Alfieri, J. | Search bioRxiv

bioRxiv2026

Dismantling Chromosomal Stasis Across the Eukaryotic Tree of Life

Chromosome number shapes genome organization, recombination, and speciation, yet how fast it evolves across the tree of life has never been measured. We analyzed 63,682 karyotypes across 55 eukaryotic clades and found that dysploidy rates vary by 844-fold, from approximately 0.0008 to 0.7 events per million years. This variation does not follow kingdom boundaries or deep phylogeny; intraclade variance exceeds interclade differences by more than an order of magnitude. Even birds, the textbook example of chromosomal stasis, exceed the global median rate once microchromosome dynamics are resolved. Contrasting the stasis of Odonata with the volatility of Orchidaceae reveals that life history and population structure, rather than deep phylogenetic constraints, govern the tempo of karyotypic change.

evolutionary biology↗

bioRxiv2024

Genome assembly of the southern pine beetle (Dendroctonus frontalis Zimmerman) reveal the origins of gene content reduction in Dendroctonus

Dendroctonus frontalis, also known as southern pine beetle (SPB), represents the most damaging forest pest in the southeastern United States. Strategies to predict, monitor and suppress SPB outbreaks have had limited success. Genomic data are critical to inform on pest biology and to identify molecular targets to develop improved management approaches. Here, we produced a chromosome-level genome assembly of SPB using long-read sequencing data. Synteny analyses confirmed the conservation of the core coleopteran Stevens elements and validated the bona fide SPB X chromosome. Transcriptomic data were used to obtain 39,588 transcripts corresponding to 13,354 putative protein-coding loci. Comparative analyses of gene content across 14 beetle and 3 other insects revealed several losses of conserved genes in the Dendroctonus clade and gene gains in SPB and Dendroctonus that were enriched for loci encoding membrane proteins and extracellular matrix proteins. While lineage-specific gene losses contributed to the gene content reduction observed in Dendroctonus, we also showed that widespread misannotation of transposable elements represents a major cause of the apparent gene expansion in several non-Dendroctonus species. Our findings uncovered distinctive features of the SPB gene complement and disentangled the role of biological and annotation-related factors contributing to gene content variation across beetles.

genomics↗