Correction: ORFanID: A web-based search engine for the discovery and identification of orphan and taxonomically restricted genes.

[This corrects the article DOI: 10.1371/journal.pone.

A single cell RNA sequence atlas of the early Drosophila larval eye.

The Drosophila eye has been an important model to understand principles of differentiation, proliferation, apoptosis and tissue morphogenesis. However, a single cell RNA sequence resource that captures gene expression dynamics from the initiation of differentiation to the specification of different cell types in the larval eye disc is lacking. Here, we report transcriptomic data from 13,000 cells that cover six developmental stages of the larval eye.

ORFanID: A web-based search engine for the discovery and identification of orphan and taxonomically restricted genes.

With the numerous genomes sequenced today, it has been revealed that a noteworthy percentage of genes in a given taxon of organisms in the phylogenetic tree of life do not have orthologous sequences in other taxa. These sequences are commonly referred to as "orphans" or "ORFans" if found as single occurrences in a single species or as "taxonomically restricted genes" (TRGs) when found at higher taxonomic levels. Quantitative and collective studies of these genes are necessary for understanding their biological origins.

The Genetic Mechanisms Underlying the Concerted Expression of the and Genes in Complex Patterns on the Abdomen and Wings of .

How complex morphological patterns form is an intriguing question in developmental biology. However, the mechanisms that generate complex patterns remain largely unknown. Here, we sought to identify the genetic mechanisms that regulate the () gene in a multi-spotted pigmentation pattern on the abdomen and wings of .

The regulation of a pigmentation gene in the formation of complex color patterns in Drosophila abdomens.

Changes in the control of developmental gene expression patterns have been implicated in the evolution of animal morphology. However, the genetic mechanisms underlying complex morphological traits remain largely unknown. Here we investigated the molecular mechanisms that induce the pigmentation gene yellow in a complex color pattern on the abdomen of Drosophila guttifera.

DrosoPhyla: Resources for Drosophilid Phylogeny and Systematics.

The vinegar fly Drosophila melanogaster is a pivotal model for invertebrate development, genetics, physiology, neuroscience, and disease. The whole family Drosophilidae, which contains over 4,400 species, offers a plethora of cases for comparative and evolutionary studies. Despite a long history of phylogenetic inference, many relationships remain unresolved among the genera, subgenera, and species groups in the Drosophilidae.

The modular expression patterns of three pigmentation genes prefigure unique abdominal morphologies seen among three Drosophila species.

To understand how novel animal body colorations emerged, one needs to ask how the development of color patterns differs among closely related species. Here we examine three species of fruit flies - Drosophila guttifera (D. guttifera), D.