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49 results for “gene family evolution”
Data for phylogenomic analysis of chelicerate gene family evolution
<p>We used phylogenomics to investigate patterns of gene family evolution across ticks and other chelicerates, which include a diverse array of parasites. We used phylogenetic profiling and trait-association tests to predict gene families that may enable parasitic species to feed on hosts undetected for prolonged periods (>1 day). This release accompanies the pub, “<a href="https://doi.org/10.57844/arcadia-4e3b-bbea">Comparative phylogenomic analysis of Chelicerates points to gene families associated with long-term suppression of host detection</a>." Please see the pub for more information.</p> <ul> <li>chelicerata-v1-10062023.zip contains the outputs from NovelTree that are needed as inputs for phylogenetic profiling.</li> <li>annotated.zip contains gene annotations used to do orthogroup filtering.</li> <li>tx2gene.tsv has presence/absence of expression for each Amblyomma americanum transcript. </li> <li>chelicerate_proteome_preprocessing_outputs.zip contains the outputs of chelicerate protein data curation.</li> <li>chelicerata-v1-parameterfile.json & chelicerata-v1-samplesheet.csv were inputs for setting up the initial NovelTree run.</li> <li>2024-06-24-all-chelicerate-noveltree-proteins.fasta has the full set of chelicerate protein sequences.</li> <li>summary_of_noveltree_results.zip contains summary figures from the outputs of the NovelTree run.</li> <li>chelicerate-samples.tsv is the sample sheet used in proteome curation upstream of NovelTree.</li> </ul>
Data from: The multilocus multispecies coalescent: a flexible new model of gene family evolution
<p>Incomplete lineage sorting (ILS), the interaction between coalescence and speciation, can generate incongruence between gene trees and species trees, as can gene duplication (D), transfer (T) and loss (L). These processes are usually modelled independently, but in reality, ILS can affect gene copy number polymorphism, i.e., interfere with DTL. This has been previously recognised, but not treated in a satisfactory way, mainly because DTL events are naturally modelled forward-in-time, while ILS is naturally modelled backwards-in-time with the coalescent. Here we consider the joint action of ILS and DTL on the gene tree/species tree problem in all its complexity. In particular, we show that the interaction between ILS and duplications/transfers (without losses) can result in patterns usually interpreted as resulting from gene loss, and that the realised rate of D, T and L becomes non-homogeneous in time when ILS is taken into account. We introduce algorithmic solutions to these problems. Our new model, the <em>multilocus multispecies coalescent</em> (MLMSC), which also accounts for any level of linkage between loci, generalises the multispecies coalescent model and offers a versatile, powerful framework for proper simulation and inference of gene family evolution.</p>
Data from: Targeted enrichment of large gene families for phylogenetic inference: phylogeny and molecular evolution of photosynthesis genes in the Portullugo clade (Caryophyllales)
Hybrid enrichment is an increasingly popular approach for obtaining hundreds of loci for phylogenetic analysis across many taxa quickly and cheaply. The genes targeted for sequencing are typically single-copy loci, which facilitate a more straightforward sequence assembly and homology assignment process. However, this approach limits the inclusion of most genes of functional interest, which often belong to multi-gene families. Here we demonstrate the feasibility of including large gene families in hybrid enrichment protocols for phylogeny reconstruction and subsequent analyses of molecular evolution, using a new set of bait sequences designed for the "portullugo" (Caryophyllales), a moderately sized lineage of flowering plants (∼2200 species) that includes the cacti and harbors many evolutionary transitions to C4 and CAM photosynthesis. Including multi-gene families allowed us to simultaneously infer a robust phylogeny and construct a dense sampling of sequences for a major enzyme of C4 and CAM photosynthesis, which revealed the accumulation of adaptive amino acid substitutions associated with C4 and CAM origins in particular paralogs. Our final set of matrices for phylogenetic analyses included 75–218 loci across 74 taxa, with ∼50% matrix completeness across datasets. Phylogenetic resolution was greatly improved across the tree, at both shallow and deep levels. Concatenation and coalescent-based approaches both resolve the sister lineage of the cacti with strong support: Anacampserotaceae + Portulacaceae, two lineages of mostly diminutive succulent herbs of warm, arid regions. In spite of this congruence, BUCKy concordance analyses demonstrated strong and conflicting signals across gene trees. Our results add to the growing number of examples illustrating the complexity of phylogenetic signals in genomic-scale data.
