Plant genome size varies hundreds of times over, and often this has nothing to do with gene number and everything to do with the accumulation of repetitive sequences. Mobile elements (transposons) can drive explosive genome expansion, but how this affects gene regulation and the emergence of new traits remains unclear, especially in non-model species. The Sapotaceae family offers a convenient system: its species are evolutionarily close yet differ sharply in genome size and repeat content. Studying the sapodilla with its gigantic genome lets us see the consequences of recent transposon activity.
DNA from the leaves of a tree growing on the IISER Bhopal campus was sequenced on Oxford Nanopore (long reads) and Illumina (short reads) platforms, and a Hi-C library was also prepared to determine the spatial organization of the chromosomes. Assembly was done with HiFiasm and YAHS, and quality was checked using BUSCO, Merqury and LAI. Repeats were annotated with the EDTA program, and the insertion times of retrotransposons were estimated from the divergence of their long terminal repeats. Cytosine methylation in CpG, CHG and CHH contexts was determined from nanopore signals using Dorado and Modkit. Genomes of four other sapotaceous species and grape were used for comparison.
The sapodilla genome was assembled to telomere-to-telomere (T2T) level, with a size of 1.63 billion base pairs distributed across 13 chromosomes. Repeats accounted for 78.61% of the genome, of which 53.09% were retroelements, with LTR-Gypsy dominating. Insertion times revealed two peaks of activity: Copia around 0.36 million years ago and Gypsy around 0.09 million years ago. Genes with LTR insertions in their introns were expressed slightly lower than control genes. DNA methylation in the sapodilla was higher than in M. longifolia in all contexts, especially in symmetric CpG and CHG. The age dynamics of Gypsy methylation differed: in the sapodilla, CHH methylation increased with element age, pointing to sustained suppression. Among the duplicated genes, 5736 were classified as transposed duplications; they are enriched in flavonoid and phenylpropanoid metabolism pathways.
The work shows that a recent burst of retrotransposons can quickly double genome size without changing gene number, while rearranging the epigenetic landscape. Enhanced methylation of repetitive elements stabilizes the genome, and transposed gene duplications contribute to metabolic diversity. This changes how we think about the way plants generate phenotypic novelty: not only through point mutations, but also through the mobilization of repetitive elements and epigenetic regulation.
As new chromosome-level assemblies of sapotaceous species appear, it will become possible to refine the ancestral karyotype and trace the evolution of each chromosomal fusion. Studying the role of individual transposon families in regulating neighboring genes will become feasible with spatial transcriptomics and epigenome editing. Comparison with other species that have extremely large genomes will help identify general principles of adaptation to genomic obesity.
The results matter for breeding tropical fruit crops, because they link genomic rearrangements to the metabolic pathways responsible for flavor and medicinal properties. Understanding the epigenetic control of transposons could help create varieties with improved traits without transgenesis.
Sequence additional sapotaceous species with different genome sizes to test how universal the explosive expansion model is. Run functional experiments activating or suppressing specific Gypsy and Copia families to assess their influence on the expression of neighboring genes.
It remains an open question why some species accumulate transposons while others efficiently remove them. The mechanisms that set the balance between insertion and removal of mobile elements, along with their epigenetic inheritance, are key unsolved problems in plant genomics.
The sapodilla genome is only 1.6 times larger than the human genome, yet it contains just about 35 thousand genes versus 20 thousand in humans: the difference in size is almost entirely due to repeats, not gene number.
Not published on arXiv. Here are its page, the PDF and the formalization: you can check it yourself, not only read our account.