Biology subjects

Yu, J.

Publications and source records attributed to Yu, J..

At least 19 recordsLinked to original sources

bioRxiv2018

Regrowth-delay Body as a Bacterial Subcellular Structure marking multidrug tolerant Persisters

Bacteria have long been recognized to be capable of entering a phenotypically non-growing persister state, in which the cells exhibit an extended regrowth lag and a multidrug tolerance, thus posing a great challenge in treating infectious diseases. Owing to their non-inheritability, low abundance of existence, lack of metabolic activities, and high heterogeneity, properties of persisters remain poorly understood. Here, we report our accidental discovery of a hitherto unreported subcellular structure that we term the regrowth-delay body, which is formed only in non-growing bacterial cells and sequesters multiple key proteins. As of now, this structure, that dissolves when the cell resumes growth, is the most distinguishable subcellular structure marking persisters. Our studies also indicate that persisters exhibit different depth of persistence, as determined by the status of their regrowth-delay bodies. Our findings imply that suppressing the formation and/or promoting the dissolution of regrowth-delay bodies could be viable strategies for eradicating persisters.

microbiology↗

bioRxiv2018

Stable biphasic interfaces for open microfluidic platforms

We present an open microfluidic platform that enables stable flow of an organic solvent over an aqueous solution. The device features apertures connecting a lower aqueous channel to an upper solvent compartment that is open to air, enabling easy removal of the solvent for analysis. We have previously shown that related open biphasic systems enable steroid hormone extraction from human cells in microscale culture and secondary metabolite extraction from microbial culture; here we build on our prior work by determining conditions under which the system can be used with extraction solvents of ranging polarities, a critical feature for applying this extraction platform to diverse classes of metabolites. We develop an analytical model that predicts the limits of stable aqueous-organic interfaces based on analysis of Laplace pressure. With this analytical model and experimental testing, we developed generalized design rules for creating stable open microfluidic biphasic systems with solvents of varying densities, aqueous-organic interfacial tensions, and polarities. The stable biphasic interfaces afforded by this device will enable on-chip extraction of diverse metabolite structures and novel applications in microscale biphasic chemical reactions.

bioengineering↗

bioRxiv2018

Integrative analyses of multi-tissue Hi-C and eQTL data demonstrate close spatial proximity between eQTLs and their target genes

Gene regulation is important for cells and tissues to function. At the genomic level, it has been studied from two aspects, the identification of expression quantitative trait loci (eQTLs) and identification of long-range chromatin interactions. It is important to understand their relationship, such as whether eQTLs regulate their target genes through physical chromatin interaction. Although previous studies have suggested enrichment of eQTLs in regions with a high chromatin interaction frequency, it is unclear whether this relationship is consistent across different tissues and cell lines and whether there would be any tissue-specific patterns. Here, we performed integrative analyses of eQTL and high-throughput chromatin conformation capture (Hi-C) data from 11 human primary tissue types and 2 human cell lines. We found that chromatin interaction frequency is positively correlated with the number of genes having eQTLs, and eQTLs and their target genes are more likely to fall in the same topologically associating domains than that expected from randomly generated control datasets. These results are consistent across all tissues and cell lines we evaluated. Moreover, in dorsolateral prefrontal cortex, spleen, hippocampus, pancreas and aorta, tissue-specific eQTLs are enriched in tissue-specific frequently interacting regions. These results reveal a more detailed picture of the complicated relationship between different mechanisms of gene regulation.\n\nAuthor summaryWhole-genome gene regulation has been studied in tissues and cell lines from multiple perspectives, including identification of expression quantitative trait loci (eQTLs) and identification of long-range chromatin interactions. These two complementary approaches focus on different aspects of gene regulation, one being statistical across individuals while the other being physical within a sample. Integrating results from these two approaches will help us understand their relationships, such as whether eQTLs regulate their target genes through physical chromatin interaction. We performed comprehensive analyses using data from multiple human tissues and cell lines, and showed that chromatin interaction frequency is positively associated with eQTL results in all evaluated tissues and cell lines. The observed relationships also displayed tissue-specific pattern in some tissues. Our results revealed a more detailed picture of the complicated relationship between the different mechanisms of gene regulation.

