Flowering genes identification, network analysis, and database construction for 837 plants.

Flowering is one of the most important biological phenomena in the plant kingdom, which not only has important ecological significance, but also has substantial horticultural ornamental value. In this study, we undertook an exhaustive review of the advancements in our understanding of plant flowering genes. We delved into the identification and conducted comparative analyses of flowering genes across virtually all sequenced angiosperm plant genomes. Furthermore, we established an extensive angiosperm flowering atlas, encompassing a staggering 183 720 genes across eight pathways, along with 10 155 ABCDE mode genes, which play a pivotal role in plant flowering regulation. Through the examination of expression patterns, we unveiled the specificities of these flowering genes. An interaction network between flowering genes of the ABCDE model and their corresponding upstream genes offered a blueprint for comprehending their regulatory mechanisms. Moreover, we predicted the miRNA and target genes linked to the flowering processes of each species. To culminate our efforts, we have built a user-friendly web interface, named the Plant Flowering-time Gene Database (PFGD), accessible at http://pfgd.bio2db.com/. We firmly believe that this database will serve as a cornerstone in the global research community, facilitating the in-depth exploration of flowering genes in the plant kingdom. In summation, this pioneering endeavor represents the first comprehensive collection and comparative analysis of flowering genes in plants, offering valuable resources for the study of plant flowering genetics.

Vascularized organoid-on-a-chip: design, imaging, and analysis.

Vascularized organoid-on-a-chip (VOoC) models achieve substance exchange in deep layers of organoids and provide a more physiologically relevant system in vitro. Common designs for VOoC primarily involve two categories: self-assembly of endothelial cells (ECs) to form microvessels and pre-patterned vessel lumens, both of which include the hydrogel region for EC growth and allow for controlled fluid perfusion on the chip. Characterizing the vasculature of VOoC often relies on high-resolution microscopic imaging. However, the high scattering of turbid tissues can limit optical imaging depth. To overcome this limitation, tissue optical clearing (TOC) techniques have emerged, allowing for 3D visualization of VOoC in conjunction with optical imaging techniques. The acquisition of large-scale imaging data, coupled with high-resolution imaging in whole-mount preparations, necessitates the development of highly efficient analysis methods. In this review, we provide an overview of the chip designs and culturing strategies employed for VOoC, as well as the applicable optical imaging and TOC methods. Furthermore, we summarize the vascular analysis techniques employed in VOoC, including deep learning. Finally, we discuss the existing challenges in VOoC and vascular analysis methods and provide an outlook for future development.

Evaluation of InSAR Tropospheric Delay Correction Methods in the Plateau Monsoon Climate Region Considering Spatial-Temporal Variability.

The tropospheric delay caused by the temporal and spatial variation of meteorological parameters is the main error source in interferometric synthetic aperture radar (InSAR) applications for geodesy. To minimize the impact of tropospheric delay errors, it is necessary to select the appropriate tropospheric delay correction method for different regions. In this study, the interferogram results of the InSAR, corrected for tropospheric delay using the Linear, Generic Atmospheric Correction Online Service for InSAR (GACOS) and ERA-5 atmospheric reanalysis dataset (ERA5) methods, are presented for the study area of the junction of the Hengduan Mountains and the Yunnan-Kweichow Plateau, which is significantly influenced by the plateau monsoon climate. Four representative regions, Eryuan, Binchuan, Dali, and Yangbi, are selected for the study and analysis. The phase standard deviation (STD), phase-height correlation, and global navigation satellite system (GNSS) data were used to evaluate the effect of tropospheric delay correction by integrating topographic, seasonal, and meteorological factors. The results show that all three methods can attenuate the tropospheric delay, but the correction effect varies with spatial and temporal characteristics.

Large-scale analysis of trihelix transcription factors reveals their expansion and evolutionary footprint in plants.

