Biology subjects

Rodriguez-Terrones, D.

Publications and source records attributed to Rodriguez-Terrones, D..

3 recordsLinked to original sources

bioRxiv2026

Recursive Repeat Extender (RRE): A recursive approach to automatically extend repeat element models

Repetitive elements, including transposable elements (TEs), are integral structural components of eukaryotic genomes; consequently, their identification and classification are crucial to their study. Several approaches have been developed to perform de novo genome-wide repeat identification through pairwise sequence comparisons; however, they often generate truncated repeat models due to their sampling strategies and the substantial fragmentation of many of the older repeat copies in the genome. To improve repeat models generated de novo, several algorithms have been developed that increase model length via the BEEA (BLAST-Extend-Extract-Align) approach, in which genomic instances of each repeat are identified with BLAST, their coordinates are extended, and a refined model is generated by aligning the extended sequences. Nevertheless, these extension algorithms exhibit two key limitations that hinder the reconstruction of highly degenerate and fragmented repeats: the use of BLAST as a search algorithm - which limits their sensitivity in detecting highly diverged sequences - and the use of a single search step, which precludes the reconstruction of extensively fragmented repeat models. In this work, we present a novel approach to extend repeat models, called RRE (Recursive Repeat Extender), which uses profile hidden Markov models (HMMs) to search for repeat elements with high sensitivity and employs a recursive extension strategy that iteratively searches and extends the repeat model, using the extended model from each round as input for the next and continuing until no additional sequence can be incorporated. We apply RRE to repeat libraries generated de novo from five model organisms, and our results show that RRE-generated repeat libraries contain fewer but longer repeat models and can identify a larger proportion of the genomes as repetitive than RepeatModeler2-generated repeat libraries. Notably, RRE can reconstruct highly degenerate repeats such as CR1_Mam, producing a model that achieves similar coverage to the reference Dfam model while extending it by an additional 131 bp that were not captured in the reference model. Overall, RRE enables the automatic improvement of de novo repeat libraries and the reconstruction of highly degenerate and fragmented repeats.

bioinformatics↗

bioRxiv2024

The dynamic genomes of Hydra and the anciently active repeat complement of animal chromosomes

Many animal genomes are characterized by highly conserved chromosomal homologies that pre-date the ancient origin of this clade. Despite such conservation, the evolutionary forces behind the retention, expansion, and contraction of chromosomal elements, and the resulting macro-evolutionary implications, are unknown. Here we present a comprehensive stem-cell resolved genomic and transcriptomic study of the fresh-water cnidarian Hydra, an animal characterized by its high regenerative capacity, the ability to propagate clonally, and an apparent lack of aging. Using single-haplotype telomere-to-telomere genome assemblies of two recently diverged hydra strains, we show how the macro-evolutionary history of chromosomal elements is shaped by both old and recent transposable element (TE) expansions. Unique features of hydra biology allowed us to compare the individual genomes of hydras three stem cell lineages. We show that distinct TE families are active at both transcriptional and genomic levels via non-random insertions in the genomes of each of these lineages. In transcriptomes, over 14,000 transcripts were composed of nearly complete TE sequences, and further classification into families, subfamilies, and individual loci reveals cell type-specific TE expression. The active TEs include elements that differentially contribute to changes in the genome size as well as persistent structural variants around loci associated with cell proliferation. Our study reveals 14 active TE families that primarily act in this role and are predominantly composed of DNA elements. Evolutionary analysis revealed that these families constitute a highly conserved TE core in eukaryotic and metazoan genomes. Our results suggest an ancient role for these core TEs as self-renewing genomic components that persist beyond ancient chromosomal homologies.

genomics↗

bioRxiv2022

Formation of sulfoquinovosyl diacylglycerol by acylation of sulfoquinovosyl glycerol

Sulfoquinovosyl diacylglycerol (SQDG) is a membrane-forming lipid present in photosynthetic organisms as well as in distinct bacteria growing in phosphate-limited environments. Four genes for SQDG biosynthesis were previously identified in Rhodobacter sphaeroides, the operon sqdBDC and sqdA. In this work, we found that SMc02490 of Sinorhizobium meliloti is an SqdA orthologue. Expression of the S. meliloti sqdBDC operon in Escherichia coli results in formation of sulfoquinovosyl glycerol (SQGro), while co-expression of this operon together with smc02490 (sqdA) results in formation of SQDG. Furthermore, SqdA allows for incorporation of exogenous SQGro into SQDG in S. meliloti and in E. coli cultures, suggesting that presence of SqdA in bacteria permit them to use environmental SQGro for the biosynthesis of the membrane lipid SQDG. An in vitro enzymatic assay for the acyltransferase SqdA was developed. Cell-free crude extracts of E. coli expressing sqdA can efficiently convert [35S]-sulfoquinovosyl monoacylglycerol into SQDG using as acyl donor acyl carrier protein. Bioinformatic analyses reveal that this sulfoquinovose acylation pathway for SQDG biosynthesis is delimited to the Hyphomicrobiales (Rhizobiales) and Rhodobacterales orders of Alphaproteobacteria.

microbiology↗