systems biology↗

bioRxiv2018

Web-based design and analysis tools for CRISPR base editing

BackgroundAs a result of its simplicity and high efficiency, the CRISPR-Cas system has been widely used as a genome editing tool. Recently, CRISPR base editors, which consist of deactivated Cas9 (dCas9) or Cas9 nickase (nCas9) linked with a cytidine or a guanine deaminase, have been developed. Base editing tools will be very useful for gene correction because they can produce highly specific DNA substitutions without the introduction of any donor DNA, but dedicated web-based tools to facilitate the use of such tools have not yet been developed.\n\nResultsWe present two web tools for base editors, named BE-Designer and BE-Analyzer. BE-Designer provides all possible base editor target sequences in a given input DNA sequence with useful information including potential off-target sites. BE-Analyzer, a tool for assessing base editing outcomes from next generation sequencing (NGS) data, provides information about mutations in a table and interactive graphs. Furthermore, because the tool runs client-side, large amounts of targeted deep sequencing data (>100MB) do not need to be uploaded to a server, substantially reducing running time and increasing data security. BE-Designer and BE-Analyzer can be freely accessed at http://www.rgenome.net/bedesigner/ and http://www.rgenome.net/be-analyzer/respectively\n\nConclusionWe develop two useful web tools to design target sequence (BE-Designer) and to analyze NGS data from experimental results (BE-Analyzer) for CRISPR base editors.

bioinformatics↗

bioRxiv2018

Phenogenon: Gene to Phenotype Associations for Rare Genetic Diseases

As genome sequencing is increasingly applied to molecular diagnosis of rare Mendelian disorders, large number of patients with diverse phenotypes have their genomic and phenotypic data pooled together to uncover new genotype - phenotype relations. We introduce Phenogenon, a method that combines: the power of Human Phenotype Ontology for describing patient phenotypes, gnomAD for estimating rare variant population frequency, and CADD for variant pathogenicity prediction. By using a divide and conquer approach, we demonstrate here that Phenogenon is able to uncover true gene to phenotype relations, such as \"ABCA4 - Macular dystrophy\" and \"SCN1A - Seizures\". Additionally, it accurately infers mode of inheritance, such as a recessive mode of inheritance in the case of the \"ABCA4 - Macular dystrophy\" relationship and a dominant mode of inheritance with the \"SCN1A - Seizures\" relationship. We also found that CADD has more power to detect early-onset rare genetic diseases than late-onset diseases. In this study, we ran Phenogenon against a diverse cohort of 3288 patients. Among the top 13 gene-phenotype relations, seven were previously known. We also highlight four potentially novel gene - phenotype relations such as \"SIPA1L3 - Abnormal electroretinogram\".

bioinformatics↗

bioRxiv2018

Insight into relationship between micro-consortia, nitrogen source and petroleum degradation at low temperature anaerobic condition

Biostimulation by addition nutrients has been proved to be an effective bioremediation strategies. Revealing response law of nitrogen source and structure characteristics of anaerobic petroleum degrading microorganisms microbial population will help us optimize nutrient to promote oil degradation. Anaerobic micro-consortia characteristics in the enrichment marine sediment samples with different nitrogen source, combining with analysis of the oil degradation rates were studied in this paper, as well as functional genes involved in petroleum degradation were also analyzed. On the basis of optimizing the best inorganic nitrogen sources and organic nitrogen sources, an effective medium was designed by response surface methodology that used for enriching petroleum degradation micro-consortia. Amplicon sequencing analysis showed that the population of microorganisms migrated obviously when enriched with different nitrogen sources. With the increase of oil degradation rate, the microbial diversity was significantly decreased, and concentrated on a limited number of genera. The reasonable proportions of GammaProteobacteria, Bacteroidetes and Fusobacteria made the greatest contribution to petroleum degradation. Metagenomic analysis unveiled the mixed nitrogen source promoted the expression of functional genes related to petroleum degradation such as the transfer of succinyl-CoA, synthesis of acetyl CoA and {beta}-oxidation cycle, and was beneficial to degradation of petroleum at low temperature anaerobic condition.\n\nOriginality Significance StatementAddition of nutrients can promote growth of indigenous petroleum degradation-related bacteria and be helpful to the rapid degradation of petroleum. Previous studies accurately characterized aerobic microorganisms on petroleum degradation. However, we still known little about anaerobic microorganisms in marine environment. Most biostimulation methods use inorganic salt as the main nutritional supplement to improve the efficiency of petroleum degradation, but effects of different nitrogen sources on diversity of microorganisms and distribution of functional genes related to petroleum degradation at anaerobic conditions are still unknown. In this research, the effects of nitrogen on petroleum biodegradation, anaerobic microconsortium structure and distribution of genes related to petroleum degradation were unveiled by using amplicon sequencing and metagenomic analysis.