The trihelix transcription factor (TTF) gene family is an important class of transcription factors that play key roles in regulating developmental processes and responding to various stresses. To date, no comprehensive analysis of the TTF gene family in large-scale species has been performed. A cross-genome exploration of its origin, copy number variation, and expression pattern in plants is also unavailable. Here, we identified and characterized the TTF gene family in 110 species representing typical plant phylogenetic taxa. Interestingly, we found that the number of TTF genes was significantly expanded in Chara braunii compared to other species. Based on the available plant genomic datasets, our comparative analysis suggested that the TTF gene family likely originated from the GT-1-1 group and then expanded to form other groups through duplication or deletion of some domains. We found evidence that whole-genome duplication/triplication contributed most to the expansion of the TTF gene family in dicots, monocots and basal angiosperms. In contrast, dispersed and proximal duplications contributed to the expansion of the TTF gene family in algae and bryophyta. The expression patterns of TTF genes and their upstream and downstream genes in different treatments showed a functional divergence of TTF-related genes. Furthermore, we constructed the interaction network between TTF genes and the corresponding upstream and downstream genes, providing a blueprint for their regulatory pathways. This study provided a cross-genome comparative analysis of TTF genes in 110 species, which contributed to understanding their copy number expansion and evolutionary footprint in plants.

The effect of training on sensitivity and stability of double fusion in Panum's limiting case.

Panum's limiting case is a phenomenon of monocular occlusion in binocular vision. This occurs when one object is occluded by the other object for one eye, but the two objects are both visible for the other eye. Although previous studies have found that vertical gradient of horizontal disparity and cue conflict are two important factors for double fusion, the effect of training on the sensitivity and stability of Panum's limiting case remains unknown. The current study trained 26 participants for 5 days with several of Panum's configurations (Gilliam, Frisby, and Wang series). The latency and duration of double fusion were recorded to examine the effects of training on sensitivity and stability of double fusion in Panum's limiting case. For each level of vertical gradient of horizontal disparity and cue conflict, the latency of double fusion decreased and the duration of double fusion increased with each additional training session. The results showed that vertical gradient of horizontal disparity and cue conflict interacted, and the duration of high cue conflict was significantly shorter than that of medium and low cue conflict for each level of vertical gradient of horizontal disparity. The findings suggest that there is an effect of training for vertical gradient of horizontal disparity and cue conflict in Panum's limiting case, and that the three factors jointly affect the sensitivity and stability of double fusion.

On-chip clearing for live imaging of 3D cell cultures.

Three-dimensional (3D) cell cultures provide an important model for various biological studies by bridging the gap between two-dimensional (2D) cell cultures and animal tissues. Microfluidics has recently provided controllable platforms for handling and analyzing 3D cell cultures. However, on-chip imaging of 3D cell cultures within microfluidic devices is hindered by the inherent high scattering of 3D tissues. Tissue optical clearing techniques have been used to address this concern but remain limited to fixed samples. As such, there is still a need for an on-chip clearing method for imaging live 3D cell cultures. Here, to achieve on-chip clearing for live imaging of 3D cell cultures, we conceived a simple microfluidic device by integrating a U-shaped concave for culture, parallel channels with micropillars, and differentiated surface treatment to enable on-chip 3D cell culture, clearing, and live imaging with minimal disturbance. The on-chip tissue clearing increased the imaging performance of live 3D spheroids with no influence on cell viability or spheroid proliferation and demonstrated robust compatibility with several commonly used cell probes. It allowed dynamic tracking of lysosomes in live tumor spheroids and enabled quantitative analysis of their motility in the deeper layer. Our proposed method of on-chip clearing for live imaging of 3D cell cultures provides an alternative for dynamic monitoring of deep tissue on a microfluidic device and has the potential to be used in 3D culture-based assays for high-throughput applications.

Nitrogen level induces sex-specific cadmium phloem remobilization and cell wall segregation in Populus cathayana.

