Molecular biology and evolution最新文献

Our understanding of the vertebrate immune system is dominated by a few model organisms such as mice. This use of a few model systems is reasonable if major features of the immune systems evolve slowly and are conserved across most vertebrates, but may be problematic if there is substantial macroevolutionary change in immune responses. Here, we present a test of the macroevolutionary stability, across 14 species of ray-finned fishes, of the transcriptomic response to a standardized immune challenge. Intraperitoneal injection of an immune adjuvant (alum) induces a fibrosis response in nearly all jawed fishes, which in some species contributes to anti-helminth protection. Despite this conserved phenotypic response, the underlying transcriptomic response is highly inconsistent across species. Although many gene orthogroups exhibit differential expression between saline versus alum-injected fish in at least one species, few orthogroups exhibit consistent differential expression across species. This result suggests that although the phenotypic response to alum (fibrosis) is highly conserved, the underlying gene regulatory architecture is very flexible and cannot readily be extrapolated from any one species to fishes (or vertebrates) more broadly. The vertebrate immune response is remarkably changeable over macroevolutionary time, requiring a diversity of model organisms to describe effectively.

The multispecies coalescent (MSC) model provides a framework for detecting gene flow using genomic data, including between sister species. However, the robustness of the inference to violations of model assumptions are poorly understood. Here, we use simulation to study the false positive rate of a Bayesian test of gene flow under the MSC with multiple influencing factors including recombination, natural selection, discrete versus continuous gene flow, variable species divergence time, and gene flow involving sister versus non-sister lineages. We find that in almost all scenarios examined the test has very low false positives. However, the test of gene flow between sister lineages may be prone to high false positives in cases of very recent species divergence and very high recombination rate. At low recombination rates, the test is robust to selective sweeps, background selection and balancing selection, although prolonged balancing selection can lead to false signals of gene flow between sister lineages. The impact of excessive recombination on the test of gene flow between sisters may be assessed by using a smaller number of sequences for each species and by considering shorter sequences at each locus. Recent species divergence alone (with no recombination) does not cause false positives in tests of gene flow, contrary to previous claims. The test of gene flow between non-sister lineages is robust to recombination at all divergence levels. Our findings provide guidance for reliable inference of gene flow using coalescent methods and highlight the need for care in conducting and interpreting simulation experiments.

Recombination suppression often evolves around sex-determining loci and extends stepwise, resulting in adjacent regions with different levels of divergence between sex chromosomes, called evolutionary strata. In Ascomycota fungi, evolutionary strata around the mating-type (MAT) locus have been reported only in pseudo-homothallic species, which have a diploid-like life cycle with mycelia carrying nuclei of both mating types. In contrast, no recombination suppression has been observed in heterothallic fungi, where colonies contain only a single mating type. Here, we investigated the evolution of recombination suppression in a clade of dung fungi encompassing 16 pseudo-homothallic and three heterothallic sibling species from the Schizothecium genus (Ascomycota, Sordariales). The analysis of genetic divergence based on genome sequencing indicated recombination suppression around the MAT locus in all 13 pseudo-homothallic species examined. The non-recombining region ranged from 600 kb to 1.6 Mb and harbored multiple evolutionary strata, varying in size and number among species. The clustering of alleles according to mating type in gene genealogies, the high linkage disequilibrium and an inversion in one species supported the lack of recombination in the MAT-proximal region in pseudo-homothallic species. The overall lack of trans-specific polymorphism suggested multiple independent recombination suppression events or occasional recombination/genic conversion. Progeny analyses showed the occurrence of recombination close to the MAT locus in heterothallic strains. We thus revealed here multiple, likely independent evolutionary strata, associated with an extended diploid-like stage in Schizothecium fungi, making this genus a valuable model for research on sex-related chromosome evolution.