microbiology↗

bioRxiv2018

Cryo-EM structure of the benzodiazepine-sensitive α1β1γ2 heterotrimeric GABAA receptor in complex with GABA illuminates mechanism of receptor assembly and agonist binding

Fast inhibitory neurotransmission in the mammalian nervous system is largely mediated by GABAA receptors, chloride-selective members of the superfamily of pentameric Cys-loop receptors. Native GABAA receptors are heteromeric assemblies sensitive to many important drugs, from sedatives to anesthetics and anticonvulsive agents, with mutant forms of GABAA receptors implicated in multiple neurological diseases, including epilepsy. Despite the profound importance of heteromeric GABAA receptors in neuroscience and medicine, they have proven recalcitrant to structure determination. Here we present the structure of the triheteromeric 1{beta}1{gamma}2EM GABAA receptor in complex with GABA, determined by single particle cryo-EM at 3.1-3.8 [A] resolution, elucidating the molecular principles of receptor assembly and agonist binding. Remarkable N-linked glycosylation on the 1 subunit occludes the extracellular vestibule of the ion channel and is poised to modulate receptor assembly and perhaps ion channel gating. Our work provides a pathway to structural studies of heteromeric GABAA receptors and a framework for the rational design of novel therapeutic agents.

biophysics↗

bioRxiv2018

Long noncoding RNA ANRIL supports proliferation of adult T-cell leukemia cells through cooperation with EZH2

Adult T-cell leukemia (ATL) is a highly aggressive T-cell malignancy induced by human T-cell leukemia virus type 1 (HTLV-1) infection. Long noncoding RNA (lncRNA) plays a critical role in the development and progression of multiple human cancers. However, the function of lncRNA on HTLV-1-induced oncogenesis has not been elucidated. In the present study, we show that the expression of the lncRNA ANRIL was elevated in HTLV-1 infected cell lines and clinical ATL samples. E2F1 induced ANRIL transcription by enhancing its promoter activity. Knocking down of ANRIL in ATL cells repressed cellular proliferation and increased apoptosis in vitro and in vivo. As a mechanism for these actions, we found that ANRIL targeted EZH2, and activated the NF-{kappa}B pathway in ATL cells. This activation was independent of the histone methyltransferase (HMT) activity of EZH2, but required the formation of an ANRIL/EZH2/p65 ternary complex. Chromatin immunoprecipitation assay revealed that ANRIL/EZH2 enhanced p65 DNA binding capability. In addition, we observed that ANRIL/EZH2 complex repressed p21/CDKN1A transcription through H3K27 trimethylation of the p21/CDKN1A promoter. Taken together, our results implicate that lncRNA ANRIL, by cooperating with EZH2, supports the proliferation of HTLV-1 infected cells, which is thought to be critical for oncogenesis.\n\nIMPORTANCEHuman T-cell leukemia virus type 1 (HTLV-1) is the pathogen that causes adult T-cell leukemia (ATL), which is a unique malignancy of CD4+ T cells. A role for long noncoding RNA (lncRNA) in HTLV-1-mediated cellular transformation has not been described. In this study, we demonstrated that lncRNA ANRIL was important for maintaining proliferation of ATL cells in vitro and in vivo. ANRIL was shown to activate NF-{kappa}B signaling through forming a ternary complex with EZH2 and p65. Further, epigenetic inactivation of p21/CDKN1A was involved in the oncogenic function of ANRIL. To the best of our knowledge, this is the first study to address the regulatory role of the lncRNA ANRIL in ATL and provides an important clue to prevent or treat HTLV-1 associated human diseases.

cancer biology↗

bioRxiv2018

The effector of Hippo signaling, Taz, is required for formation of the micropyle and fertilization in zebrafish

