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      Bioarchaeological and palaeogenomic portrait of two Pompeians that died during the eruption of Vesuvius in 79 AD

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          Abstract

          The archaeological site of Pompeii is one of the 54 UNESCO World Heritage sites in Italy, thanks to its uniqueness: the town was completely destroyed and buried by a Vesuvius’ eruption in 79 AD. In this work, we present a multidisciplinary approach with bioarchaeological and palaeogenomic analyses of two Pompeian human remains from the Casa del Fabbro. We have been able to characterize the genetic profile of the first Pompeian’ genome, which has strong affinities with the surrounding central Italian population from the Roman Imperial Age. Our findings suggest that, despite the extensive connection between Rome and other Mediterranean populations, a noticeable degree of genetic homogeneity exists in the Italian peninsula at that time. Moreover, palaeopathological analyses identified the presence of spinal tuberculosis and we further investigated the presence of ancient DNA from Mycobacterium tuberculosis. In conclusion, our study demonstrates the power of a combined approach to investigate ancient humans and confirms the possibility to retrieve ancient DNA from Pompeii human remains. Our initial findings provide a foundation to promote an intensive and extensive paleogenetic analysis in order to reconstruct the genetic history of population from Pompeii, a unique archaeological site.

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          The Sequence Alignment/Map format and SAMtools

          Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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            Fast gapped-read alignment with Bowtie 2.

            As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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              Fast and accurate short read alignment with Burrows–Wheeler transform

              Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk
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                Author and article information

                Contributors
                gabrielescor@gmail.com
                pierfrancesco.fabbri@unisalento.it
                fmacciar@uci.edu
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                26 May 2022
                26 May 2022
                2022
                : 12
                : 6468
                Affiliations
                [1 ]GRID grid.6530.0, ISNI 0000 0001 2300 0941, Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, , University of Rome “Tor Vergata”, ; 00133 Rome, Italy
                [2 ]GRID grid.5254.6, ISNI 0000 0001 0674 042X, Lundbeck Foundation GeoGenetics Centre, Globe Institute, , University of Copenhagen, ; Copenhagen, Denmark
                [3 ]GRID grid.9906.6, ISNI 0000 0001 2289 7785, Department of Cultural Heritage, , University of Salento, ; 73100 Lecce, Italy
                [4 ]GRID grid.8430.f, ISNI 0000 0001 2181 4888, Laboratório de Biodiversidade e Evolução Molecular (LBEM), , Universidade Federal de Minas Gerais, ; Belo Horizonte, Brazil
                [5 ]GRID grid.266093.8, ISNI 0000 0001 0668 7243, Laboratory of Molecular Psychiatry, Department of Psychiatry and Human Behavior, , University of California, ; Irvine, CA 92868 USA
                Article
                10899
                10.1038/s41598-022-10899-1
                9135728
                35618734
                f55adda8-d42b-478c-99b1-ec876baea879
                © The Author(s) 2022

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 17 December 2021
                : 8 April 2022
                Funding
                Funded by: National Scientific Coordinator and Principal Investigator OR: Biological and cultural heritage of the central-southern Italian population trough 30 thousand Years EPIC
                Award ID: prot.2010EL8TXP
                Award Recipient :
                Categories
                Article
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                © The Author(s) 2022

                Uncategorized
                genetics,population genetics
                Uncategorized
                genetics, population genetics

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