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Xu et al. (2021) recently recommended a new parameterization of as a superior alternative to the widely-used algorithm to map ancient DNA sequencing data. Here, we compare the parameterization recommended by Xu et al. with the best-performing alignment methods determined in the recent benchmarks of Oliva and colleagues (2021), demonstrating that is still the gold-standard for ancient DNA read alignment .
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http://dx.doi.org/10.1002/ece3.8297 | DOI Listing |
ACS Omega
September 2025
Genetics and Cellular Biology Laboratory, Center for Biodiversity Studies, Federal University of Pará, Belém 66075-110, Pará, Brazil.
Histone genes contain sequences responsible for coding five types of proteins (H1, H2A, H2B, H3, and H4) that are of great importance for chromatin organization. Their transcriptional regulation through DNA methylation has been little studied. Testudines are ancient reptiles with high cytogenetic diversity (2 = 26-68), with a large number of histone gene loci in their karyotype.
View Article and Find Full Text PDFEcol Evol
September 2025
Aquatic Systems Biology Unit TUM School of Life Sciences, Technical University of Munich Freising Germany.
Historically, the thick-shelled river mussel ( agg. complex) was considered a single, widespread species across Europe. However, recent phylogenetic taxonomic revisions have delineated 12 species from this complex, including (s.
View Article and Find Full Text PDFNat Ecol Evol
September 2025
Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
Ageing Res Rev
September 2025
Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Rome, Italy; Department of Medicine and Surgery, LUM University, Casamassima, Italy. Electronic address:
Nuclear insertions of mitochondrial DNA (mtDNA) segments (NUMTs) represent an evolutionarily conserved phenomenon originating from the ancient endosymbiotic relationship between mitochondria and host cells. These insertions predominantly localize near intergenic or regulatory regions and are often enriched in tissues with high metabolic activity. Once regarded as inert pseudogenes or genomic artifacts, NUMTs are now recognized as dynamic elements capable of modulating nuclear architecture and cellular function.
View Article and Find Full Text PDFMol Cell
September 2025
Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria. Electronic address:
PIWI-clade Argonaute proteins and their associated PIWI-interacting RNAs (piRNAs) are essential guardians of genome integrity, silencing transposable elements through distinct nuclear and cytoplasmic pathways. Nuclear PIWI proteins direct heterochromatin formation at transposon loci, while cytoplasmic PIWIs cleave transposon transcripts to initiate piRNA amplification. Both processes rely on target RNA recognition by PIWI-piRNA complexes, yet how this leads to effector recruitment is unclear.
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