Ming Zou

Silurus duanensis is a narrowly distributed freshwater catfish that lacks a chromosome-level reference genome, limiting genome-scale studies of its evolutionary history and genetic diversity. Here, we generated the first chromosome level genome assembly of S. duanensis using PacBio HiFi long reads and Hi-C data. Assembly of the HiFi reads followed by removal of redundant sequences produced a purged primary assembly of 820.59 Mb with a contig N50 of 18.97 Mb. Hi-C scaffolding and manual curation produced a final chromosome-level assembly spanning 820.69 Mb, with 99.98% of the total contig sequence anchored to 30 pseudochromosomes and a scaffold N50 of 30.96 Mb. The purged primary assembly contained 97.0% complete actinopterygian BUSCOs. Illumina short reads and PacBio HiFi reads mapped to the purged primary assembly at rates of 99.96% and 99.99%, respectively. Merqury analyses yielded QV estimates of 49.78 based on the independent Illumina reads and 61.72 based on the HiFi reads used for genome assembly. Repetitive sequences accounted for 34.35% of the assembly, and 25,210 protein-coding genes were predicted. This chromosome-level assembly substantially expands the genomic resources available for Silurus and provides a foundation for comparative genomics, evolutionary studies and genetic diversity analyses of S. duanensis and related catfishes.

The stickleback system offers a powerful model for investigating the evolutionary dynamics of sex chromosome differentiation. Although a ZW sex determination mechanism has previously been reported in sticklebacks, its origin and evolutionary history remain poorly resolved. Here, integrated multiomics analyses were applied to elucidate the evolutionary trajectory of the ZW system in Pungitius sinensis and Pungitius bussei . Using two newly assembled genomes and family-based segregation data, the sex-determining region (SDR) was delineated with high resolution. Several canonical genes implicated in sex determination pathways were located within the identified SDR, although the primary sex-determining gene could not be definitively identified. Phylogenomic evidence indicated that the ZW system emerged in Pungitius sticklebacks at least 5.0 million years ago. The absence of strong selective pressure may account for the limited differentiation between Z and W chromosomes. These findings define the evolutionary framework of the ZW system in Pungitius and contribute to a broader understanding of the extensive sex chromosome diversity in teleosts.

Regression traits such as pigmentation loss in cave-dwelling species offer powerful models for understanding evolutionary mechanisms under extreme environments. In this study, we investigated the genetic and evolutionary mechanisms underlying pigmentation loss in the cavefish Triplophysa rosa, a depigmented, eyeless species endemic to subterranean habitats. Compared with its surface-dwelling relative T. stenura, T. rosa exhibited significantly reduced expression of melanogenesis genes, indicating transcriptional repression of pigmentation pathways. Further analysis revealed a novel splicing site mutation in melanocyte inducing transcription factor a (mitfa), which results in a 63-nt deletion and loss of 21 amino acids in the activation domain. Functional rescue assays in zebrafish confirmed that the loss of 21 amino acids in Mitfa severely compromises melanin synthesis. Additionally, a premature stop codon in tyrosinase-related protein 1a (tyrp1a) was detected, which may also contribute to the depigmented phenotype. Evolutionary analyses indicated that pigmentation-specific genes in the T. rosa lineage are under relaxed purifying selection, consistent with weakened selective constraints on pigmentation in cave environments. Collectively, our findings indicate that a splice-site mutation in mitfa, acting against a background of relaxed selection on pigmentation genes, contributes to pigmentation loss in T. rosa, offering integrated proximate (molecular) and evolutionary insights into the troglomorphic traits in cavefish.

Whole-genome duplication (WGD), or polyploidization, is a major contributor to biodiversity. However, the establishment and survival of WGDs are often considered to be stochastic, since elucidating the processes of WGD establishment remains challenging. In the current study, we explored the processes leading to polyploidy establishment in snow carp (Cyprinidae: Schizothoracinae), a predominant component of the ichthyofauna of the Tibetan Plateau and its surrounding areas. Using large-scale genomic data from isoform sequencing, we analyzed ohnolog genealogies and divergence in hundreds to thousands of gene families across major snow carp lineages. Our findings demonstrated that independent autopolyploidization subsequent to speciation was prevalent, while autopolyploidization followed by speciation also occurred in the diversification of snow carp. This was further supported by matrilineal divergence and drainage evolution evidence. Contrary to the long-standing hypothesis that ancient polyploidization preceded the diversification of snow carp, we determined that polyploidy in extant snow carp was established by recurrent autopolyploidization events during the Pleistocene. These findings indicate that the diversification of extant snow carp resembles a coordinated duet: first, the uplift of the Tibetan Plateau orchestrated the biogeography and diversification of their diploid progenitors; then, the extensive Pliocene–Pleistocene climate changes acted as relay runners, further fueling diversification through recurrent autopolyploidization. Overall, this study not only reveals a hitherto unrecognized recent WGD lineage in vertebrates but also advances current understanding of WGD processes, emphasizing that WGD establishment is a nonstochastic event, emerging from numerous adaptations to environmental challenges and recurring throughout evolutionary history rather than merely in plants.

