Biology subjects

Jin, H.

Publications and source records attributed to Jin, H..

At least 109 records · Page 6Linked to original sources

bioRxiv2023

Botrytis cinerea small RNAs are associated with tomato AGO1 and silence tomato target genes supporting cross-kingdom RNAi between the fungal pathogen B. cinerea and its tomato host

Cross-kingdom or cross-species RNA interference (RNAi) is broadly present in many interacting systems between microbes/parasites and their plant and animal hosts. A recent study by Qin et al. (2022) performed correlation analysis using global sRNA- and mRNA-deep sequencing data of cultured B. cinerea and B. cinerea-infected tomato leaves and claimed that cross-kingdom RNAi may not occur in B. cinerea-tomato interaction (Qin et al., 2022). Here, we use experimental evidence and additional bioinformatics analysis of the datasets produced by Qin et al. (2022) to identify the key reasons why a discrepancy between the conclusion of Qin et al. 2022 and previously published findings occurred. We also provided additional experimental evidence to support the presence of cross-kingdom RNAi between tomato and B. cinerea. We believe it is important to clarify the basic concept and mechanism of cross-kingdom/cross-species sRNA trafficking and illustrate proper bioinformatics analyses in this regard for all the scientists and researchers in this field.

plant biology↗

bioRxiv2022

md_harmonize: a Python package for atom-level harmonization of public metabolic data-bases

SummaryA big challenge to integrating public metabolic resources is the use of different nomenclatures by individual databases. This paper presents md_harmonize, an open-source Python package for harmonizing compounds and metabolic reactions across various metabolic databases. md_harmonize utilizes a neighborhood-specific graph coloring method for generating a unique identifier for each compound via atom identifiers based on the compound structure. The resulting harmonized compounds and reactions can be used to construct metabolic networks and models for various downstream analyses, including metabolic flux analysis. AvailabilityThe md_harmonize package is implemented in Python and freely available at https://github.com/MoseleyBioinformaticsLab/md_harmonize Contacthunter.moseley@uky.edu Supplementary informationSupplementary data are available at https://doi.org/10.6084/m9.figshare.21699683.

bioinformatics↗

bioRxiv2022

Utilization of an Artery-on-a-chip to unravel novel regulators and therapeutic targets in vascular diseases

IntroductionOrgans-on-chips represent novel in vitro models that have the capacity to emulate aspects of human physiology and pathophysiology by incorporating features like tissue-multicellularity and exposure to organ-relevant physical environment. We developed an artery-on-a-chip with the objective to recapitulate the structure of the arterial wall composed of intimal and medial layers and the relevant hemodynamic forces that affect luminal cells. ResultsBy comparing arteries-on-chips exposed either to in vivo-like shear stress values or kept in static conditions, we identified a panel of novel genes modulated by shear stress. We next measured the expression pattern of shear stress-modulated genes in areas of the vascular tree affected by atherosclerotic plaques and aortic aneurysms, where disease development and progression are induced by alterations of shear stress. We obtained biopsies from patients affected by carotid artery disease (CAD), comprising the atherosclerotic plaque (diseased artery) and the adjacent region (non-diseased artery). From patients with abdominal aortic aneurysms (AAA), we obtained the aneurysmal portion (diseased aorta) and non-dilated adjacent segment (non-diseased aorta). Genes modulated by shear stress followed the same expression pattern in non-diseased segments of human vessels and were expressed by endothelial and smooth muscle cells as evidenced by immunofluorescence analysis and single cell RNA sequencing. Using mice and porcine models of vascular CAD and AAA, we confirmed that shear stress mediated targets are important in discriminating diseased and non-diseased vessel portions in vivo. Furthermore, we showed that our artery-on-a-chip can serve as a platform for drug-testing. We were able to reproduce the effects of a therapeutic agent previously used in AAA animal models in artery-on-a-chip systems and extend our understanding of its therapeutic effect through a multicellular structure. ConclusionsOur novel in vitro model is capable of mimicking important physiological aspects of human arteries, such as the response to shear stress, and can further shed light on the mechanism of action of potential therapeutics before they enter the clinical stage. TeaserThe artery-on-a-chip is a novel in vitro platform that enables the mimicry of human arteries and can be used to gain insights into the development and therapeutic targeting of vascular diseases.

