Qi Zhou

Sex chromosome evolution is among the most dynamic genomic innovations in vertebrates, yet why some lineages evolve XY while others evolve ZW remains unclear. Using chromosome-level genomes from 19 geckos, we found that gecko sex chromosomes originated independently from 16 ancestral chromosomes. Their origins are nonrandom in both time and direction. Five of 11 datable origins coincide near the Middle Miocene Climatic Transition (~10 million years ago). Ancestral gene content is associated with the direction of evolution, with testis-enriched regions tending to evolve into ZW and testis-depleted regions into XY, a pattern observed across multiple amniote sex chromosome origins. Geckos with genetic sex determination repeatedly evolve partial dosage balance through up-regulation in the heterogametic sex. Sex chromosome evolution thus follows constraints from ancestral genomic predisposition and environmental context.

The widespread and regulated production of infertile parasperm assisting fertilization of eusperm provides a compelling model for elucidating the mechanisms of cellular innovation and altruism. Here we identify two specific parasperm lineages in Drosophila pseudoobscura that are segregated in development from the eusperm lineage by their single-cell transcriptomes. Most X-linked genes, except for species-specific new genes, show testis-specific repressive epigenetic modifications and become downregulated upon meiotic entry, supporting meiotic X chromosome inactivation. Between sperm classes, nearly half of the known ‘meiotic arrest’ genes and their downstream targets are differentially transcribed, with over 200 genes displaying a gradient of transcription levels correlated with that of tail lengths. New genes are overrepresented throughout the hierarchical regulatory network of sperm divergence and over 60% of them exhibit a new cell-level expression compared to their parental copies. These results together indicate that new genes play a prominent role in the emergence of low-cost parasperm that shield the eusperm until fertilization.

Natural selection has sculpted tetrapod limbs and digits into a tremendous morphological diversity, but the underlying developmental mechanism remains unclear. This leads to an enduring debate concerning the identity of the three digits of bird wing. Here we use comparative digit transcriptomics across six tetrapod species to examine gene expression signatures of digit evolution. Here we show that the avian wing digits are homologous to reptilian forelimb digits 1,3,4. We find that birds uniquely increase fore-hindlimb transcriptome divergence during development, relaxing constraints and facilitating wing and foot digit specialization. We identify many limb- or digit- identity associated genes that have a biased expression between fore- or hind-limb, or toward specific digits. There are more limb and digit biased genes among the avian lineages than in other tetrapod lineages. Our work reveals ancient regulatory networks that maintain limb and digit molecular identity through persistent differential expression. We also show that this conserved network does not preclude independent digit evolution, especially when developmental constraints are reduced.

The functional integrity of a mammalian chromosome is shaped by its long-term, co-evolution with species-specific nuclear environment. How chromosomes co-adapt with their native environment to define 3D architecture and transcriptional activity remain poorly understood, largely due to a lack of experimental models capable of systematically dissecting this co-evolution relationship. Here, we report a cross-species chromosome substitution (CROSS) method, a robust genomic engineering method that enables the stable, scarless replacement of host chromosomes with evolutionarily divergent orthologs. By integrating microcell-mediated chromosome transfer with CRISPR/Cas9, we imported the intact 158-Mb rat X chromosome into mouse embryonic stem cells, and subsequently achieved targeted substitution of its endogenous mouse counterpart, maintaining stability and integrity. Using this model, we found that rat-specific LINE1 and RatSatRep2 repeats failed to adequately recruit host SETDB1 in mouse cells, leading to localized erosion of H3K9me3 heterochromatin. This further triggered 3D structural remodeling, characterized by the de novo formation of topologically associating domain (TAD) boundaries that aberrantly activated adjacent genes—including Rhox5 , the master regulator of the Rhox cluster—impairing cellular differentiation. Our method provides a powerful chromosome engineering platform for dissecting how genomic sequences and epigenetic mechanisms cooperate in regulating chromosome architecture and function, and for evaluating the structural and functional fidelity of large-scale synthetic or heterologous DNA across species.

The amniote digits have undergone recurrent modifications with the diversified molecular mechanisms more studied among mammals than reptiles. Here we focus on the emu wings and ostrich feet, both of which experienced species specific digit changes driven respectively by secondary flight loss and adaptation to running. By comparing their digit transcriptomes to those of chicken and alligator, we identified different gene networks in skeleton/muscle development responsible for the degenerated digits in archosaur ancestor and emu, but those in epidermal development for the load-bearing digit of ostrich. These results provide new clues for developmental programs of different cell types between different digits, on which natural selection can convergently operate.

Chromosomes of mammals and reptiles have diverged extensively in sequence and three-dimensional (3D) nuclear organization since their last common amniote ancestor. The fine-scale evolutionary patterns and mechanisms underlying this divergence and the relationship between chromosome rearrangements and 3D genome architecture remain unclear. Here we reconstruct ancestral linkage groups (ALGs) of the amniote ancestor and its descendent nodes using chromosome-level assemblies from 36 species, including two newly generated genomes. We infer that most microchromosomes originated in the jawed vertebrate ancestor were retained as distinct ALGs across all ancestral amniote nodes. They were mainly involved in fusions with each other in reptiles, but underwent frequent translocations with the larger ALGs (macro-ALGs) during the mammalian evolution. Despite extensive rearrangements, sequences derived from micro-ALGs consistently occupy nuclear interior positions in both reptiles and mammals, likely enriched near nuclear speckles, supported by published lamina-positioning data and our lamin-B1 ChIP-seq data. In contrast, mammals independently evolved interchromosomal interactions associated with lineage specific transposable elements, reflecting local innovations in nuclear architecture. Together, these results reveal contrasting rearrangement regimes in mammals and reptiles, yet a conserved higher-order nuclear organization linked to ancient micro- versus macro-ALG chromatin segregation, suggesting deep constraints on chromosome evolution.

A few species have evolved multiple sex chromosome systems with more than two Xs or Ys due to sex chromosome-autosome translocations. Among vertebrates, frogs (Anura) have the highest known number of such neo-sex chromosome systems, making them interesting for studying how such systems evolve. In this work, we investigated two Leptodactylus species, L. pentadactylus (LPE) and L. paraensis (LPA), with large ring multivalents in male meiosis, using genomic and cytogenetic investigation of repetitive DNA sequences, including satellite DNAs (satDNAs), and transposable elements (TEs). SatDNA mapping identify individual chromosomes in the LPE ring, and morphologies suggest that all chromosomes are shared with the LPA ring although a common ring origin is not firmly supported. In situ mapping suggests recent satDNA accumulation in subtelomeric regions since the split from the outgroups, likely unrelated to the translocations that created sex-linkage, which probably involved breaks in the pericentromeric regions.