Venom has independently evolved across many lineages, yet relatively few have been studied in detail, particularly among insects. Of these, Neuroptera (lacewings, antlions and relatives) remain largely unexplored, despite being widespread with agriculturally important groups such as green lacewings. While adults are non-venomous, neuropteran larvae are ferocious predators that use pincer-like mouthparts to inject paralysing and liquefying venom to subdue and consume their prey. Here, we provide a comprehensive investigation of the venom system in Neuroptera by integrating a high-quality genome, long-read transcriptomes spanning all life stages, microCT-reconstruction of venom glands, tissue-specific expression analyses, venom proteomics, and functional assays of the common green lacewing Chrysoperla carnea. We provide a re-description of the neuropteran venom system, demonstrate the venom's insecticidal and cytotoxic activity, and show the venom comprises diverse toxin gene families and is richer and more similar to the venom of antlions than previously proposed. We show that this toxin arsenal is the result of a multitude of evolutionary events that include co-option, recruitment following gene duplication, diversification of toxin-paralogs by gene duplication, and functional innovation of new paralogs through both small structural and large architectural changes. In addition, we find that alternative splicing of toxin genes is an important contributor to the biochemical arsenal, which is a mechanism rarely documented among venomous animals. Our results demonstrate how multiple genomic and evolutionary mechanisms together contribute to the emergence and evolution of a complex molecular trait, and provide new insights into the evolution of venom in insects.

The growing availability of genomes from non-model organisms offers new opportunities to identify functional loci underlying trait variation through comparative genomics. While cis-regulatory regions drive much of phenotypic evolution, linking them to specific functions remains challenging. We identified 514 cis-regulatory motifs enriched in regulatory regions of five diverse grass species, with 73% consistently enriched across all, suggesting a deeply conserved regulatory code. Leveraging 57 new contig-level genome assemblies, we then quantified shared occupancy of specific motif instances within gene-proximal regions across 589 grass species, revealing widespread gain and loss over evolutionary time. Shared occupancy declined rapidly over the first few million years of divergence, yet ∼50% of motif instances were shared back to the origin of grasses ∼100 million years ago. We used phylogenetic mixed models to identify motif gains and losses associated with ecological niche transitions. Our models revealed significant environmental associations across 1282 motif-orthogroup combinations, including convergent gains of HSF/GARP motifs at an Alpha-N-acetylglucosaminidase gene associated with occurrence in temperate environments. Our findings support a "stable motifs, variable binding sites" model in which cis-regulatory evolution involves turnover of thousands of individual binding site instances while largely preserving transcription factors' binding preferences. Our results highlight the potential of comparative genomics and phylogenetic mixed models to reveal the genetic basis of complex traits.

Paraspeckles are nuclear bodies essential for gene regulation and stress response, and they are built upon the long non-coding RNA NEAT1. Together with the syntenic MALAT1, these are the only lncRNAs that use the tRNA-processing machinery for maturation, yet they differ in function and evolutionary conservation. To investigate these differences, we identified NEAT1 and MALAT1 orthologs across 545 mammals. For NEAT1, we found that G-quadruplexes, short motifs interacting with DBHS proteins and TDP-43, long gene length, and self-complementary regions are highly conserved features that likely stabilize paraspeckle integrity. Transposable elements also contributed structural modules potentially recognized by DBHS proteins, underscoring their role in NEAT1 evolution. The NEAT1Short isoform was present in all orthologs, and the TDP-43-mediated isoform switch appears to be conserved. In contrast, MALAT1 function likely relies on its conserved primary sequence and regions under purifying selection. This is the first large-scale phylogenetic study of NEAT1 - a lncRNA that lacks sequence similarity between orthologs while maintaining functional and syntenic conservation.

Heterostyly is a floral polymorphism controlled by an S-locus supergene in several angiosperm families. Most heterostylous species are self-incompatible. Here, we investigate the genomic architecture of distyly in self-compatible Cordia subcordata in which incompatibility has apparently been lost. We assembled chromosome-level genomes of floral morphs and conducted population genomic analyses to locate the S-locus region. We used transcriptomic analyses of floral organs and functional validation by gene overexpression to identify genes controlling floral dimorphism. The tempo and mode of origin of S-locus genes was also investigated to determine whether gene duplication facilitated supergene assembly. The candidate S-locus in C. subcordata contained 12 genes, eight of which were restricted to the S-morph. CsGA2ox6 deactivates gibberellins and was exclusively expressed in S-morph pistils. Overexpression of CsGA2ox6 in transgenic tobacco produced flowers with shortened styles and an apparently functioning self-incompatibility system. The genomic locations of paralogs and estimations of duplication age suggested that the S-locus genes may have arisen through stepwise duplications, although an origin via segmental duplication could not be excluded. Our study revealed molecular convergence with several other distylous families in hemizygous structure and possibly in the mode of supergene origins. We also identified a molecular pathway for style-length control, likely through gibberellin deactivation by CsGA2ox6, which may have also controlled the expression of self-incompatibility in transgenic plants.