cell biology↗

bioRxiv2022

Targeting long non-coding RNA NUDT6 enhances smooth muscle cell survival and limits vascular disease progression

Long non-coding RNAs (lncRNAs) orchestrate various biological processes and regulate the development of cardiovascular diseases. Their potential therapeutic benefit to tackle disease progression has recently been extensively explored. Our study investigates the role of lncRNA Nudix Hydrolase 6 (NUDT6) and its antisense target Fibroblast Growth Factor 2 (FGF2) in two vascular pathologies: abdominal aortic aneurysms (AAA) and carotid artery disease. Using tissue samples from both diseases, we detected a substantial increase of NUDT6, whereas FGF2 was downregulated. Targeting Nudt6 in vivo with antisense oligonucleotides in three murine and one porcine animal models of carotid artery disease and AAA limited disease progression. Restoration of FGF2 upon Nudt6 knockdown improved vessel wall morphology and fibrous cap stability. Overexpression of NUDT6 in vitro impaired smooth muscle cell (SMC) migration, while limiting their proliferation and augmenting apoptosis. By employing RNA pulldown followed by mass spectrometry as well as RNA immunoprecipitation, we identified Cysteine and Glycine Rich Protein 1 (CSRP1) as another direct NUDT6 interaction partner, regulating cell motility and SMC differentiation. Overall, the present study identifies NUDT6 as a well-conserved antisense transcript of FGF2. NUDT6 silencing triggers SMC survival and migration and could serve as a novel RNA-based therapeutic strategy in vascular diseases.

molecular biology↗

bioRxiv2022

Depletion of collagen IX alpha2 interferes osteochondral homeostasis of the knee joint which ultimately causing osteoarthritis-like articular cartilage damage

As one of the branched chains of Type IX collagen (Col9), Collagen IX alpha2 (Col92) has been reported to be associated with several orthopedic conditions. To probe the relationship between Col92 and knee osteoarthritis (KOA), we performed a systematic analysis of Col92-deficient (Col9-/-) mice using whole-mount skeletal staining, Micro-CT (CT), biomechanics, histomorphometry, immunohistochemistry (IHC), immunofluorescence (IF) and Enzyme-linked immunosorbent (Elisa). Although whole-mount skeletal staining displayed no difference in bone length and ossification between Col9-/- mice and wild-type (Col92+/+) mice at mid-gestation and adult stages, the knee joint exhibited dramatic discrepancies. Specifically, the subchondral bone (SCB) in the knee joint of Col9-/- mice became sparse and deformed in the early stage, with altered bone morphometric parameters, reduced load-bearing capacity, dysfunctional bone homeostasis (decreased osteogenesis capacity and elevated bone resorption capacity), diminished cartilage proteoglycans and disrupted cartilage extracellular matrix (ECM) anabolism and catabolism compared with the Col92+/+ mice. In the late stage, the cartilage degeneration in Col92-/- mice were particularly pronounced compared to Col92+/+ mice, as evidenced by severe cartilage destruction and a marked reduction in cartilage thickness and area. Overall, Col92 is essential for maintaining osteochondral homeostasis in the knee joint of mice, and the absence of this gene is accompanied by distinct sclerosis of the SCB and a reduction in load-bearing capacity; in the late stage, in the lack of SCB stress inhibition, excessive load is consistently exerted on the cartilage, ultimately leading to osteoarthritic-like articular cartilage damage. Hence, Col92 may serve as a potential candidate biomarker associated with KOA.

