Patterns of intron gain and conservation in eukaryotic genes

Background:  

The presence of introns in protein-coding genes is a universal feature of eukaryotic genome organization, and the genes of multicellular eukaryotes, typically, contain multiple introns, a substantial fraction of which share position in distant taxa, such as plants and animals. Depending on the methods and data sets used, researchers have reached opposite conclusions on the causes of the high fraction of shared introns in orthologous genes from distant eukaryotes. Some studies conclude that shared intron positions reflect, almost entirely, a remarkable evolutionary conservation, whereas others attribute it to parallel gain of introns. To resolve these contradictions, it is crucial to analyze the evolution of introns by using a model that minimally relies on arbitrary assumptions.     

Evolutionary conservation suggests a regulatory function of AUG triplets in 5'-UTRs of eukaryotic genes

By comparing sequences of human, mouse and rat orthologous genes, we show that in 5′-untranslated regions (5′-UTRs) of mammalian cDNAs but not in 3′-UTRs or coding sequences, AUG is conserved to a significantly greater extent than any of the other 63 nt triplets. This effect is likely to reflect, primarily, bona fide evolutionary conservation, rather than cDNA annotation artifacts, because the excess of conserved upstream AUGs (uAUGs) is seen in 5′-UTRs containing stop codons in-frame with the start AUG and many of the conserved AUGs are found in different frames, consistent with the location in authentic non-coding sequences. Altogether, conserved uAUGs are present in at least 20–30% of mammalian genes. Qualitatively similar results were obtained by comparison of orthologous genes from different species of the yeast genus Saccharomyces. Together with the observation that mammalian and yeast 5′-UTRs are significantly depleted in overall AUG content, these findings suggest that AUG triplets in 5′-UTRs are subject to the pressure of purifying selection in two opposite directions: the uAUGs that have no specific function tend to be deleterious and get eliminated during evolution, whereas those uAUGs that do serve a function are conserved. Most probably, the principal role of the conserved uAUGs is attenuation of translation at the initiation stage, which is often additionally regulated by alternative splicing in the mammalian 5′-UTRs. Consistent with this hypothesis, we found that open reading frames starting from conserved uAUGs are significantly shorter than those starting from non-conserved uAUGs, possibly, owing to selection for optimization of the level of attenuation.     

A probabilistic measure for alignment-free sequence comparison

MOTIVATION: Alignment-free sequence comparison methods are still in the early stages of development compared to those of alignment-based sequence analysis. In this paper, we introduce a probabilistic measure of similarity between two biological sequences without alignment. The method is based on the concept of comparing the similarity/dissimilarity between two constructed Markov models. RESULTS: The method was tested against six DNA sequences, which are the thrA, thrB and thrC genes of the threonine operons from Escherichia coli K-12 and from Shigella flexneri; and one random sequence having the same base composition as thrA from E.coli. These results were compared with those obtained from CLUSTAL W algorithm (alignment-based) and the chaos game representation (alignment-free). The method was further tested against a more complex set of 40 DNA sequences and compared with other existing sequence similarity measures (alignment-free). AVAILABILITY: All datasets and computer codes written in MATLAB are available upon request from the first author.     

Y chromosomal fertility genes of Drosophila: a new type of eukaryotic genes

The Y chromosomal fertility genes of Drosophila are required for sperm differentiation. They are active only in primary spermatocytes where they form giant lampbrush loops. The molecular structure of these genes was investigated and revealed an unusual composition of DNA. Short, tandemly repeated sequence clusters are interrupted by longer and more heterogeneous sequences, which probably all represent transposable elements. No indication of the presence of protein-coding regions has been found within the fertility genes. However, the lampbrush loops bind site-specific proteins recognized by immunofluorescence techniques. This, together with other experimental data, led to the hypothesis that the Y chromosomal genes have a function in binding chromosomal proteins. The data and arguments in support of this gene model are summarized in this paper.     

Detecting interspecific recombination with a pruned probabilistic divergence measure

MOTIVATION: A promising sliding-window method for the detection of interspecific recombination in DNA sequence alignments is based on the monitoring of changes in the posterior distribution of tree topologies with a probabilistic divergence measure. However, as the number of taxa in the alignment increases or the sliding-window size decreases, the posterior distribution becomes increasingly diffuse. This diffusion blurs the probabilistic divergence signal and adversely affects the detection accuracy. The present study investigates how this shortcoming can be redeemed with a pruning method based on post-processing clustering, using the Robinson-Foulds distance as a metric in tree topology space. RESULTS: An application of the proposed scheme to three synthetic and two real-world DNA sequence alignments illustrates the amount of improvement that can be obtained with the pruning method. The study also includes a comparison with two established recombination detection methods: Recpars and the DSS (difference of sum of squares) method. AVAILABILITY: Software, data and further supplementary material are available at the following website: http://www.bioss.sari.ac.uk/~dirk/Supplements/     

yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes

Your Gene structure Annotation Tool for Eukaryotes (yrGATE) provides an Annotation Tool and Community Utilities for worldwide web-based community genome and gene annotation. Annotators can evaluate gene structure evidence derived from multiple sources to create gene structure annotations. Administrators regulate the acceptance of annotations into published gene sets. yrGATE is designed to facilitate rapid and accurate annotation of emerging genomes as well as to confirm, refine, or correct currently published annotations. yrGATE is highly portable and supports different standard input and output formats. The yrGATE software and usage cases are available at .     

