Asymmetric and parallel subgenome selection co-shape common carp domestication.

BACKGROUND: The common carp (Cyprinus carpio) might best represent the domesticated allopolyploid animals. Although subgenome divergence which is well-known to be a key to allopolyploid domestication has been comprehensively characterized in common carps, the link between genetic architecture underlying agronomic traits and subgenome divergence is unknown in the selective breeding of common carps globally. RESULTS: We utilized a comprehensive SNP dataset in 13 representative common carp strains worldwide to detect genome-wide genetic variations associated with scale reduction, vibrant skin color, and high growth rate in common carp domestication. We identified numerous novel candidate genes underlie the three agronomically most desirable traits in domesticated common carps, providing potential molecular targets for future genetic improvement in the selective breeding of common carps. We found that independently selective breeding of the same agronomic trait (e.g., fast growing) in common carp domestication could result from completely different genetic variations, indicating the potential advantage of allopolyploid in domestication. We observed that candidate genes associated with scale reduction, vibrant skin color, and/or high growth rate are repeatedly enriched in the immune system, suggesting that domestication of common carps was often accompanied by the disease resistance improvement. CONCLUSIONS: In common carp domestication, asymmetric subgenome selection is prevalent, while parallel subgenome selection occurs in selective breeding of common carps. This observation is not due to asymmetric gene retention/loss between subgenomes but might be better explained by reduced pleiotropy through transposable element-mediated expression divergence between ohnologs. Our results demonstrate that domestication benefits from polyploidy not only in plants but also in animals.

Prevalent Introgression Underlies Convergent Evolution in the Diversification of Pungitius Sticklebacks.

New mutations and standing genetic variations contribute significantly to repeated phenotypic evolution in sticklebacks. However, less is known about the role of introgression in this process. We analyzed taxonomically and geographically comprehensive genomic data from Pungitius sticklebacks to decipher the extent of introgression and its consequences for the diversification of this genus. Our results demonstrate that introgression is more prevalent than suggested by earlier studies. Although gene flow was generally bidirectional, it was often asymmetric and left unequal genomic signatures in hybridizing species, which might, at least partly, be due to biased hybridization and/or population size differences. In several cases, introgression of variants from one species to another was accompanied by transitions of pelvic and/or lateral plate structures-important diagnostic traits in Pungitius systematics-and frequently left signatures of adaptation in the core gene regulatory networks of armor trait development. This finding suggests that introgression has been an important source of genetic variation and enabled phenotypic convergence among Pungitius sticklebacks. The results highlight the importance of introgression of genetic variation as a source of adaptive variation underlying key ecological and taxonomic traits. Taken together, our study indicates that introgression-driven convergence likely explains the long-standing challenges in resolving the taxonomy and systematics of this small but phenotypically highly diverse group of fish.

Contrasting population differentiation in two sympatric Triplophysa loaches on the Qinghai-Tibet Plateau.

Genetic differentiation in aquatic organisms is usually shaped by drainage connectivity. Sympatric aquatic species are thus expected to show similar population differentiation patterns and similar genetic responses to their habitats. Water bodies on the Qinghai-Tibet Plateau (QTP) have recently experienced dramatic physicochemical changes, threatening the biodiversity of aquatic organisms on the "roof of the world." To uncover ecological genetics in Tibetan loaches (Triplophysa)-the largest component of the QTP ichthyofauna-we characterized population differentiation patterns and adaptive mechanisms to salinity change in two sympatric and phylogenetically closely related Tibetan loaches, T. stewarti and T. stenura, by integrating population genomic, transcriptomic, and electron probe microanalysis approaches. Based on millions of genome-wide SNPs, the two Tibetan loach species show contrasting population differentiation patterns, with highly geographically structured and clear genetic differentiation among T. stewarti populations, whereas there is no such observation in T. stenura, which is also supported by otolith microchemistry mapping. While limited genetic signals of parallel adaption to salinity changes between the two species are found from either genetic or gene expression variation perspective, a catalog of genes involved in ion transport, energy metabolism, structural reorganization, immune response, detoxification, and signal transduction is identified to be related to adaptation to salinity change in Triplophysa loaches. Together, our findings broaden our understanding of the population characteristics and adaptive mechanisms in sympatric Tibetan loach species and would contribute to biodiversity conservation and management of aquatic organisms on the QTP.

