Biology subjects

Yang, Y.

Publications and source records attributed to Yang, Y..

At least 1,297 records · Page 72Linked to original sources

bioRxiv2019

Disentangling Sources of Gene Tree Discordance in Phylotranscriptomic Datasets: A Case Study from Amaranthaceae s.l.

Gene tree discordance in large genomic datasets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-based molecular data. The dataset included seven genomes and 88 transcriptomes, 17 generated for this study. We examined gene-tree discordance using coalescent-based species trees and network inference, gene tree discordance analyses, site pattern tests of introgression, topology tests, synteny analyses, and simulations. We found that a combination of processes might have generated the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. Furthermore, we found evidence that three consecutive short internal branches produce anomalous trees contributing to the discordance. Overall, our results suggest that Amaranthaceae s.l. might be a product of an ancient and rapid lineage diversification, and remains, and probably will remain, unresolved. This work highlights the potential problems of identifiability associated with the sources of gene tree discordance including, in particular, phylogenetic network methods. Our results also demonstrate the importance of thoroughly testing for multiple sources of conflict in phylogenomic analyses, especially in the context of ancient, rapid radiations. We provide several recommendations for exploring conflicting signals in such situations.

evolutionary biology↗

bioRxiv2019

Integration of locomotion and auditory signals in the mouse inferior colliculus

The inferior colliculus (IC) is the major midbrain auditory integration center, where virtually all ascending auditory inputs converge. Although the IC has been extensively studied for sound processing, little is known about the neural activity of the IC in moving subjects, as frequently happens in natural hearing conditions. Here we show, by recording the IC neural activity in walking mice, the activity of IC neurons is strongly modulated by locomotion in the absence of sound stimulus presentation. Similar modulation was also found in deafened mice, demonstrating that IC neurons receive non-auditory, locomotion-related neural signals. Sound-evoked activity was attenuated during locomotion, and the attenuation increased frequency selectivity across the population, while maintaining preferred frequencies. Our results suggest that during behavior, integrating movement-related and auditory information is an essential aspect of sound processing in the IC.

neuroscience↗

bioRxiv2019

A tissue-specific collaborative mixed model for jointly analyzing multiple tissues in transcriptome-wide association studies

Transcriptome-wide association studies (TWAS) integrate expression quantitative trait loci (eQTLs) studies with genome-wide association studies (GWASs) to prioritize candidate target genes for complex traits. Several statistical methods have been recently proposed to improve the performance of TWAS in gene prioritization by integrating the expression regulatory information imputed from multiple tissues, and made significant achievements in improving the ability to detect gene-trait associations. The major limitation of these methods is that they cannot be used to elucidate the specific functional effects of candidate genes across different tissues. Here, we propose a tissue-specific collaborative mixed model (TisCoMM) for TWAS, leveraging the co-regulation of genetic variations across different tissues explicitly via a unified probabilistic model. TisCoMM not only performs hypothesis testing to prioritize gene-trait associations, but also detects the tissue-specific role of candidate target genes in complex traits. To make use of widely available GWAS summary statistics, we extend TisCoMM to use summary-level data, namely, TisCoMM-S2. Using extensive simulation studies, we show that type I error is controlled at the nominal level, the statistical power of identifying associated genes is greatly improved, and false positive rate (FPR) for non-causal tissues is well controlled at decent levels. We further illustrate the benefits of our methods in applications to summary-level GWAS data of 33 complex traits. Notably, apart from better identifying potential trait-associated genes, we can elucidate the tissue-specific role of candidate target genes. The follow-up pathway analysis from tissue-specific genes for asthma shows that the immune system plays an essential function for asthma development in both thyroid and lung tissues.

bioinformatics↗

bioRxiv2019

Simultaneous and precise generation of Zebra3 and Wsl5 mutations in rice using CRISPR/Cas9-mediated adenine base editors

