Pineal progenitors originate from a non-neural territory limited by FGF signalling

BuffExDb: web-based tissue-specific gene expression resource for breeding and conservation programmes in Bubalus bubalis

Amidst the global challenge of extreme poverty, the livestock sector can significantly contribute to global sustainable development goals by enhancing resilience, smallholder productivity, and market participation. The Indian livestock sector is one of the largest in the world with a total livestock population of 535.82 million, ∼10.7% of the world's livestock population. Buffalo (Bubalus bubalis) holds significant importance in India and other Asian countries, notably contributing to their economies by surpassing cattle in milk production and providing various valuable products. The limited availability of genomic and transcriptomic resources for buffaloes hinders the efforts to enhance their traits for increased milk and meat production. To address this gap, this study adopted the state-of-the-art bioinformatics tools to analyse 2429 transcriptomes representing 438 BioSamples from 23 BioProjects obtained from a public domain database, representing 76 different types of tissues and cell types from all major organ systems in buffalo species (river and swamp). The outcome of this exhaustive genomic data led to the development of a relational buffalo expression database based on a three-tier architecture named as BuffExDb (http://46.202.167.198/buffex/). The user-friendliness and flexibilities in retrieval of tissue-specific genes (TSGs) and their functional annotation are the major characteristics of BuffExDb. This is the first of its kind that offers an effortlessly navigable and filterable database, enabling users to examine and visualize the expression levels of each tissue across multiple samples, simultaneously. It also provides the Tau score parameter for the identification of TSGs along with their essential roles in tissue development, maintenance, and function as observed through the enrichment test for gene ontologies. The exhaustive outcome of this work would pave the way for the biological, functional, and evolutionary studies for easy access. This prior information based on tissue-specific mechanisms can be used for future genomic research, especially in association studies in endeavour of enhanced buffalo breeding and conservation programmes. Database URL: http://46.202.167.198/buffex/.

Neural plate progenitors give rise to both anterior and posterior pituitary cells

The pituitary is the master neuroendocrine gland, which regulates body homeostasis. It consists of the anterior pituitary/adenohypophysis harboring hormones producing cells and the posterior pituitary/neurohypophysis, which relays the passage of hormones from the brain to the periphery. It is accepted that the adenohypophysis originates from the oral ectoderm (Rathke's pouch), whereas the neural ectoderm contributes to the neurohypophysis. Single-cell transcriptomics of the zebrafish pituitary showed that cyp26b1-positive astroglial pituicytes of the neurohypophysis and prop1-positive adenohypophyseal progenitors expressed common markers implying lineage relatedness. Genetic tracing identifies that, in contrast to the prevailing dogma, neural plate precursors of zebrafish (her4.3+) and mouse (Sox1+) contribute to both neurohypophyseal and a subset of adenohypophyseal cells. Pituicyte-derived retinoic-acid-degrading enzyme Cyp26b1 fine-tunes differentiation of prop1+ progenitors into hormone-producing cells. These results challenge the notion that adenohypophyseal cells are exclusively derived from non-neural ectoderm and demonstrate that crosstalk between neuro- and adeno-hypophyseal cells affects differentiation of pituitary cells.

OTX Genes in Adult Tissues

OTX homeobox genes have been extensively studied for their role in development, especially in neuroectoderm formation. Recently, their expression has also been reported in adult physiological and pathological tissues, including retina, mammary and pituitary glands, sinonasal mucosa, in several types of cancer, and in response to inflammatory, ischemic, and hypoxic stimuli. Reactivation of OTX genes in adult tissues supports the notion of the evolutionary amplification of functions of genes by varying their temporal expression, with the selection of homeobox genes from the "toolbox" to drive or contribute to different processes at different stages of life. OTX involvement in pathologies points toward these genes as potential diagnostic and/or prognostic markers as well as possible therapeutic targets.

A 3D molecular map of the cavefish neural plate illuminates eye-field organization and its borders in vertebrates

The vertebrate retinas originate from a specific anlage in the anterior neural plate called the eye field. Its identity is conferred by a set of ‘eye transcription factors’, whose combinatorial expression has been overlooked. Here, we use the dimorphic teleost Astyanax mexicanus, which develops proper eyes in the wild type and smaller colobomatous eyes in the blind cavefish embryos, to unravel the molecular anatomy of the eye field and its variations within a species. Using a series of markers (rx3, pax6a, cxcr4b, zic1, lhx2, emx3 and nkx2.1a), we draw a comparative 3D expression map at the end of gastrulation/onset of neurulation, which highlights hyper-regionalization of the eye field into sub-territories of distinct sizes, shapes, cell identities and combinatorial gene expression levels along the three body axes. All these features show significant variations in the cavefish natural mutant. We also discover sub-domains within the prospective telencephalon and characterize cell identities at the frontiers of the eye field. We propose putative fates for some of the characterized eye-field subdivisions, and suggest the existence of a trade-off between some subdivisions in the two Astyanax morphs on a micro-evolutionary scale.