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Phylogeny of Normal and Abnormal Hemoglobin Genes
Published in S. K. Dutta, DNA Systematics, 2019
Two of the major factors which appear to have contributed to the evolution of those globin genes which we today recognize as normal are gene duplication and concerted evolution. Gene duplication was vigorously promoted 20 years ago by Ohno et al.35 as a major mechanism of evolution. There seems to be little question that this process was indeed the mechanism by which many of the features of the globin genome arose. These features will be discussed below in the appropriate sections. The process called concerted evolution is a much newer concept.46 It proposes that when two homologous genes lie adjacent to one another on a chromosome, they may exchange segments of DNA so that they tend to evolve as a pair rather than diverge. Hess and co-workers83 have recently found that 5′ to 3′ homology gradients exist in the human a-chain cluster which support a polar correction process in which crossovers originate at “hotspots” and extend for random distances in the 3′ direction. Such a mechanism would clearly serve to buffer the effects of mutation since the pair could rid itself of an unfavorable mutation by replacing it with an unmutated segment from the sister gene or conversely, preserving and amplifying a desirable mutation. The situation would be somewhat analogous to the practice in computer operation whereby a backup copy of a program is made before experimenting with modification. If the modification produces the desired improvement, the backup copy can be improved by transferring the appropriate section of the program to it. If the modification proves to be undesirable, the operator can replace it from the backup copy.
Chloroplast DNA and Phylogenetic Relationships
Published in S. K. Dutta, DNA Systematics, 2019
Several features of its evolution increase the systematic value of the chloroplast genome, particularly in comparison to the nuclear genome. Most nuclear genes in animals16,17,102–104 and in plants,105,106 even those once thought to be “single copy”, are actually members of small repeated gene families. A number of evolutionary processes such as gene duplication and deletion, concerted evolution, and pseudogene formation have been associated with such repeat families. All of these processes tend to distort the evolutionary history of DNA sequences relative to that of organisms. Therefore, particular care must be taken to understand as completely as possible the evolutionary history of a given nuclear gene and its family members before using sequence changes in these genes to imply organismal phylogeny. In contrast, there is no evidence that any of these processes occur in chloroplast DNA in such a way as to confound phylogenetic interpretation. The two repeat elements present in the only significant repeat family in angiosperm chloroplast genomes, i.e., the large inverted repeat discussed previously, do undergo concerted evolution, but this appears to occur so rapidly as to be unresolvable within interspecific19,21,24,28 and even laboratory107 time scales. The net result is that the two repeats evolve essentially as one genetic unit with a single, undistorted evolutionary history. The chloroplast genome is evolving quite slowly at the nucleotide sequence level.11–13,19,27,28,85,86 This fact, together with the absence of any mutational imbalances, such as the extreme transition-transversion bias found in animal mitochondrial DNA,14,15,108 is reflected by the extremely low incidence of parallel and convergent restriction site mutations found in studies at the interspecific level.19,23,28 Different portions of the chloroplast genome are evolving at different rates,11–13,85,86 thus providing a range of molecular yardsticks with which to measure evolutionary distances and determine relationships.
Metagenomic analysis reveals distinct patterns of gut lactobacillus prevalence, abundance, and geographical variation in health and disease
Published in Gut Microbes, 2020
Tarini Shankar Ghosh, Jerome Arnoux, Paul W. O’Toole
The genus Lactobacillus encompasses an unusually diverse number of species that share the property of being found in nutrient-rich environments.14 Lactobacilli have been exploited extensively for food preservation, 15 for biotechnological applications, 16 and as health-promoting “probiotics”.17 The phenotypic diversity of the genus Lactobacillus is reflected in extraordinarily high genomic diversity, approaching that of other bacterial families. 18,19 The isolation sources for most lactobacilli may be broadly categorized as humans, animals, plants, food and environment, and major “lifestyle” assignment groupings coincide remarkably with phylogenomic clades, 20 indicating concerted evolution for niche adaptation.
Phylogenetic analysis of Uncaria species based on internal transcribed spacer (ITS) region and ITS2 secondary structure
Published in Pharmaceutical Biology, 2018
Shuang Zhu, Qiwei Li, Shanchong Chen, Yesheng Wang, Lin Zhou, Changqing Zeng, Jun Dong
Previous studies indicated that the ITS and ITS2 regions evolve rapidly, leading to genetic changes similar to those in plastid DNA barcodes (such as matK, rbcL, psbA-trnH, et al.) (Kress et al. 2005; China Plant BOL Group 2011). However, the well-documented concerns and limitations of ITS include: (1) divergent paralogous copies within individuals lead by incomplete concerted evolution, (2) difficulties in amplifying and sequencing in some sample sets such as gymnosperms, and (3) fungal contamination (China Plant BOL Group 2011; Hollingsworth et al. 2011). Although they are imperfect, we believe that the ITS and ITS2 regions have sufficient ability to identify Uncaria species using best match and best close match techniques.
Pedigree Analysis of Nonhomologous Sequence Recombination of HBA1 and HBA2 Genes
Published in Hemoglobin, 2020
Shi-Qiang Luo, Xing-Yuan Chen, Ning Tang, Jun Huang, Qing-Yan Zhong, Ren Cai, Ti-Zhen Yan
The human α-globin gene cluster is located on chromosome 16 pterp13.3 and arranged in the following order: 5′-ζ2-ψζ1-ψα2-ψα1-α2-α1-θ1-3′ [1]. α-Thalassemia (α-thal) is caused by a deletion or a mutation of α-globin genes that are mainly distributed among the Mediterranean countries, Southeast Asia, Africa, the Middle East and in the Indian subcontinent [2]. Despite their ancient origin, the resultant HBA1 and HBA2 genes have maintained a remarkable sequence homology to each other over time. Unequal homologous recombination is common between the two α-globin genes of this cluster, due to the extensive sequence homology between the HBA1 (α1-globin) and HBA2 (α2-globin) genes. Sequence homology at the α-globin gene cluster promotes unequal crossovers [3]. Several models have been suggested for this concerted evolution of the α-globin gene cluster. The most prominent gene conversions and crossover fixation were the –α4.2 (leftward) and αααanti3.7 and αααanti4.2. In 2006, Law et al. [4] first reported the HBA1 and HBA2 gene conversion and determined that the cause was recurrent gene conversion or crossover fixation events. In 2014, Borgio et al. [5] found the α12 allele in a Saudi population and amended the conclusions of Law et al. [4]. Whether the α12 allele has had an effect on the expression of the α2-globin gene, has not yet been determined. In this study, we identified a gene conversion on the HBA2 gene, called α12 (HBA12), and for the first time reported the impact of the α12 allele with Hb Quong Sze (Hb QS, HBA2: c377T>C) and α-thal on clinical phenotype.