A transcript perspective on evolution

SimSpliceEvol2: alternative splicing-aware simulation of biological sequence evolution and transcript phylogenies

BACKGROUND

SimSpliceEvol is a tool for simulating the evolution of eukaryotic gene sequences that integrates exon-intron structure evolution as well as the evolution of the sets of transcripts produced from genes. It takes a guide gene tree as input and generates a gene sequence with its transcripts for each node of the tree, from the root to the leaves. However, the sets of transcripts simulated at different nodes of the guide gene tree lack evolutionary connections. Consequently, SimSpliceEvol is not suitable for evaluating methods for transcript phylogeny inference or gene phylogeny inference that rely on transcript conservation.

RESULTS

Here, we introduce SimSpliceEvol2, which, compared to the first version, incorporates an explicit model of transcript evolution for simulating alternative transcripts along the branches of a guide gene tree, as well as the transcript phylogenies inferred. We offer a comprehensive software with a graphical user interface and an updated version of the web server, ensuring easy and user-friendly access to the tool.

CONCLUSION

SimSpliceEvol2 generates synthetic datasets that are useful for evaluating methods and tools for spliced RNA sequence analysis, such as spliced alignment methods, methods for identifying conserved transcripts, and transcript phylogeny reconstruction methods. The web server is accessible at https://simspliceevol.cobius.usherbrooke.ca , where you can also download the standalone software. Comprehensive documentation for the software is available at the same address. For developers interested in the source code, which requires the installation of all prerequisites to run, it is provided at  https://github.com/UdeS-CoBIUS/SimSpliceEvol .

Orthology and Paralogy Relationships at Transcript Level

Eukaryotic genes undergo a mechanism called alternative processing, resulting in transcriptome diversity by allowing the production of multiple distinct transcripts from a gene. More than half of human genes are affected, and the resulting transcripts are highly conserved among orthologous genes of distinct species. In this work, we present the definition of orthology and paralogy between transcripts of homologous genes, together with an algorithm to compute clusters of conserved orthologous and paralogous transcripts. Gene-level homology relationships are utilized to define various types of homology relationships between transcripts originating from the same ancestral transcript. A Reciprocal Best Hits approach is employed to infer clusters of isoorthologous and recent paralogous transcripts. We applied this method to transcripts from simulated gene families as well as real gene families from the Ensembl-Compara database. The results are consistent with those from previous studies that compared orthologous gene transcripts. Furthermore, our findings provide evidence that searching for conserved transcripts between homologous genes, beyond the scope of orthologous genes, is likely to yield valuable information.

From pairwise to multiple spliced alignment

Motivation

Alternative splicing is a ubiquitous process in eukaryotes that allows distinct transcripts to be produced from the same gene. Yet, the study of transcript evolution within a gene family is still in its infancy. One prerequisite for this study is the availability of methods to compare sets of transcripts while accounting for their splicing structure. In this context, we generalize the concept of pairwise spliced alignments (PSpAs) to multiple spliced alignments (MSpAs). MSpAs have several important purposes in addition to empowering the study of the evolution of transcripts. For instance, it is a key to improving the prediction of gene models, which is important to solve the growing problem of genome annotation. Despite its essentialness, a formal definition of the concept and methods to compute MSpAs are still lacking.

Results

We introduce the MSpA problem and the SplicedFamAlignMulti (SFAM) method, to compute the MSpA of a gene family. Like most multiple sequence alignment (MSA) methods that are generally greedy heuristic methods assembling pairwise alignments, SFAM combines all PSpAs of coding DNA sequences and gene sequences of a gene family into an MSpA. It produces a single structure that represents the superstructure and models of the gene family. Using real vertebrate and simulated gene family data, we illustrate the utility of SFAM for computing accurate gene family superstructures, MSAs, inferring splicing orthologous groups and improving gene-model annotations.

Availability and implementation

The supporting data and implementation of SFAM are freely available at https://github.com/UdeS-CoBIUS/SpliceFamAlignMulti.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.

