WASTER: Practicalde novophylogenomics from low-coverage short reads

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 24, 2025

The advent of affordable whole-genome sequencing has spurred numerous large-scale projects aimed at inferring the tree life, yet achieving a complete species-level phylogeny remains distant goal due to significant costs and computational demands. Traditional species inference methods, though effective, are hampered by need for high-coverage sequencing, high-quality genomic alignments, extensive resources. To address these challenges, this study introduces WASTER, novel de novo tool trees directly from short-read sequences. WASTER employs k-mer based approach identifying variable sites, circumventing genome assembly alignment. Using simulations, we demonstrate that achieves accuracy comparable traditional alignment-based even low depth, substantially higher than other alignment-free methods. We validate WASTER's efficacy on real data, where it accurately reconstructs phylogenies eukaryotic with as depth 1.5X. provides fast efficient solution estimation in cases and/or alignment may bias analyses or is challenging, example depth. It also method generating guide tree-based algorithms. ability estimate low-coverage data without relying will lead reduced phylogenomic projects.

Language: Английский

---

The human genome encodes a multitude of novel miRNAs

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(4)

Published: Feb. 8, 2025

Abstract Human cells generate a vast complexity of noncoding RNAs, the “RNA dark matter,” which includes small RNA (sRNA) transcriptome. The biogenesis, biological relevance, and mechanisms action most these transcripts remain unknown, they are widely assumed to represent degradation products. Here, we aimed functionally characterize human sRNA transcriptome by attempting answer following question—can significant number novel sRNAs correspond members known classes, specifically, microRNAs (miRNAs)? By developing validating miRNA discovery pipeline, show that at least 2726 canonical miRNAs, majority families, exist in just one cell line compared 1914 loci. Moreover, potentially tens thousands miRNAs be discovered. Strikingly, many map exons protein-coding genes emphasizing complex interleaved architecture genome. existence so functional class suggest harbors multitude regulatory molecules. Overall, results very beginning understanding true component matter.”

Language: Английский

---

New remarkably complete skeleton of Mixodectes reveals arboreality in a large Paleocene primatomorphan mammal following the Cretaceous-Paleogene mass extinction

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: March 11, 2025

Abstract Mixodectids are poorly understood placental mammals from the Paleocene of western North America that have variably been considered close relatives euarchontan (primates, dermopterans, and scandentians) with hypothesized relationships to colugos, extinct plagiomenids, and/or microsyopid plesiadapiforms. Here we describe most complete dentally associated skeleton yet recovered for a mixodectid, specifically Mixodectes pungens early San Juan Basin, New Mexico. A partial skull all teeth erupted axial skeleton, forelimbs, hind limbs, epiphyses fused, indicate it was mature adult. Results cladistic analyses incorporating new data robustly support primatomorphan (Primates + Dermoptera) affinities Mixodectidae, but within Euarchonta less clear, as stem primatomorphan, dermopteran, or primate. Analyses postcrania suggest M. relatively large (~ 1.3 kg), claw-climbing arborealist capable frequent clinging on diameter vertical supports. With suggesting an omnivorous diet included leaves, occupied unique ecological niche in differed contemporary, arboreal plesiadapiforms were smaller more frugivorous. Euarchontans thus diverse radiation Cenozoic than previously appreciated.

Language: Английский

---

Evolution and development of vocal communication in primates

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

---

Complete omission of exon 21 from Slc12a2 transcripts in mice results in hearing loss

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: April 28, 2025

Language: Английский

---