The evolutionary direction of gonochorism and hermaphroditism is an intriguing mystery to be solved. The special transient hermaphroditic stage makes the little yellow croaker (Larimichthys polyactis, L. polyactis) an appealing model for studying the formation of hermaphrodites. On the other hand, as the most famous commercial fish species in East Asia, the origin and evolutionary relationship of L. polyactis and Larimichthys crocea remain unclear. Here, we report the genome sequence of L. polyactis, with a size of ~706 Mb (contig N50 = 1.21 Mb and scaffold N50 = 4.52 Mb) and 25,233 protein-coding genes. Phylogenomic analysis suggests that L. polyactis diverged from the common ancestor of Larimichthys crocea ~25.4 million years ago. Our high-quality genome assembly enabled comparative genomic analysis, which revealed a number of within-chromosome rearrangements and translocations without major chromosome fission or fusion events between the two species. The dmrt1 gene was identified as the candidate sex determination gene in L. polyactis. The expression of dmrt1 and its upstream regulatory gene rnf183 were both sexually dimorphic in the transcriptome analysis. Rnf183, unlike its two paralogues rnf223 and rnf225, is only present in Larimichthys but not in other teleost species, suggesting that it originated from a lineage-specific duplication or was lost in other teleosts. Phylogenetic analysis shows that the hermaphrodite stage in male L. polyactis may be explained by the sequence evolution of dmrt1. Decoding the L. polyactis genome not only provides insight into the genetic underpinnings of hermaphrodite evolution but also provides valuable information for enhancing fish aquaculture.

Temperature is an important climatic factor that shapes the distribution of eurythermal species. Thermal adaptation of species is important to both evolutionary biology and climate-change biology because it frequently leads to latitudinal gradients of various phenotypes among populations. Spotted sea bass (Lateolabrax maculatus) has a broad latitudinal distribution range along the marginal seas of the Northwest Pacific, providing an excellent teleost model for climate adaptation studies. We generated over 8.57 million SNP loci using whole genome re-sequencing from 100 samples collected at 14 geographic loci. We built the phylogeographic structure and demographic history of L. maculatus and determined sea surface temperature as the key environmental factor and major driving force for genetic divergence and local adaptation. We also identified distinct selective signatures and functional genes underlying adaptive mechanisms and ecological tradeoffs in the southernmost and northernmost populations inhabiting distinct climatic and latitudinal zones. The results offer an opportunity to better understand the genetic basis of the phenotypic variation in eurythermal fishes inhabiting different climatic regions.

The diploid Poropuntius huangchuchieni in the cyprinid family, which is widely distributed in the Mekong and Red River basins, is one of the most closely related diploid progenitor-like species of allotetraploid common carp, which was generated by merging of two diploid genomes during evolution. Therefore, the P. huangchuchieni genome is essential for polyploidy evolution studies in Cyprinidae. Here, we report a high-quality chromosome-level genome assembly of P. huangchuchieni by integrating Oxford Nanopore and Hi-C technology. The assembled genome size was 1021.38 Mb, 895.66 Mb of which was anchored onto 25 chromosomes with a N50 of 32.93 Mb. The genome contained 486.28 Mb repetitive elements and 24,099 protein-coding genes. Approximately 95.9% of the complete BUSCOs were detected, suggesting a high completeness of the genome. Evolutionary analysis revealed that P. huangchuchieni diverged from Cyprinus carpio at approximately 12 Mya. Genome comparison between P. huangchuchieni and the B subgenome of C. carpio provided insights into chromosomal rearrangements during the allotetraploid speciation. With the complete gene set, 17,474 orthologous genes were identified between P. huangchuchieni and C. carpio, providing a broad view of the gene component in the allotetraploid genome, which is critical for future genetic analyses. The high-quality genomic dataset created for P. huangchuchieni provides a diploid progenitor-like reference for the evolution and adaptation of allotetraploid carps.