Biology subjects

Mansour, T. A.

Publications and source records attributed to Mansour, T. A..

3 recordsLinked to original sources

bioRxiv2024

EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE DURING THE EMERGENCE OF DIGITS AND GENITALS

The transition from fins to limbs has been a rich source of discussion for more than a century. One open and important issue is understanding how the mechanisms that pattern digits arose during vertebrate evolution. In this context, the analysis of Hox gene expression and functions to infer evolutionary scenarios has been a productive approach to explain the changes in organ formation, particularly in limbs. In tetrapods, the transcription of Hoxd genes in developing digits depends on a well-characterized set of enhancers forming a large regulatory landscape1,2. This control system has a syntenic counterpart in zebrafish, even though they lack bona fide digits, suggestive of deep homology3 between distal fin and limb developmental mechanisms. We tested the global function of this landscape to assess ancestry and source of limb and fin variation. In contrast to results in mice, we show here that the deletion of the homologous control region in zebrafish has a limited effect on the transcription of hoxd genes during fin development. However, it fully abrogates hoxd expression within the developing cloaca, an ancestral structure related to the mammalian urogenital sinus. We show that similar to the limb, Hoxd gene function in the urogenital sinus of the mouse also depends on enhancers located in this same genomic domain. Thus, we conclude that the current regulation underlying Hoxd gene expression in distal limbs was co-opted in tetrapods from a preexisting cloacal program. The orthologous chromatin domain in fishes may illustrate a rudimentary or partial step in this evolutionary co-option.

evolutionary biology↗

bioRxiv2023

Multiple embryonic sources converge to form the pectoral girdle skeleton in zebrafish

The morphological transformation of the pectoral/shoulder girdle is fundamental to the water-to-land transition in vertebrate evolution. Although previous studies have resolved the embryonic origins of the tetrapod shoulder girdle, those of the fish pectoral girdle remain uncharacterized, creating a gap in the understanding of girdle transformation mechanisms from fish to modern tetrapods. Here, we identified the embryonic origins of the pectoral girdle of zebrafish (Danio rerio), including the cleithrum as an ancestral pectoral girdle element lost in extant tetrapods. Our combinatorial approach of photoconversion and genetic cell lineage tracing mapped that cleithrum development combines three adjoining embryonic populations: cranial neural crest cells and lateral plate mesoderm-derivatives (trunk lateral plate mesoderm and cardiopharyngeal mesoderm-associated cells). The topographical position of the cleithrum at the head/trunk interface is a shared characteristic among cleithrum-bearing fish, thus its multiple embryonic origins are likely a conserved feature. Moreover, a comparison of the pectoral girdle progenitors between aquatic fish and extant amniotes suggests that cleithrum loss is associated with the disappearance of its unique developmental environment by the insertion of the neck lateral plate mesoderm into the head/trunk interface. Overall, our study establishes an embryological framework for pectoral/shoulder girdle formation and their evolutionary trajectories from their origin in water to diversification on land.

developmental biology↗

bioRxiv2020

MQF and buffered MQF: Quotient filters for efficient storage of k-mers with their counts and metadata

BackgroundSpecialized data structures are required for online algorithms to efficiently handle large sequencing datasets. The counting quotient filter (CQF), a compact hashtable, can efficiently store k-mers with a skewed distribution. ResultHere, we present the mixed-counters quotient filter (MQF) as a new variant of the CQF with novel counting and labeling systems. The new counting system adapts to a wider range of data distributions for increased space efficiency and is faster than the CQF for insertions and queries in most of the tested scenarios. A buffered version of the MQF can offload storage to disk, trading speed of insertions and queries for a significant memory reduction. The labeling system provides a flexible framework for assigning labels to member items while maintaining good data locality and a concise memory representation. These labels serve as a minimal perfect hash function but are ~10 fold faster than BBhash, with no need to re-analyze the original data for further insertions or deletions. ConclusionThe MQF is a flexible and efficient data structure that extends our ability to work with high throughput sequencing data.

bioinformatics↗