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This study explicates molecular insights commencing Self-Incompatibility (SI) and CC (cross-compatibility/fertilization) in self (SP) and cross (CP) pollinated pistils of tea. The fluorescence microscopy analysis revealed ceased/deviated pollen tubes in SP, while successful fertilization occurred in CP at 48 HAP. Global transcriptome sequencing of SP and CP pistils generated 109.7 million reads with overall 77.9% mapping rate to draft tea genome. Furthermore, concatenated de novo assembly resulted into 48,163 transcripts. Functional annotations and enrichment analysis (KEGG & GO) resulted into 3793 differentially expressed genes (DEGs). Among these, de novo and reference-based expression analysis identified 195 DEGs involved in pollen-pistil interaction. Interestingly, the presence of 182 genes [PT germination & elongation (67), S-locus (11), fertilization (43), disease resistance protein (30) and abscission (31)] in a major hub of the protein-protein interactome network suggests a complex signaling cascade commencing SI/CC. Furthermore, tissue-specific qRT-PCR analysis affirmed the localized expression of 42 DE putative key candidates in stigma-style and ovary, and suggested that LSI initiated in style and was sustained up to ovary with the active involvement of csRNS, SRKs & SKIPs during SP. Nonetheless, COBL10, RALF, FERONIA-rlk, LLG and MAPKs were possibly facilitating fertilization. The current study comprehensively unravels molecular insights of phase-specific pollen-pistil interaction during SI and fertilization, which can be utilized to enhance breeding efficiency and genetic improvement in tea.
Pubmed ID: 30696008
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Software that estimates expression at transcript-level resolution and controls for variability evident across replicate libraries.
View all literature mentionsPassive and active source waveform data, event (earthquake) catalog, channel response data is available. This comprehensive data store of raw geophysical time-series data is collected from a large variety of sensors, courtesy of a vast array of US and International scientific networks, including seismometers (permanent and temporary), tilt and strain meters, infrasound, temperature, atmospheric pressure and gravimeters, to support basic research aimed at imaging the Earth's interior. IRIS also provides data and software for educational purposes. This consortium of over 100 US universities is dedicated to the operation of science facilities for the acquisition, management, and distribution of seismological data. IRIS programs contribute to scholarly research, education, earthquake hazard mitigation, and verification of the Comprehensive Nuclear-Test-Ban Treaty. Data is stored at the IRIS Data Management Center in Seattle, Washington. They currently manage a large archive from over tens of thousands of seismic stations and ship hundreds of terabytes of data yearly.
View all literature mentionsA database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories). eggNOG's database currently counts 1.7 million orthologous groups in 3686 species, covering over 7.7 million proteins (built from 9.6 million proteins). (Jan 30, 2014)
View all literature mentionsSoftware platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
View all literature mentionsComprehensive plant transcription factor database. Interface to allow users to search the database by IDs or free texts, to make sequence similarity search against TFs of all or individual species, and to download TF sequences for local analysis.PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors
View all literature mentionsDatabase of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive linkouts from data pages to other Arabidopsis resources. The data can be searched, viewed and analyzed. Datasets can also be downloaded. Pages on news, job postings, conference announcements, Arabidopsis lab protocols, and useful links are provided.
View all literature mentionsSoftware repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.
View all literature mentionsA web-based tool and database for the gene ontology analysis. Its focus is on agricultural species and is user-friendly. The agriGO is designed to provide deep support to agricultural community in the realm of ontology analysis. Compared to other available GO analysis tools, unique advantages and features of agriGO are: # The agriGO especially focuses on agricultural species. It supports 45 species and 292 datatypes currently. And agriGO is designed as an user-friendly web server. # New tools including PAGE (Parametric Analysis of Gene set Enrichment), BLAST4ID (Transfer IDs by BLAST) and SEACOMPARE (Cross comparison of SEA) were developed. The arrival of these tools provides users with possibilities for data mining and systematic result exploration and will allow better data analysis and interpretation. # The exploratory capability and result visualization are enhanced. Results are provided in different formats: HTML tables, tabulated text files, hierarchical tree graphs, and flash bar graphs. # In agriGO, PAGE and SEACOMPARE can be used to carry out cross-comparisons of results derived from different data sets, which is very important when studying multiple groups of experiments, such as in time-course research. Platform: Online tool
View all literature mentionsIntegrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies.
View all literature mentionsBioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.
View all literature mentionsSoftware tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions.
View all literature mentionsThe main purpose of Cufflinks.cuffmerge is to merge together several Cufflinks assemblies, making it easier to produce an assembly GTF file suitable for use with Cufflinks.cuffdiff. Cufflinks.cuffmerge also runs Cuffcompare in the background and automatically filters out transcribed fragments (transfrags) that are likely to be artifacts. Trapnell C, Hendrickson D,Sauvageau S, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nature Biotechnology. 2013;31:46-53.
View all literature mentionsSoftware tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV.
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