A hidden layer of the silkworm genome has now been mapped in unprecedented detail, revealing a surprisingly stable but evolutionarily active landscape of repetitive DNA. In a comprehensive study of the domesticated silkworm, Bombyx mori, researchers analyzed satellite DNA across seven strains and compared their findings with the species’ reference genome assembly. The investigation identified 35 satellite DNA families, all of which were detected in every strain examined. Twenty-nine of these families were also found in Bombyx mandarina, the wild ancestor of the domesticated silkworm, suggesting that much of the satellite DNA repertoire predates domestication and has remained remarkably conserved through the species’ evolutionary history.
Satellite DNA, or satDNA, consists of highly repetitive sequences arranged in tandem arrays or distributed across chromosomes. For decades, these sequences were often dismissed as genomic “junk” because they do not typically encode proteins. Modern genomics, however, has shown that satDNA can influence chromosome structure, centromere function, genome stability, gene regulation and the behavior of sex chromosomes. In B. mori, a species of major economic importance in silk production and a widely used model for genetics, the satDNA fraction had remained poorly characterized. The new analysis provides the first broad survey of this repetitive component across multiple domesticated strains, offering a clearer view of how repetitive sequences contribute to genome architecture.
The researchers found that satellite DNA makes up only a small fraction of the B. mori genome. Its average abundance was approximately 0.85 percent in males and 0.91 percent in females, with variation among strains. Although modest in overall quantity, this fraction displayed several distinctive molecular features. The satellite sequences were enriched in adenine and thymine, the two DNA bases connected by only two hydrogen bonds, which generally makes A+T-rich DNA less thermally stable than regions rich in guanine and cytosine. The satDNA families also showed considerable variation in monomer length, meaning that the basic repeated units differed substantially in size. Such variability can arise through replication errors, unequal crossing-over, mutation and the gradual rearrangement of repetitive arrays.
Unlike the tightly clustered satellite arrays frequently associated with centromeres and other specialized chromosomal regions, most of the B. mori satDNAs appeared to have a predominantly dispersed organization. Instead of being concentrated into a few large blocks, copies were distributed across multiple genomic locations. This pattern suggests that the silkworm satellitome—the complete collection of satellite DNA families in its genome—has been shaped by mechanisms that move or redistribute repetitive sequences. Dispersed satDNA can originate through the propagation of short repeated fragments, the insertion of mobile elements, chromosome rearrangements or the expansion of sequences at multiple independent sites. Its distribution may also affect local chromatin structure, potentially influencing how nearby regions are packaged and regulated.
Sequence divergence patterns offered clues about the age of these repetitive families. By comparing related copies within and among satDNA families, the scientists generated divergence landscapes that revealed predominantly ancient amplification events. In other words, much of the satellite DNA appears to have expanded deep in the evolutionary past rather than through continuous, recent bursts. Only a limited number of families showed evidence of more recent homogenization, a process in which repeated copies become increasingly similar through mechanisms such as unequal recombination or gene conversion. The coexistence of ancient divergence and occasional homogenization indicates that the silkworm satellitome is neither static nor rapidly changing, but instead experiences intermittent episodes of expansion and sequence renewal.
The study also found surprisingly little differentiation among the seven B. mori strains. Despite their distinct breeding histories and geographic backgrounds, the strains shared the same 35 satellite DNA families and displayed generally low levels of strain-specific divergence. This genomic stability contrasts with the rapid changes often observed in repetitive DNA, which can expand or contract over relatively short evolutionary timescales. The result suggests that domestication and strain diversification have not dramatically reshaped the core satellitome of B. mori. Because the same families are largely retained across strains, they may be subject to structural constraints or may perform roles that favor their long-term maintenance.
