The genome and genome annotation version 1 of Mesotaenium endlicherianum can be downloaded by the link provided on the published paper by (Cheng et al., 2019). You can download the files of genome annotation version 2 below:

Version 2 (V2) annotation files

Protein domain annotation, GO and KEGG assingment, functional annotation using Interproscan

We used InterProScan-5.59-91.0 to find protein domains in Mesotaenium endlicherianum proteins (annotation V2). It is large table, we suggest to handle it with care (do not use excel if possible).

Comparison of annotation V1 and V2

If you are interested in a specific gene, we highly recommend to visualize the genome using a genome browser and load both V1 and V2 gff files to investigate the gene structure in detail. However, we provide a table that summerize the relationship between gene IDs in V1 and V2.

We compared the annotation V2 to the annotation V1 to get a “mapping table” between annotations. This was done using gffcompare v0.12.6. You can download the results below. If you do not know how to read the tables, you can read the gffcompare documentaiton. If it is to complicated (or you do not have time and/or enthusiasm), please open V1_as_ref_.tracking with a text editor and use find method to find any gene ID that you are interested in. On the 4th column of this table there is a letter code which can be understood using gffcompare documentation figure.

For the above comparison we took, the annotation V1 as the reference and compared V2 to it. If you are interested in the reverse comparison (V2 as the reference and V1 as query), you can download the results using the link below.

KEGG orthology

We used KAAS to assign KEGG ortholog ID to each protein sequence. The result and input parameters are available below. You can use the clusterProfiler package and R to perform KEGG enrichment.

Functional annotation using eggNOG-mapper

We also performed functional annotation using eggNOG-mapper. You can download the result using the button below.