Comprehensive CircRNA Profiling and Selection of Key CircRNAs Reveal the Potential Regulatory Roles of CircRNAs throughout Ovarian Development and Maturation in Cynoglossus semilaevis.

CircRNAs are novel endogenous non-coding small RNAs involved in the regulation of multiple biological processes. However, little is known regarding circRNAs in ovarian development and maturation of fish. Our study, for the first time, provides the genome-wide overview of the types and relative abundances of circRNAs in tongue sole tissues during three ovarian developmental stages. We detected 6790 circRNAs in the brain, 5712 in the pituitary gland, 4937 in the ovary and 4160 in the liver. Some circRNAs exhibit tissue-specific expression, and qRT-PCR largely confirmed 6 differentially expressed (DE) circRNAs. Gene Ontology and KEGG pathway analyses of DE mRNAs were performed. Some DE circRNA parental genes were closely associated with biological processes in key signalling pathways and may play essential roles in ovarian development and maturation. We found that the selected circRNAs were involved in 10 pathways. RNase R digestion experiment and Sanger sequencing verified that the circRNA had a ring structure and was RNase R resistant. qRT-PCR results largely confirmed differential circRNA expression patterns from the RNA-seq data. These findings indicate that circRNAs are widespread in terms of present in production-related tissues of tongue sole with potentially important regulatory roles in ovarian development and maturation.

Transcriptome analysis on chlorpyrifos detoxification in Uronema marinum (Ciliophora, Oligohymenophorea).

Chlorpyrifos (CPF) pollution has drawn widespread concerns in aquatic environments due to its risks to ecologic system, however, the response mechanisms of ciliates to CPF pollution were poorly studied. In our current work, the degradation of CPF by ciliates and the morphological changes of ciliates after CPF exposure were investigated. In addition, the transcriptomic profiles of the ciliate Uronema marinum, with and without exposure with CPF, were detected using digital gene expression technologies. De novo transcriptome assembly 166,829,634 reads produced from three groups (untreated, CPF treatment at 12 h and 24 h) by whole transcriptome sequencing (RNA-Seq). Gene ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways were analyzed in all unigenes and different expression genes to identify their biological functions and processes. Furthermore, the results indicated that genes related to the stress response, cytoskeleton and cell structure proteins, and antioxidant systems might play an important role in the resistance mechanism of ciliates. The enzyme activities of SOD and GST after CPF stress were also analyzed, and the result showed the good antioxidant capacity of SOD and GST in ciliates inferred from the increase of the activities of the two enzymes. The ciliate Uronema marinum showed a resistance response to chlorpyrifos stress at the transcriptomic level in the present work, which indicates that ciliates can be considered as a potential bioremediation agent.

The oxidative stress response of oxytetracycline in the ciliate Pseudocohnilembus persalinus.

Oxytetracycline (OTC) is commonly employed in fish farms to prevent bacterial infections in China, and because of their widely and intensive use, the potential harmful effects on organisms in aquatic environment are of great concern. Ciliates play an important role in aquatic food webs as secondary producers, and Pseudocohnilembus persalinus, is one kind of them which are easily found in fish farms, surviving in polluted water. Therefore, using P. persalinus as experimental models, this study investigated the effects of oxytetracycline (OTC) on the growth, antioxidant system and morphological damage in pollution-resistant ciliates species. Our results showed that the 96-h EC50 values for OTC of P. persalinus was 21.38mgL-1. The increased level of SOD and GSH during 96h OTC stress was related to an adaptive response under oxidative stress induced in ciliates. Additionally, sod1, sod2 and sod3 exhibited a significant increased expression level compared to control group at 24h treatment, indicating a promoting of dense system in ciliates at this exposure time. However, only sod1 and sod2 showed raised expression level at 48h stress, showing the different sensitive of gene isoforms to some extent. With OTC treatment, damage of regular wrinkles, shrunk, twisted on the cell surface, even forming cyst of scuticociliatid ciliate cells were firstly observed by SEM (scanning electron microscope) in this study. Overall, physiological, molecular and morphological information on the toxicological studies of ciliates and more information on possibility of ciliates as indicators of contamination were provided in this study.