The mechanisms that ensure fertilization of eggs by a single sperm are not fully understood. In all teleosts, a channel called the micropyle is the only route of entry for sperm to enter and fertilize the egg. The micropyle forms by penetration of the developing vitelline envelope by a single specialized follicle cell, the micropylar cell, which subsequently degenerates. The mechanisms underlying micropylar cell specification and micropyle formation are poorly understood. Here, we show that an effector of the Hippo signaling pathway, the Transcriptional co-activator with a PDZ-binding domain (Taz), plays crucial roles in micropyle formation and fertilization in zebrafish. Genome editing mutants affecting taz can grow to adults, however, eggs from homozygous taz females are not fertilized even though oocytes in mutant females are histologically normal with intact animal-vegetal polarity, complete meiosis and proper ovulation. However, taz mutant eggs have no micropyle. We show that Taz protein is specifically enriched from mid-oogenesis onwards in two follicle cells located at the animal pole of the oocyte, and co-localizes with the actin and tubulin cytoskeleton. Taz protein and micropylar cell are not detected in taz mutant ovaries. Our work identifies a novel role for the Hippo/Taz pathway in micropylar cell specification in zebrafish, and uncovers the molecular basis of micropyle formation in teleosts.

developmental biology↗

bioRxiv2018

Engineering Nitrogen Fixation Activity in an Oxygenic Phototroph

Biological nitrogen fixation is catalyzed by nitrogenase, a complex metalloenzyme found only in prokaryotes. N2 fixation is energetically highly expensive, and an energy generating process such as photosynthesis can meet the energy demand of N2 fixation. However, synthesis and expression of nitrogenase is exquisitely sensitive to oxygen. Thus, engineering nitrogen fixation activity in photosynthetic organisms that produce oxygen is challenging. Cyanobacteria are oxygenic photosynthetic prokaryotes, and some of them also fix N2. Here, we demonstrate a feasible way to engineer nitrogenase activity in the non-diazotrophic cyanobacterium Synechocystis sp. PCC 6803 through the transfer of 35 nitrogen fixation (nif) genes from the diazotrophic cyanobacterium Cyanothece sp. ATCC 51142. In addition, we have identified the minimal nif cluster required for such activity in Synechocystis 6803. Moreover, nitrogenase activity was significantly improved by increasing the expression levels of nif genes. Importantly, the O2 tolerance of nitrogenase was enhanced by introduction of uptake hydrogenase genes, showing this to be a functional way to improve nitrogenase enzyme activity under micro-oxic conditions. To date, our efforts have resulted in engineered Synechocystis 6803 strains that remarkably have more than 30% N2-fixation activity compared to that in Cyanothece 51142, the highest such activity established in any non-diazotrophic oxygenic photosynthetic organism. This study establishes a baseline towards the ultimate goal of engineering nitrogen fixation ability in crop plants.\n\nIMPORTANCEApplication of chemically synthesized nitrogen fertilizers has revolutionized agriculture. However, the energetic costs of such production processes as well as the wide spread application of fertilizers have raised serious environmental issues. A sustainable alternative is to endow crop plants the ability to fix atmospheric N2 in situ. One long-term approach is to transfer all nif genes from a prokaryote to plant cells, and express nitrogenase in an energy-producing organelle, chloroplast or mitochondrion. In this context, Synechocystis 6803, the non-diazotrophic cyanobacterium utilized in this study, provides a model chassis for rapid investigation of the necessary requirements to establish diazotrophy in an oxygenic phototroph.

synthetic biology↗

bioRxiv2018

Population Pharmacokinetics Study of Morinidazole in Patients with Moderate Hepatic Impairment

ObjectiveMorinidazole is a novel third generation 5-nitroimidazole antimicrobial drug which has demonstrated substantial antibacterial activity against clinical isolates of anaerobe. The aim of this study was to build population pharmacokinetic (PPK) model of morinidazole among patients with hepatic impairment and to provide dosage adjustment strategy for morinidazole in patients with hepatic impairment and/or renal dysfunction.\n\nMethodsThe nonlinear mixed effects modeling tool NONMEM (version7.3, ICON Development Solutions) was used to develop the PPK model of morinidazole.\n\nResultsOne-compartment model was conducted to establish the morinidazole PPK model. Disease condition was the significant covariate for CL and weight was the significant covariate for V. The AUC0-{infty} was 120.44{+/-}37.05 (79.25-207.20) gxh/mL in hepatic impairment group and was 79.46{+/-}23.71 (42.94-116.75) gxh/mL in control group. The AUC0-{infty} was 164.9{+/-}44.8 gxh/mL and 77.2{+/-}23.1 gxh/mLin in the 3 subjects with both hepatic impairment and mild renal impairment and in the 3 matched healthy subjects, respectively.\n\nConclusionIt is not necessary to adjust morinidazole dosage for patients with moderate hepatic impairment without confirmed renal dysfunction. For patient with moderate hepatic and mild renal impairment, morinidazole regimen should be considered as 500mg every 24 hours. When used in patients with moderate/severe hepatic impairment combined with renal dysfunction, both dosage and interval adjustment of morinidazole should be considered.

