GeneNoteBook, a collaborative notebook for comparative genomics

SUMMARY: Analysis and comparison of genomic and transcriptomic datasets have become standard procedures in biological research. However, for non-model organisms no efficient tools exist to visually work with multiple genomes and their metadata, and to annotate such data in a collaborative way. Here we present GeneNoteBook: a web based collaborative notebook for comparative genomics. GeneNoteBook allows experimental and computational researchers to query, browse, visualize and curate bioinformatic analysis results for multiple genomes. GeneNoteBook is particularly suitable for the analysis of non-model organisms, as it allows for comparing newly sequenced genomes to those of model organisms. AVAILABILITY AND IMPLEMENTATION: GeneNoteBook is implemented as a node.js web application and depends on MongoDB and NCBI BLAST. Source code is available at https://github.com/genenotebook/genenotebook. Additionally, GeneNoteBook can be installed through Bioconda and as a Docker image. Full installation instructions and online documentation are available at https://genenotebook.github.io. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.</p

Gene phylogenies based on Bayesian analysis

Phylogenetic analyses of genes of interest (EPR, HB, NFP, HCT, EPR, NIN, and RPG). Amino acid sequence alignments were generated using MAFFT version 7.017. Analyses were performed using MrBayes version 3.2.6 running 2.2 million generations, setting gamma-distributed rate variation and integrating over different models of amino acid sequence evolution (aamodelpr=mixed). For NFP analyses were based on the full-length sequences as well as separately on the kinase domain only

Phylogenetic analyses of Cannabaceae

Nucleotide alignments were generated using MAFFT version 7.017. The first phylogenetic reconstruction of Cannabaceae (MarkerData) was based on four plastid markers with five optimal partitions and models of sequence evolution: atpB-rbcL combined with trnL-F (GTR+I+G); first codon position of rbcL (GTR+I+G); second position of rbcL (SYM+I+G); third position of rbcL (GTR+G); rps16 (GTR+G). The second phylogenetic reconstruction of Cannabaceae (GenomeData) was based on whole chloroplast genomes with eight optimal partitions and models of sequence evolution: tRNA sequence (HKY+I), rRNA sequence (GTR+I), long single copy region (LSC) coding sequence (GTR+I+G), LSC non-coding sequence (GTR+G), short single copy region (SSC) coding sequence (GTR+G), SSC non-coding sequence (GTR+G), inverted repeat region (IR) coding sequence (GTR+G), and IR non-coding sequence (GTR+G)

Draft genomes of Parasponia and Trema species

Draft genome assemblies of Parasponia rigida, Parasponia rugosa, Trema levigata, and Trema orientalis accession RG16 based on medium-coverage sequence data. Read data are available at GenBank under bioprojects PRJNA272486 (P. rigida), PRJNA272880 (P. rugosa) PRJNA38059 (T. levigata), and PRJNA272878 (T. orientalis RG16). Assembly was performed with the iterative de Bruijn graph assembler IDBA-UD version 1.1.1, iterating from 30-mers to 120-mers, with incremental steps of 20

GeneNoteBook, a collaborative notebook for comparative genomics

SUMMARY: Analysis and comparison of genomic and transcriptomic datasets have become standard procedures in biological research. However, for non-model organisms no efficient tools exist to visually work with multiple genomes and their metadata, and to annotate such data in a collaborative way. Here we present GeneNoteBook: a web based collaborative notebook for comparative genomics. GeneNoteBook allows experimental and computational researchers to query, browse, visualize and curate bioinformatic analysis results for multiple genomes. GeneNoteBook is particularly suitable for the analysis of non-model organisms, as it allows for comparing newly sequenced genomes to those of model organisms. AVAILABILITY AND IMPLEMENTATION: GeneNoteBook is implemented as a node.js web application and depends on MongoDB and NCBI BLAST. Source code is available at https://github.com/genenotebook/genenotebook. Additionally, GeneNoteBook can be installed through Bioconda and as a Docker image. Full installation instructions and online documentation are available at https://genenotebook.github.io. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.</p

The Effect of Exogenous Nitrate on LCO Signalling, Cytokinin Accumulation, and Nodule Initiation in Medicago truncatula