eGOB: eukaryotic Gene Order Browser

A large number of genomes have been sequenced, allowing a range of comparative studies. Here, we present the eukaryotic Gene Order Browser with information on the order of protein and non-coding RNA (ncRNA) genes of 74 different eukaryotic species. The browser is able to display a gene of interest together with its genomic context in all species where that gene is present. Thereby, questions related to the evolution of gene organization and non-random gene order may be examined. The browser also provides access to data collected on pairs of adjacent genes that are evolutionarily conserved. AVAILABILITY: eGOB as well as underlying data are freely available at http://egob.biomedicine.gu.se SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: tore.samuelsson@medkem.gu.se.     

Genomics for conservation: a case study of behavioral genes in the Tasmanian devil

The increased availability of genomic resources for many species has expanded perspectives on problems in conservation by helping to design management strategies for threatened species. Tasmanian devils (Sarcophilus harrisii) are an iconic and endangered marsupial with an intensively managed breeding program aimed at preventing extinction in the wild caused by devil facial tumour disease. Between 2015 and 2017, 85 devils from this program were released to three sites in Tasmania to support wild populations. Of these, 26 were known to have been killed by vehicles shortly after release. A previous analysis indicated that increased generations in captivity was a positive predictor of vehicle strike, with possible behavioural change hypothesised. Here we use 39 resequenced devil genomes to characterise diversity at 35 behaviour-associated genes, which contained 826 single nucleotide polymorphisms (24 were non-synonymous). We tested for a predictor of survival by examining three genes (AVPR1B, OXT and SLC6A4) in 62 released devils with known fates (survived, N?=?39; died, N?=?23), and genome-wide associations via reduced-representation sequencing (1727 single nucleotide polymorphisms [SNPs]), in 55 devils with known fates (survived, N?=?38; died, N?=?17). Overall, there was little evidence of an association between genetic profile and probability of being struck by a vehicle. Despite previous evidence of low genetic diversity in devils, the 35 behaviour-associated genes contained variation that may influence their functions. Our dataset can be used for future research into devil behavioural ecology, and adds to the increasing body of research applying genomics to conservation problems.

     

Individual fertility rate: a new individual fertility measure for small populations

Fertility measurement in small preindustrial societies is hampered by small numbers and the lack of some essential data. Most measures of fertility are collective and require large enough populations to permit grouped data analysis. Existing individual measures of fertility are often unsatisfactory. This paper presents a new measure of individual fertility, the Individual Fertility Rate (IFR), which is constructed by dividing parity by reproductive span in years and multiplying the product by 100. The result is a number which may be used as a dependent individual or cumulative variable to study the effects of health and socioeconomic factors on fertility.     

Cloning of eukaryotic genes in single-strand phage vectors: the human interferon genes

Using oligonucleotide probes with defined sequences, we have selected clones from a human lymphocyte cDNA library which represent human leukocyte (HuIFN-α) and fibroblast (HuIFN-β) interferon gene sequences. Double-stranded f1 phage DNA was used as the vector for initial cloning of cDNA. Clones carrying interferon gene sequences were identified by hybridization with the oligonucleotide probes. The same oligonucleotide probes were used as primers for dideoxy chain termination sequencing of the clones. One HuIFN-α clone, 201, has a nucleotide sequence different from published HuIFN-α sequences. Under control of the lacUV5 promoter, the 201 gene has been used to express biologically active HuIFN-α in Escherichia coli.     

Remarkable interkingdom conservation of intron positions and massive,lineage-specific intron loss and gain in eukaryotic evolution

Sequencing of eukaryotic genomes allows one to address major evolutionary problems, such as the evolution of gene structure. We compared the intron positions in 684 orthologous gene sets from 8 complete genomes of animals, plants, fungi, and protists and constructed parsimonious scenarios of evolution of the exon-intron structure for the respective genes. Approximately one-third of the introns in the malaria parasite Plasmodium falciparum are shared with at least one crown group eukaryote; this number indicates that these introns have been conserved through >1.5 billion years of evolution that separate Plasmodium from the crown group. Paradoxically, humans share many more introns with the plant Arabidopsis thaliana than with the fly or nematode. The inferred evolutionary scenario holds that the common ancestor of Plasmodium and the crown group and, especially, the common ancestor of animals, plants, and fungi had numerous introns. Most of these ancestral introns, which are retained in the genomes of vertebrates and plants, have been lost in fungi, nematodes, arthropods, and probably Plasmodium. In addition, numerous introns have been inserted into vertebrate and plant genes, whereas, in other lineages, intron gain was much less prominent.     

