Comparison of diploid and triploid Carassius auratus provides insights into adaptation to environmental change

Focusing on adaptation of aquatic organisms, especially fish, can help elucidate complex dynamics in freshwater ecology. The differences in genetic and epigenetic regulation between diploid and triploid Carassius auratus affect survival under eutrophication. To identify the underlying mechanisms that lead to better adaption of triploids than diploids, we compared mRNA and microRNA(miRNA) expressions in liver tissue of diploid and triploid individuals obtained from the Dongting lake water system in central China. Differential expression analysis revealed that 566 transcripts were significantly up-regulated, whereas758 were down-regulated in triploids; of these differentially expressed transcripts, 33 transcripts including cacna1 d, nfkb2, hspa1 and fgfr4 were involved in the MAPK signaling pathway, and eight transcripts were determined to be regulated by seven miRNAs. Additionally, four of 25 differential expressed(DE) transcripts(mhc1, irf7, nfkb2 and pik3 c) involving the viral carcinogenesis pathway were regulated by four miRNAs. Furthermore, genetic polymorphisms analysis showed that more heterozygous mutations were detected in triploids than diploids. The d N/d S results revealed that 21 genes were under positive selection(d N/d S>1) in C. auratus complex. We hypothesize that these changes related to genetic and epigenetic regulation may be caused by abiotic stresses, and facilitate adaptation to environmental changes.

Diverse transcriptional patterns of homoeologous recombinant transcripts in triploid fish(Cyprinidae)

Homoeologous recombination(HR),the exchange of homoeologous chromosomes,contributes to subgenome adaptation to diverse environments by producing various phenotypes.However,the potential relevance of HR and innate immunity is rarely described in triploid cyprinid fish species.In our study,two allotriploid genotypes(R_(2)C and RC_(2)),whose innate immunity was stronger than their inbred parents(Carassius auratus red var.and Cyprinus carpio L.),were obtained from backcrossing between male allotetraploids of C.auratus red var.×C.carpio L.and females of their two inbred parents,respectively.The work detected 140 HRs shared between the two triploids at the genomic level.Further,transcriptions of 54 homoeologous recombinant genes(HRGs)in R_(2)C and 65 HRGs in RC_(2) were detected using both Illumina and PacBio data.Finally,by comparing expressed recombinant reads to total expressed reads in each of the genes,a range of 0.1%-10% was observed in most of the 99-193 HRGs,of which six recombinant genes were classified as"response to stimulus".These results not only provide a novel way to predict HRs in allopolyploids based on cross prediction at both genomic and transcriptional levels,but also insight into the potential relationship between HRs related to innate immunity and adaptation of the triploids and allotetraploids.

HIGH-PERFORMANCE COMPUTATION AND ARTIFICIAL INTELLIGENCE IN PESTICIDE DISCOVERY: STATUS AND OUTLOOK

1 INTRODUCTION Pesticides are extremely important in global crop,food and ecological safety.Use of pesticides can prevent around 20%to 30%of global crop loss every year.The continuous growth of population and the limited acreage of agricultural land require increasing crop yields to feed people.Pesticides are important for protecting crops and preventing yield losses.With the increasing concerns over environmental protection,ecofriendly pesticides are needed to replace some higher risk ones.It is slow and difficult to successfully discover new pesticides with the standard random screening.New technologies and methods,such as high-performance computation and artificial intelligence(AI),can dramatically facilitate in the pesticide discovery process.