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Plant DNA: Contents and Systematics
Published in S. K. Dutta, DNA Systematics, 2019
Many more such cases as the examples cited above may be presently uninvestigated. However, a word of caution may be added that genetic divergence and quantitative DNA alterations do not always go together, in view of the instances in which speciation has occurred without any appreciable alterations in DNA content as also massive DNA variation is present in species with close genetic relationship.
Mitochondrial DNAs and Phylogenetic Relationships
Published in S. K. Dutta, DNA Systematics, 2019
Mitochondrial DNA diversity is especially suited to the study of phylogeny at a within-species level since it is a sensitive discriminator of genetical differentiation within subdivided populations and closely related species. Hence we can expect mtDNA variation to be of value in the assessment of the degree of genetic isolation for ecologically defined population subdivisions of a species. The investigation of more distant phylogenetic relationships presents some difficulties since the high rate of evolution will cause multiple base pair substitutions to be overlooked, so underestimating the actual number of events between two species or genera.183,184 The degree of underestimation will be greatest for silent site substitutions and regions of the genome subject to low evolutionary constraint. Additionally, small length mutations relative to two identical restriction sites will cause a number of site differences to apparently vary when the length mutation is within the limits of technique. This feature is a probable explanation for hypervariable restriction sites noted by Lansman et al.185 in populations of Peromyscus maniculatus. Such problems in the estimation of genetical divergence were discussed by Aquadro and Greenberg146 in a detailed evaluation of genetic divergence from nucleotide sequence data. Base pair substitution in mitochondrial DNA shows a marked excess (32-fold) of transitions over transversions and is the most likely cause of convergent evolution of restriction sites. In their analysis of a 900 bp region of human mtDNA Aquadro and Greenberg identified the convergent loss of a site 3 times in their sample of 7 individuals. In another instance mutation caused the loss of an Mnll restriction site and the formation of a new Mnll site two nucleotides away. Hence, evolutionary divergence, when it is estimated from mtDNA restriction map data, is progressively underestimated with increasing phylogenetic distance.
Molecular characterization of G2P[4] and G9P[8] rotaviruses strains isolated from Moroccan children fully vaccinated with Rotarix™ between 2013 and 2014
Published in Alexandria Journal of Medicine, 2019
Hassan Boulahyaoui, Sanaa Alaoui Amine, Marouane Melloul, Chafiqa Loutfi, Reda Tagajdid, Hicham El Annaz, Nadia Touil, Yashpal Singh Malik, Elmostafa El Fahime, Saad Mrani
G9P [5] genotype was also found to emerge as the second most prevalent strain after 3 years of immunization in Morocco (15% vs. 7.8% 11.3%) [8]. Both G9 genotypes were found close to the Italian ITA/BA29/2012 and ITA/JES11/2010; a G9P [5] rotavirus strains circulating in Italy between 2010 and 2011 [20,21]; showing high similarities between clinical and environmental strains. However, they presented the most genetic divergence, with a separate clustering pattern for encoding VP4 genes. Their P [5] segregate into a separate sub-cluster, allowing to hypothesize a possible intra-genotype reassortment event at the base of the formation of the modern Moroccan G9P [5] strains. This hypothesis is supported by the substitutions found at the level of their aa. Whether this is the reason why RV-1 vaccine could not provide any protection against the partly heterotypic rotavirus strains remains to be clarified.
The evolution and competitive strategies of Akkermansia muciniphila in gut
Published in Gut Microbes, 2022
Ji-Sun Kim, Se Won Kang, Ju Huck Lee, Seung-Hwan Park, Jung-Sook Lee
Since the ANI value between the KGMB strains was 99.99–100% and their genome sequences were almost identical, the complete genome of KGMB01988 was selected among the KGMB strains for comparative analysis between the A. muciniphila genomes. Twenty-five complete sequences of A. muciniphila were obtained from GenBank (www.ncbi.nlm.nih.gov/genome/browser). Comparative analysis was performed using only A. muciniphila strains with complete genomic sequence to obtain accurate results. Phylogenetic analysis was performed using A. glycaniphila APytT, which is the closest to A. muciniphila, as an outgroup. Most of A. muciniphila strains used in this analysis were isolated from the feces of Homo sapiens, but A. muciniphila YL44, YL44_sDMDMm2, and ‘139’ were isolated from mice (Table 3). The genome sizes ranged between 2.66 Mb and 2.84 Mb, and the GC content ranged from 55.23–55.76%. Interestingly, KGMB01988 had the largest genome size after strain CBA5201, among the A. muciniphila strains used in this study. None of the 27 strains contained additional amplicons besides a chromosome and had an average of 2,262 CDSs, as predicted using the prodigal program (Table 3). To analyze the genomic distance between strain KGMB01988 and A. muciniphila reference strains, dDDH (digital DNA-DNA hybridization) and ANI values were calculated (Table 4). As a result, the ANI and dDDH values for pair-wise comparisons were in the range of 97.44–99.90% and 77.70–98.90%, respectively. These results revealed that genetic divergence exists between A. muciniphila.
Genomic diversity and differentiation of Alu insertion polymorphisms in a native British and four South Asian migrant populations
Published in Annals of Human Biology, 2023
Rebekah Beaumont, Liz Akam, Puneetpal Singh, Jasvinder Singh Bhatti, Sarabjit Mastana
In conclusion, Alu insertions are stable and easy to genotype genetic markers which could be used as an effective tool in population genomics and exploration of population relationships, migration patterns, and ancestry. The results of this study emphasised the genetic divergence between European and South Asian populations, based on geographical location, migration patterns, endogamy, and ancestral lineage.