Computational Methods for Pseudogene Annotation Based on Sequence Homology

Harrison, Paul M.

doi:10.1007/978-1-0716-1503-4_3

Cited by 6 publications

(3 citation statements)

References 62 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Table 4) apart from Pachon. The correct annotation of pseudogenes "non-functional" genes across species is a persistent problem, and especially deserves further attention in cave species genomes given its importance in understanding troglomorphic genetic adaptation (HARRISON 2021). While all these newly annotated A. mexicanus genomes are improved over prior assemblies (WARREN et al 2021), estimates of non-coding genes were substantially improved (a 36-fold increase; Suppl.…”

Section: )mentioning

confidence: 99%

Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery

Warren,

Rice,

Maggs

et al. 2023

Preprint

View full text Add to dashboard Cite

The ability of organisms to adapt to sudden extreme environmental changes produces some of the most drastic examples of rapid phenotypic evolution. The Mexican Tetra,Astyanax mexicanus, is abundant in the surface waters of northeastern Mexico, but repeated colonizations of cave environments have resulted in the independent evolution of troglomorphic phenotypes in several populations. Here, we present three chromosome-scale assemblies of this species, for one surface and two cave populations, enabling the first whole-genome comparisons between independently evolved cave populations to evaluate the genetic basis for the evolution of adaptation to the cave environment. Our assemblies represent the highest quality of sequence completeness with predicted protein-coding and non-coding gene metrics far surpassing prior resources and, to our knowledge, all long-read assembled teleost genomes, including zebrafish. Whole genome synteny alignments show highly conserved gene order among cave forms in contrast to a higher number of chromosomal rearrangements when compared to other phylogenetically close or distant teleost species. By phylogenetically assessing gene orthology across distant branches of amniotes, we discover gene orthogroups unique toA. mexicanus.When compared to a representative surface fish genome, we find a rich amount of structural sequence diversity, defined here as the number and size of insertions and deletions as well as expanding and contracting repeats across cave forms. These new more complete genomic resources ensure higher trait resolution for comparative, functional, developmental, and genetic studies of drastic trait differences within a species.

show abstract

Section: )mentioning

confidence: 99%

Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery

Warren,

Rice,

Maggs

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…The annotation of genes that do not encode functional proteins have been described as an ongoing problem because these copies of genes are disabled by premature stop codons, sequence disablements, and protein domain truncations. 3 These genes are commonly referred to as pseudogenes and are of 3 types, namely: processed pseudogenes, duplicated/unprocessed pseudogenes, and unitary/disabled pseudogenes. 4 The processed genes arise from retrotransposition, which is an mRNA reverse-transcription and genomic DNA reintegration process; they have poly-A tail at the 3′ end, extensions such as flanking direct repeats but lack introns and promoters.…”

Section: Introductionmentioning

confidence: 99%

“…4,5 It is biologically important that these genes are well annotated for proper discrimination from those that have protein coding ability, and to provide clues to organismal evolution and history, and show patterns that demonstrate loss of coding ability, transcription, codon, or splice sites. 3…”

Section: Introductionmentioning

confidence: 99%

Expression, Interaction, and Role of Pseudogene Adh6-ps1 in Cancer and other Disease Phenotypes

Nwadiugwu

2021

Bioinform Biol Insights

View full text Add to dashboard Cite

Pseudogenes have been classified as functionless and their annotation is an ongoing problem. The Adh6-ps1—a mouse pseudogene belonging to the alcohol dehydrogenase gene complex (Adh) was analyzed to review the conservation, homology, expression, and interactions and identify any role it plays in disease phenotypes using bioinformatics databases. Results showed that Adh6-ps1 have 2 transcripts (processed and unprocessed) which may have emerged from a transposition and duplication event, respectively, and that induced inversions (Uox gene, In(3)11Rk) involving gene complexes associated with Adh6-ps1 have been implicated in a diverse range of diseases. Adh6-ps1 is highly conserved in vertebrates particularly rodents and expressed in the liver. The top 5 MirRNA targets were Mir455, Mir511, Mir1903, Mir361, and Mir669o markers. While much is unknown about Mir1903 and Mir669o, the silencing of Mir455 and Mir511 is linked with hepatocellular carcinoma (HCC), and Mir361 is implicated in endometrial cancers. Given the identified MirRNA interactions with Adh6-ps1 and its expression in HCC and reproductive systems, it may well have a role in tumorigenesis and disease phenotypes. Nonetheless, further studies are required to establish these facts to add to the growing efforts to understand pseudogenes and their potential involvement in disease conditions.

show abstract

The reconstruction of evolutionary dynamics of processed pseudogenes indicates deep silencing of “retrobiome” in naked mole rat

Kogan,

Molodtsov,

Fleyshman

et al. 2024

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Approximately half of mammalian genomes are occupied by retrotransposons, highly repetitive interspersed genetic elements expanded through the mechanism of reverse transcription. The evolution of this “retrobiome” involved a series of explosive amplifications, presumably associated with high mutation rates, interspersed with periods of silencing. A by-product of retrotransposon activity is the formation of processed pseudogenes (PPGs)—intron-less, promoter-less DNA copies of messenger RNA (mRNA). We examined the proportion of PPGs with varying degrees of deviation from their ancestor mRNAs as an indicator of the intensity of retrotranspositions at different times in the past. Our analysis revealed a high proportion of “young’’ (recently acquired) PPGs in the DNA of mice and rats, indicating significant retrobiome activity during the recent evolution of these species. The ongoing process of new PPG entries in mouse germ line DNA was confirmed by identifying diversity in PPG content within the single strain of mice, C57BL/6. In contrast, the highly abundant PPGs of the naked mole rat (NMR) exhibited substantial deviation from their mRNAs, with a near-complete lack of PPGs without mutations, indicative of the silencing of the retrobiome in the most recent evolutionary past, preceded by a period of high activity. This distinctive feature of the NMR genome was confirmed through the analysis of a broad range of mammalian species. The peculiar evolutionary dynamics of PPGs in the NMR, an organism with exceptional longevity and resistance to cancer, may reflect the role played by the retrobiome in aging and cancer.

show abstract

Computational Methods for Pseudogene Annotation Based on Sequence Homology

Cited by 6 publications

References 62 publications

Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery

Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery

Expression, Interaction, and Role of Pseudogene Adh6-ps1 in Cancer and other Disease Phenotypes

The reconstruction of evolutionary dynamics of processed pseudogenes indicates deep silencing of “retrobiome” in naked mole rat

Contact Info

Product

Resources

About