Divergent evolution and purifying selection of the flaA gene sequences in Aeromonas

Common bean (Phaseolus vulgaris L.) is an important source of dietary protein and minerals worldwide. Genes conditioning variability for mineral contents are not clearly understood. Our ultimate goal is to identify genes conditioning genetic variation for Zn and Fe content. To establish mapping populations for this objective, we tested mineral content of 29 common bean genotypes. Chemical analyses revealed significant genetic variability for seed Zn and Fe contents among the genotypes. Genetic diversity was evaluated with 49 primer pairs, of which 23 were simple sequence repeats (SSR), 16 were developed from tentative consensus (TC) sequences, and 10 were generated from common bean NBS-LRR gene sequences. The discriminatory ability of molecular markers for identifying allelic variation among genotypes was estimated by polymorphism information content (PIC) and the genetic diversity was measured from genetic similarities between genotypes. Primers developed from NBS-LRR gene sequences were highly polymorphic in both PIC values and number of alleles (0.82 and 5.3), followed by SSRs (0.56 and 3.0), and markers developed from TC (0.39 and 2.0). genetic similarity values between genotypes ranged from 14.0 (JaloEEP558 and DOR364) to 91.4 (MIB152 and MIB465). Cluster analysis clearly discriminated the genotypes into Mesoamerican and Andean gene pools. Common bean genotypes were selected to include in crossing to enhance seed Zn and Fe content based on genetic diversity and seed mineral contents of the genotypes. Key words: Common bean, genetic diversity, mineral nutrients, breeding

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Gene conversion and purifying selection of a placenta-specific ERV-V envelope gene during simian evolution

BMC Evolutionary Biology ◽

10.1186/1471-2148-8-266 ◽

2008 ◽

Vol 8 (1) ◽

pp. 266 ◽

Cited By ~ 19

Author(s):

Anders L Kjeldbjerg ◽

Palle Villesen ◽

Lars Aagaard ◽

Finn Skou Pedersen

Keyword(s):

Gene Conversion ◽

Purifying Selection ◽

Envelope Gene ◽

Selection Of

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Purifying Selection of mtDNA and the Shape of Human Evolution

Human Mutation ◽

10.1002/humu.22668 ◽

2015 ◽

Vol 36 (11) ◽

pp. v-v

Author(s):

Maria Pala

Keyword(s):

Human Evolution ◽

Purifying Selection ◽

Selection Of

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Purifying selection of mtDNA and its implications for understanding evolution and mitochondrial disease

Nature Reviews Genetics ◽

10.1038/nrg2396 ◽

2008 ◽

Vol 9 (9) ◽

pp. 657-662 ◽

Cited By ~ 111

Author(s):

James Bruce Stewart ◽

Christoph Freyer ◽

Joanna L. Elson ◽

Nils-Göran Larsson

Keyword(s):

Mitochondrial Disease ◽

Purifying Selection ◽

Selection Of

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Nuclear DNA-encoded fragments of mitochondrial DNA (mtDNA) confound analysis of selection of mtDNA mutations in human primordial germ cells.

10.1101/2021.10.18.464832 ◽

2021 ◽

Author(s):

Melissa Franco ◽

Zoe Fleischmann ◽

Sofia Annis ◽

Konstantin Khrapko ◽

Jonathan L. Tilly ◽

...

Keyword(s):

Mitochondrial Dna ◽

Germ Cells ◽

Nuclear Dna ◽

Mutational Analysis ◽

Primordial Germ Cells ◽

Purifying Selection ◽

Mutational Pressure ◽

Mtdna Mutations ◽

Reported Effect ◽

Selection Of

The resilience of the mitochondrial genome to a high mutational pressure depends, in part, on purifying selection against detrimental mutations in the germline. It is crucial to understand the mechanisms of this process. Recently, Floros et al. concluded that much of the purifying selection takes place during the proliferation of primordial germ cells (PGCs) because, according to their analysis, the synonymity of mutations in late PGCs was seemingly increased compared to those in early PGCs. We re-analyzed the Floros et al. mutational data and discovered a high proportion of sequence variants that are not true mutations, but originate from NUMTs, the latter of which are segments of mitochondrial DNA (mtDNA) inserted into nuclear DNA, up to millions of years ago. This is a well-known artifact in mtDNA mutational analysis. Removal of these artifacts from the Floros et al. dataset abolishes the reported effect of purifying selection in PGCs. We therefore conclude that the mechanism of germline selection of mtDNA mutations remains open for debate, and more research is needed to fully elucidate the timing and nature of this process.

