A chromosome-level reference genome assembly of the Reeve's moray eel (Gymnothorax reevesii)

Genomics comparisons provide new insights into the evolution of karyotype and body patterns in Anguilliformes species

Anguilliformes species not only possess distinctive appearance (such as body elongation and absence of pectoral and/or pelvic fins), but also display diversity in chromosome number, supporting them as a suitable model for studying karyotype evolution and related molecular mechanisms of evolutionary body patterns. However, the ancestral chromosomes and evolutionary chromosomal reorganization in various eels have not been reported yet. The most regulatory or related genes of their distinctive appearance are still unknown. Here, we predicted an eel-based ancestral chromosome karyotype for the first time, and revealed multiple chromosomal fusion and fission events that reduced the ancestral chromosome number from haploid n = 21 to the commonly extant n = 19 within the Anguilla lineage. Moreover, we carried out a genome-wide comparison of two significant gene families including homeobox (Hox) and T-box (tbx), revealing genomic loss of some Hox genes (such as HoxB9β and HoxD13α) and variation of certain tbx gene (i.e., tbx5) may be responsible for the evolutionary development of pectoral fins. Interestingly, loss of certain secretory calcium-binding phosphoprotein (SCPP) genes was identified in various eel genomes, which possibly contribute to the common reduction of scales. Overall, our current findings provide new insights into evolutionary karyotype and body pattern evolution across diverse Anguilliformes species.

A complete telomere-to-telomere chromosome-level genome assembly of X-ray tetra (Pristella maxillaris)

X-ray tetra (Pristella maxillaris) originates from the lower Amazon basin in South America. It is renowned for its strikingly transparent body, which has drawn significant interests in biomedical research and the world ornamental fish industry. Nevertheless, genomic resources for this interesting fish species remains scarce, hindering exploration of the molecular basis behind its unique transparency. To address this gap, we constructed the first complete telomere-to-telomere (T2T) chromosome-scale genome assembly of the X-ray tetra by integration of PacBio HiFi, ONT ultra-long, and Hi-C sequencing technologies. This haplotypic assembly spans approximately 1.1 Gb, with a contig N50 of 42.8 Mb. It is anchored onto 25 chromosomes, highlighting a complete set of 50 telomeres and 25 centromeres. We predicted 514.3 Mb of repetitive sequences and annotated 28,456 protein-coding genes in the assembled genome. Subsequent BUSCO analysis discovered high genome completeness (98.0%). This high-quality T2T genome assembly provides a valuable genetic resource for investigating the molecular mechanisms underlying transparency, and supporting in-depth studies on functional genomics, genetic diversity, and selective breeding for this economically important species.

Chromosome-level genome assembly and annotation of pawak croaker (Pennahia pawak)

The diversity of fish coloration is a fascinating scientific question. The pawak croaker (Pennahia pawak) is distinguished by its silver-white colour, setting it apart from other Sciaenidae species. However, the genomic information of this genus remains largely unexplored. This study aims to advance our understanding by assembling and annotating the genome of P. pawak at the chromosome level using multi-platform sequencing data. The assembled genome size of P. pawak is 613.02 Mb, closely matching the estimated size of 570.32 Mb from 21-mer analysis. The assembly features a scaffold N50 of 27.09 Mb, with 24 chromosomes successfully constructed using Hi-C technology, achieving a mounting rate of 99.31%. Genome annotation revealed that 26.20% of the genome consists of repetitive sequences and identified 26,361 protein-coding genes, of which 25,885 have functional annotations. This chromosome-level genome assembly of P. pawak provides valuable resources for comparative genomic studies within the Sciaenidae family and offers foundational data for researchers to understand its unique silver-white pigmentation.

Chromosome-level genome assemblies of vulnerable male and female elongate loach (Leptobotia elongata)

Endemic to the upper and middle reaches of the Yangtze River in China, elongate loach (Leptobotia elongata) has become a vulnerable species mainly due to overfishing and habitat destruction. Thus far, no genome data of this species are reported. As a result, lacking of such genomic information has restricted practical conservation and utilization of this economic fish. Here, we constructed chromosome-level genome assemblies for both male and female elongate loach by integration of MGI, PacBio HiFi and Hi-C sequencing technologies. Two primary genome assemblies (586-Mb and 589-Mb) were obtained for female and male fishes, respectively. Indeed, 98.22% and 98.61% of the contig sequences were anchored onto 25 chromosomes, with identification of 26.22% and 25.92% repeat contents in both assembled genomes. Meanwhile, a total of 25,215 and 25,253 protein-coding genes were annotated, of which 97.41% and 98.8% could be predicted with functions. Taken together, our genome data presented here provide a valuable genomic resource for in-depth evolutionary and functional research, as well as molecular breeding and conservation of this economic fish species.

Chromosome-level genome assembly and annotation of eel goby (Odontamblyopus rebecca)

The eel gobies fascinate researchers with many important features, including its unique body structure, benthic lifestyle, and degenerated eyes. However, genome assembly and exploration of the unique genomic composition of the eel gobies are still in their infancy. This has severely limited research progress on gobies. In this study, multi-platform sequencing data were generated and used to assemble and annotate the genome of O. rebecca at the chromosome-level. The assembled genome size of O. rebecca is 918.57 Mbp, which is similar to the estimated genome size (903.03 Mbp) using 17-mer. The scaffold N50 is 41.67 Mbp, and 23 chromosomes were assembled using Hi-C technology with a mounting rate of 99.96%. Genome annotation indicates that 53.29% of the genome is repetitive sequences, and 22,999 protein-coding genes are predicted, of which 21,855 have functional annotations. The chromosome-level genome of O. rebecca will not only provide important genomic resources for comparative genomic studies of gobies, but also expand our knowledge of the genetic origin of their unique features fascinating researchers for decades.