Shared fusions between ancestral chromosomal linkage groups have previously been used to support phylogenetic groupings, notably sponges with cnidarians and bilaterians to the exclusion of ctenophores, rendering ctenophores the sister group to all other animals. The linkage groups used to identify these fusions were assessed for statistical significance relative to a model of randomly shuffled genes. I argue that the method of random shuffling treated all species as equally distant from each other, and so over-estimated the significance of the observed linkages. I calculate alternative statistics, and further argue that there are likely to be real linkage groups which are not identified as significant. If linkage groups are not supported statistically, they cannot reliably be used to identify shared derived chromosomal rearrangements, and hence phylogenetic hypotheses derived from them are suspect.

The insulin and insulin-like growth factor (IGF) system regulates essential biological functions such as growth, metabolism, and development. While its physiological roles are well characterized, the evolutionary origins and molecular diversification of its ligands and receptors remain incompletely defined. Here, we present the most comprehensive phylogenetic and sequence conservation analysis of this system to date, using over 1,000 sequences from vertebrates, invertebrates, and viruses. Our analyses reveal that insulin, IGF-1, and IGF-2 form distinct monophyletic clades that diverged after the emergence of vertebrates, with IGF-1 being the most conserved ligand. We show that IGF1R-binding residues, especially in the A- and B-domains of IGF-1, are highly conserved across vertebrates, while insulin's Site 2 residues, which overlap with its dimerization and hexamerization surface, are more variable-correlating with the loss of hexamer formation in hystricomorphs, reptiles, and jawless fish. Unexpectedly, we identify a 12-amino acid insert in the insulin receptor (IR) of turtles and tortoises, previously thought to be unique to mammalian IR-B isoform, challenging the view that receptor isoform diversity is a mammalian innovation. We also show that marsupials and monotremes retain ancestral receptor domain features shared with reptiles and birds, and that avian insulins, particularly A-chain residues, are unusually conserved. Viral insulin/IGF-like peptides (VILPs) fall into two distinct clades that resemble either IGFs or insulin. Together, these findings illuminate the evolutionary architecture of the insulin/IGF system, highlight unexpected lineage-specific adaptations, and provide a framework for understanding hormone-receptor function across biology and therapeutic design.

Humans differ from other primates in various traits, despite nearly identical protein-coding sequences. Understanding the evolution of these differences requires studying transcriptional regulation. Here, we examine ZEB2, a transcription factor crucial for immune and neural development, to explore its regulatory divergence across great apes. Using B-lymphoblastoid cells, chosen as experimental model system due to the availability of biological replicates for three great ape species, we show that, in addition to conserved ZEB2 targets, human ZEB2 is distinct in regulating a larger repertoire of genes implicated in neuronal development. ZEB2 knock-down in human, chimpanzee, and orangutan B-lymphoblastoid cells followed by transcriptome profiling uncovered human-specific regulatory differences, especially in nervous system-related genes. Additional analysis using single-cell RNA-Seq and brain organoid data identified cell-type-specific differences in ZEB2 expression and regulated genes between humans and other apes, most pronounced in ventral progenitors and neurons. Moreover, human-specific ZEB2 targets are enriched in non-coding genes, suggesting an expanded and possibly rewired regulatory network. Our study demonstrates that species differences in ZEB2 regulation can be detected in a controlled cell system and validated in neural contexts. More broadly, we provide new insights into the functional divergence of TFs across closely related species and how regulatory shifts can contribute to phenotypic evolution.