The evolution of multi-gene families and metabolic pathways in the evening primroses (Oenothera: Onagraceae): a comparative transcriptomics approach
<p>The plant genus <em>Oenothera</em> has played an important role in the study of genome evolution and plant defense and reproduction. Here, we built on the 1kp transcriptomic dataset and developed a molecular resource of 63 transcriptomes and present a large-scale comparative study across 29 <em>Oenothera</em> species. We produced 2.3 million transcripts and 25.4 Mb of total length assembly per individual. We used this transcriptome resource to examine genome-wide evolutionary patterns and functional diversification by searching for orthologous genes and performed gene family evolution analysis. We found wide heterogeneity in gene family evolution across the genus, with section <em>Oenothera </em>exhibiting the most pronounced evolutionary changes. Overall, more significant expansions occurred than contractions. We also analyzed the molecular evolution of phenolic metabolism by retrieving proteins annotated for phenolic enzymatic complexes. We identified 1,568 phenolic genes arranged into 83 multigene families that varied widely across the genus. All taxa experienced rapid phenolic evolution involving 33 gene families, which exhibited large expansions, gaining about 2-fold more genes than they lost. Upstream enzymes phenylalanine ammonia-lyase (PAL) and 4-coumaroyl: CoA ligase (4CL) accounted for most of the significant expansions and contractions. Our results suggest that adaptive responses to environmental stress coupled with non-adaptive evolutionary forces have contributed to <em>Oenothera </em>diversification and rapid gene family evolution.</p>
Data from: The effect of copy number hemiplasy on gene family evolution
<p>The evolution of gene families is complex, involving gene-level evolutionary events such as gene duplication, horizontal gene transfer, and gene loss (DTL), and other processes such as incomplete lineage sorting (ILS). Because of this, topological differences often exist between gene trees and species trees. A number of models have been recently developed to explain these discrepancies, the most realistic of which attempt to consider both gene-level events and ILS. When unified in a single model, the interaction between ILS and gene-level events can cause polymorphism in gene copy number, which we refer to as copy number hemiplasy (CNH).</p> <p>In this paper we extend the Wright-Fisher process to include duplications and losses over several species, and show that the probability of CNH for this process can be significant. We study how well two unified models --- MLMSC (MultiLocus MultiSpecies Coalescent), which models CNH, and DLCoal (Duplication, Loss, and Coalescence), which does not --- approximate the Wright-Fisher process with duplication and loss.</p> <p>We then study the effect of CNH on gene family evolution by comparing MLMSC and DLCoal. We generate comparable gene trees under both models, showing significant differences in various summary statistics; most importantly, CNH reduces the number of gene copies greatly. If this is not taken into account, the traditional method of estimating duplication rates (by counting the number of gene copies) becomes inaccurate. The simulated gene trees are also used for species tree inference with the summary methods ASTRAL and ASTRAL-Pro, demonstrating that their accuracy, based on CNH-unaware simulations calibrated on real data, may have been overestimated.}</p>
A new genome of an African weakly electric fish (Campylomormyrus compressirostris, Mormyridae) indicates rapid gene family evolution in Osteoglossomorpha
Background <p>Teleost fishes comprise more than half of the vertebrate species. Within teleosts, most phylogenies consider the split between Osteoglossomorpha and Euteleosteomorpha/Otomorpha as basal, preceded only by the derivation of the most primitive group of teleosts, the Elopomorpha. While Osteoglossomorpha are generally species-poor, the taxon contains the African weakly electric fish (Mormyroidei), which have radiated into numerous species. Within the mormyrids, the genus <em>Campylomormyrus</em> is mostly endemic to the Congo Basin. <em>Campylomormyrus</em> serves as a model to understand mechanisms of adaptive radiation and ecological speciation, especially with regard to its highly diverse species-specific electric organ discharges (EOD). Currently, there are few well-annotated genomes available for electric fish in general and mormyrids in particular. Our study aims at producing a high-quality genome and to use this to examine genome evolution in relation to other teleosts. This will facilitate further understanding of the evolution of the osteoglossomorph fish in general and of electric fish in particular.</p> Results <p>A high-quality weakly electric fish (<em>C. compressirostris</em>) genome was produced from a single individual with a genome size of 862Mb, consisting of 1,497 contigs with an N50 of 1,399 kb and a GC-content of 43.69%. Gene predictions identified 34,492 protein-coding genes, which is a higher number than in the two other available Osteoglossomorpha genomes of <em>Paramormyrops</em> <em>kingsleyae</em> and <em>Scleropages</em> <em>formosus</em>. A CAFE5 analysis of gene family evolution comparing 33 teleost fish genomes suggests an overall faster gene family turnover rate in Osteoglossomorpha than in Otomorpha and Euteleosteomorpha. Moreover, the ratios of expanded/contracted gene family numbers in Osteoglossomorpha are significantly higher than in the other two taxa, except for species that had undergone an additional genome duplication (<em>Cyprinus</em> <em>carpio</em> and <em>Oncorhynchus</em> <em>mykiss</em>). As potassium channel proteins are hypothesized to play a key role in EOD diversity among species, we put a special focus on them, and manually curated 16 Kv1 genes. We identified a tandem duplication in the KCNA7a gene in the genome of <em>C</em>. <em>compressirostris</em>.</p> Conclusions <p>We present the fourth genome of an electric fish and the third well-annotated genome for Osteoglossomorpha, enabling us to compare gene family evolution among major teleost lineages. Osteoglossomorpha appears to exhibit rapid gene family evolution, with more gene family expansions than contractions. The curated Kv1 gene family showed seven gene clusters, which is more than in other analyzed fish genomes outside Osteoglossomorpha. The KCNA7a, encoding for a potassium channel central for EOD production and modulation, is tandemly duplicated which may related to the diverse EOD observed among <em>Campylomormyrus</em> species.</p>
