Biology subjects

Raja, K. K. B.

Publications and source records attributed to Raja, K. K. B..

4 recordsLinked to original sources

bioRxiv2024

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. Our data show cell clusters that correspond to all major cell types present in the eye disc ranging from the initiation of the morphogenetic furrow to the differentiation of each photoreceptor cell type as well as early cone cells. We identify dozens of cell type-specific genes whose function in different aspects of eye development have not been reported. These single cell data will greatly aid research groups studying different aspects of early eye development and will facilitate a deeper understanding of the larval eye as a model system.

genomics↗

bioRxiv2022

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. However, the current software for identifying orphan genes is limited in its functionality, database search range, and very complex algorithmically. Thus, researchers studying orphan genes must harvest their data from many disparate sources. ORFanID is a graphical web-based search engine that facilitates the efficient identification of both orphan genes and TRGs at all taxonomic levels, from DNA or amino acid sequences in the NCBI database cluster and other large bioinformatics repositories. The software allows users to identify genes that are unique to any taxonomic rank, from species to domain, using NCBI systematic classifiers. It provides control over NCBI database search parameters, and the results are presented in a spreadsheet as well as a graphical display. The tables in the software are sortable, and results can be filtered using the fuzzy search functionality. The visual presentation can be expanded and collapsed by the taxonomic tree to its various branches. Example results from searches on five species and gene expression data from specific orphan genes are provided in the Supplementary Information. Availability and ImplementationThe ORFanID web application and database can be accessed at http://www.orfangenes.com/. The website provides textual and video instructions on how to use the tool. The Source Code for ORFanID is available at https://github.com/orfanid.

bioinformatics↗

bioRxiv2020

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

Changes in cis-regulatory modules (CRMs) that control developmental gene expression patterns have been implicated in the evolution of animal morphology1-6. However, the genetic mechanisms underlying complex morphological traits remain largely unknown. Here we investigated the molecular mechanisms that induce the pigmentation gene yellow (y) in a complex spot and shade pattern on the abdomen of the quinaria group species Drosophila guttifera. We show that the y expression pattern is controlled by only one CRM, which contains a stripe-inducing CRM at its core. We identified several developmental genes that may collectively interact with the CRM to orchestrate the patterning in the pupal abdomen of D. guttifera. We further show that the core CRM is conserved among D. guttifera and the closely related quinaria group species Drosophila deflecta, which displays a similarly spotted abdominal pigment pattern. Our data suggest that besides direct activation of patterns in distinct spots, abdominal spot patterns in Drosophila species may have evolved through partial repression of an ancestral stripe pattern, leaving isolated spots behind. Abdominal pigment patterns of extant quinaria group species support the partial repression hypothesis and further emphasize the modularity of the D. guttifera pattern.

developmental biology↗

bioRxiv2020

From simplicity to complexity: The gain or loss of spot rows underlies the morphological diversity of three Drosophila species

To understand how novel animal patterning emerged, one needs to ask how the development of color patterns has changed among diverging species. Here we examine three species of fruit flies - Drosophila guttifera (D. guttifera), Drosophila palustris (D. palustris), and Drosophila subpalustris (D. subpalustris) - displaying a varying number of abdominal spot rows that were either gained or lost throughout evolutionary time. Through in situ hybridization, we examine the mRNA expression patterns for the pigmentation genes Dopa decarboxylase (Ddc), tan (t), and yellow (y) during pupal development. Our results show that Ddc, t, and y are co-expressed in identical patterns, each foreshadowing the adult abdominal spots in D. guttifera, D. palustris, and D. subpalustris.

developmental biology↗