Nitrogen (N) fertilization can improve the phytoremediation of contaminated soils. However, limited information is available on the effects and mechanisms of N availability on Cadmium (Cd) phytoextraction by dioecious plants. This study employed female and male Populus cathayana to examine sex-specific long-distance transport and cell wall Cd sequestration. Females had a greater ability to transport Cd from roots to shoots and accumulated more Cd in leaves, but had less Cd bound to the cell wall and S-containing ligands than males, irrespective of N availability. N availability affected the sex-specific ability to transport Cd and chelate it within cell walls and with S-containing ligands. Low N promoted phloem-mediated upward and downward Cd transport and total Cd accumulation in both sexes, and such effects on phloem-mediated downward Cd transport were greater than those on upward Cd transport in males. However, low-N concentration-induced Cd phloem transport was more significant in females than males. In females, low N reduced Cd accumulation in leaves via increased phloem-mediated Cd downward transport, and this Cd was subsequently sequestered in the bark and root cell walls. In contrast, for males, high N promoted xylem-mediated Cd transport to shoots and Cd sequestration in the bark but reduced phloem-mediated Cd downward transport and subsequent sequestration in root cell walls. Sex-specific genes related to root Cd transport and translocation from roots to shoots were also affected by N supply in roots. These results suggested that N availability reduced the sex-based difference in total Cd accumulation, translocation and Cd detoxification, and males showed stronger Cd tolerance than females at both N availabilities.

Genome-wide characterization and functional identification of MYB genes in Malus sieversii infected by Valsa mali.

Among the most important transcription factors in plants, the v-myb avian myeloblastosis viral oncogene homolog (MYB) regulates the expression network of response genes under stresses such as fungal infection. In China, the canker disease Valsa mali threatens the survival of Malus sieversii, an ancestor of cultivated apples. Using the M. sieversii genome, we identified 457 MsMYB and 128 R2R3-MsMYB genes that were randomly distributed across 17 chromosomes. Based on protein sequence and structure, the R2R3-MsMYB genes were phylogenetically divided into 29 categories, and 26 conserved motifs were identified. We further predicted cis-elements in the 2000-kb promoter region of R2R3-MsMYBs based on the genome. Transcriptome analysis of M. sieversii under V. mali infection showed that 27 R2R3-MsMYBs were significantly differentially expressed, indicating their key role in the response to V. mali infection. Using transient transformation, MsMYB14, MsMYB24, MsMYB39, MsMYB78, and MsMYB108, which were strongly induced by V. mali infection, were functionally identified. Among the five MsMYBs, MsMYB14 and MsMYB78 were both important in enhancing resistance to diseases, whereas MsMYB24 inhibited resistance. Based on the results of this study, we gained a better understanding of the MsMYB transcription factor family and laid the foundation for a future research program on disease prevention strategies in M. sieversii.

A versatile vessel casting method for fine mapping of vascular networks using a hydrogel-based lipophilic dye solution.

Efficient labeling of the vasculature is important for understanding the organization of vascular networks. Here, we propose VALID, a vessel-labeling method that enables visualization of vascular networks with tissue clearing and light-sheet microscopy. VALID transforms traditional lipophilic dye solution into hydrogel by introducing gelatin and restrains the dye aggregation, resulting in complete and uniform vessel-labeling patterns with high signal-to-background ratios. VALID also enhances the compatibility of lipophilic dyes with solvent-based tissue-clearing protocols, which was hard to achieve previously. Using VALID, we combined lipophilic dyes with solvent-based tissue-clearing techniques to perform 3D reconstructions of vasculature within mouse brain and spinal cord. We also employed VALID for 3D visualization and quantification of microvascular damage in a middle cerebral artery occlusion mouse model. VALID should provide a simple, cost-effective vessel-labeling protocol that would significantly widen the applications of lipophilic dyes in research on cerebrovascular complications.