physiology↗

bioRxiv2022

A dynamic template complex mediates Munc18-chaperoned SNARE assembly

Munc18 chaperones assembly of three membrane-anchored soluble N-ethylmaleimide- sensitive factor attachment protein receptors (SNAREs) into a four-helix bundle to mediate membrane fusion between vesicles and plasma membranes, leading to neurotransmitter or insulin release, GLUT4 translocation, or other exocytotic processes. Yet, the molecular mechanism underlying chaperoned SNARE assembly is not well understood. Recent evidence suggests that Munc18-1 and Munc18-3 simultaneously bind their cognate SNAREs to form ternary template complexes - Munc18-1:Syntaxin-1:VAMP2 for synaptic vesicle fusion and Munc18-3:Syntaxin-4:VAMP2 for GLUT4 translocation and insulin release, which facilitate binding of SNAP-25 or SNAP-23 to conclude SNARE assembly. Here, we further investigate the structure, dynamics, and function of the template complexes using optical tweezers. Our results suggest that the synaptic template complex transitions to an activated state with a rate of [~]0.05 s-1 and [~]6.8 kBT higher energy for efficient SNAP-25 binding. The transition depends upon the linker region of syntaxin-1 upstream of its helical bundle-forming SNARE motif. In addition, the template complex is stabilized by a poorly characterized disordered loop region in Munc18-1. While the synaptic template complex efficiently binds both SNAP-25 and SNAP-23, the GLUT4 template complex strongly favors SNAP-23 over SNAP-25, despite similar stabilities of their assembled SNARE bundles. Together, our data demonstrate that a highly dynamic template complex mediates efficient and specific SNARE assembly. SignificanceMunc18-1 chaperones coupled folding and assembly of three synaptic SNAREs, syntaxin-1, VAMP2, and SNAP-25, into a four-helix bundle to mediate membrane fusion and neurotransmitter release. Recent evidence suggests that Munc18-1, syntaxin-1, and VAMP2 first form a weak template complex and then bind to SNAP-25 to complete SNARE assembly. However, the dynamics and function of the template complex are not well understood. Using optical tweezers, we found that the template complex undergoes a conformational change to bind SNAP-25 in a way dependent upon the syntaxin linker region and that Munc18 kinetically proofreads SNARE pairing not governed by its thermodynamic stability. Our study reveals a more dynamic template complex than that seen in its cryo-EM structure.

biophysics↗

bioRxiv2022

lncRNA-WAL Promotes Aggressiveness of Triple-Negative Breast Cancer via inducing β-Catenin nuclear translocation.

Because of its insensitive to existing radiotherapy, chemotherapy and targeted treatments, Triple-negative breast cancer (TNBC) remains a great challenge to overcome. More and more evidence has indicated abnormal wnt/{beta}-catenin pathway activation in TNBC but not luminal or her2+ breast cancer, and lncRNAs play a key role in a variety of cancers. Through lncRNA microarray profiling between Activated and inactivated Wnt/{beta}-catenin pathway of TNBC tissues, lnc-WAL (Wnt/{beta}-catenin associated lncRNA; WAL) was selected as the top up-regulated lncRNA in Wnt/{beta}-catenin pathway activation compared with the inactivation group. RIP-seq was analyzed between {beta}-catenin and IgG groups of, where lnc-WAL could interact with {beta}-catenin. Clinically, increased lnc-WAL in the TNBC tumor tissue was associated with shorter survival. lnc-WAL promoted the EMT, the ability of breast cancer stem cells (BCSC), proliferation, migration and invasion of TNBC cells. Mechanistically, lnc-WAL inhibited {beta}-catenin protein degradation via Axin-mediated phosphorylation at serine 45. Subsequently, {beta}-catenin was accumulated in nuclear and activated the target genes. Importantly, Wnt/{beta}-catenin pathway activation stimulated the transcription of lnc-WAL. These results pointed to a master regulatory role of lnc-WAL/Axin/{beta}-catenin in the malignant progression of TNBC. Our findings provide important clinical translational evidence that lnc-WAL maybe as potential therapeutic target against TNBC.

