Biology subjects

Ranz, J. M.

Publications and source records attributed to Ranz, J. M..

4 recordsLinked to original sources

bioRxiv2025

Dichotomous transcriptome divergence at the cell-type level between the Drosophila male and female germlines

Gene expression evolution in reproductive organs plays a central role in species divergence, yet cell-type-resolved patterns in invertebrates remain poorly understood. We used single-nucleus RNA-sequencing to profile testis and ovary transcriptomes from the sibling species Drosophila melanogaster and D. simulans. Despite conserved cellular composition, we observed highly cell-type-specific expression and coexpression network divergence between species. In the testis, mitotic cells were conserved across species, mirroring patterns in mammals, while divergence peaked in late spermatocytes. In the ovary, divergence was less pronounced, peaking in early germline and late-stage follicle cells, and enriched on the X chromosome, consistent with a faster-X effect driven by positive selection. Genes expressed in these cell types exhibited narrower expression breadth, younger phylogenetic age, and elevated rates of protein evolution in both tissues. Our findings reveal contrasting evolutionary regimes in male and female germlines, shaped by adaptive and non-adaptive mechanisms, contingent on cell type and chromosomal context.

evolutionary biology↗

bioRxiv2024

Gene age shapes functional and evolutionary properties of the Drosophila seminal fluid proteome

Seminal fluid proteins (Sfps) are crucial for animal reproductive success, with most Sfps-encoding genes believed to be evolutionarily young and rapidly evolving. By employing estimates of the phylogenetic origin of each Drosophila melanogaster Sfp gene based on genomic resources that include outgroup species to the Drosophila genus, we examined the functional attributes and evolutionary characteristics of Sfp genes relative to their evolutionary age. Contrary to common belief, 62% of Sfp genes existed in the genome of the ancestor to such genus. These ancient genes have broadened their expression profiles, expanded their biological roles, and formed a denser network of interactions with non-Sfp genes. This increased pleiotropy has imposed constraints on the rate of sequence evolution in ancient Sfp genes compared to younger ones. Within the Sfp interactome, we identified a fast-evolving core sub-network of younger genes with more restricted tissue expression and functions. Our findings uncover a large, previously unrecognized set of ancient Sfp genes with distinct genomic, functional, and evolutionary characteristics compared to the younger, more commonly studied Sfp genes.

evolutionary biology↗

bioRxiv2020

Genome-Wide Architecture of Adaptation in Experimentally Evolved Drosophila

The molecular basis of adaptation remains elusive even with the current ease of sequencing the genome and transcriptome. We used experimentally evolved populations of Drosophila in conjunction with statistical learning tools to explore interactions between the genome, the transcriptome, and phenotypes. Our results indicate that transcriptomic measures from adult samples can predict phenotypic characters at many adult ages. Importantly, when comparing the genome and transcriptome in predicting phenotypic characters, we find that the two types of data are comparably useful. When using genome sites as predictors for the expression of the transcriptome, we find that gene expression is influenced by genomic regions across all large chromosome arms. Conversely, we found many genomic regions influencing the expression of numerous genes, which is consistent with widespread pleiotropy. Our results also highlight the power of the combination of experimental evolution, next-generation sequencing, and statistical learning tools in exploring the molecular basis of adaptation.

evolutionary biology↗

bioRxiv2020

A De Novo Genome Assembly, Gene Annotation, And Expression Atlas For The Monarch Butterfly Danaus plexippus

The monarch butterfly epitomizes insect biodiversity decline. Understanding the genetic basis of the adaptation of the monarch to a changing environment requires genomic and transcriptomic resources that better reflect its genetic diversity while being informative about gene functionality during life cycle. We report a reference-quality genome assembly from an individual resident at a nonmigratory colony in Mexico, and a new gene annotation and expression atlas for 14,865 genes, including 492 unreported long noncoding RNA (lncRNA) genes, based on RNA-seq data from 14 larval and pupal stages, plus adult morphological sections. Two thirds of the genes show significant expression changes associated with a life stage or section, with lncRNAs being more finely regulated during adulthood than protein-coding genes, and male-biased expression being four times more common than female-biased. The two portions of the heterochromosome Z display distinct patterns of differential expression between the sexes, reflecting that dosage compensation is either absent or incomplete -depending on the sample- in the ancestral but not in the novel portion of the Z. This study represents a major advance in the genomic and transcriptome resources available for D. plexippus while providing the first systematic analysis of its transcriptional program across most of its life cycle.

genomics↗