Nitrogen fixation by rhizobia is a highly energy-demanding process. Therefore, nodule initiation in legumes is tightly regulated. Environmental nitrate is a potent inhibitor of nodulation. However, the precise mechanism by which this agent (co)regulates the inhibition of nodulation is not fully understood. Here, we demonstrate that in Medicago truncatula the lipo-chitooligosaccharide-induced accumulation of cytokinins is reduced in response to the application of exogenous nitrate. Under permissive nitrate conditions, perception of rhizobia-secreted signalling molecules leads to an increase in the level of four cytokinins (i.e., iP, iPR, tZ, and tZR). However, under high-nitrate conditions, this increase in cytokinins is reduced. The ethylene-insensitive mutant Mtein2/sickle, as well as wild-type plants grown in the presence of the ethylene biosynthesis inhibitor 2-aminoethoxyvinyl glycine (AVG), is resistant to the inhibition of nodulation by nitrate. This demonstrates that ethylene biosynthesis and perception are required to inhibit nodule organogenesis under high-nitrate conditions

Host- and stage-dependent secretome of the arbuscular mycorrhizal fungus Rhizophagus irregularis

Arbuscular mycorrhizal fungi form the most wide‐spread endosymbiosis with plants. There is very little host‐specificity in this interaction, however host preferences as well as varying symbiotic efficiencies have been observed. We hypothesize that secreted proteins (SPs) may act as fungal effectors to control symbiotic efficiency in a host‐dependent manner. Therefore, we studied whether AM fungi adjust their secretome in a host‐ and stage‐dependent manner to contribute to their extremely wide host‐range. We investigated the expression of SP‐encoding genes of Rhizophagus irregularis in three evolutionary distantly‐related plant species, Medicago truncatula, Nicotiana benthamiana and Allium schoenoprasum. In addition we used laser microdissection in combination with RNAseq to study SP expression at different stages of the interaction in Medicago. Our data indicate that most expressed SPs show roughly equal expression levels in the interaction with all three host plants. In addition, a subset shows significant differential expression depending on the host plant. Furthermore, SP expression is controlled locally in the hyphal network in response to host dependent cues. Overall, this study presents a comprehensive analysis of the R. irregularis secretome, which now offers a solid basis to direct functional studies on the role of fungal SPs in AM symbiosis

The BOP-type co-transcriptional regulator NODULE ROOT1 promotes stem secondary growth of the tropical Cannabaceae tree Parasponia andersonii

Tree stems undergo a massive secondary growth in which secondary xylem and phloem tissues arise from the vascular cambium. Vascular cambium activity is driven by endogenous developmental signalling cues and environmental stimuli. Current knowledge regarding the genetic regulation of cambium activity and secondary growth is still far from complete. The tropical Cannabaceae tree Parasponia andersonii is a non-legume research model of nitrogen-fixing root nodulation. Parasponia andersonii can be transformed efficiently, making it amenable for CRISPR-Cas9-mediated reverse genetics. We considered whether P. andersonii also could be used as a complementary research system to investigate tree-related traits, including secondary growth. We established a developmental map of stem secondary growth in P. andersonii plantlets. Subsequently, we showed that the expression of the co-transcriptional regulator PanNODULE ROOT1 (PanNOOT1) is essential for controlling this process. PanNOOT1 is orthologous to Arabidopsis thaliana BLADE-ON-PETIOLE1 (AtBOP1) and AtBOP2, which are involved in the meristem-to-organ-boundary maintenance. Moreover, in species forming nitrogen-fixing root nodules, NOOT1 is known to function as a key nodule identity gene. Parasponia andersonii CRISPR-Cas9 loss-of-function Pannoot1 mutants are altered in the development of the xylem and phloem tissues without apparent disturbance of the cambium organization and size. Transcriptomic analysis showed that the expression of key secondary growth-related genes is significantly down-regulated in Pannoot1 mutants. This allows us to conclude that PanNOOT1 positively contributes to the regulation of stem secondary growth. Our work also demonstrates that P. andersonii can serve as a tree research system

Reverse genetics using CRISPR-Cas9 in the tropical tree Parasponia andersonii revealed a promotive role for PanNODULE ROOT1 in stem secondary growth

NODULE ROOT (NOOT), BLADE-ON-PETIOLE (BOP), COCHLEATA (COCH)-LIKE (NBCL) are plant-specific developmental regulator participating in many developmental process of the primary growth. NBCL contribute to the meristem-to-organ-boundaries maintenance by inhibiting meristematic activities and promoting adjacent tissues initiation, development and determinacy. To determine if NBCL contribute to the regulation of tree secondary growth, we studied the impact of the PanNODULE ROOT1 (PanNOOT1) gene loss-of-function on the secondary growth of Parasponia andersonii (P. andersonii)