Improving Gene Annotation of the Peanut Genome by Integrated Proteogenomics Workflow

Peanut
(Arachis hypogaea L.) is
a staple crop in semiarid tropical and subtropical regions. Although
the genome of peanut has been fully sequenced, the current gene annotations
are still incomplete. New technologies in genomics and proteomics
have resulted in the emergence of proteogenomics, which can integrate
genomic, transcriptomic, and proteomic data for improving gene annotation.
In the present study, we collected RNA-seq and proteomic data from
multiple tissues such as seed, shell, and gynophore of peanut and
utilized a proteogenomic approach to improve the gene annotation of
peanut based on these data. A total of 1 935 655 904
RNA-seq reads and 7 490 280 MS/MS spectra were collected.
Ultimately, 13 767 annotated genes were found with evidence
at the protein level, and seven novel protein-coding genes were found
with both RNA-seq and proteomics evidence. In addition, 35 gene models
were updated based on proteomics data. Proteogenomic approaches improved
the gene annotation in certain aspects by integrating both RNA-seq
and proteomic data. We expect that these approaches could help improve
existing genome annotations of other species.