pharmacology and toxicology↗

bioRxiv2018

Visualizing Wnt secretion from endoplasmic reticulum to filopodia

Wnts are a family of secreted palmitoleated glycoproteins that play a key role in cell to cell communications during development and regulate stem cell compartments in adults. Wnt receptors, downstream signaling cascades and target pathways have been extensively studied while less is known about how Wnts are secreted and move from producing cells to receiving cells. We used the synchronization system called Retention Using Selective Hook (RUSH) to study Wnt trafficking from endoplasmic reticulum to Golgi and then to plasma membrane and filopodia in real time. Consistent with prior studies, inhibition of porcupine (PORCN) or knockout of Wntless (WLS) blocked Wnt exit from the ER. Indeed, WLS was rate-limiting for Wnt ER exit. Wnt-containing vesicles paused at sub-cortical regions of the plasma membrane before exiting the cell. Wnt-containing vesicles were transported to adjacent cells associated with filopodia. Increasing the number of filopodia by expression of LGR5 in the producing cell increased the ability of a cell to send a Wnt signal. The RUSH system is a powerful tool to provide new insights into the Wnt secretory pathway.

cell biology↗

bioRxiv2018

Fast and simple comparison of semi-structured data, with emphasis on electronic health records

We present a locality-sensitive hashing strategy for summarizing semi-structured data (e.g., in JSON or XML formats) into data fingerprints: highly compressed representations which cannot recreate details in the data, yet simplify and greatly accelerate the comparison and clustering of semi-structured data by preserving similarity relationships. Computation on data fingerprints is fast: in one example involving complex simulated medical records, the average time to encode one record was 0.53 seconds, and the average pairwise comparison time was 3.75 microseconds. Both processes are trivially parallelizable.\n\nApplications include detection of duplicates, clustering and classification of semi-structured data, which support larger goals including summarizing large and complex data sets, quality assessment, and data mining. We illustrate use cases with three analyses of electronic health records (EHRs): (1) pairwise comparison of patient records, (2) analysis of cohort structure, and (3) evaluation of methods for generating simulated patient data.

bioinformatics↗

bioRxiv2018

Arsenite exposure inhibits histone acetyltransferase p300 for attenuating H3K27ac at enhancers in low-dose exposed mouse embryonic fibroblast cells

Epidemiological investigations have validated the positive relationships between arsenic in drinking water and several cancers, including skin, liver and lung cancers. Besides genotoxicity, arsenic exposure-related pathogenesis of disease is widely considered through epigenetic mechanisms; however, the underlying mechanistic insight remains elusive. Herein we explore the initial epigenetic changes via acute low-dose arsenite exposures of mouse embryonic fibroblast (MEF) cells and Dot1L knockout MEF (Dot1L-/- for abbreviation) cells. Our RNA-seq and Western blot data demonstrated that, in both cell lines, acute low-dose arsenite exposure abolished histone acetyltransferase p300 at the RNA level and subsequent protein level. Consequently, p300-specific main target histone H3K27ac, a marker separating active from poised enhancers, decreased dramatically as validated by both Western blot and ChIP-seq analyses. Concomitantly, H3K4me1 as another well-known marker for enhancers also showed significant decreases, suggesting an underappreciated crosstalk between H3K4me1 and H3K27ac involved in arsenite exposure. Significantly, arsenite exposure-reduced H3K27ac and H3K4me1 inhibit the expression of genes including EP300 itself and Kruppel Like Factor 4(Klf4), a tumor suppressor gene. Collectively, our investigations identify p300 as an internal bridging factor within cells to sense external environmental arsenite exposure to alter chromatin, thereby changing gene transcription for disease pathogenesis.

pharmacology and toxicology↗

bioRxiv2018

Human Puf-A, a Novel Component of 90S Pre-ribosome, Links Ribosome Biogenesis to Cancer Progression