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Section 7: Bioinformatics: Bioinformatics and its Impact on Clinical Research Methods

Yearbook of Medical Informatics ◽

10.1055/s-0038-1638478 ◽

2006 ◽

Vol 15 (01) ◽

pp. 104-106

Author(s):

E. Lang ◽

Keyword(s):

Microarray Data ◽

Clinical Findings ◽

Biological Functions ◽

Gene Sequences ◽

Strong Trend ◽

Healthy State ◽

Excellent Research ◽

Experimental Findings ◽

Text And Data Mining ◽

Selection Of

SummaryTo summarize current excellent research in the field of bioinformatics.Synopsis of the articles selected for the IMIA Yearbook 2006. Results: Current research in the field of bioinformatics clearly shows ongoing unification of experimental findings and clinical outcomes. Microarray data, gene sequences and clinical data are more and more perceived as different but related facets of one entity. Significant work is done in the area of text and data mining in order to bring together patient data and biochemical phenomena by means of ontologies. A strong trend in the clinical field is performance of exhaustive studies on DNA material derived from patients that suffer from diseases that are already known to be inherited. Examination of appropriate methods covers data and text mining, ontologies as well as machine learning and classification.The best paper selection of articles on bioinformatics shows examples of excellent research on methods used for studying inherited diseases and their underlying genetic dispositions. Clinical studies, inclusion of experimental findings like microarray data, and of knowledge representation formats all lead to a better understanding the linkage between gene sequences, biological functions and clinical findings in the form of healthy state or physiological disorders.

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Divergent Evolutional Mode and Purifying Selection of the KIT Gene in European and Asian Domestic Pig Breeds

BioMed Research International ◽

10.1155/2018/8932945 ◽

2018 ◽

Vol 2018 ◽

pp. 1-10

Author(s):

Lili Niu ◽

KeYu Shi ◽

Jing-Jing Xie ◽

Sen Liu ◽

Tao Zhong

Keyword(s):

Purifying Selection ◽

Coat Colour ◽

Blood Parameters ◽

Domestic Pigs ◽

Kit Gene ◽

History Of ◽

Geographic Expansion ◽

Phenotype Formation ◽

White Colour ◽

Selection Of

The recent geographic expansion of wild boars and the even more recent development of numerous domestic pigs have spurred exploration on pig domestic origins. The porcine KIT gene has been showed to affect pleiotropic effects, blood parameters, and coat colour phenotypes, especially the white colour phenotype formation in European commercial breeds. Here, we described the use of SNPs to identify different selection patterns on the porcine KIT gene and the phylogenetic relationships of the inferred haplotypes. The phylogenetic tree revealed four clades in European and Asian wild and domestic pigs: two major clades with European and Asian origins and one minor clade with Iberian origins as well as the other minor clade in Asia, consistent with the major introgression of domestic Asian pigs in Europe around 18th -19th century. The domestication history of pigs, which occurred in the domestication centers (Europe and Asia), has also been demonstrated by mtDNA analysis. Furthermore, both Asian and European domestic pigs evolved under purifying selection. This study indicated that domestic pigs in Europe and Asia have different lineage origins but the porcine KIT gene was undergoing a purifying selection during their evolutional histories.

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Insights into the genomic evolution of insects from cricket genomes

Communications Biology ◽

10.1038/s42003-021-02197-9 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Guillem Ylla ◽

Taro Nakamura ◽

Takehiko Itoh ◽

Rei Kajitani ◽

Atsushi Toyoda ◽

...

Keyword(s):

Dna Methylation ◽

Purifying Selection ◽

Field Cricket ◽

Genomic Evolution ◽

Gryllus Bimaculatus ◽

Class V ◽

Insect Genome ◽

Element Activity ◽

Complete Metamorphosis ◽

Selection Of

AbstractMost of our knowledge of insect genomes comes from Holometabolous species, which undergo complete metamorphosis and have genomes typically under 2 Gb with little signs of DNA methylation. In contrast, Hemimetabolous insects undergo the presumed ancestral process of incomplete metamorphosis, and have larger genomes with high levels of DNA methylation. Hemimetabolous species from the Orthopteran order (grasshoppers and crickets) have some of the largest known insect genomes. What drives the evolution of these unusual insect genome sizes, remains unknown. Here we report the sequencing, assembly and annotation of the 1.66-Gb genome of the Mediterranean field cricket Gryllus bimaculatus, and the annotation of the 1.60-Gb genome of the Hawaiian cricket Laupala kohalensis. We compare these two cricket genomes with those of 14 additional insects and find evidence that hemimetabolous genomes expanded due to transposable element activity. Based on the ratio of observed to expected CpG sites, we find higher conservation and stronger purifying selection of methylated genes than non-methylated genes. Finally, our analysis suggests an expansion of the pickpocket class V gene family in crickets, which we speculate might play a role in the evolution of cricket courtship, including their characteristic chirping.

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