- Intron and gene size expansion during nervous system evolution. - Background: The evolutionary radiation of animals was accompanied by extensive expansion of gene and genome sizes, increased isoform diversity, and complexity of regulation.. - Conclusions: We find that intron and gene size expansion is a feature of many genes whose expression is enriched in nervous systems. - The evolutionary consequences of gene size expansion are still being uncovered. - This phenomenon, termed intron delay, biases patterns of expression and evolution of gene structure for a substantial portion of the transcriptome [12, 13]. - To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.. - The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.. - expression of the longest genes is enriched in neuronal tissues [7, 14–17]. - Additionally, we show that net expansion of neuronal intron and gene size is a feature of many nervous systems.. - We examined gene expression as a function of gene length (see Gene Expression Analysis in Methods) in multiple tissues for diverse animals and found that as gene length increases, so does expression enrichment in neuronal tissues (Fig. - As observed in comparing read counts in different tissues with annotated gene lengths, both assembled genomes exhibit enrichment for neur- onal transcripts in size ranges at the high end of the gene-length distribution (e.g. - Together, these observa- tions support either an ancient origin of neuronal long gene preference dating back to the evolution of the first nervous systems or convergence toward this phenomenon in multiple animal lineages.. - 2-fold, Additional file 3: Figure S2).. - elegans genes is evident, as is some indication of neuronal enrichment in the longest genes (Fig. - A detailed tissue-specific intron and gene length analysis was also possible for Zea mays (Fig. - We chose a measurement of gene length span- ning the start of the first exon to the end of the last exon, in part to avoid known differences in annotation completeness of untranslated regions (UTRs) [39]. - Gene length variation was most dramatic for the top 10% lon- gest genes, which were an order of magnitude longer in vertebrates ( x kb) compared to non- animal eukaryotes ( x kb)(Fig. - Consist- ent with other reports [39, 40], the vast majority of the increases in gene length are intronic (Fig. - 2c), with in- creases in intron length coinciding with increases in the average number of exons per gene (Fig. - Additional file 8: Figure S7). - Many of the observed differences were consistent within species of the same clade, some of which include more extensively annotated organisms (e.g. - Although the evolutionary dynamics of gene size expan- sion alone do not explain how the longest genes became enriched for neuronal expression in particular, the ob- served median sizes are consistent with metazoan gene size expansion beginning during the evolutionary diver- gence of animals in the Precambrian eon [41]. - Together with evidence of neuronal long gene expression in verte- brates and invertebrates, this suggests that intron and gene size expansion of neuronal genes could have begun during the evolution of the first nervous systems.. - Determining the individual and collective contribution of these forces is not trivial, with a primary challenge coming from the currently necessary use of static distri- butions of gene sizes across Eukarya as presented here.. - These previous observations have contributed to hypotheses regarding the role of alternative splicing in the evolution of overall phenotypic complexity [45, 46]. - 1 Neuronal intron and gene size expansion in diverse animal species. - a Expression of the longest genes is enriched in neuronal tissues of vertebrates and invertebrates. - Genes were segregated into 100 bins according to gene length, and points show average gene length of each bin. - Branch lengths for the phylogenetic tree were obtained from TimeTree.org [22]. - Genes with only slight expression fold-difference of the top expressing tissue over the next highest-expressing tissue (<. - Conversely, hagfish (Eptatretus burgeri) have one of the larger median gene lengths (Fig. - While these examples highlight several parameters potentially affecting the dy- namics of gene and genome size evolution at the organ- ismal level, our study indicates that biological parameters at the tissue and cellular level may also shape aspects of gene and genome architecture.. - The molecular components of nervous systems are similar across animals despite vast differences in ner- vous system complexity, with some of the same sets of proteins and signaling molecules being used re- peatedly in different contexts [53]. - Intron and gene size expansion provide one mechanism by which existing components can be modified to increase transcriptomic potential from a limited gene comple- ment, contributing to the evolution of novelty [6, 54]. - In this study, we show that many of the longest genes are preferentially expressed