The CRISPR/Cas9-mediated base editing technology can efficiently generate point mutations in the genome without introducing double-strand break (DSB) or supplying a DNA donor template for homology-dependent repair (HDR). In this study, adenine base editors (ABEs) were used for rapid generation of precise point mutations in two distinct genes, OsWsl5, and OsZebra3 (Z3), in rice protoplasts and regenerated plants. The precisely engineered point mutations were stably inherited to subsequent generations. These single nucleotide alterations resulted in single amino acid changes and associated wsl5 and z3 phenotypes as evidenced by white stripe leaf and light green/dark green leaf pattern, respectively. Through selfing and segregation, transgene-free, base edited wsl5 and z3 mutants were readily obtained in a short period of time. We noticed a novel mutation (V540A) in Z3 locus could mimic the phenotype of Z3 mutation (S542P). Furthermore, we observed unexpected non-A/G or T/C mutations in the ABE editing window in a few of the edited plants. The ABE vectors and the method from in this study could be used to simultaneously generate point mutations in multiple genes in a single transformation and serve as a useful base editing tool for crop improvement as well as basic studies in plant biology.\n\nHighlightsAdenine base editors were adapted for plant base editing that can generate precise and heritable point mutations in rice genome without indel formation. The base editing approach allows rapid generation of transgene-free rice mutants with expected phenotypic changes.

plant biology↗

bioRxiv2019

Angle-tuned Coil: A Focal Spot-size Adjustable Transcranial Magnetic Stimulator

BackgroundConventional transcranial magnetic stimulation (TMS) coils are limited by the depth-focality tradeoff rule and the emission field intensity from coils with either small or large apertures will diverge quickly at less than one aperture diameter distance away from the coil. To utilize a better depth-focality tradeoff rule and accomplish deep and focused stimulation, a new approach needs to be employed.\n\nObjectivesWe report a new TMS coil design that can deliver deep and spot size adjustable stimulation to deep brain regions.\n\nMethodsIn our design, we introduce a magnetic core at the center of a coil to help confine the magnetic field and prevent leakage. We further tilted the wire wrapping angle of the coil to break its ring symmetry and accomplish tunable focusing by adjusting the tilting angle.\n\nResultsBy comparing the electric field decay curves of five types of coils, our results concluded the proposed novel method to improve the coils depth-focality profile. Both theoretical calculations and experimental data collectively demonstrated that by using a larger tilting angle, we were able to accomplish a more tightly focused stimulation at any distance away from the coil.\n\nConclusionEnlarging the tilting angle of the coil wire wrapping and applying magnetic core significantly improved the spatial resolution of the field without inducing considerable effect on field decay speed. Our novel TMS coil design plots a new curve in the depth-focality profile with better performance than the existing conventional coil designs in the tradeoff rule.

bioengineering↗

bioRxiv2019

Succinylation Links Metabolic Reductions to Amyloid and Tau Pathology

Abnormalities in glucose metabolism and misfolded protein deposits composed of the amyloid-{beta} peptide (A{beta}) and tau are the three most common neuropathological hallmarks of Alzheimers disease (AD), but their relationship(s) to the disease process or to each other largely remains unclear. In this report, the first human brain quantitative lysine succinylome together with a global proteome analysis from controls and patients reveals that lysine succinylation contributes to these three key AD-related pathologies. Succinylation, a newly discovered protein post-translational modification (PTM), of multiple proteins, particularly mitochondrial proteins, declines with the progression of AD. In contrast, amyloid precursor protein (APP) and tau consistently exhibit the largest AD-related increases in succinylation, occurring at specific sites in AD brains but never in controls. Transgenic mouse studies demonstrate that succinylated APP and succinylated tau are detectable in the hippocampus concurrent with A{beta} assemblies in the oligomer and insoluble fiber assembly states. Multiple biochemical approaches revealed that succinylation of APP alters APP processing so as to promote A{beta} accumulation, while succinylation of tau promotes its aggregation and impairs its microtubule binding ability. Succinylation, therefore, is the first single PTM that can be added in parallel to multiple substrates, thereby promoting amyloidosis, tauopathy, and glucose hypometabolism. These data raise the possibility that, in order to show meaningful clinical benefit, any therapeutic and/or preventative measures destined for success must have an activity to either prevent or reverse the molecular pathologies attributable to excess succinylation.

