A novel Giraffidae-specific interspersed repeat with a microsatellite, originally found in an intron of a ruminant paralogous p97bcnt gene

The ruminant-specific p97bcnt gene (bcnt^p97) is a paralogous gene that includes a region derived from a retrotransposable element 1 (RTE-1). The region comprises an exon (RTE-1 exon) encoding 325 amino acids in the middle of the p97bcnt protein. To understand how the bcnt^p97 paralog evolved, we examined its organization in several ruminants. We found a 700-base pair (bp) insert in the 5′ intron of the RTE-1 exon in giraffe bcnt^p97. This insert is missing in the corresponding regions of bovine and sika deer. Furthermore, the sequence of the insert is interspersed in the genome of giraffe but not bovine and also contains a (GA)n microsatellite. A highly homologous insert harboring significantly different (GA)n microsatellite was detected in the corresponding region of okapi bcnt^p97. Therefore, the interspersed fragments with (GA)n microsatellite might serve as a marker for tracking how duplicated genes evolve in a family-specific manner.     

A natural case of RIP: degeneration of the DNA sequence in an ancestral tandem duplication.

5S rRNA genes of Neurospora crassa are generally dispersed in the genome and are unmethylated. The xi-eta region of Oak Ridge strains represents an informative exception. Most of the cytosines in this region, which consists of a diverged tandem duplication of a 0.8-kilobase-pair segment including a 5S rRNA gene, appear to be methylated (E. U. Selker and J. N. Stevens, Proc. Natl. Acad. Sci. USA 82:8114-8118, 1985). Previous work demonstrated that the xi-eta region functions as a portable signal for de novo DNA methylation (E. U. Selker and J. N. Stevens, Mol. Cell. Biol. 7:1032-1038, 1987; E. U. Selker, B. C. Jensen, and G. A. Richardson, Science 238:48-53, 1987). To identify the structural basis of this property, we have isolated and characterized an unmethylated allele of the xi-eta region from N. crassa Abbott 4. The Abbott 4 allele includes a single 5S rRNA gene, theta, which is different from all previously identified Neurospora 5S rRNA genes. Sequence analysis suggests that the xi-eta region arose from the theta region by duplication of a 794-base-pair segment followed by 267 G.C to A.T mutations in the duplicated DNA. The distribution of these mutations is not random. We propose that the RIP process of N. crassa (E. U. Selker, E. B. Cambareri, B. C. Jensen, and K. R. Haack, Cell 51:741-752, 1987; E. U. Selker, and P. W. Garrett, Proc. Natl. Acad. Sci. USA 85:6870-6874, 1988; E. B. Cambareri, B. C. Jensen, E. Schabtach, and E. U. Selker, Science 244:1571-1575, 1989) is responsible for the numerous transition mutations and DNA methylation in the xi-eta region. A long homopurine-homopyrimidine stretch immediately following the duplicated segment is 9 base pairs longer in the Oak Ridge allele than in the Abbott 4 allele. Triplex DNA, known to occur in homopurine-homopyrimidine sequences, may have mediated the tandem duplication.     

A hotspot of gene order rearrangement by tandem duplication and random loss in the vertebrate mitochondrial genome

Most reported examples of change in vertebrate mitochondrial (mt) gene order could be explained by a tandem duplication followed by random loss of redundant genes (tandem duplication-random loss [TDRL] model). Under this model of evolution, independent loss of genes arising from a single duplication in an ancestral species are predicted, and remnant pseudogenes expected, intermediate states that may remain in rearranged genomes. However, evidence for this is rare and largely scattered across vertebrate lineages. Here, we report new derived mt gene orders in the vertebrate "WANCY" region of four closely related caecilian amphibians. The novel arrangements found in this genomic region (one of them is convergent with the derived arrangement of marsupials), presence of pseudogenes, and positions of intergenic spacers fully satisfy predictions from the TDRL model. Our results, together with comparative data for the available vertebrate complete mt genomes, provide further evidence that the WANCY genomic region is a hotspot for gene order rearrangements and support the view that TDRL is the dominant mechanism of gene order rearrangement in vertebrate mt genomes. Convergent gene rearrangements are not unlikely in hotspots of gene order rearrangement by TDRL.     

A tandem segmental duplication (TSD) in green revolution gene Rht-D1b region underlies plant height variation

? Rht-D1c (Rht10) carried by Chinese wheat (Triticum aestivum) line Aibian 1 is an allele at the Rht-D1 locus. Among the Rht-1 alleles, little is known about Rht-D1c although it determines an extreme dwarf phenotype in wheat. ? Here, we cloned and functionally characterized Rht-D1c using a combination of Southern blotting, target region sequencing, gene expression analysis and transgenic experiments. ? We found that the Rht-D1c allele was generated through a tandem segmental duplication (TSD) of a >?1?Mb region, resulting in two copies of the Rht-D1b. Two copies of Rht-D1b in the TSD were three-fold more effective in reducing plant height than a single copy, and transformation with a segment containing the tandemly duplicated copy of Rht-D1b resulted in the same level of reduction of plant height as the original copy in Aibian 1. ? Our results suggest that changes in gene copy number are one of the important sources of genetic diversity and some of these changes could be directly associated with important traits in crops.     

Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergence

Background  

Oxidative phosphorylation is central to the energy metabolism of the cell. Due to adaptation to different life-styles and environments, fungal species have shaped their respiratory pathways in the course of evolution. To identify the main mechanisms behind the evolution of respiratory pathways, we conducted a phylogenomics survey of oxidative phosphorylation components in the genomes of sixty fungal species.     

A novel fatty acid-binding protein (FABP) gene resulting from tandem gene duplication in mammals: transcription in rat retina and testis

We have identified a new member of the FABP gene family, designated FABP12. FABP12 has the same structure as other FABP genes and resides in a cluster with FABP4/5/8/9 within 300,000 bp chromosomal region. FABP12 orthologs are found in mammals, but not in the zebrafish or chicken genomes. We demonstrate that FABP12 is expressed in rodent retina and testis, as well as in human retinoblastoma cell lines. In situ hybridization of adult rat retinal tissue indicates that FABP12 mRNA is expressed in ganglion and inner nuclear layer cells. Analysis of adult rat testis reveals a pattern of expression that is different from that of the known testis FABP (FABP9) in the testicular germ cells, suggesting distinct roles for these two genes during mammalian spermatogenesis. We propose that FABP12 arose as the result of tandem gene duplication, a mechanism that may have been instrumental to the expansion of the FABP family.     

A possible new type of chromosome rearrangement: telomere-centromere translocation (tct) followed by double duplication

Summary The reassessment of a case of complex interchromosomal rearrangement after breakage at centromeric and telomeric regions, and the comparison with four other independently published cases suggested the existence of a new type of rearrangement. It would consist of: formation of an isochromosome after breakage at a centromeric region, duplication of the telomeric region of another chromosome, and reassociation of the nonduplicated arm of the first chromosome with the duplicated telomeric region of the second chromosome.     

Two rounds of whole genome duplication in the ancestral vertebrate

The hypothesis that the relatively large and complex vertebrate genome was created by two ancient, whole genome duplications has been hotly debated, but remains unresolved. We reconstructed the evolutionary relationships of all gene families from the complete gene sets of a tunicate, fish, mouse, and human, and then determined when each gene duplicated relative to the evolutionary tree of the organisms. We confirmed the results of earlier studies that there remains little signal of these events in numbers of duplicated genes, gene tree topology, or the number of genes per multigene family. However, when we plotted the genomic map positions of only the subset of paralogous genes that were duplicated prior to the fish–tetrapod split, their global physical organization provides unmistakable evidence of two distinct genome duplication events early in vertebrate evolution indicated by clear patterns of four-way paralogous regions covering a large part of the human genome. Our results highlight the potential for these large-scale genomic events to have driven the evolutionary success of the vertebrate lineage.     

Perforin evolved from a gene duplication of MPEG1, followed by a complex pattern of gene gain and loss within Euteleostomi

ABSTRACT: BACKGROUND: The pore-forming protein perforin is central to the granule-exocytosis pathway used by cytotoxic lymphocytes to kill abnormal cells. Although this mechanism of killing is conserved in bony vertebrates, cytotoxic cells are present in other chordates and invertebrates, and their cytotoxic mechanism has not been elucidated. In order to understand the evolution of this pathway, here we characterize the origins and evolution of perforin. RESULTS: We identified orthologs and homologs of human perforin in all but one species analysed from Euteleostomi, and present evidence for an earlier ortholog in Gnathostomata but not in more primitive chordates. In placental mammals perforin is a single copy gene, but there are multiple perforin genes in all lineages predating marsupials, except birds. Our comparisons of these many-to-one homologs of human perforin show that they mainly arose from lineagespecific gene duplications in multiple taxa, suggesting acquisition of new roles or different modes of regulation. We also present evidence that perforin arose from duplication of the ancient MPEG1 gene, and that it shares a common ancestor with the functionally related complement proteins. CONCLUSIONS: The evolution of perforin in vertebrates involved a complex pattern of gene, as well as intron, gain and loss. The primordial perforin gene arose at least 500 million years ago, at around the time that the major histocompatibility complex-T cell receptor antigen recognition system was established. As it is absent from primitive chordates and invertebrates, cytotoxic cells from these lineages must possess a different effector molecule or cytotoxic mechanism.     

Functional divergence of Populus MYB158 and MYB189 gene pair created by whole genome duplication

Whole genome duplication (WGD) providesnew genetic material for genome evolution. After a WGD event, some duplicates are lost, while other duplicates still persist and evolve diverse functions. A particular challenge is to understand how this diversity arises. This study identified two WGD-derived duplicates, MYB158 and MYB189, from Populus tomentosa. Populus MYB158 and MYB189 had expression divergence. Populus tomentosa overexpressing MYB158 or MYB189 had similar phenotypes: creep growth, decreased width of xylem and secondary cell wall thickness. Compared to wild-type, neither myb158 mutant nor myb158 myb189 double mutant showed obvious phenotypic variation in P. tomentosa. Although MYB158 and MYB189 proteins could repress the same structural genes involved in lignin, cellulose, and xylan biosynthesis, the two proteins had their own specific regulatory targets. Populus MYB158 could act as the upstream regulator of secondary cell wall NAC master switch and directly represses the expression of the SND1-B2 gene. Taken together, Populus MYB158 and MYB189 have retained similar functions in negatively regulating secondary cell wall biosynthesis, but have evolved partially distinct functions in direct regulation of NAC master switch, with MYB158 playing a more crucial role. Our findings provide new insights into the evolutionary and functional divergence of WGD-derived duplicate genes.