Contribution of Pseudogenes to Sequence Diversity

Vihinen, Mauno

doi:10.1007/978-1-4939-0835-6_2

Cited by 7 publications

(7 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In humans, olfactory receptor genes (387) form one of the largest gene families, which has numerous pseudogenes (415). It is hypothesized that the development of color vision reduced the importance of odor sensing and resulted in the pseudogenization of numerous olfactory receptor genes (Vihinen, ).…”

Section: Introductionmentioning

confidence: 99%

The pseudogenes of barley

et al. 2018

View full text Add to dashboard Cite

Pseudogenes have a reputation of being 'evolutionary relics' or 'junk DNA'. While they are well characterized in mammals, studies in more complex plant genomes have so far been hampered by the absence of reference genome sequences. Barley is one of the economically most important cereals and has a genome size of 5.1 Gb. With the first high-quality genome reference assembly available for a Triticeae crop, we conducted a whole-genome assessment of pseudogenes on the barley genome. We identified, characterized and classified 89 440 gene fragments and pseudogenes scattered along the chromosomes, with occasional hotspots and higher densities at the chromosome ends. Full-length pseudogenes (11 015) have preferentially retained their exon-intron structure. Retrotransposition of processed mRNAs only plays a marginal role in their creation. However, the distribution of retroposed pseudogenes reflects the Rabl configuration of barley chromosomes and thus hints at founding mechanisms. While parent genes related to the defense-response were found to be under-represented in cultivated barley, we detected several defense-related pseudogenes in wild barley accessions. The percentage of transcriptionally active pseudogenes is 7.2%, and these may potentially adopt new regulatory roles.The barley genome is rich in pseudogenes and small gene fragments mainly located towards chromosome tips or as tandemly repeated units. Our results indicate non-random duplication and pseudogenization preferences and improve our understanding of the dynamics of gene birth and death in large plant genomes and the mechanisms that lead to evolutionary innovations.

show abstract

Section: Introductionmentioning

confidence: 99%

The pseudogenes of barley

et al. 2018

View full text Add to dashboard Cite

show abstract

“…While the origin of pseudogenes in the human genome and their role during evolution and speciation have been extensively studied for years ( 6 – 8 ), most of the known pseudogene functions have been discovered quite recently in the context of human cancer, where pseudogenic DNA, RNA, and peptides/proteins have been shown to exert parental gene-related and unrelated functions (for an overview, please refer to Figure 1 ).…”

Section: Introductionmentioning

confidence: 99%

Pseudogenes in Human Cancer

2015

View full text Add to dashboard Cite

Recent advances in the analysis of RNA sequencing data have shown that pseudogenes are highly specific markers of cell identity and can be used as diagnostic and prognostic markers. Furthermore, genetically engineered mouse models have recently provided compelling support for a causal link between altered pseudogene expression and cancer. In this review, we discuss the most recent milestones reached in the pseudogene field and the use of pseudogenes as cancer classifiers.

show abstract

“…They originate with three mechanisms [ 24 ]. Duplicated pseudogenes are produced via tandem duplication or uneven crossing over and processed pseudogenes arise by retrotransposition, when an mRNA sequence or part of it is reverse transcribed to DNA and inserted into the genome [ 25 ]. The human genome contains > 14 700 duplicated or retroposed pseudogenes according to the GENCODE database Release version 41 ( , accessed on 10 August 2022).…”

Section: Genes and Genomementioning

confidence: 99%

“…Despite nonfunctional sequences, the accumulation of variations does not occur at random rate in some pseudogenes, and they display evolutionary selection. Pseudogenes have functions, e.g., as regulatory elements at DNA, RNA, and protein level; they provide a reservoir of genetic material for increased genetic diversity, and some pseudogenes are translated [ 24 , 25 ].…”

Section: Genes and Genomementioning

confidence: 99%

Individual Genetic Heterogeneity

Vihinen

2022

Genes

Self Cite

View full text Add to dashboard Cite

Genetic variation has been widely covered in literature, however, not from the perspective of an individual in any species. Here, a synthesis of genetic concepts and variations relevant for individual genetic constitution is provided. All the different levels of genetic information and variation are covered, ranging from whether an organism is unmixed or hybrid, has variations in genome, chromosomes, and more locally in DNA regions, to epigenetic variants or alterations in selfish genetic elements. Genetic constitution and heterogeneity of microbiota are highly relevant for health and wellbeing of an individual. Mutation rates vary widely for variation types, e.g., due to the sequence context. Genetic information guides numerous aspects in organisms. Types of inheritance, whether Mendelian or non-Mendelian, zygosity, sexual reproduction, and sex determination are covered. Functions of DNA and functional effects of variations are introduced, along with mechanism that reduce and modulate functional effects, including TARAR countermeasures and intraindividual genetic conflict. TARAR countermeasures for tolerance, avoidance, repair, attenuation, and resistance are essential for life, integrity of genetic information, and gene expression. The genetic composition, effects of variations, and their expression are considered also in diseases and personalized medicine. The text synthesizes knowledge and insight on individual genetic heterogeneity and organizes and systematizes the central concepts.

show abstract

Contribution of Pseudogenes to Sequence Diversity

Cited by 7 publications

References 38 publications

The pseudogenes of barley

The pseudogenes of barley

Pseudogenes in Human Cancer

Individual Genetic Heterogeneity

Contact Info

Product

Resources

About