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      Revisiting the heterogeneous global genomic population structure of Leishmania infantum

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          Abstract

          Leishmania infantum is the main causative agent responsible for visceral leishmaniasis (VL), a disease with global distribution. The genomic structure and genetic variation of this species have been widely studied in different parts of the world. However, in some countries, this information is still yet unknown, as is the genomic behaviour of the main antigens used in VL diagnosis (rK39 and rK28), which have demonstrated variable sensitivity and specificity in a manner dependent on the geographic region analysed. The objective of this study was to explore the genomic architecture and diversity of four Colombian L. infantum isolates obtained in this study and to compare these results with the genetic analysis of 183 L. infantum isolates from across the world (obtained from public databases), as well as to analyse the whole rK39 and rK28 antigen sequences in our dataset. The results showed that, at the global level, L. infantum has high genetic homogeneity and extensive aneuploidy. Furthermore, we demonstrated that there are distinct populations of L. infantum circulating in various countries throughout the globe and that populations of distant countries have close genomic relationships. Additionally, this study demonstrated the high genetic variability of the rK28 antigen worldwide. In conclusion, our study allowed us to (i) expand our knowledge of the genomic structure of global L. infantum; (ii) describe the intra-specific genomic variability of this species; and (iii) understand the genomic characteristics of the main antigens used in the diagnosis of VL. Additionally, this is the first study to report whole-genome sequences of Colombian L. infantum isolates.

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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            Interactive Tree Of Life (iTOL) v4: recent updates and new developments

            Abstract The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. The current version introduces four new dataset types, together with numerous new features. Annotation options have been expanded and new control options added for many display elements. An interactive spreadsheet-like editor has been implemented, providing dataset creation and editing directly in the web interface. Font support has been rewritten with full support for UTF-8 character encoding throughout the user interface. Google Web Fonts are now fully supported in the tree text labels. iTOL v4 is the first tool which supports direct visualization of Qiime 2 trees and associated annotations. The user account system has been streamlined and expanded with new navigation options, and currently handles >700 000 trees from more than 40 000 individual users. Full batch access has been implemented allowing programmatic upload and export of trees and annotations.
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              Detecting the number of clusters of individuals using the software structure: a simulation study

              The identification of genetically homogeneous groups of individuals is a long standing issue in population genetics. A recent Bayesian algorithm implemented in the software STRUCTURE allows the identification of such groups. However, the ability of this algorithm to detect the true number of clusters (K) in a sample of individuals when patterns of dispersal among populations are not homogeneous has not been tested. The goal of this study is to carry out such tests, using various dispersal scenarios from data generated with an individual-based model. We found that in most cases the estimated 'log probability of data' does not provide a correct estimation of the number of clusters, K. However, using an ad hoc statistic DeltaK based on the rate of change in the log probability of data between successive K values, we found that STRUCTURE accurately detects the uppermost hierarchical level of structure for the scenarios we tested. As might be expected, the results are sensitive to the type of genetic marker used (AFLP vs. microsatellite), the number of loci scored, the number of populations sampled, and the number of individuals typed in each sample.
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                Author and article information

                Journal
                Microb Genom
                Microb Genom
                mgen
                mgen
                Microbial Genomics
                Microbiology Society
                2057-5858
                2021
                7 September 2021
                7 September 2021
                : 7
                : 9
                Affiliations
                [ 1] departmentCentro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR) , Facultad de Ciencias Naturales, Universidad del Rosario , Bogotá, Colombia
                [ 2] departmentPrograma de Estudios y Control de Enfermedades Tropicales (PECET) , Facultad de Medicina, Universidad de Antioquia , Medellín, Colombia
                [ 3] departmentGrupo de Investigaciones Biomédicas , Universidad de Sucre , Sincelejo, Colombia
                [ 4] Candidata a doctor en Medicina Tropical, Universidad de Cartagena-SUE Caribe , Colombia
                Author notes

                The four samples sequenced for this study were deposited in the EBI European Nucleotide Archive (ENA) under project number PRJEB42749.

                *Correspondence: Juan David Ramírez, juand.ramirez@ 123456urosario.edu.co
                Article
                000640
                10.1099/mgen.0.000640
                8715437
                34491157
                0be663c1-4186-4b92-96f7-0afcb2fb154d
                © 2021 The Authors

                This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License.

                Product
                Funding
                Funded by: Universidad del Rosario
                Award ID: Internal Funds
                Award Recipient : DAVID RAMIREZJUAN
                Categories
                Research Articles
                Pathogens and Epidemiology
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                aneuploidy,genomic diversity,leishmania,whole genome sequencing

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