Transcripts' Evolutionary History and Structural Dynamics Give Mechanistic Insights into the Functional Diversity of the JNK Family

Alternative splicing and alternative initiation/termination transcription sites have the potential to greatly expand the proteome in eukaryotes by producing several transcript isoforms from the same gene. Although these mechanisms are well described at the genomic level, little is known about their contribution to protein evolution and their impact at the protein structure level. Here, we address both issues by reconstructing the evolutionary history of transcripts and by modeling the tertiary structures of the corresponding protein isoforms. We reconstruct phylogenetic forests relating 60 protein-coding transcripts from the c-Jun N-terminal kinase (JNK) family observed in seven species. We identify two alternative splicing events of ancient origin and show that they induce subtle changes in the protein's structural dynamics. We highlight a previously uncharacterized transcript whose predicted structure seems stable in solution. We further demonstrate that orphan transcripts, for which no phylogeny could be reconstructed, display peculiar sequence and structural properties. Our approach is implemented in PhyloSofS (Phylogenies of Splicing Isoforms Structures), a fully automated computational tool freely available at https://github.com/PhyloSofS-Team/PhyloSofS.

SimSpliceEvol: alternative splicing-aware simulation of biological sequence evolution

Background

It is now well established that eukaryotic coding genes have the ability to produce more than one type of transcript thanks to the mechanisms of alternative splicing and alternative transcription. Because of the lack of gold standard real data on alternative splicing, simulated data constitute a good option for evaluating the accuracy and the efficiency of methods developed for splice-aware sequence analysis. However, existing sequence evolution simulation methods do not model alternative splicing, and so they can not be used to test spliced sequence analysis methods.

Results

We propose a new method called SimSpliceEvol for simulating the evolution of sets of alternative transcripts along the branches of an input gene tree. In addition to traditional sequence evolution events, the simulation also includes gene exon-intron structure evolution events and alternative splicing events that modify the sets of transcripts produced from genes. SimSpliceEvol was implemented in Python. The source code is freely available at https://github.com/UdeS-CoBIUS/SimSpliceEvol.

Conclusions

Data generated using SimSpliceEvol are useful for testing spliced RNA sequence analysis methods such as methods for spliced alignment of cDNA and genomic sequences, multiple cDNA alignment, orthologous exons identification, splicing orthology inference, transcript phylogeny inference, which requires to know the real evolutionary relationships between the sequences.

Aligning coding sequences with frameshift extension penalties

BACKGROUND

Frameshift translation is an important phenomenon that contributes to the appearance of novel coding DNA sequences (CDS) and functions in gene evolution, by allowing alternative amino acid translations of gene coding regions. Frameshift translations can be identified by aligning two CDS, from a same gene or from homologous genes, while accounting for their codon structure. Two main classes of algorithms have been proposed to solve the problem of aligning CDS, either by amino acid sequence alignment back-translation, or by simultaneously accounting for the nucleotide and amino acid levels. The former does not allow to account for frameshift translations and up to now, the latter exclusively accounts for frameshift translation initiation, not considering the length of the translation disruption caused by a frameshift.

RESULTS

We introduce a new scoring scheme with an algorithm for the pairwise alignment of CDS accounting for frameshift translation initiation and length, while simultaneously considering nucleotide and amino acid sequences. The main specificity of the scoring scheme is the introduction of a penalty cost accounting for frameshift extension length to compute an adequate similarity score for a CDS alignment. The second specificity of the model is that the search space of the problem solved is the set of all feasible alignments between two CDS. Previous approaches have considered restricted search space or additional constraints on the decomposition of an alignment into length-3 sub-alignments. The algorithm described in this paper has the same asymptotic time complexity as the classical Needleman-Wunsch algorithm.

CONCLUSIONS

We compare the method to other CDS alignment methods based on an application to the comparison of pairs of CDS from homologous human, mouse and cow genes of ten mammalian gene families from the Ensembl-Compara database. The results show that our method is particularly robust to parameter changes as compared to existing methods. It also appears to be a good compromise, performing well both in the presence and absence of frameshift translations. An implementation of the method is available at https://github.com/UdeS-CoBIUS/FsePSA.