Data from: Evolution of five environmentally responsive gene families in a pine-feeding sawfly, Neodiprion lecontei (Hymenoptera: Diprionidae)
<p>A central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly <em>Neodiprion lecontei</em>, a non-eusocial hymenopteran and exemplar of a pine-specialized lineage evolved from angiosperm-feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions before characterizing their genomic distributions and molecular evolution. We find evidence of recent expansions of bitter gustatory receptor (GR), clan 3 cytochrome P450 (CYP3), olfactory receptor (OR), and antimicrobial peptide (AMP) subfamilies, with strong evidence of positive selection among paralogs in a clade of gustatory receptors possibly involved in the detection of bitter compounds. In contrast, these gene families had little evidence of recent contraction via pseudogenization. Overall, our results are consistent with the hypothesis that in response to novel selection pressures, gene families that mediate ecological interactions may expand and contract predictably. Testing this hypothesis will require the comparative analysis of high-quality annotation data from phylogenetically and ecologically diverse insect species and functionally diverse gene families. To this end, increasing sampling in under-sampled hymenopteran lineages and environmentally responsive gene families and standardizing manual annotation methods should be prioritized.</p>
Tudor genes of Holozoa: Early evolution and within Metazoa diversification of a multifaceted protein family
<p>Early metazoan evolution was characterized by the expansion of many gene families involved in novel multicellularity-related functions, like the Tudor family. In eukaryotes, Tudor genes are numerous and heterogeneous, mostly associated with gene expression regulation. However, the family underwent a lineage-specific expansion in animals, with novel elements almost exclusively involved in the germline-specific regulation of retrotransposons through piRNAs (as spatiotemporal regulators of the key-element Piwi, another previously supposedly animal-specific gene). In the present analysis, we used online-available proteomes for a total of 25 major taxonomic groups to characterize the Tudor gene family at a holozoan-wide level, and we confirmed the apomorphic expansion of piRNA-related Tudor genes in animals. However, we could also interestingly observe the presence of elements of the piRNA pathway, both Tudor and Piwi genes, in some Ichthyosporea species, suggesting that some elements of the pathway were already present in the last common ancestor of Holozoa. Moreover, we observed an outstanding variability (34-fold) of Tudor gene number both between and within metazoan phyla, that could be associated with convergent genomic and phenotypic evolutions. Expansions were usually sided by whole genome duplications and/or life history traits such as parthenogenesis, possibly leading to the expansion of retrotransposon silencing pathways. Reductions were instead mostly associated with overall phenotypic and genomic simplifications, like almost all endoparasites of our dataset. Lastly, we phylogenetically tested a previously proposed model for the evolution of the three possible secondary structures of the Tudor domains and we could mostly (but not completely) confirm the model.</p>
Evolution of repetitive genomic content and gene families over geo-climatic gradients in Brassicaceae
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Data from: Targeted enrichment of large gene families for phylogenetic inference: phylogeny and molecular evolution of photosynthesis genes in the Portullugo clade (Caryophyllales)
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A new genome of an African weakly electric fish (Campylomormyrus compressirostris, Mormyridae) indicates rapid gene family evolution in Osteoglossomorpha
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Data from: The multilocus multispecies coalescent: a flexible new model of gene family evolution
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Data from: The effect of copy number hemiplasy on gene family evolution
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Tudor genes of Holozoa: Early evolution and within Metazoa diversification of a multifaceted protein family
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Structural evolution drives diversification of the large LRR-RLK gene family
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Data from: Evolution of five environmentally responsive gene families in a pine-feeding sawfly, Neodiprion lecontei (Hymenoptera: Diprionidae)
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The evolution of multi-gene families and metabolic pathways in the evening primroses (Oenothera: Onagraceae): a comparative transcriptomics approach
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Evolution of chemosensory and detoxification gene families across herbivorous Drosophilidae
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High rate of gene family evolution in close proximity to the origin of ectomycorrhizal symbiosis in Inocybaceae
<p>Annotations, aligned rthologoious gene sets and CAFE outputs used in the article "High rate of gene family evolution in close proximity to the origin of ectomycorrhizal symbiosis in Inocybaceae."</p>
Evolution and amplification of the trehalose-6-phosphate synthase gene family in Theaceae
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Allen Brain Atlas
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