in neuronal tissues across diverse verte- brates and invertebrates. - Orthologs of the human NRXN1 gene were obtained by using the Drosophila RNAi Screening Center Integrative Ortholog Prediction Tool (DIOPT, version which integrates ortholog predictions from Ensembl Compara, HomoloGene, Inparanoid, Isobase, OMA, orthoMCL, Phylome, RoundUp, and TreeFam. - Gene expression analysis. - Smoothed conditional means of gene expression con- ditional on gene length (or gene length percentiles) were estimated using the ‘geom_smooth’ function from R package ggplot2 version 2.2.1 [63]. - 2 Differential gene size expansion during animal evolution. - a Phylogenomic tree showing median gene length of the top 10% longest genes in each genome as a bargraph. - Branch lengths were obtained from TimeTree.org [22], and scale bar shows 100 million years. - b Boxplots of median gene length of long genes of each genome in kilobases aggregated by clade. - This extends similar analyses by Lynch et al. - Gene start posi- tions were subtracted from gene end positions to obtain a measure of gene length for each gene that excludes 5′. - The branch lengths obtained from TimeTree.org [22]. - were combined with gene length annotations using the. - Supplementary information accompanies this paper at https://doi.org/10.. - Additional file 1: Figure S1. - Additional file 2: Table S1. - Additional file 3: Figure S2. - Additional file 4: Figure S3. - Non-smooth-quantile-normalized gene ex- pression conditional on gene length. - (A) Genes were segregated into 100 bins according to gene length (kb), and points show average gene length of each bin. - Additional file 5: Figure S4. - Non-smooth-quantile-normalized gene ex- pression conditional on gene length quantiles. - (A) Genes were segregated into 100 bins according to gene length, and points show average gene length of each bin. - (B) Loess smoothing of gene expres- sion conditional on gene length quantiles. - (C) Generalized additive model of gene expression conditional on gene length quantiles.. - Additional file 6: Figure S5. - Smooth-quantile-normalized gene expres- sion conditional on gene length. - Additional file 7: Figure S6. - Smooth-quantile-normalized gene expres- sion conditional on gene length quantiles. - (A) Genes were segre- gated into 100 bins according to gene length, and points show average gene length of each bin. - (B) Loess smoothing of gene expression condi- tional on gene length quantiles. - Additional file 8: Figure S7. - Joy plots showing distribution of gene features (median gene length, median intron length, median exon length, median number of exons per gene, and number of genes).. - MJM conceived of the study. - The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.. - Gene length and expression level shape genomic novelties. - Available from: https://elifesciences.org/articles/38619.. - Transcript length mediates developmental timing of gene expression across Drosophila. - Gene Length Matters in Neurons. - an R package for interactive gene length dependent analysis for neuronal identity. - Petryszak R, Keays M, Tang YA, Fonseca NA, Barrera E, Burdett T, et al.. - Expression atlas update — an integrated database of gene and protein expression in humans, animals and plants. - Papatheodorou I, Fonseca NA, Keays M, Tang YA, Barrera E, Bazant W, et al.. - Available from:. - https://commons.wikimedia.org/wiki/File:Female_shadow.png. - Depiction by MJM, https://creativecommons.org/publicdomain/zero/1.0/legalcode.. - Available from: https://commons.wikimedia.org/wiki/File:Cow_female_black_. - Depiction by MJM, https://creativecommons.org/publicdomain/. - Available from: https://commons.wikimedia.org/wiki/File:Monodelphis_domestica93-3 00.jpg. - Available from: https://commons.wikimedia.org/wiki/File:Gallus_gallus_. - Depiction by MJM, https://creativecommons.org/licenses/. - Available from: https://commons.wikimedia.org/wiki/File:Green_anole.jpg. - Depiction by MJM, https://creativecommons.org/licenses/by-sa/3.0/legalcode.. - Available from: https://commons.wikimedia.org/wiki/File:. - creativecommons.org/publicdomain/zero/1.0/legalcode.. - creativecommons.org/licenses/by-sa/2.5/legalcode.. - Available from: https://. - commons.wikimedia.org/wiki/File:Zea_mays_004.JPG. - The anatomy of the nervous system of Octopus vulgaris. - Available from: https://doi.org . - On the formation of novel genes by duplication in the Caenorhabditis elegans genome. - Sequence, structural and expression divergence of duplicate genes in the bovine genome. - The evolution of gene expression levels in mammalian organs. - Evolutionary dynamics of gene and isoform regulation in mammalian tissues. - Massively parallel sequencing of the polyadenylated transcriptome of C. - RNA sequencing of laser-capture microdissected compartments of the maize kernel identifies regulatory modules associated with endosperm cell differentiation. - Available from: https://colorbrewer2.org/#.
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