Origin and fate of supergenes in Atlantic cod

Supergenes are sets of genes that are inherited as a single marker and encode complex phenotypes through their joint action. They are identified in an increasing number of organisms, yet their origins and evolution remain enigmatic. In Atlantic cod, four large supergenes have been identified and linked to migratory lifestyle and environmental adaptations. Here, we investigate the origin and fate of these four supergenes through analysis of whole-genome-sequencing data, including a new long-read-based genome assembly for a non-migratory Atlantic cod individual. We corroborate that chromosomal inversions underlie all four supergenes, and show that they originated separately, between 0.40 and 1.66 million years ago. While introgression was not involved in the origin of the four supergenes, we reveal gene flow between inverted and noninverted supergene haplotypes, occurring both through gene conversion and double crossover. Moreover, the presence of genes linked to salinity adaptations in a sequence transferred through double crossover indicates that these sequences exchanged between the haplotypes are subject to selection. Our results suggest that the fate of supergenes is comparable to that of hybridizing species, by depending on the degree to which separation is maintained through purging of introduced genetic variation.

Transcriptome analysis of Fenneropenaeus chinensis (Decapoda: Penaeidae) after low-salinity exposure identifies differentially expressed genes in pathways potentially related to osmoregulation

Ability to tolerate low salinity is a key factor affecting the distribution of the Chinese shrimp (Fenneropenaeus chinensis). Although previous studies have investigated the mechanisms underlying adaptations to low salinity in some crustaceans, little is known about low-salinity adaptations in F. chinensis, particularly at the molecular level. Here, to identify genes potentially associated with the molecular response of F. chinensis to low-salinity exposure, we compared the transcriptomes of F. chinensis in low-salinity (5 ppt) and normal-salinity (20 ppt) environments. In total, 45,297,936 and 44,685,728 clean reads were acquired from the low-salinity and control groups, respectively. De novo assembly of the clean reads yielded 159,130 unigenes, with an average length of 662.82 bp. Of these unigenes, only a small fraction (10.5% on average) were successfully annotated against six databases. We identified 3,658 differentially expressed genes (DEGs) between the low-salinity group and the control group: 1,755 DEGs were downregulated in the low-salinity group as compared to the control, and 1,903 were upregulated. Of these DEGs, 282 were significantly overrepresented in 38 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. Notably, several DEGs were associated with pathways important for osmoregulation, including the mineral absorption pathway (ATP1A, Sodium/potassium-transporting ATPase subunit alpha; CLCN2, Chloride channel 2; HMOX2, Heme oxygenase 2; SLC40A1/FPN1, Solute carrier family 40 iron-regulated transporter, member 1), the vasopressin-regulated water reabsorption pathway (AQP4, Aquaporin-4; VAMP2, Vesicle-associated membrane protein 2; RAB5, Ras-related protein Rab-5) and the ribosome pathway. Our results help to clarify the molecular basis of low-salinity adaptations in F. chinensis.