neuroscience↗

bioRxiv2019

Chromosome-scale de novo assembly and phasing of a Chinese indigenous pig genome

Chinese indigenous pigs differ significantly from Western commercial pig breeds in phenotypic and genomic characteristics. Thus, building a high-quality reference genome for Chinese indigenous pigs is pivotal to exploring gene function, genome evolution and improving genetic breeding in pigs. Here, we report an ultrahigh-quality phased chromosome-scale genome assembly for a male Luchuan pig, a representative Chinese domestic breed, by generating and combining data from PacBio Sequel reads, Illumina paired-end reads, high-throughput chromatin conformation capture and BioNano optical map. The primary assembly is [~] 2.58 Gb in size with contig and scaffold N50s of 18.03 Mb and 140.09 Mb, respectively. Comparison between primary assembly and alternative haplotig reveals numerous haplotype-specific alleles, which provide a rich resource to study the allele-specific expression, epigenetic regulation, genome structure and evolution of pigs. Gene enrichment analysis indicates that the Luchuan-specific genes are predominantly enriched in Gene Ontology terms for phosphoprotein phosphatase activity, signaling receptor activity and phosphatidylinositol binding. We provide clear molecular evolutionary evidence that the divergence time between Luchuan and Duroc pigs is dated back to about 1.7 million years ago. Meanwhile, Luchuan exhibits fewer events of gene family expansion and stronger gene family contraction than Duroc. The positively selected genes (PSGs) in Luchuan pig significantly enrich for protein tyrosine kinase activity, microtubule motor activity, GTPase activator activity and ubiquitin-protein transferase activity, whereas the PSGs in Duroc pig enrich for G-protein coupled receptor activity. Overall, our findings not only provide key benchmark data for the pig genetics community, but also pave a new avenue for utilizing porcine biomedical models to study human health and diseases.

genomics↗

bioRxiv2019

Offspring production of ovarian organoids derived from spermatogonial stem cells by chromatin reorganization

Fate determination of germline stem cells remains poorly understood at the chromatin structure level1,2. Here, we demonstrate successful production of offspring from oocytes transdifferentiated from mouse spermatogonial stem cells (SSCs) with tracking of transplanted SSCs in vivo, single cell whole exome sequencing, and in 3D cell culture reconstitution of the process of oogenesis derived from SSCs. Furthermore, we demonstrate direct induction of germline stem cells (iGSCs) differentiated into functional oocytes by transduction of H19, Stella, and Zfp57 and inactivation of Plzf in SSCs after screening with ovarian organoids. Using high throughput chromosome conformation, we uncovered extensive chromatin reorganization during SSC conversion into iGSCs, which was highly similar to female germline stem cells. We observed that although topologically associating domains were stable during SSC conversion, chromatin interactions changed in a striking manner, altering 35% of inactive and active chromosomal compartments throughout the genome. These findings have important implications in various areas including mammalian gametogenesis, genetic and epigenetic reprogramming, biotechnology, and medicine.

