Biology subjects

Pinhal, D.

Publications and source records attributed to Pinhal, D..

3 recordsLinked to original sources

bioRxiv2026

Environmental DNA/RNA metabarcoding in estuaries of Sao Paulo, Brazil, reveals fish diversity and the presence of invasive species

Tropical estuaries within the Brazilian Atlantic Forest are biodiversity hotspots facing escalating anthropogenic pressures, yet their ichthyofaunal assemblages remain incompletely documented. We evaluated the combined use of environmental DNA (eDNA) and environmental RNA (eRNA) metabarcoding to characterize fish communities in two estuaries with contrasting levels of urbanization (the Juqueriquere and Escuro rivers) on the northern coast of Sao Paulo, Brazil. Targeting the mitochondrial 12S rRNA (MiFish) fragment, we detected a diverse vertebrate assemblage totaling 93 species. eDNA identified 32 fish species across both systems, while eRNA detected 22 species in the preserved estuary, providing robust signals of metabolically active assemblages. The less impacted estuary exhibited significantly higher diversity indices and a more heterogeneous taxonomic composition. In contrast, the urbanized system displayed clear molecular signatures of anthropogenic influence, including the presence of invasive species (Oreochromis niloticus, O. aureus, and Clarias gariepinus) and domestic animals. This study constitutes the first application of fish eRNA metabarcoding in Brazil and demonstrates that integrating eDNA and eRNA refines ecological interpretation by coupling biodiversity detection with improved inference about contemporary community composition. Our findings highlight the potential of multi-molecule metabarcoding for routine, non-invasive biodiversity assessment in megadiverse and conservation-priority coastal ecosystems.

ecology↗

bioRxiv2021

A switch in the development: microRNA arm usage screening in zebrafish suggests an important role of arm switching events in ontogenesis

In metazoan, regulatory molecules tightly control gene expression. Among them, microRNAs (miRNAs) are key regulators of several important features, like cell proliferation, differentiation, and homeostasis. During miRNA biogenesis, the canonical strand that loads onto RISC can be switched, in a process called "arm switching." Due to the miRNA-to-target pairing peculiarities, switching events can lead to changes on the gene-targeted repertoire, promoting the modulation of a distinct set of biological routes. To understand how these events affect cell regulation, we conducted an extensive and detailed in silico analysis of RNA-seq datasets from several tissues and key developmental stages of zebrafish. We identified interesting patterns of miRNA arm switching occurrence, mainly associated with the control of protein coding genes during embryonic development. Additionally, our data show that miRNA isoforms (isomiRs) play an important role in differential arm usage. Our findings provide new insights on how such events emerge and coordinate gene expression regulation, opening perspectives for novel investigations in the area.

bioinformatics↗

bioRxiv2021

Genome assembly and annotation of the tambaqui (Colossoma macropomum): an emblematic fish of the Amazon River basin

Colossoma macropomum known as "tambaqui" is the largest Characiformes fish in the Amazon River Basin and a leading species in Brazilian aquaculture and fisheries. Good quality meat and great adaptability to culture systems are some of its remarkable farming features. To support studies into the genetics and genomics of the tambaqui, we have produced the first high-quality genome for the species. We combined Illumina and PacBio sequencing technologies to generate a reference genome, assembled with 39X coverage of long reads and polished to a QV=36 with 130X coverage of short reads. The genome was assembled into 1,269 scaffolds to a total of 1,221,847,006 bases, with a scaffold N50 size of 40 Mb where 93% of all assembled bases were placed in the largest 54 scaffolds that corresponds to the diploid karyotype of the tambaqui. Furthermore, the NCBI Annotation Pipeline annotated genes, pseudogenes, and non-coding transcripts using the RefSeq database as evidence, guaranteeing a high-quality annotation. A Genome Data Viewer for the tambaqui was produced which benefits any groups interested in exploring unique genomic features of the species. The availability of a highly accurate genome assembly for tambaqui provides the foundation for novel insights about ecological and evolutionary facets and is a helpful resource for aquaculture purposes.

genomics↗