to social interactions in sticklebacks and fruit fly. There was stronger evidence for this hypothesis for one type of social behavior – a territorial challenge – than for a social interaction at the opposite end of the continuum: a courtship opportunity. In chapter three and chapter four I tracked the temporal dynamics of neurogenomic plasticity in male sticklebacks. I focused on two brains regions (diencephalon and telencephalon), which contain several nuclei of the social decision-making network. The third chapter focused on the transcriptomic and epigenomic responses to a territorial challenge. Results showed that the genome dynamically responds to a territorial challenge, with waves of transcription associated with different functions, e.g. hormone activity and immune response. The fourth chapter focused on males’ transition to fatherhood, and compared and contrasted the neurogenomics of paternal care with the neurogenomics of the response to a territorial challenge. Males experienced dramatic neurogenomic shifts while they were providing paternal care. Genes related to hormones that change in mammalian mothers during pregnancy and maternal care, were differentially expressed in stickleback fathers. Gene regulatory analysis suggested that shared regulators were responsive to both a territorial challenge and paternal care and these were regulated differently along with their targets. This analysis offers a glimpse into how genes differentially acting within the social decision-making network in the brain can generate responses to opposing social stimuli. Altogether, this thesis adds to the growing repertoire of studies examining social behavior at the molecular level and draws attention to the neurogenomic dynamics associated with behavioral plasticity

Understanding mechanisms underlying changes in parental care behaviour in response to perceived paternity in sunfish

Parental care is essential for the survival of many young animals but presents significant costs to the caring parent. To mitigate these costs, parental care systems have evolved to optimize survival and fitness. According to parental investment theory, care allocation is influenced by the offspring’s value, which is often linked to their relatedness to the parent. In this thesis, I explore how hormones and gene expression influence parental care, focusing on bluegill sunfish (Lepomis macrochirus) and the hybrids they produce with pumpkinseed sunfish (Lepomis gibbosus). By manipulating direct and indirect paternity cues – swapping eggs between nests for the former and simulating cuckoldry for the latter – I investigated changes in parental investment via care behaviour. To do so, I examined variations in circulating endogenous 11-ketotestosterone, prolactin, and gene expression. I found that while 11KT levels in bluegill respond to paternity cues, they do not directly regulate parental care behaviour. Rather, these levels seem to indicate preparations for future reproductive events. In contrast, prolactin emerges as a critical hormone in fish parental care, with circulating levels correlating with nurturing behaviour and adjusting in response to perceived paternity. Additionally, I used whole-brain RNA sequencing to determine that gene expression associated with energy transport, immune response, and stress varies in response to paternity perception. Focusing on hybrids, known to provide care despite low genetic relatedness, I found they maintain distinct hormonal profiles and gene expression patterns. Specifically, they exhibit higher prolactin and lower 11-ketotestosterone levels compared to bluegills, pointing to a species-specific regulation of parental care, shaped by evolutionary and environmental factors. Overall, my thesis advances our understanding of parental care regulation in species with male-only care and complex reproductive systems. It underscores the significance of considering a range of endocrine, genomic, and environmental factors in understanding the evolution and maintenance of parental care, thereby enriching our knowledge within evolutionary biology and the neuroendocrine regulation of parental behaviour