genetics↗

bioRxiv2019

A novel xenograft model of human HCC in immunocompetent mouse

Hepatocellular carcinoma (HCC) is one of the most common malignant tumors that threaten human health; thus, the establishment of an animal model with clinical features similar to human liver cancer is of important practical significance. Taking advantage of the novel microcarrier-6, human HCC cells was injected into immunocompetent mice to establish a novel human HCC patient-derived xenograft (PDX) model. Primary HCC cells were isolated from fresh liver cancer tissues, which were subsequently co-cultured with microcarrier-6 to construct a three-dimensional tumor cell culture model in vitro. The HCC-microcarrier complex was implanted into mice by subcutaneous inoculation, and the tumor formation time, tumor formation rate, and pathological manifestation were recorded. Changes of immune parameters in mice were detected by flow cytometry. The success rate was 60% (6/10) in the establishment of liver cancer PDX mouse model, and the total tumor formation rate of the tumor-forming model is 80-100%. H&E staining and immunohistochemical experiments indicate that the model well retained the characteristics of the primary tumor. Interestingly, M2 macrophages in tumor-bearing mice increased significantly, and the levels of CD4+ T cells were significantly reduced. Through the application of the microcarrier-6 in immunocompetent mice, we successfully established a novel human HCC PDX model, which can be used to better study and further elucidate the occurrence and pathogenic mechanism of HCC.

cancer biology↗

bioRxiv2019

Identification of the Repressive Domain of the Negative Circadian Clock Component CHRONO

Circadian rhythm is an endogenous, self-sustainable oscillation that participates in regulating organisms physiological activities. Key to this oscillation is a negative feedback by main clock components Periods and Cryptochromes that repress transcriptional activity of BMAL1/CLOCK complexes. In addition, a novel repressor, CHRONO, has been identified recently, but details of CHRONOs function during repressing the circadian cycle remain unclear. Here we report that a domain of CHRONO mainly composed of -helixes is critical to repression through the exploitation of protein-protein interactions according to luciferase reporter assays, co-immunoprecipitation, immunofluorescence, genome editing and structural information analysis via circular dichroism spectroscopy. This repression is fulfilled by interactions between CHRONO with a region on the BMAL1 C-terminus where Cryptochrome and CBP bind. Our results indicate that CHRONO and PER differentially function as BMALA/CLOCK-dependent repressors. We further suggest a repression model of how PER, CRY and CHRONO proteins associate with BMAL1, respectively.

molecular biology↗

bioRxiv2019

Streptococcus pyogenes Cas9 displays biased one-dimensional diffusion on dsDNA to search for a target

The RNA-guided Streptococcus pyogenes Cas9 (spCas9) is a sequence-specific DNA endonuclease that works as one of the most powerful genetic editing tools. However, how the Cas9 locates its target among huge amounts of dsDNAs remains controversial. Here, combining biochemical and single-molecule assays, we revealed that Cas9 uses both three-dimensional and one-dimensional diffusion to find its target. We further observed a surprising biased one-dimensional diffusion of Cas9 from 3 to 5 end of the non-target strand under physiological salt condition, whereas low ionic concentration or mutations on PAM recognition residues induce unbiased one-dimensional diffusion of Cas9 along dsDNA. We quantified the diffusion length of 27 bp, which accelerates the target search efficiency of Cas9 by [~] 10 folds. Our results reveal a unique searching mechanism of Cas9 at physiological salt conditions, and provide important guidance for both in-vitro and in-vivo applications of Cas9.

biochemistry↗

bioRxiv2019

Pumilio Proteins Exert Distinct Biological Functions and Multiple Modes of Post-Transcriptional Regulation in Embryonic Stem Cell Pluripotency and Early Embryogenesis