genetics↗

bioRxiv2022

Multi-Domain Characterization and Rapid Detection Technology for Cocaine and Methamphetamine Acute Abuse based on EEG

Multi-domain characterization and a new fast detection method for acute illegal psychostimulants abuse detection based on waking-state EEG of mice is proposed in this paper. To get corftical electroencephalogram (EEG), three groups of mice were injected with cocaine (Coca), methamphetamine (Meth), and saline (Sali) respectively following the experimental paradigm of drug abuse. The EEG features were extracted out by multi-domain views, including time, frequency, complexity, dynamics, and independent domains to obtain acute drug abuse effects on the brain. New strategy combing time domain with frequency domain is developed as multi-domain input and by means of dimension transformation approach preserving temporal information, the performance of drug abuse detection is greatly improved with deep learning models of ResNet50. Results show that comparing to support vector machine (SVM), k nearest neighbor (kNN), random forest (RF), and long short-term memory fully convolutional networks (LSTM-FCN), ResNet50 based on our proposed multi-domain features has best F1-score of 95.10%. This promising method provides a low-cost, fast, and widely assisted technology for psychostimulants abuse identification.

bioinformatics↗

bioRxiv2022

Monoallelically-expressed Noncoding RNAs form nucleolar territories on NOR-containing chromosomes and regulate rRNA expression

Out of the several hundred copies of rRNA genes that are arranged in the nucleolar organizing regions (NOR) of the five human acrocentric chromosomes, [~]50% remain transcriptionally inactive. NOR-associated sequences and epigenetic modifications contribute to differential expression of rRNAs. However, the mechanism(s), controlling the dosage of active versus inactive rRNA genes in mammals is yet to be determined. We have discovered a family of ncRNAs, SNULs (Single NUcleolus Localized RNA), which form constrained sub-nucleolar territories on individual NORs and influences rRNA expression. Individual members of the SNULs monoallelically associate with specific NOR-containing chromosome. SNULs share sequence similarity to pre-rRNA and localize in the sub-nucleolar compartment with pre-rRNA. Finally, SNULs control rRNA expression by influencing pre-rRNA sorting to the DFC compartment and pre-rRNA processing. Our study discovered a novel class of ncRNAs that by forming constrained nucleolar territories on individual NORs contribute to rRNA expression.

cell biology↗

bioRxiv2022

Variation in morpho-physiological and metabolic responses to low nitrogen stress across the sorghum association panel

Access to biologically available nitrogen is a key constraint on plant growth in both natural and agricultural settings. Variation in tolerance to nitrogen deficit stress and productivity in nitrogen limited conditions exists both within and between plant species. Here we quantified variation in the metabolic, physiological, and morphological responses of a sorghum association panel assembled to represent global genetic diversity to long term, moderate, nitrogen deficit stress and the relationship of these responses to grain yield under both conditions. Grain yield exhibits substantial genotype by environment interaction while many other morphological and physiological traits exhibited consistent responses to nitrogen stress across the population. Large scale nontargeted metabolic profiling for a subset of lines in both conditions identified a range of metabolic responses to long term nitrogen deficit stress as well as several metabolites associated with variation in the degree of yield plasticity specific sorghum genotypes exhibited in response to nitrogen deficit stress.

plant biology↗

bioRxiv2022

Efficacy of Parainfluenza Virus 5 (PIV5)-vectored Intranasal COVID-19 Vaccine as a Single Dose Vaccine and as a Booster against SARS-CoV-2 Variants