EuSplice: a unified resource for the analysis of splice signals and alternative splicing in eukaryotic genes

MOTIVATION: Despite increased availability of genome annotation data, a comprehensive resource for in-depth analysis of splice signal distributions and alternative splicing (AS) patterns in eukaryote genomes is still lacking. To meet this need, we have developed EuSplice--a unique splice-centric database which provides reliable splice signal and AS information for 23 eukaryotes. RESULTS: The EuSplice database contains 95,822 AS events and 2.1 million splice signals associated with over 270,000 protein-coding genes. The intuitive, user-friendly EuSplice web interface has powerful data mining and graphics capabilities for inter-genomic comparative analysis of splice signals, putative cryptic splice sites and AS events. Moreover, the seamless integration of splicing data to extensive gene-specific annotations, such as homolog annotations, functional information, mutations and sequence details makes EuSplice a powerful one-stop information resource for investigating the molecular mechanisms of complex splicing events, disease associations and the evolution of splicing in eukaryotes. AVAILABILITY: http://66.170.16.154/EuSplice. SUPPLEMENTARY INFORMATION: Supplementary tables and figures at Bioinfo online.     

Genome SEGE: A database for 'intronless' genes in eukaryotic genomes

Background  

A number of completely sequenced eukaryotic genome data are available in the public domain. Eukaryotic genes are either 'intron containing' or 'intronless'. Eukaryotic 'intronless' genes are interesting datasets for comparative genomics and evolutionary studies. The SEGE database containing a collection of eukaryotic single exon genes is available. However, SEGE is derived using GenBank. The redundant, incomplete and heterogeneous qualities of GenBank data are a bottleneck for biological investigation in comparative genomics and evolutionary studies. Such studies often require representative gene sets from each genome and this is possible only by deriving specific datasets from completely sequenced genome data. Thus Genome SEGE, a database for 'intronless' genes in completely sequenced eukaryotic genomes, has been constructed.     

Inhibitor of apoptosis proteins in eukaryotic evolution and development: a model of thematic conservation

The past decade and a half has witnessed the discovery of a large, evolutionarily conserved family of cellular genes bearing homology to the prototype baculovirus Inhibitor of Apoptosis (IAP). The logical decision in the field to also refer to these cellular proteins as IAPs fails to do justice to this versatile group of factors that play a wide range of roles in eukaryotic development and homeostasis which include, but are not limited to, the regulation of programmed cell death. Here we describe the shared functional characteristics of several well-characterized IAPs whose defining motifs place them more in the category of multifunctional modular protein interaction domains.     

A general tendency for conservation of protein length across eukaryotic kingdoms

Protein elongation can occur in many ways, such as domain duplication or insertion and as recruitment of a transposable element fragment into the coding region, and it is believed to be a general tendency in protein evolution. Indeed, a previous study showed that yeast proteins are, on average, longer than their orthologs in bacteria, and in this study, we found that proteins in yeast, nematode, Drosophila, human, and Arabidopsis are, on average, longer than their orthologs in Escherichia coli. Surprisingly, however, we found conservation of protein sequence length across eukaryotic kingdoms. We collected 1,252 orthologous proteins from yeast, nematode, Drosophila, human, and Arabidopsis and found that the total length of these proteins is very similar among the five species and that there is no general tendency for a protein to increase or decrease in length. Furthermore, although paralogous proteins tend to undergo more sequence-length changes, there is also no general tendency for length increase. However, proteins that are commonly shared by Drosophila and human but not by yeast are, on average, substantially longer than proteins that are shared by yeast, Drosophila, and human. This is a puzzle that begs for an answer.     

Widespread conservation of genetic redundancy during a billion years of eukaryotic evolution

Genetic redundancy means that two genes can perform the same function. Using a comprehensive phylogenetic analysis, we show here in both Saccharomyces cerevisiae and Caenorhabditis elegans that genetic redundancy is not just a transient consequence of gene duplication, but is often an evolutionary stable state. In multiple examples, genes have retained redundant functions since the divergence of the animal, plant and fungi kingdoms over a billion years ago. The stable conservation of genetic redundancy contrasts with the more rapid evolution of genetic interactions between unrelated genes and can be explained by theoretical models including a 'piggyback' mechanism in which overlapping redundant functions are co-selected with nonredundant ones.     

Evolution of the intron-exon structure of eukaryotic genes

The origin and evolution of intron-exon structures continue to be controversial topics. Two alternative theories, the ‘exon theory of genes’ and the ‘insertional theory of introns’, debate the presence or absence of introns in primordial genes. Both sides of the argument have focused on the positions of introns with respect to protein and gene structures. A new approach has emerged in the study of the evolution of intron-exon structures: a population analysis of genes. One example is the statistical analysis of intron phases — the position of introns within or between codons. This analysis detected a significant signal of exon shuffling in the DNA sequence database containing both ancient and modern exon sequences: intron phase correlations, that is, the association together within genes of introns of the same phase. The results of this analysis suggest that exon shuffling played an important role in the origin of both ancient and modern genes.