Chromosome-level wild Hevea brasiliensis genome provides new tools for genomic-assisted breeding and valuable loci to elevate rubber yield.

The rubber tree (Hevea brasiliensis) is grown in tropical regions and is the major source of natural rubber. Using traditional breeding approaches, the latex yield has increased by sixfold in the last century. However, the underlying genetic basis of rubber yield improvement is largely unknown. Here, we present a high-quality, chromosome-level genome sequence of the wild rubber tree, the first report on selection signatures and a genome-wide association study (GWAS) of its yield traits. Population genomic analysis revealed a moderate population divergence between the Wickham clones and wild accessions. Interestingly, it is suggestive that H. brasiliensis and six relatives of the Hevea genus might belong to the same species. The selective sweep analysis found 361 obvious signatures in the domesticated clones associated with 245 genes. In a 15-year field trial, GWAS identified 155 marker-trait associations with latex yield, in which 326 candidate genes were found. Notably, six genes related to sugar transport and metabolism, and four genes related to ethylene biosynthesis and signalling are associated with latex yield. The homozygote frequencies of the causal nonsynonymous SNPs have been greatly increased under selection, which may have contributed to the fast latex yield improvement during the short domestication history. Our study provides insights into the genetic basis of the latex yield trait and has implications for genomic-assisted breeding by offering valuable resources in this new domesticated crop.

UVMS task-priority planning framework for underwater task goal classification optimization.

This paper presents a task prioritization strategy based on a generic underwater task goal classification transformation for multitasking underwater operational tasks: attitude control, floating manipulation, collision-free motion, especially optimizing trajectory of the end-effector of an underwater vehicle manipulator system (UVMS) in a complex marine environment. The design framework aims to divide the complex underwater operational tasks into UVMS executable generic task combinations and optimize the resource consumption during the whole task. In order to achieve the corresponding underwater task settings, the system needs to satisfy different task scheduling structures. We consider the actual application scenarios of the operational goals and prioritize and define each category of task hierarchy accordingly. Multiple tasks simultaneously enable fast adaptation to UVMS movements and planning to complete UVMS autonomous movements. Finally, an underwater vehicle manipulator system implements the task prioritization planning framework for a practical scenario with different constraints on different goals. We quickly and precisely realize the interconversion of different tasks under goal constraints. The autonomous motion planning and real-time performance of UVMS are improved to cope with the increasing operational task requirements and the complex and changing practical engineering application environments.

PRECISION.array: An R Package for Benchmarking microRNA Array Data Normalization in the Context of Sample Classification.

We present a new R package PRECISION.array for assessing the performance of data normalization methods in connection with methods for sample classification. It includes two microRNA microarray datasets for the same set of tumor samples: a re-sampling-based algorithm for simulating additional paired datasets under various designs of sample-to-array assignment and levels of signal-to-noise ratios and a collection of numerical and graphical tools for method performance assessment. The package allows users to specify their own methods for normalization and classification, in addition to implementing three methods for training data normalization, seven methods for test data normalization, seven methods for classifier training, and two methods for classifier validation. It enables an objective and systemic evaluation of the operating characteristics of normalization and classification methods in microRNA microarrays. To our knowledge, this is the first such tool available. The R package can be downloaded freely at https://github.com/LXQin/PRECISION.array.

GGDB: A Grameneae genome alignment database of homologous genes hierarchically related to evolutionary events.