Immunization with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines has greatly reduced coronavirus disease 2019 (COVID-19)-related deaths and hospitalizations, but waning immunity and the emergence of variants capable of immune escape indicate the need for novel SARS-CoV-2 vaccines. An intranasal parainfluenza virus 5 (PIV5)-vectored COVID-19 vaccine CVXGA1 has been proven efficacious in animal models and blocks contact transmission of SARS-CoV-2 in ferrets. CVXGA1 vaccine is currently in human clinical trials in the United States. This work investigates the immunogenicity and efficacy of CVXGA1 and other PIV5-vectored vaccines expressing additional antigen SARS-CoV-2 nucleoprotein (N) or SARS-CoV-2 variant spike (S) proteins of beta, delta, gamma, and omicron variants against homologous and heterologous challenges in hamsters. A single intranasal dose of CVXGA1 induces neutralizing antibodies against SARS-CoV-2 WA1 (ancestral), delta variant, and omicron variant and protects against both homologous and heterologous virus challenges. Compared to mRNA COVID-19 vaccine, neutralizing antibody titers induced by CVXGA1 were well-maintained over time. When administered as a boost following two doses of a mRNA COVID-19 vaccine, PIV5-vectored vaccines expressing the S protein from WA1 (CVXGA1), delta, or omicron variants generate higher levels of cross-reactive neutralizing antibodies compared to three doses of a mRNA vaccine. In addition to the S protein, the N protein provides added protection as assessed by the highest body weight gain post-challenge infection. Our data indicates that PIV5-vectored COVID-19 vaccines, such as CVXGA1, can serve as booster vaccines against emerging variants. ImportanceWith emerging new variants of concern (VOC), SARS-CoV 2 continues to be a major threat to human health. Approved COVID-19 vaccines have been less effective against these emerging VOCs. This work demonstrates the protective efficacy, and strong boosting effect, of a new intranasal viral-vectored vaccine against SARS-CoV-2 variants in hamsters.

microbiology↗

bioRxiv2022

A kinase-independent function of cyclin-dependent kinase 6 promotes outer radial glia expansion and neocortical folding

The neocortex, the center for higher brain function, first emerged in mammals and has become massively expanded and folded in humans, constituting almost half the volume of the human brain. Primary microcephaly, a developmental disorder in which the brain is smaller than normal at birth, mainly results from the number of neurons in the neocortex being reduced because of defects in neural progenitor cells (NPCs). Outer radial glia (oRGs), NPCs that are abundant in gyrencephalic species but rare in lisencephalic species, are thought to play key roles in the expansion and folding of the neocortex. However, how oRGs expand, whether they are necessary for neocortical folding, and whether defects in oRGs cause microcephaly remain important questions in the study of brain development, evolution, and disease. Here, we show that oRG expansion in mice, ferrets, and human cerebral organoids requires cyclin-dependent kinase 6 (CDK6), the mutation of which causes primary microcephaly via an unknown mechanism. In a mouse model in which increased Hedgehog signaling expands oRGs and intermediate progenitor cells and induces neocortical folding, CDK6 loss selectively decreased oRGs and abolished neocortical folding. Remarkably, this function of CDK6 in oRG expansion did not require its kinase activity, was not shared by the highly similar CDK4 and CDK2, and was disrupted by the mutation causing microcephaly. Therefore, our results indicate that CDK6 is conserved to promote oRG expansion; that oRGs are necessary for neocortical folding; and that defects in oRG expansion may cause primary microcephaly. Significance StatementPrimary microcephaly, a disorder in which the brain is smaller than normal at birth, disproportionately affects the neocortex. Although outer radial glia (oRGs) expansion is hypothesized to be important in neocortical expansion and folding, it remains unknown whether oRGs are necessary for neocortical folding and whether defective oRGs cause microcephaly. Moreover, how oRGs expand is not well understood. A mutation in CDK6 causes microcephaly via an unknown mechanism. Here, we show that CDK6 promotes oRG expansion and neocortical folding. This function of CDK6 does not require its kinase activity but is disrupted by a mutation that causes microcephaly. Our findings show that CDK6 is conserved to expand oRGs and provide evidence that oRG defects disrupt neocortical growth and folding.

neuroscience↗

bioRxiv2022

Deaza-modification of MR1 ligands modulates recognition by MR1-restricted T cells

