Population Genomic Analysis of ALMS1 in Humans Reveals a Surprisingly Complex Evolutionary History

AbstractHuman tuberculosis is caused by members of the Mycobacterium tuberculosis Complex (MTBC). The MTBC comprises several human-adapted lineages known as M. tuberculosis sensu stricto as well as two lineages (L5 and L6) traditionally referred to as M. africanum. Strains of L5 and L6 are largely limited to West Africa for reasons unknown, and little is known on their genomic diversity, phylogeography and evolution. Here, we analyzed the genomes of 365 L5 and 326 L6 strains, plus five related genomes that had not been classified into any of the known MTBC lineages, isolated from patients from 21 African countries.Our population genomic and phylogeographical analyses show that the unclassified genomes belonged to a new group that we propose to name MTBC Lineage 9 (L9). While the most likely ancestral distribution of L9 was predicted to be East Africa, the most likely ancestral distribution for both L5 and L6 was the Eastern part of West Africa. Moreover, we found important differences between L5 and L6 strains with respect to their phylogeographical substructure, genetic diversity and association with drug resistance. In conclusion, our study sheds new light onto the genomic diversity and evolutionary history of M. africanum, and highlights the need to consider the particularities of each MTBC lineage for understanding the ecology and epidemiology of tuberculosis in Africa and globally.

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Faculty Opinions recommendation of Population genomic analysis of base composition evolution in Drosophila melanogaster.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.717982880.793472060 ◽

2013 ◽

Author(s):

Hiroshi Akashi

Keyword(s):

Drosophila Melanogaster ◽

Base Composition ◽

Genomic Analysis ◽

Population Genomic

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Genetic Diversity of Rice stripe necrosis virus and New Insights into Evolution of the Genus Benyvirus

Viruses ◽

10.3390/v13050737 ◽

2021 ◽

Vol 13 (5) ◽

pp. 737

Author(s):

Issiaka Bagayoko ◽

Marcos Giovanni Celli ◽

Gustavo Romay ◽

Nils Poulicard ◽

Agnès Pinel-Galzi ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Sierra Leone ◽

Evolutionary History ◽

Molecular Diversity ◽

Genomic Data ◽

Gene Recombination ◽

Necrosis Virus ◽

History Of ◽

Complex Evolutionary History

The rice stripe necrosis virus (RSNV) has been reported to infect rice in several countries in Africa and South America, but limited genomic data are currently publicly available. Here, eleven RSNV genomes were entirely sequenced, including the first corpus of RSNV genomes of African isolates. The genetic variability was differently distributed along the two genomic segments. The segment RNA1, within which clusters of polymorphisms were identified, showed a higher nucleotidic variability than did the beet necrotic yellow vein virus (BNYVV) RNA1 segment. The diversity patterns of both viruses were similar in the RNA2 segment, except for an in-frame insertion of 243 nucleotides located in the RSNV tgbp1 gene. Recombination events were detected into RNA1 and RNA2 segments, in particular in the two most divergent RSNV isolates from Colombia and Sierra Leone. In contrast to BNYVV, the RSNV molecular diversity had a geographical structure with two main RSNV lineages distributed in America and in Africa. Our data on the genetic diversity of RSNV revealed unexpected differences with BNYVV suggesting a complex evolutionary history of the genus Benyvirus.

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Rhizobial plasmids — replication, structure and biological role

Open Life Sciences ◽

10.2478/s11535-012-0058-8 ◽

2012 ◽

Vol 7 (4) ◽

pp. 571-586 ◽

Cited By ~ 8

Author(s):

Andrzej Mazur ◽

Piotr Koper

Keyword(s):

Genome Organization ◽

Soil Bacteria ◽

Evolutionary History ◽

Bacterial Genome ◽

Biological Role ◽

Genome Architecture ◽

Genomic Knowledge ◽

History Of ◽

Cryptic Plasmids ◽

Complex Evolutionary History

AbstractSoil bacteria, collectively named rhizobia, can establish mutualistic relationships with legume plants. Rhizobia often have multipartite genome architecture with a chromosome and several extrachromosomal replicons making these bacteria a perfect candidate for plasmid biology studies. Rhizobial plasmids are maintained in the cells using a tightly controlled and uniquely organized replication system. Completion of several rhizobial genome-sequencing projects has changed the view that their genomes are simply composed of the chromosome and cryptic plasmids. The genetic content of plasmids and the presence of some important (or even essential) genes contribute to the capability of environmental adaptation and competitiveness with other bacteria. On the other hand, their mosaic structure results in the plasticity of the genome and demonstrates a complex evolutionary history of plasmids. In this review, a genomic perspective was employed for discussion of several aspects regarding rhizobial plasmids comprising structure, replication, genetic content, and biological role. A special emphasis was placed on current post-genomic knowledge concerning plasmids, which has enriched the view of the entire bacterial genome organization by the discovery of plasmids with a potential chromosome-like role.

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Organellar phylogenomics inform systematics in the green algal family Hydrodictyaceae (Chlorophyceae) and provide clues to the complex evolutionary history of plastid genomes in the green algal tree of life

American Journal of Botany ◽

10.1002/ajb2.1066 ◽

2018 ◽

Vol 105 (3) ◽

pp. 315-329 ◽

Cited By ~ 7

Author(s):

Hilary A. McManus ◽

Karolina Fučíková ◽

Paul O. Lewis ◽

Louise A. Lewis ◽

Kenneth G. Karol

Keyword(s):

Evolutionary History ◽

Tree Of Life ◽

Green Algal ◽

Plastid Genomes ◽

History Of ◽

Complex Evolutionary History

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Population genomic analysis reveals domestication of cultivated rye from weedy rye

Molecular Plant ◽

10.1016/j.molp.2021.12.015 ◽

2021 ◽

Author(s):

Yanqing Sun ◽

Enhui Shen ◽

Yiyu Hu ◽

Dongya Wu ◽

Yu Feng ◽

...

Keyword(s):

Genomic Analysis ◽

Population Genomic

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Runs of homozygosity for autozygosity estimation and genomic analysis in production animals

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2018000900001 ◽

2018 ◽

Vol 53 (9) ◽

pp. 975-984 ◽

Cited By ~ 1

Author(s):

Arnaldo Basso Rebelato ◽

Alexandre Rodrigues Caetano

Keyword(s):

Evolutionary History ◽

Genomic Analysis ◽

Runs Of Homozygosity ◽

Demographic Information ◽

Genomic Information ◽

Selection Signatures ◽

Effective Population ◽

High Frequencies ◽

Production Animals ◽

Genealogical Information

Abstract: Runs of homozygosity (ROHs) are long stretches of homozygous genomic segments, identifiable by molecular markers, which can provide genomic information for accurate estimates to characterize populations, determine evolutionary history and demographic information, estimate levels of consanguinity, and identify selection signatures in production animals. This review paper aims to perform a survey of the works on the efficiency of ROHs for these purposes. Factors such as genetic drift, natural or artificial selection, founder effect, and effective population size directly influence the size and distribution of ROHs along the genome. Individually, genome estimates of consanguinity based on ROHs can be obtained using the FROH index, which is generally considered more accurate than indexes based on other types of genomic or genealogical information. High frequencies of specific ROHs in a population can be used to identify selection signatures. The results of recent studies with ROHs in domestic animals have shown the efficiency of their use to characterize herds in a reliable and accessible way, using genomic information.

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