Gene regulation in embryonic stem cells (ESCs) has been extensively studied at the epigenetic-transcriptional levels, but not at the post-transcriptional levels. Pumilio (Pum) proteins are among the few known translational regulators required for stem cell maintenance in invertebrates and plants. Here we report the essential function of two murine Pum proteins, Pum1 and Pum2, in ESCs and early embryogenesis. Pum1/2 double mutants are developmentally delayed at the morula stage and lethal by embryonic day 8.5 (e8.5). Correspondingly, Pum1/2 double mutant ESCs display severely reduced self-renewal and differentiation, revealing the combined function of Pum1 and Pum2 in ESC pluripotency. Remarkably, Pum1-deficient ESCs show increased expression of pluripotency genes but not differentiation genes, indicating that Pum1 mainly promote differentiation; whereas Pum2-deficient ESCs show decreased expression of pluripotency genes and accelerated differentiation, indicating that Pum2 promotes self-renewal. Thus, Pum1 and Pum2 each uniquely contributes to one of the two complementary aspects of pluripotency. Furthermore, we show that Pum1 and Pum2 achieve ESC functions by forming a negative auto- and inter-regulatory feedback loop that directly regulates at least 1,486 mRNAs. Pum1 and Pum2 regulate target mRNAs not only by repressing translation as expected but also by promoting translation and enhancing or reducing mRNA stability of different target mRNAs. Together, these findings reveal the distinct roles of individual mammalian Pum proteins in ESCs and their collectively essential functions in ESC pluripotency and embryogenesis. Moreover, they demonstrate three novel modes of regulation of Pum proteins towards target mRNAs.\n\nSIGNIFICANCE STATEMENTThis report demonstrates the essential functions of mammalian Pumilio (Pum) proteins for embryonic stem cells (ESCs) pluripotency and embryogenesis. Moreover, it reveals the contrasting but complementary function of individual Pum proteins in regulating distinct aspects of ESC pluripotency, despite their largely overlapping expression and extremely high homology. Furthermore, it unravels a complex regulatory network in which Pum1 and Pum2 form a negative auto- and inter-regulatory feedback loop that regulates 1,486 mRNAs not only by translational repression as expected but also by promoting translation and enhancing or reducing stability of different target mRNAs, which reveals novel modes of post-transcriptional regulation mediated by Pum.

developmental biology↗

bioRxiv2019

Genome sequencing and neurotoxin diversity of a wandering spider Pardosa pseudoannulata (pond wolf spider)

Spiders constitute an extensive and diverse branch of the phylum Arthropoda. Whereas the genomes of four web-weaver spider species and a single cave-living spider have been determined, similar studies have not been reported previously for a wandering spider. The pond wolf spider, Pardosa pseudoannulata, is a wandering hunter that immobilizes prey using venom rather than a web. It is also an important predator against a range of agriculturally important insect pests. The increasing interest in its wandering lifestyle and in the potential of spider venom as a tool for pest control have prompted a detailed study on this wandering spider species. We have generated a high-quality genome sequence of P. pseudoannulata and analysed genes associated with the production of silk and venom toxins. Sequencing reveals that P. pseudoannulata has a large genome of 4.26 Gb. The presence of only 16 spidroin genes and four types of silk glands is consistent with the moderate use of silk and the lack of a prey-catching web. A large number of genes encode neurotoxins and there is evidence that the majority are highly selective for invertebrates. Comparison between spider species reveals a correlation between spider neurotoxin selectivity for target organisms and spider prosoma size, suggesting a possible coevolution of these two features. The genome data provides valuable insights into the biology of P. pseudoannulata and its potential role as a natural enemy in pest control.

genomics↗

bioRxiv2019

Endothelial pannexin 1 channels control inflammation by regulating intracellular calcium