MR1-restricted T (MR1T) cells recognize microbial small molecule metabolites presented on the MHC Class I-like molecule MR1 and have been implicated in early effector responses to microbial infection. As a result, there is considerable interest in identifying chemical properties of metabolite ligands that permit recognition by MR1T cells, for consideration in therapeutic or vaccine applications. Here, we made chemical modifications to known MR1 ligands to evaluate the effect on MR1T cell activation. Specifically, we modified 6,7-dimethyl-8-D-ribityllumazine (DMRL) to generate 6,7-dimethyl-8-D-ribityldeazalumazine (DZ), and then further derivatized DZ to determine the requirements for retaining MR1 surface stabilization and agonistic properties. Interestingly, the IFN-{gamma} response toward DZ varied widely across a panel of T cell receptor (TCR)-diverse MR1T cell clones; while one clone was agnostic toward the modification, most displayed either an enhancement or depletion of IFN-{gamma} production when compared with its response to DMRL. To gain insight into a putative mechanism behind this phenomenon, we used in silico molecular docking techniques for DMRL and its derivatives and performed molecular dynamics simulations of the complexes. In assessing the dynamics of each ligand in the MR1 pocket, we found that DMRL and DZ exhibit differential dynamics of both the ribityl moiety and the aromatic backbone, which may contribute to ligand recognition. Together, our results support an emerging hypothesis for flexibility in MR1:ligand-MR1T TCR interactions and enable further exploration of the relationship between MR1:ligand structures and MR1T cell recognition for downstream applications targeting MR1T cells.

immunology↗

bioRxiv2022

Accurate and sensitive mutational signature analysis with MuSiCal

Mutational signature analysis is a recent computational approach for interpreting somatic mutations in the genome. Its application to cancer data has enhanced our understanding of mutational forces driving tumorigenesis and demonstrated its potential to inform prognosis and treatment decisions. However, methodological challenges remain for discovering new signatures and assigning proper weights to existing signatures, thereby hindering broader clinical applications. Here we present MuSiCal (Mutational Signature Calculator), a rigorous analytical framework with novel algorithms that solves major problems in the standard workflow. Our simulation studies demonstrate that MuSiCal outperforms state-of-the-art algorithms for both signature discovery and assignment. By reanalyzing over 2,700 cancer genomes, we provide an improved catalog of signatures and their assignments, discover nine indel signatures absent in the current catalog, resolve long-standing issues with the ambiguous flat signatures, and give insights into signatures with unknown etiologies. We expect MuSiCal and the improved catalog to be a step towards establishing best practices for mutational signature analysis.

genomics↗

bioRxiv2022

Association Mapping Across a Multitude of Traits Collected in Diverse Environments Identifies Pleiotropic Loci in Maize.

Classical genetic studies have identified many cases of pleiotropy where mutations in individual genes alter many different phenotypes. Quantitative genetic studies of natural genetic variants frequently examine one or a few traits, limiting their potential to identify pleiotropic effects of natural genetic variants. Widely adopted community association panels have been employed by plant genetics communities to study the genetic basis of naturally occurring phenotypic variation in a wide range of traits. High-density genetic marker data - 18M markers - from two partially overlapping maize association panels comprising 1,014 unique genotypes grown in field trials across at least seven US states and scored for 162 distinct trait datasets enabled the identification of of 2,154 suggestive marker-trait associations and 697 confident associations in the maize genome using a resampling-based genome-wide association strategy. The precision of individual marker-trait associations was estimated to be three genes based a reference set of genes with known phenotypes. Examples were observed of both genetic loci associated with variation in diverse traits (e.g. above-ground and below-ground traits), as well as individual loci associated with the same or similar traits across diverse environments. Many significant signals are located near genes whose functions were previously entirely unknown or estimated purely via functional data on homologs. This study demonstrates the potential of mining community association panel data using new higher density genetic marker sets combined with resampling-based genome-wide association tests to develop testable hypotheses about gene functions, identify potential pleiotropic effects of natural genetic variants, and study genotype by environment interaction.