The genomes of Gramineae plants have been preferentially sequenced owing to their economic value. These genomes are often quite complex, for example harboring many duplicated genes, and are the main source of genetic innovation and often the result of recurrent polyploidization. Deciphering these complex genome structures and linking duplicated genes to specific polyploidization events are important for understanding the biology and evolution of plants. However, efforts have been hampered by the complexity of analyzing these genomes. Here, we analyzed 29 well-assembled and up-to-date Gramineae genome sequences by hierarchically relating duplicated genes in collinear regions to specific polyploidization or speciation events. We separated duplicated genes produced by each event, established lists of paralogous and orthologous genes, and ultimately constructed an online database, GGDB (http://www.grassgenome.com/). Homologous gene lists from each plant and between plants can be displayed, searched, and downloaded from the database. Interactive comparison tools are deployed to demonstrate homology among user-selected plants and to draw genome-scale or local alignment figures and gene-based phylogenetic trees corrected by exploiting gene collinearity. Using these tools and figures, users can easily detect structural changes in genomes and explore the effects of paleo-polyploidy on crop genome structure and function. The GGDB will provide a useful platform for improving our understanding of genome changes and functional innovation in Gramineae plants.

Altered resting state dynamic functional connectivity of amygdala subregions in patients with autism spectrum disorder: A multi-site fMRI study.

BACKGROUND: Autism spectrum disorder (ASD) is associated with altered brain connectivity. Previous studies have focused on the static functional connectivity pattern from amygdala subregions in ASD while ignoring its dynamics. Considering that dynamic functional connectivity (dFC) can provide different perspectives, the present study aims to investigate the dFC pattern of the amygdala subregions in ASD patients. METHODS: Data of 618 ASD patients and 836 typical controls (TCs) of 30 sites were obtained from the Autism Brain Imaging Data Exchange (ABIDE) database. The sliding window approach was applied to conduct seed-based dFC analysis. The seed regions were bilateral basolateral (BLA) and centromedial-superficial amygdala (CSA). A two-sample t-test was done at each site. Image-based meta-analysis (IBMA) based on the results from all sites was performed. Correlation analysis was conducted between the dFC values and the clinical scores. RESULTS: The ASD patients showed lower dFC between the left BLA and the bilateral inferior temporal (ITG)/left superior frontal gyrus, between the right BLA and right ITG/right thalamus/left superior temporal gyrus, and between the right CSA and middle temporal gyrus. The ASD patients showed higher dFC between the left BLA and temporal lobe/right supramarginal gyrus, between the right BLA and left calcarine gyrus, and between the left CSA and left calcarine gyrus. Correlation analysis revealed that the symptom severity was positively correlated with the dFC between the bilateral BLA and ITG in ASD. CONCLUSIONS: Abnormal dFC of the specific amygdala subregions may provide new insights into the pathological mechanisms of ASD.

The Brassicaceae genome resource (TBGR): A comprehensive genome platform for Brassicaceae plants.

The Brassicaceae is an important plant family. We built a user-friendly, web-based, comparative, and functional genomic database, The Brassicaceae Genome Resource (TBGR, http://www.tbgr.org.cn), based on 82 released genomes from 27 Brassicaceae species. The TBGR database contains a large number of important functional genes, including 4,096 glucosinolate genes, 6,625 auxin genes, 13,805 flowering genes, 36,632 resistance genes, 1,939 anthocyanin genes, and 1,231 m6A genes. A total of 1,174,049 specific guide sequences for clustered regularly interspaced short palindromic repeats and 5,856,479 transposable elements were detected in Brassicaceae. TBGR also provides information on synteny, duplication, and orthologs for 27 Brassicaceae species. The TBGR database contains 1,183,851 gene annotations obtained using the TrEMBL, Swiss-Prot, Nr, GO, and Pfam databases. The BLAST, Synteny, Primer Design, Seq_fetch, and JBrowse tools are provided to help users perform comparative genomic analyses. All the genome assemblies, gene models, annotations, and bioinformatics results can be easily downloaded from the TBGR database. We plan to improve and continuously update the database with newly assembled genomes and comparative genomic studies. We expect the TBGR database to become a key resource for the study of the Brassicaceae.

Chromosome-level pepino genome provides insights into genome evolution and anthocyanin biosynthesis in Solanaceae.

