Pseudogene

About: Pseudogene is a research topic. Over the lifetime, 5528 publications have been published within this topic receiving 336634 citations. The topic is also known as: Ψ & pseudogenes.

Phylogeny, Recombination, and Mechanisms of Stepwise Mitochondrial Genome Reorganization in Mantellid Frogs from Madagascar

Abstract: In Malagasy frogs of the family Mantellidae, the genus Mantella is known to possess highly reorganized mitochondrial (mt) genomes with the following characteristics: 1) some rearranged gene positions, 2) 2 distinct genes and a pseudogene corresponding to the transfer RNA gene for methionine (trnM), and 3) 2 control regions (CRs) with almost identical nucleotide sequences. These unique genomic features were observed concentrated between the duplicated CRs surrounding cytochrome b (cob) and nicotinamide adenine dinucleotide dehydrogenase subunit 2 (cnad2) genes. To elucidate the mechanisms and evolutionary pathway that yielded the derived genome condition, we surveyed the reorganized genomic portion for all 12 mantellid genera. Our results show that the mt genomes of 7 genera retain the ancestral condition. In contrast, adding to Mantella, 4 genera of the subfamily Mantellinae, Blommersia, Guibemantis, Wakea, and Spinomantis, share several derived genomic characters. Furthermore, mt genomes of these mantellines showed additional structural divergences, resulting in different genome conditions between them. The high frequency of genomic reorganization does not correlate with nucleotide substitution rate. The encountered mt genomic conditions also suggest the occurrences of stepwise gene duplication and deletion events during the evolution of mantellines. Simultaneously, the majority of duplication events seems to be mediated by general (homologous) or illegitimate recombination, and general recombination also plays a role in concerted sequence evolution between multiple CRs. Considering our observations and recent conditional evidences, the following outlines can be expected for recombination processes in mt genome reorganization. 1) The CR is the "hot spot" of recombination; 2) highly frequent recombination between CRs may be mediated by a replication fork barrier lying in the CR; 3) general recombination has a potential to cause gene rearrangement in upstream regions of multiple CRs as the results of gene conversion and unequal crossing over processes. Our results also suggest that recombination activity is not a direct cause of convergent gene rearrangement; rather, homoplasious gene rearrangement seems to be mediated by persistence of a copied genomic condition through several lineage splits and subsequent parallel deletions.

The IgH locus of the channel catfish, Ictalurus punctatus, contains multiple constant region gene sequences: different genes encode heavy chains of membrane and secreted IgD.

Abstract: The δ-chain of catfish IgD was initially characterized as a unique chimeric molecule containing a rearranged VDJ spliced to Cμ1, seven C domain-encoding exons (δ1–δ7), and a transmembrane tail. The presence of cDNA forms showing splicing of δ7 to an exon encoding a secretory tail was interpreted to indicate that membrane (δm) and secreted (δs) forms were likely expressed from a single gene by alternative RNA processing. Subsequent cloning and sequence analyses have unexpectedly revealed the presence of three δ C region genes, each linked to a μ gene or pseudogene. The first ( IGHD1 ) is located 1.6 kb 3′ of the functional Cμ ( IGHM1 ). The second ( IGHD3 ) is positioned immediately downstream of a pseudo Cμ ( IGHM3P ), ∼725 kb 5′ of IGHM1 . These two δ genes are highly similar in sequence and each contains a tandem duplication of δ2-δ3-δ4. However, IGHD1 has a terminal exon encoding the transmembrane region, whereas IGHD3 has a single terminal exon encoding a secreted tail. The occurrence of IGHD3 immediately downstream of a μ pseudogene indicates that the putative δs product may not be expressed as a chimeric μδ molecule. Western blots and protein sequencing data indicate that an IGHD3 -encoded protein is expressed in catfish serum. Thus, catfish δm transcripts appear to originate from IGHD1 , whereas δs transcripts originate from IGHD3 rather than, as previously inferred, from a single expressed δ gene. The third δ ( IGHD2 ) is associated with a pseudo Cμ ( IGHM2P ); its presence is inferred by Southern blot analyses.

Evolutionary dynamics of olfactory receptor genes in chordates: interaction between environments and genomic contents.

Abstract: Olfaction is essential for the survival of animals. Versatile odour molecules in the environment are received by olfactory receptors (ORs), which form the largest multigene family in vertebrates. Identification of the entire repertories of OR genes using bioinformatics methods from the whole-genome sequences of diverse organisms revealed that the numbers of OR genes vary enormously, ranging from ~1,200 in rats and ~400 in humans to ~150 in zebrafish and ~15 in pufferfish. Most species have a considerable fraction of pseudogenes. Extensive phylogenetic analyses have suggested that the numbers of gene gains and losses are extremely large in the OR gene family, which is a striking example of the birth-and-death evolution. It appears that OR gene repertoires change dynamically, depending on each organism's living environment. For example, higher primates equipped with a well-developed vision system have lost a large number of OR genes. Moreover, two groups of OR genes for detecting airborne odorants greatly expanded after the time of terrestrial adaption in the tetrapod lineage, whereas fishes retain diverse repertoires of genes that were present in aquatic ancestral species. The origin of vertebrate OR genes can be traced back to the common ancestor of all chordate species, but insects, nematodes and echinoderms utilise distinctive families of chemoreceptors, suggesting that chemoreceptor genes have evolved many times independently in animal evolution.