plant biology↗

bioRxiv2021

Sorghum Association Panel Whole-Genome Sequencing Establishes Pivotal Resource for Dissecting Genomic Diversity

Association mapping panels represent foundational resources for understanding the genetic basis of phenotypic diversity and serve to advance plant breeding by exploring genetic variation across diverse accessions with distinct histories of evolutionary divergence and local adaptation. We report the whole-genome sequencing (WGS) of 400 sorghum [Sorghum bicolor (L.) Moench] accessions from the Sorghum Association Panel (SAP) at an average coverage of 38X (25X-72X), enabling the development of a high-density genomic-marker set of 43,983,694 variants including SNPs (~ 38 million), indels (~ 5 million), and CNVs (170,000). We observe slightly more deletions among indels and a much higher prevalence of deletions among copy number variants compared to insertions. This new marker set enabled the identification of several putatively novel genomic associations for plant height and tannin content, which were not identified when using previous lower-density marker sets. WGS identified and scored variants in 5 kb bins where available genotyping-by-sequencing (GBS) data captured no variants, with half of all bins in the genome falling into this category. The predictive ability of genomic best unbiased linear predictor (GBLUP) models was increased by an average of 30% by using WGS markers rather than GBS markers. We identified 18 selection peaks across subpopulations that formed due to evolutionary divergence during domestication, and we found six Fst peaks resulting from comparisons between converted lines and breeding lines within the SAP that were distinct from the peaks associated with historic selection. This population has been and continues to serve as a significant public resource for sorghum research and demonstrates the value of improving upon existing genomic resources. Author summary

plant biology↗

bioRxiv2021

Moving Beyond Processing and Analysis-Related Variation in Neuroscience

When fields lack consensus standard methods and accessible ground truths, reproducibility can be more of an ideal than a reality. Such has been the case for functional neuroimaging, where there exists a sprawling space of tools and processing pipelines. We provide a critical evaluation of the impact of differences across five independently developed minimal preprocessing pipelines for functional MRI. We show that even when handling identical data, inter-pipeline agreement was only moderate, critically shedding light on a factor that limits cross-study reproducibility. We show that low inter-pipeline agreement mainly becomes appreciable when the reliability of the underlying data is high, which is increasingly the case as the field progresses. Crucially, we show that when inter-pipeline agreement is compromised, so too are the consistency of insights from brainwide association studies. We highlight the importance of comparing analytic configurations, as both widely discussed and commonly overlooked decisions can lead to marked variation.

neuroscience↗

bioRxiv2021

Genomic analysis based on chromosome-level genome assembly reveals an expansion of terpene biosynthesis of Azadirachta indica

Azadirachta indica (neem), an evergreen tree of the Meliaceae family, is a source of the potent biopesticide azadirachtin. The lack of a chromosome-level assembly impedes the understanding of in-depth genomic architecture and the comparative genomic analysis of A. indica. Here, a high-quality genome assembly of A. indica was constructed using a combination of data from Illumina, PacBio, and Hi-C technology, which is the first chromosome-scale genome assembly of A. indica. The genome size of A. indica is 281 Mb anchored to 14 chromosomes (contig N50=6 Mb and scaffold N50=19 Mb). The genome assembly contained 115 Mb repetitive elements and 25,767 protein-coding genes. Evolutional analysis revealed that A. indica didnt experience any whole-genome duplication (WGD) event after the core eudicot {gamma} event, but some genes and genome segment might undergo recent duplications. The secondary metabolite clusters, TPS genes, and CYP genes were also identified. Comparative genomic analysis revealed that most of the A. indica-specific TPS genes and CYP genes were located on the terpene-related clusters on chromosome 13. It is suggested that chromosome 13 may play an important role in the specific terpene biosynthesis of A. indica. And the gene duplication events may be responsible for the terpene biosynthesis expansion in A. indica. This will shed light on terpene biosynthesis in A. indica and facilitate comparative genomic research of the family Meliaceae.

genomics↗