Pepino (Solanum muricatum, 2n = 2x = 24), a member of the Solanaceae family, is an important globally grown fruit. Herein, we report high-quality, chromosome-level pepino genomes. The 91.67% genome sequence is anchored to 12 chromosomes, with a total length of 1.20 Gb and scaffold N50 of 87.03 Mb. More than half the genome comprises repetitive sequences. In addition to the shared ancient whole-genome triplication (WGT) event in eudicots, an additional new WGT event was present in the pepino. Our findings suggest that pepinos experienced chromosome rearrangements, fusions, and gene loss after a WGT event. The large number of gene removals indicated the instability of Solanaceae genomes, providing opportunities for species divergence and natural selection. The paucity of disease-resistance genes (NBS) in pepino and eggplant has been explained by extensive loss and limited generation of genes after WGT events in Solanaceae. The outbreak of NBS genes was not synchronized in Solanaceae species, which occurred before the Solanaceae WGT event in pepino, tomato, and tobacco, whereas it was almost synchronized with WGT events in the other four Solanaceae species. Transcriptome and comparative genomic analyses revealed several key genes involved in anthocyanin biosynthesis. Although an extra WGT event occurred in Solanaceae, CHS genes related to anthocyanin biosynthesis in grapes were still significantly expanded compared with those in Solanaceae species. Proximal and tandem duplications contributed to the expansion of CHS genes. In conclusion, the pepino genome and annotation facilitate further research into important gene functions and comparative genomic analysis in Solanaceae.

Large-scale analyses of heat shock transcription factors and database construction based on whole-genome genes in horticultural and representative plants.

Heat shock transcription factor (Hsf) plays a critical role in regulating heat resistance. Here, 2950 Hsf family genes were identified from 111 horticultural and representative plants. More Hsf genes were detected in higher plants than lower plants. Based on all Hsf genes, we constructed a phylogenetic tree, which indicated that Hsf genes of each branch evolved independently after species differentiation. Furthermore, we uncovered the evolutionary trajectories of Hsf genes by motif analysis. There were only 6 motifs (M1 to M6) in lower plants, and then 4 novel motifs (M7-M10) appeared in higher plants. However, the motifs of some Hsf genes were lost in higher plant, indicating that Hsf genes have undergone sequence variation during the evolution. The number of Hsf gene loss was more than duplication after whole-genome duplication in higher plants. The heat response network was constructed using 24 Hsf genes, 2421 downstream, and 222 upstream genes of Arabidopsis. Further enrichment analysis revealed that Hsf genes and other transcription factors interacted with each other to response heat resistance. The global expression maps were illustrated for Hsf genes under various abiotic, biotic stresses, and several developmental stages in Arabidopsis. The syntenic and phylogenetic analyses were conducted using Hsf genes of Arabidopsis and Pan-genome of 18 Brassica rapa accessions. We also performed the expression pattern analysis of Hsf and six Hsp family genes using expression values from different tissues and heat treatments in B. rapa. The interaction network between Hsf and Hsp gene families was constructed in B. rapa, and several core genes were detected in the network. Finally, we constructed a Hsf database (http://hsfdb.bio2db.com) for researchers to retrieve Hsf gene family information. Therefore, our study will provide rich resources for the evolution and functional study of Hsf genes.

A highly specific aptamer probe targeting PD-L1 in tumor tissue sections: Mutation favors specificity.

