Biology subjects

Rincon, G.

Publications and source records attributed to Rincon, G..

3 recordsLinked to original sources

bioRxiv2024

Phylogeography of the electric rays of the family Narcinidae (Gill, 1862): systematic review and evidence of the dispersal routes to America.

The electric rays belonging family Narcinidae are a cosmopolitan group, which has come under increasing scrutiny in relation to the taxonomic composition of the family and its phylogenetic position within the order Torpediniformes. Phylogeographic inferences can provide important insights into the present-day distribution of the narcinid species, as well as the systematics of the group. In this context, the present study evaluates the evolutionary and biogeographic history of the family Narcinidae, inferring distribution patterns and the molecular systematics of these organisms based on the DNA barcode. The results of the analysis indicate that the electric rays originated in the Central Indo-Pacific realm, with all other dispersal events beginning from this region. Two different dispersal routes were observed for the American narcinids. The first route was from the Central Indo-Pacific realm to the Pacific Ocean and then the Caribbean Sea, prior to the closure of the Isthmus of Panama. The second route start on Central Indo-Pacific realm passed South Africa continent before crossing the Atlantic. The principal torpediniform lineages diversified between the end of the Cretaceous and the early Paleocene, with the present-day narcinid taxa arising and diversifying between 25 and 20 Mya. The present study confirms the lack of monophyly in the Narcinidae, validates the genus Narcinops, and restricts the occurrence of the genus Narcine to the coastal environments of the Americas, which emphasizes the need for the review and revalidation of the synonym Syrraxis for the narcinids of the Central/Western Indo-Pacific realm. This study also describes additional lineages for Narcine entemedor and Narcine maculata and validates the occurrence of three species (Narcinesp., Narcine brasiliensis, and Narcine bancroftii) in the Atlantic Ocean, based on the published data, and emphasizes the need for a definitive description of Narcine sp.

evolutionary biology↗

bioRxiv2022

Functional genomics of cattle through integration of multi-omics data

Functional annotation of the bovine genome was performed by characterizing the spectrum of RNA transcription using a multi-omics approach, combining long- and short-read transcript sequencing and orthogonal data to identify promoters and enhancers and to determine boundaries of open chromatin. A total number of 171,985 unique transcripts (50% protein-coding) representing 35,150 unique genes (64% protein-coding) were identified across tissues. Among them, 159,033 transcripts (92% of the total) were structurally validated by independent datasets such as PacBio Iso-seq, ONT-seq, de novo assembled transcripts from RNA-seq, or Ensembl and NCBI gene sets. In addition, all transcripts were supported by extensive independent data from different technologies such as WTTS-seq, RAMPAGE, ChIP-seq, and ATAC-seq. A large proportion of identified transcripts (69%) were novel, of which 87% were produced by known genes and 13% by novel genes. A median of two 5 untranslated regions was detected per gene, an increase from Ensembl and NCBI annotations (single). Around 50% of protein-coding genes in each tissue were bifunctional and transcribed both coding and noncoding isoforms. Furthermore, we identified 3,744 genes that functioned as non-coding genes in fetal tissues, but as protein coding genes in adult tissues. Our new bovine genome annotation extended more than 11,000 known gene borders compared to Ensembl or NCBI annotations. The resulting bovine transcriptome was integrated with publicly available QTL data to study tissue-tissue interconnection involved in different traits and construct the first bovine trait similarity network. These validated results show significant improvement over current bovine genome annotations.

bioinformatics↗

bioRxiv2019

Revisiting the evolution and taxonomy of Clostridia, a phylogenomic update

Clostridium is a large genus of obligate anaerobes belonging to the Firmicutes phylum of bacteria, most of which have a Gram-positive cell wall structure. The genus includes significant human and animal pathogens, causative of potentially deadly diseases such as tetanus and botulism. Despite their relevance and many studies suggesting that they are not a monophyletic group, the taxonomy of the group has largely been neglected. Currently, species belonging to the genus are placed in the unnatural order defined as Clostridiales, which includes the class Clostridia. Here we used genomic data from 779 strains to study the taxonomy and evolution of the group. This analysis allowed us to; (i) confirm that the group is composed of more than one genus (ii), detect major differences between pathogens classified as a single species within the group of authentic Clostridium spp. (sensu stricto), identify inconsistencies between taxonomy and toxin evolution that reflect on the pervasive misclassification of strains and, (iv) identify differential traits within central metabolism of members of what has been defined earlier and confirmed by us as cluster I. Our analysis shows that the current taxonomic classification of Clostridium species hinders the prediction of functions and traits, suggests a new classification for this fascinating class of bacteria and highlights the importance of phylogenomics for taxonomic studies.

microbiology↗