The most striking exception involved the female-specific W chromosome. In moths and butterflies, sex determination commonly follows a ZW system, in which females carry Z and W chromosomes while males carry two Z chromosomes. The researchers discovered that the W chromosome acts as a major hotspot for satellite DNA accumulation. Several satDNA families were amplified specifically in females, and their copies on the W chromosome displayed greater sequence homogeneity than satellite sequences elsewhere in the genome. This combination of enrichment and similarity may reflect recent or ongoing amplification on the W chromosome, as well as reduced recombination. Because the W chromosome is present only in females and often contains large repetitive regions, it can provide a distinct evolutionary environment in which repetitive sequences accumulate and evolve differently from those on autosomes.
The Z chromosome, by contrast, did not show a dramatic excess of satellite DNA. Its overall satDNA content was comparable to that of the autosomes, although a few families appeared to be slightly amplified on the Z. This contrasting pattern between W and Z chromosomes highlights how sex-specific inheritance can shape repetitive DNA evolution. The W chromosome’s restricted transmission, limited recombination and potentially unusual chromatin environment may promote the retention of repetitive sequences. Researchers suggest that W-associated satDNAs could contribute to chromosome condensation, structural organization or the regulation of genes located nearby. Their female-specific amplification may also provide clues about how the W chromosome has evolved and how its repetitive landscape interacts with sex determination and reproductive biology.
One of the study’s most important findings was that some silkworm satellite DNA families appear to have originated from transposable elements. Transposable elements are mobile genetic sequences capable of changing their position or generating new copies within a genome. They are major drivers of genome evolution and can create mutations, rearrangements and novel regulatory regions. Four satDNA families linked to transposable elements accounted for approximately 63 percent of the total satellite DNA content detected in B. mori. This result supports the idea that satellite DNA can emerge when fragments of transposable elements become organized into tandem repeats. Once established, these fragments may undergo amplification, mutation and homogenization, eventually becoming recognizable as independent satellite DNA families. The finding also illustrates that satellite DNA and transposable elements are not separate genomic worlds, but interconnected components of genome evolution.
The researchers describe the B. mori satellitome as a product of long-term interaction between repetitive DNA, mobile elements and chromosome-specific evolutionary forces. Its low abundance, dispersed distribution and broad stability across domesticated strains distinguish it from the massive, rapidly changing satellite arrays found in some other organisms. At the same time, the concentration of particular families on the W chromosome and the extensive contribution of transposable-element-derived sequences reveal that the silkworm genome remains structurally dynamic beneath its apparent stability. Future work will need to determine whether these satDNAs influence gene expression, chromatin accessibility, chromosome pairing or the organization of the W chromosome. By establishing a genomic baseline for satellite DNA in one of the world’s most important insects, the study opens a path toward understanding how repetitive sequences shape genome function, sex chromosome evolution and the biological diversity of Lepidoptera.
Subject of Research: Satellite DNA and genome organization in the domesticated silkworm, Bombyx mori
Article Title: Comprehensive analysis of the Bombyx mori satellitome reveals evolutionary stability, dispersed chromosomal organization, and transposable element-related origins
Article References: Rico-Porras, J.M., Mora, P., Palomeque, T. et al. Comprehensive analysis of the Bombyx mori satellitome reveals evolutionary stability, dispersed chromosomal organization, and transposable element-related origins. Heredity (2026). https://doi.org/10.1038/s41437-026-00874-1
Image Credits: AI Generated
DOI: 10.1038/s41437-026-00874-1
Keywords: Bombyx mori, silkworm, satellite DNA, satellitome, transposable elements, W chromosome, Z chromosome, sex chromosome evolution, repetitive DNA, genome architecture, Lepidoptera, genomics
Tags: chromosomal organization of satellite DNAcomparative genomics of Bombyx speciesgenome architecture and evolution of Bombyx moriimplications for silk production androle of satDNA in chromosome structure and stabilitysatellite DNA evolution in Bombyx morisatellite DNA families in Bombyx mori and wild ancestorssilkworm genomestability of repetitive DNA in domesticated insectstransposon origins in silkworm genometransposon-derived repetitive elements in silkworm