Although DNA aptamers can show comparable affinity to antibodies and have the advantage of having high batch-to-batch consistency, they often suffer from unsatisfied specificity for complex samples. The limited library size used for aptamer in vitro isolation (SELEX) has been recognized as one of the major reasons. Programmed cell death-ligand 1 (PD-L1) is both a key protein in cancer diagnostics and also immunotherapy. We report here a DNA aptamer that highly specifically binds PD-L1 expressed on the surface of various cancer cells and multiple types of tissue sections. The aptamers were selected from a DNA library containing a type II restriction endonuclease Alu I recognition site in the middle of the 40-nt random sequences, against recombinant PD-L1 rather than the whole cell or tissue section. The library enrichment was achieved by Alu I mediated-SELEX, named as REase-SELEX, in which Alu I cut off the non-binders at the recognition site and, more importantly, induced library mutations to substantially increase the library diversity. 8-60, a representative aptamer with high affinity (KD = 1.4 nM determined by SPR) successfully detected four types of cancer cells with PD-L1 expression levels from low to high by flow cytometry, normal human tonsil (gold standard for PD-L1 antibody evaluation), clinical non-small cell lung cancer (high PD-L1 expression level), and malignant melanoma (low PD-L1 expression level) tissue sections by fluorescence microscopy imaging, showing unprecedented high specificity. The results demonstrate that 8-60 is an advanced probe for PD-L1 cancer diagnostics and mutations in SELEX greatly favor aptamer specificity.

MicroRNA 223 Targeting ATG16L1 Affects Microglial Autophagy in the Kainic Acid Model of Temporal Lobe Epilepsy.

This study aimed to explore whether microRNA (miR) 223 affects microglial autophagy by targeting autophagy-related 16-like 1 (ATG16L1) in the kainic acid (KA) model of temporal lobe epilepsy (TLE). The miRNA and mRNA expression levels were quantified using quantitative real-time polymerase chain reaction (qRT-PCR), and the protein expression was investigated using western blotting. A dual-luciferase reporter assay was used to test the direct interaction between miR 223 and ATG16L1. In situ hybridization was performed to measure the hippocampal expression of miR 223. We used immunofluorescence staining to assess the expression of ATG16L1 and microtubule-associated protein light chain 3 (LC3) in the murine hippocampal microglia. Inhibitor of miR 223 was utilized to investigate the role of miR 223 in TLE, and the epileptic activity was assessed using electroencephalography (EEG). The autophagosomes were observed by transmission electron microscopy. In patients with TLE, the murine KA model of TLE, and the KA-stimulated BV2 cells, miR 223, and sequestosome 1 (SQSTM1/P62) expressions were remarkably increased, whereas ATG16L1 and LC3 levels were significantly decreased. Using a dual-luciferase reporter assay, ATG16L1 was determined as a direct target of miR 223. Treatment with antagomir 223 alleviated epilepsy, prevented abnormalities in EEG recordings and increased the ATG16L1 and LC3 levels in KA-treated mice. Inhibition of miR 223 induced increased autophagy in BV2 cells upon Rapamycin stimulation. These findings show that miR 223 affects microglial autophagy via ATG16L1 in the KA model of TLE. The miR 223/ATG16L1 pathway may offer a new treatment option for TLE.

Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants.

Simple sequence repeats (SSRs) are one of the most important genetic markers and widely exist in most species. Here, we identified 249,822 SSRs from 3,951,919 genes in 112 plants. Then, we conducted a comprehensive analysis of these SSRs and constructed a plant SSR database (PSSRD). Interestingly, more SSRs were found in lower plants than in higher plants, showing that lower plants needed to adapt to early extreme environments. Four specific enriched functional terms in the lower plant Chlamydomonas reinhardtii were detected when it was compared with seven other higher plants. In addition, Guanylate_cyc existed in more genes of lower plants than of higher plants. In our PSSRD, we constructed an interactive plotting function in the chart interface, and users can easily view the detailed information of SSRs. All SSR information, including sequences, primers, and annotations, can be downloaded from our database. Moreover, we developed Web SSR Finder and Batch SSR Finder tools, which can be easily used for identifying SSRs. Our database was developed using PHP, HTML, JavaScript, and MySQL, which are freely available at http://www.pssrd.info/ . We conducted an analysis of the Myb gene families and flowering genes as two applications of the PSSRD. Further analysis indicated that whole-genome duplication and whole-genome triplication played a major role in the expansion of the Myb gene families. These SSR markers in our database will greatly facilitate comparative genomics and functional genomics studies in the future.