Note

We classified nuclear organelle genes (NOGs), also known as intracellular gene transfer (IGT) or endosymbiotic gene transfer (EGT), into nuclear plastid genes (NPGs) and nuclear mitochondrial genes (NMGs). We developed the IGTminer pipeline (https://chenym1.github.io/IGTminer/) and applied it to construct a Poaceae NOG map recording the dynamic trajectory of 1,302 NPGCs and 431 NMGCs.

GeneBrowse

1. In the input panel, you can select the NOG type and the genome assembly you want to view. In addition, a genomic region can be inputted to obtain the NOGs located in the region.

2. The bar plot shows the counts of NOGs from different organellar genes. Green represents a coding gene, and grey represents a pseudogene.

3. The table shows genome location (i.e., chromosome, start, end, and strand), NOG ID (we assign a unique ID for each NOG), Cluster ID (multiple NOGs with short intervals are clustered into one single nuclear integration event), and Network ID (a collinear block connects NOGs or NOG clusters from different genomes). The network ID can be used as input for the Step 2 in the Microcollinearity tool.

Distribution

1. In the input panel, you can select the NOG type and the genome assembly you want to view.

2. The plots show the genomic location of NOGs in the genome assembly. You can click on the gene in the plot for detailed information.

Macrocollinearity of NOG and NMG

1. You should select one or more genomes for further analysis.

2. Input a Network ID. Each Network ID represents a collinear network that contains NOGs or NOG clusters from different genome assemblies.

3. Set number of flanking genes of the NOG.

4. One-to-many. All homologous genes will be showed, otherwise, only 1-to-1 (i.e. RBH and SBH).

5. Outout. The green blocks represent NOGs in the nucleus from the organellar genomes, and the black blocks represent nuclear genes. You can click on the gene in the plot for detailed information.