In BriefInterleukine-1 beta (IL-1{beta}) has been identified as a critical factor that contributes to the inflammatory response in cardiovascular disease (e.g., atherosclerosis). Pannexin 1 (Panx1) channel activity in endothelial cells regulates localized inflammatory cell recruitment. In response to prolonged tumor necrosis factor alpha (TNF) treatment, Yang et al. found that the Panx1 channel is targeted to the plasma membrane, where it facilitates an increase in intracellular calcium to control the production and release of cytokines including IL-1{beta}.\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC=\"FIGDIR/small/750323v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (46K):\norg.highwire.dtl.DTLVardef@59e72borg.highwire.dtl.DTLVardef@57bd5corg.highwire.dtl.DTLVardef@50ed73org.highwire.dtl.DTLVardef@1151f56_HPS_FORMAT_FIGEXP M_FIG C_FIG AbstractThe proinflammatory cytokine IL-1{beta} is a significant risk factor in cardiovascular disease that can be targeted to reduce major cardiovascular events. IL-1{beta} expression and release are tightly controlled by changes in intracellular Ca2+. In addition, purinergic signaling through ATP release has also been reported to promote IL-1{beta} production. Despite this, the mechanisms that control IL-1{beta} synthesis and expression have not been identified. The pannexin 1 (Panx1) channel has canonically been implicated in ATP release, especially during inflammation. However, resolution of purinergic signaling occurs quickly due to blood flow and the presence of ectonucleotidases. We examined Panx1 in human endothelial cells following treatment with the pro-inflammatory cytokine tumor necrosis alpha (TNF). In response to long-term TNF treatment, we identified a dramatic increase in Panx1 protein expression at the plasma membrane. Analysis by whole transcriptome sequencing (RNA-seq), qPCR, and treatment with specific kinase inhibitors, revealed that TNF signaling induced NF{kappa}{beta}-associated Panx1 transcription. Genetic inhibition of Panx1 reduced the expression and secretion of IL-1{beta}. We initially hypothesized that increased Panx1-mediated ATP release acted in a paracrine fashion to control cytokine expression. However, our data demonstrate that IL1-{beta} expression was not altered after direct ATP stimulation, following degradation of ATP by apyrase, or after pharmacological blockade of P2 receptors. These data suggest that non-purinergic pathways, involving Panx1, control IL-1{beta} production. Because Panx1 forms a large pore channel, we hypothesized it may act to passively diffuse Ca2+ into the cell upon opening to regulate IL-1{beta}. High-throughput flow cytometric analysis demonstrated that TNF treatments lead to elevated intracellular Ca2+. Genetic or pharmacological inhibition of Panx1 reduced TNF-associated increases in intracellular Ca2+, and IL-1{beta} transcription. Furthermore, we found that the Ca2+-sensitive NF{kappa}{beta}-p65 protein failed to localize to the nucleus after genetic or pharmacological block of Panx1. Taken together, our study provides the first evidence that intracellular Ca2+ regulation via the Panx1 channel induces a feed-forward effect on NF{kappa}{beta} to regulate IL-1{beta} synthesis and release in endothelium during inflammation.

cell biology↗

bioRxiv2019

Impact of ultrasonography on identifying noninvasive prenatal screening false-negative aneuploidy

PurposeTo evaluate the impact of ultrasonography (US) on identifying noninvasive prenatal screening (NIPS) false-negative aneuploidy.\n\nMethodsAnalysis of large population-based NIPS false-negative aneuploidy data comprising karyotypes, clinical outcomes, and US results.\n\nResultsFrom December 2010 to July 2018, a total of 3,320,457 pregnancies were screened by NIPS performed in BGI; among them, 69 NIPS false-negative aneuploidy cases with informed consent were confirmed, and US examination data for 48 cases were not available. Of the 21 cases with US results, 19 (90.5%) had various abnormalities on ultrasound, and 2 (9.5%) cases were shown to be normal on ultrasound. Additionally, 6 out of 7 live born fetuses (approximately 85.7%) were found to have abnormalities on ultrasound. Ventricular septal defects constituted the most frequently observed ultrasound abnormality type among the 21 NIPS false-negative aneuploidy cases.\n\nConclusionNIPS has expanded rapidly worldwide and now accounts for a large proportion of prenatal screening tests in China. This study suggests that abnormal US findings should not be neglected, even when NIPS produces a negative result. Combining NIPS with an US examination can further reduce the incidence of livebirths with aneuploidy.

genetics↗

bioRxiv2019

A systematic survey of PRMT interactomes reveals the key roles of arginine methylation in the global control of RNA splicing and translation

