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DNA, Volume 2, Issue 2 (June 2022) – 3 articles

Cover Story (view full-size image): An essential step for many bioinformatics studies is to determine the order of nucleotides in a given genome. Conventional physical mapping methods, while very effective for genome assembly, are prohibitively expensive; instead, less-contiguous genome assemblies are built using whole-genome shotgun (WGS) sequencing data. Here, we introduce Physlr—a tool that constructs next-generation physical maps using WGS linked reads. Physlr leverages long-range information in linked reads to infer a chromosome-scale physical map in the form of an overlap graph of sequenced molecules. It can be used for various genomics analyses, including scaffolding. Here, we demonstrate how physical maps can be used to substantially improve genome assemblies over state-of-the-art linked-read scaffolding tools. View this paper
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18 pages, 730 KiB  
Review
Mitochondrial DNA: Consensuses and Controversies
by Inna Shokolenko and Mikhail Alexeyev
DNA 2022, 2(2), 131-148; https://doi.org/10.3390/dna2020010 - 10 Jun 2022
Cited by 5 | Viewed by 7381
Abstract
In the course of its short history, mitochondrial DNA (mtDNA) has made a long journey from obscurity to the forefront of research on major biological processes. mtDNA alterations have been found in all major disease groups, and their significance remains the subject of [...] Read more.
In the course of its short history, mitochondrial DNA (mtDNA) has made a long journey from obscurity to the forefront of research on major biological processes. mtDNA alterations have been found in all major disease groups, and their significance remains the subject of intense research. Despite remarkable progress, our understanding of the major aspects of mtDNA biology, such as its replication, damage, repair, transcription, maintenance, etc., is frustratingly limited. The path to better understanding mtDNA and its role in cells, however, remains torturous and not without errors, which sometimes leave a long trail of controversy behind them. This review aims to provide a brief summary of our current knowledge of mtDNA and highlight some of the controversies that require attention from the mitochondrial research community. Full article
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15 pages, 4704 KiB  
Article
Physlr: Next-Generation Physical Maps
by Amirhossein Afshinfard, Shaun D. Jackman, Johnathan Wong, Lauren Coombe, Justin Chu, Vladimir Nikolic, Gokce Dilek, Yaman Malkoç, René L. Warren and Inanc Birol
DNA 2022, 2(2), 116-130; https://doi.org/10.3390/dna2020009 - 10 Jun 2022
Cited by 3 | Viewed by 2670
Abstract
While conventional physical maps helped build most of the reference genomes we use today, generating the maps was prohibitively expensive, and the technology was abandoned in favor of whole-genome shotgun sequencing (WGS). However, genome assemblies generated using WGS data are often less contiguous. [...] Read more.
While conventional physical maps helped build most of the reference genomes we use today, generating the maps was prohibitively expensive, and the technology was abandoned in favor of whole-genome shotgun sequencing (WGS). However, genome assemblies generated using WGS data are often less contiguous. We introduce Physlr, a tool that leverages long-range information provided by some WGS technologies to construct next-generation physical maps. These maps have many potential applications in genome assembly and analysis, including, but not limited to, scaffolding. In this study, using experimental linked-read datasets from two humans, we used Physlr to construct chromosome-scale physical maps (NGA50s of 52 Mbp and 70 Mbp). We also demonstrated how these physical maps can help scaffold human genome assemblies generated using various sequencing technologies and assembly tools. Across all experiments, Physlr substantially improved the contiguity of baseline assemblies over state-of-the-art linked-read scaffolders. Full article
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12 pages, 1261 KiB  
Article
Updating the Phylogeography and Temporal Evolution of Mitochondrial DNA Haplogroup U8 with Special Mention to the Basques
by Vicente M. Cabrera
DNA 2022, 2(2), 104-115; https://doi.org/10.3390/dna2020008 - 7 Apr 2022
Viewed by 3863
Abstract
Mitochondrial DNA phylogenetic and phylogeographic studies have been very useful in reconstructing the history of modern humans. In addition, recent advances in ancient DNA techniques have enabled direct glimpses of the human past. Taking advantage of these possibilities, I carried out a spatiotemporal [...] Read more.
Mitochondrial DNA phylogenetic and phylogeographic studies have been very useful in reconstructing the history of modern humans. In addition, recent advances in ancient DNA techniques have enabled direct glimpses of the human past. Taking advantage of these possibilities, I carried out a spatiotemporal study of the rare and little-studied mtDNA haplogroup U8. Today, U8, represented by its main branches U8a and U8b, has a wide western Eurasian range but both with average frequencies below 1%. It is known that, in Paleolithic times, U8 reached high frequencies in European hunter-gatherers. However, it is pertinent to precise that only lineages belonging to U8a and U8c, a sister branch of U8b, were detected at that time. In spite of its wide geographic implantation, U8c was extinct after the Last Glacial Maximum, but U8a subsisted until the present day, although it never reached its high Paleolithic frequencies. U8a is detected mainly in northern and western Europe including the Basques, testifying to a minor maternal Paleolithic continuity. In this respect, it is worth mentioning that Basques show more U8-based affinities with continental European than with Mediterranean populations. On the contrary, coalescent ages of the most ancient U8b clades point to a Paleolithic diversification in the Caucasus and the Middle Eastern areas. U8b-derived branches reached eastern Europe since the Mesolithic. Subsequent Neolithic and post-Neolithic expansions widen its ranges in continental Europe and the Mediterranean basin, including northern Africa, albeit always as a minor clade that accompanied other, more representative, mitochondrial lineages. Full article
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