We describe a novel biogenesis factor of the 90S pre-ribosome, Puf-A, which is a negative transcriptional target of p53. The expression of Puf-A is not only upregulated in advanced human lung cancer and tumors of patients especially with TP53 mutation, but also is highly prognostic for stage I lung cancer. Loss of Puf-A expression prevents KrasG12D/p53-/--induced tumor progression in the lungs and induces apoptosis in TP53- mutated cancers and c-Myc/p53-/--transformed cells as well. Overexpression of Puf-A enhances proliferation of normal cells after c-Myc induction and overcomes the cell-cycle checkpoints incurred by p53 expression. Mechanistically, Puf-A interacts with double-stranded structures of the 5.8S sequence within pre-rRNA and maintains the integrity of 90S pre-ribosomes, thereby impacting early ribosome assembly and export of ribosomes from nuclei. Silencing of Puf-A disrupts the assembly of 90S pre-ribosomes and induces the translocation of its associated nucleophosmin (NPM1) from nucleoli to the nucleoplasm, resulting in impairment of ribosome synthesis. Thus, Puf-A is crucial for over-activation of ribosome biogenesis and contributes to tumor progression and cancer growth.

cancer biology↗

bioRxiv2017

Natural Variation of OsLG3 Controls Drought Stress Tolerance in Rice by Inducing ROS Scavenging

BackgroundImproving performance of rice under drought stress has potential to significant impact on rice productivity. Previously we reported that OsLG3 positively control rice grain length and yield.\n\nResultsIn this study, we found that OsLG3 was more strongly expressed in upland rice compared to lowland rice under drought stress condition. Candidate gene association analysis showed that the natural variation in OsLG3 was associated with tolerance to water deficit stress in germinating rice seeds. Transgenic rice with enhanced OsLG3 expression exhibited improved tolerance to drought and that is most likely due to enhanced ROS scavenging efficiency. Phylogenetic analysis and pedigree records indicated that the tolerant allele of OsLG3 has potential to improve drought tolerance of japonica rice.\n\nConclusionsCollectively, our work revealed that the natural variation of OsLG3 contributes to rice drought tolerance and the elite allele of OsLG3 is a promising genetic resource for the development of drought-tolerant and high-yield rice varieties.

plant biology↗

bioRxiv2017

In vivo multiphoton fluorescence imaging with polymer dots

Deep in vivo imaging of vasculature requires small, bright, and photostable fluorophores suitable for multiphoton microscopy (MPM). Although semiconducting polymer dots (pdots) are an emerging class of highly fluorescent contrast agents with favorable advantages for the next generation of in vivo imaging, their use for deep multiphoton imaging has never before been demonstrated. Here we characterize the multiphoton properties of three pdot variants (CNPPV, PFBT, and PFPV) and demonstrate deep imaging of cortical microvasculature in C57 mice. Specifically, we measure the two-versus three-photon power dependence of these pdots and observe a clear three-photon excitation signature at wavelengths longer than 1300 nm, and a transition from two-photon to three-photon excitation within a 1060 - 1300 nm excitation range. Furthermore, we show that pdots enable in vivo two-photon imaging of cerebrovascular architecture in mice up to 850 m beneath the pial surface using 800 nm excitation. In contrast with traditional multiphoton probes, we also demonstrate that the broad multiphoton absorption spectrum of pdots permits imaging at longer wavelengths ({lambda}ex = 1,060 and 1225 nm). These wavelengths approach an ideal biological imaging wavelength near 1,300 nm and confer compatibility with a high-power ytterbium-fiber laser and a high pulse energy optical parametric amplifier, resulting in substantial improvements in signal-to-background ratio (>3.5-fold) and greater cortical imaging depths of 900 m and 1300 m. Ultimately, pdots are a versatile tool for MPM due to their extraordinary brightness and broad absorption, which will undoubtedly unlock the ability to interrogate deep structures in vivo.

bioengineering↗

bioRxiv2017

Overlooked polyploidies in lycophytes generalize their roles during the evolution of vascular plants

Seed plants and lycophytes constitute the extant vascular plants. As a model lycophyte, Selaginalla moellendroffii was deciphered its genome, previously proposed to have avoided polyploidies, as key events contributing to the origination and fast expansion of seed plants. Here, using a gold-standard streamline recently proposed to deconvolute complex genomes, we reanalyzed the S. moellendroffii genome. To our surprise, we found clear evidence of multiple paleo-polyploidies, with one being recent (~ 13-15 millions of years ago or Mya), another one occurring about ~125-142 Mya, during the evolution of lycophytes, and at least 2 or 3 events being more ancient. Besides, comparison of reconstructed ancestral genomes of lycophytes and angiosperms shows that lycophytes were likely much more affected by paleo-polyploidies than seed plants. The present analysis here provides clear and solid evidence that polyploidies have contributed the successful establishment of all vascular plants on earth.

evolutionary biology↗