Thousands of proteins undergo arginine methylation, a widespread post-translational modification catalyzed by various protein arginine methyltransferases (PRMTs). However, a full picture of the catalytic network for each PRMT is lacking and the global understanding of their biological roles remains limited. Here we systematically identified interacting proteins for all human PRMTs and demonstrated that they are functionally important for mRNA splicing and translation. We showed that the interactomes of human PRMTs are significantly overlapped with the known methylarginine containing proteins, and different PRMTs are functionally complementary with a high degree of overlap in their substrates and high similarities between their putative methylation motifs. Importantly, arginine methylation is significantly enriched in RNA binding proteins involved in regulating RNA splicing and translation, and inhibition of PRMTs leads to global alteration of alternative splicing and suppression of translation. In particular, ribosomal proteins are pervasively modified with methylarginine, and mutations on their methylation sites suppress ribosome assembly, translation, and eventually cell growth. Collectively, our study provides a novel global view of different PRMT networks and uncovers critical functions of arginine methylation in the regulation of mRNA splicing and translation.

molecular biology↗

bioRxiv2019

Genome-wide analysis of GATA factors in moso bamboo (Phyllostachys edulis) unveils that PeGATAs regulate shoot rapid-growth and rhizome development

BackgroundMoso bamboo is well-known for its rapid-growth shoots and widespread rhizomes. However, the regulatory genes of these two processes are largely unexplored. GATA factors regulate many developmental processes, but its role in plant height control and rhizome development remains unclear.\n\nResultsHere, we found that bamboo GATA factors (PeGATAs) are involved in the growth regulation of bamboo shoots and rhizomes. Bioinformatics and evolutionary analysis showed that there are 31 PeGATA factors in bamboo, which can be divided into three subfamilies. Light, hormone, and stress-related cis-elements were found in the promoter region of the PeGATA genes. Gene expression of 12 PeGATA genes was regulated by phytohormone-GA but there was no correlation between auxin and PeGATA gene expression. More than 27 PeGATA genes were differentially expressed in different tissues of rhizomes, and almost all PeGATAs have dynamic gene expression level during the rapid-growth of bamboo shoots. These results indicate that PeGATAs regulate rhizome development and bamboo shoot growth partially via GA signaling pathway. In addition, PeGATA26, a rapid-growth negative regulatory candidate gene modulated by GA treatment, was overexpressed in Arabidopsis, and over-expression of PeGATA26 significantly repressed Arabidopsis primary root length and plant height. The PeGATA26 overexpressing lines were also resistant to exogenous GA treatment, further emphasizing that PeGATA26 inhibits plant height from Arabidopsis to moso bamboo via GA signaling pathway.\n\nConclusionsOur results provide an insight into the function of GATA transcription factors in regulating shoot rapid-growth and rhizome development, and provide genetic resources for engineering plant height.

plant biology↗

bioRxiv2019

The evaluation of RNA-Seq de novo assembly by PacBio long read sequencing

RNA-Seq de novo assembly is an important method to generate transcriptomes for non-model organisms before any downstream analysis. Given many great de novo assembly methods developed by now, one critical issue is that there is no consensus on the evaluation of de novo assembly methods yet. Therefore, to set up a benchmark for evaluating the quality of de novo assemblies is very critical. Addressing this challenge will help us deepen the insights on the properties of different de novo assemblers and their evaluation methods, and provide hints on choosing the best assembly sets as transcriptomes of non-model organisms for the further functional analysis. In this article, we generate a \"real time\" transcriptome using PacBio long reads as a benchmark for evaluating five de novo assemblers and two model-based de novo assembly evaluation methods. By comparing the de novo assmblies generated by RNA-Seq short reads with the \"real time\" transcriptome from the same biological sample, we find that Trinity is best at the completeness by generating more assemblies than the alternative assemblers, but less continuous and having more misassemblies; Oases is best at the continuity and specificity, but less complete; The performance of SOAPdenovo-Trans, Trans-AByss and IDBA-Tran are in between of five assemblers. For evaluation methods, DETONATE leverages multiple aspects of the assembly set and ranks the assembly set with an average performance as the best, meanwhile the contig score can serve as a good metric to select assemblies with high completeness, specificity, continuity but not sensitive to misassemblies; TransRate contig score is useful for removing misassemblies, yet often the assemblies in the optimal set is too few to be used as a transcriptome.

bioinformatics↗