Large Yellow Croaker Male Genome Mapped to Advance Aquaculture Breeding
Researchers have produced a telomere-to-telomere (T2T) gap-free male reference genome for the Mindong population of Larimichthys crocea, commonly known as the large yellow croaker. According to the research data, the new assembly totals 747.28 megabases with a contig N50 of 31.79 megabases. This marine fish stands as one of the most economically significant species in East Asia. Until now, scientists only had chromosome-scale genome assemblies for three female (XX) geographical populations—Mindong, the South China Sea, and Daiqu. The absence of a high-quality male (XY) reference genome previously blocked researchers from exploring male-specific sequences and the core molecular mechanisms driving sex determination.
Technical Architecture of the T2T Sex Chromosomes
The genome assembly was built by integrating Oxford Nanopore ultra-long sequencing, PacBio HiFi technology, and Hi-C mapping. Scientists successfully achieved haplotype partitioning of both the X and Y sex chromosomes alongside complete telomere-to-telomere coverage. Telomeric repeats consisting of the sequence TTAGGG appeared at both termini across all 23 autosomes as well as the two sex chromosomes. Furthermore, centromeric regions showed heavy concentrations of six major transposable elements. These elements include DNA MULE, LTR Gypsy, DNA CMC-EnSpm, RC Helitron, LTR ERV1, and DNA TcMar-Tc2, which account for 76.19% to 93.42% of their total copies localized strictly within centromeres. Combined with a 42-base-pair tandem repeat designated as Cen-42, these specific elements form a complex centromeric architecture characterized by higher-order repeats.
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The new male reference genome achieved a BUSCO completeness score of 99.6% paired with a base accuracy (QV) exceeding 59.75, confirming its high technical standard for downstream molecular research.
Protein-Coding Potential and Precision Breeding Applications
Genome annotation identified 29,933 protein-coding genes across the sequence data. This functional catalog supplies a definitive genetic map of the male-specific regions. According to the study findings, this resource provides the necessary foundation for investigating sex-biased traits, tracking sex chromosome evolution, and executing precision molecular breeding programs for Larimichthys crocea.
Frequently Asked Questions
Q: What is the total size of the new large yellow croaker male genome?
A: The assembly measures 747.28 megabases with a contig N50 of 31.79 megabases.
Q: Why was a male reference genome previously unavailable?
A: Prior research efforts produced chromosome-scale assemblies exclusively for female (XX) populations from Mindong, the South China Sea, and Daiqu, leaving male-specific sequences unmapped.
Q: How many protein-coding genes were identified in the annotation?
A: The genome annotation successfully yielded 29,933 protein-coding genes.
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