Slavum lentiscoides and Chaetogeoica ovagalla are two aphid species from the subtribe Fordina of Fordini within the subfamily Eriosomatinae, and they produce galls on their primary host plants Pistacia. We assembled chromosome-level genomes of these two species using Nanopore long-read sequencing and Hi-C technology. A 332 Mb genome assembly of S. lentiscoides with a scaffold N50 of 19.77 Mb, including 11,747 genes, and a 289 Mb genome assembly of C. ovagalla with a scaffold N50 of 11.85 Mb, containing 14,492 genes, were obtained. The Benchmarking Universal Single-Copy Orthologs (BUSCO) benchmark of the two genome assemblies reached 93.7% (91.9% single-copy) and 97.0% (95.3% single-copy), respectively. The high-quality genome assemblies in our study provide valuable resources for future genomic research of galling aphids.

Genome complexity such as heterozygosity may heavily influence its de novo assembly. Sequencing somatic cells of the F1 hybrids harboring two sets of genetic materials from both of the paternal and maternal species may avoid alleles discrimination during assembly. However, the feasibility of this strategy needs further assessments. We sequenced and assembled the genome of an F1 hybrid between Silurus asotus and S. meridionalis using the SequelII platform and Hi-C scaffolding technologies. More than 300 Gb raw data were generated, and the final assembly obtained 2344 scaffolds composed of 3017 contigs. The N50 length of scaffolds and contigs was 28.55 Mb and 7.49 Mb, respectively. Based on the mapping results of short reads generated for the paternal and maternal species, each of the 29 chromosomes originating from S. asotus and S. meridionalis was recognized. We recovered nearly 94% and 96% of the total length of S. asotus and S. meridionalis. BUSCO assessments and mapping analyses suggested that both genomes had high completeness and accuracy. Further analyses demonstrated the high collinearity between S. asotus, S. meridionalis, and the related Pelteobagrus fulvidraco. Comparison of the two genomes with that assembled only using the short reads from non-hybrid parental species detected a small portion of sequences that may be incorrectly assigned to the different species. We supposed that at least part of these situations may have resulted from mitotic recombination. The strategy of sequencing the F1 hybrid genome can recover the vast majority of the parental genomes and may improve the assembly of complex genomes.

Objectives: To detect livestock-associated MRSA (LA-MRSA) ST398 from bulk tank milk in China and to determine the phenotypic and genomic characteristics of the strains.Methods: LA-MRSA ST398 strains were isolated from bulk tank milk samples in Shanghai and their susceptibilities to antimicrobials were determined using the broth dilution method. Genomic characterization of MRSA ST398 strains was performed by WGS and their evolutionary relationships were assessed by phylogenetic analysis.Results: Two LA-MRSA ST398 isolates were recovered from bulk tank milk samples in two geographically distant farms in China. Whole-genome analysis strongly suggested that the LA-MRSA ST398 strains were closely related to the highly virulent hospital-associated MRSA (HA-MRSA) ST398 strains in China.Conclusions: The presence of LA-MRSA ST398 in bulk tank milk might be a serious threat to public health, highlighting the need for active surveillance of LA-MRSA in healthy cattle in China.

Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil containing a high proportion of eleostearic acid (∼80%). Here we report a high-quality, chromosome-scale tung tree genome sequence of 1.12 Gb with 28,422 predicted genes and over 73% repeat sequences. Tung tree genome was assembled by combining Illumina short reads, PacBio single-molecule real-time long reads and Hi-C sequencing data. Insertion time analysis revealed that the repeat-driven tung tree genome expansion might be due to long standing long terminal repeat (LTR) retrotransposon bursts and lack of efficient DNA deletion mechanisms. An electronic fluorescent pictographic (eFP) browser was generated based on genomic and RNA-seq data from 17 various tissues and developmental stages. We identified 88 nucleotide-binding site (NBS)-encoding resistance genes, of which 17 genes may help the tung tree resist theFusariumwilt shortly after infection. A total of 651 oil-related genes were identified and 88 of them were predicted to be directly involved in tung oil biosynthesis. The fewer phosphoenolpyruvate carboxykinase (PEPC) genes, and synergistic effects between transcription factors and oil biosynthesis-related genes may contribute to high oil content in tung seeds. The tung tree genome should provide valuable resources for molecular breeding and genetic improvement.

Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil rich in eleostearic acid. Here, we report a high-quality chromosome-scale genome sequence of tung tree. The genome sequence was assembled by combining Illumina short reads, Pacific Biosciences single-molecule real-time long reads, and Hi-C sequencing data. The size of tung tree genome is 1.12 Gb, with 28,422 predicted genes and over 73% repeat sequences. The V. fordii underwent an ancient genome triplication event shared by core eudicots but no further whole-genome duplication in the subsequent ca. 34.55 million years of evolutionary history of the tung tree lineage. Insertion time analysis revealed that repeat-driven genome expansion might have arisen as a result of long-standing long terminal repeat retrotransposon bursts and lack of efficient DNA deletion mechanisms. The genome harbors 88 resistance genes encoding nucleotide-binding sites; 17 of these genes may be involved in early-infection stage of Fusarium wilt resistance. Further, 651 oil-related genes were identified, 88 of which are predicted to be directly involved in tung oil biosynthesis. Relatively few phosphoenolpyruvate carboxykinase genes, and synergistic effects between transcription factors and oil biosynthesis-related genes might contribute to the high oil content of tung seed. The tung tree genome constitutes a valuable resource for understanding genome evolution, as well as for molecular breeding and genetic improvements for oil production.