KIPEs3: Automatic annotation of biosynthesis pathways

Abstract

Background: Flavonoids and carotenoids are pigments involved in stress mitigation and numerous other processes. Both pigment classes can contribute to flower and fruit coloration. Carotenoids and flavonoid aglycons are produced by a pathway that is largely conserved across land plants. Glycosylations, acylations, and methylations of the flavonoid aglycones can be species-specific and lead to a plethora of biochemically diverse flavonoids. We previously developed KIPEs for the automatic annotation of biosynthesis pathways and presented an application on the flavonoid aglycone biosynthesis. Findings: KIPEs3 is an improved version with additional features and the potential to identify not just the core biosynthesis players, but also candidates involved in the decoration steps and in the transport of flavonoids. Functionality of KIPEs3 is demonstrated through the analysis of the flavonoid biosynthesis in Arabidopsis thaliana Nd-1, Capsella grandiflora, and Dioscorea dumetorum. We demonstrate the applicability of KIPEs to other pathways by adding the carotenoid biosynthesis to the repertoire. As a proof of concept, the carotenoid biosynthesis was analyzed in the same species and Daucus carota. KIPEs3 is available as an online service to enable access without prior bioinformatics experience. Conclusion: KIPEs3 facilitates the automatic annotation and analysis of biosynthesis pathways with a consistent and high quality in a large number of plant species. Numerous genome sequencing projects are generating a huge amount of data sets that can be analyzed to identify evolutionary patterns and promising candidate genes for biotechnological and breeding applications.

Apiaceae FNS I originated from F3H through tandem gene duplication

“…Functional annotation of the Daucus carota genes (Dcarota_388_v2.0) was inferred from Arabidopsis thaliana based on reciprocal best BLAST hits of the representative peptide sequences as previously described [29,46]. This co-expression analysis was implemented in a Python script (coexp3.py) which is available via github [34] and as an online service [47].…”

Genetic factors explaining anthocyanin pigmentation differences

“…In order to facilitate the identification of candidate genes, encoded peptide sequences were inferred from the transcriptome assembly using a previously established approach[137] that combines Transdecoder[138], ORFfinder[139], and ORFpredictor[140]. Knowledge-based Identification of Pathway Enzymes (KIPEs3) v0.34[141,142] was applied to identify the structural genes involved in the flavonoid biosynthesis. Flavonoid biosynthesis regulating R2R3-MYB genes were identified via MYB_annotator v0.3[143].…”

“…ORFfinder [139], and ORFpredictor [140]. Knowledge-based Identification of Pathway Enzymes (KIPEs3) v0.34 [141,142] was applied to identify the structural genes involved in the flavonoid biosynthesis. Flavonoid biosynthesis regulating R2R3-MYB genes were identified via MYB_annotator v0.3 [143].…”

Identification of annotation artifacts concerning theCHALCONE SYNTHASE(CHS)

“…Numerous plant genomes are sequenced every year [9] and the rapid development of long read sequencing technologies enables the generation of high quality genome sequences [10]. Since an automatic annotation of all genes in the flavonoid biosynthesis and many regulators is possible [11, 12], it is feasible to perform large scale analyses of gene families acting in this pathway. Analyses at this scale are inherently prone to errors concerning individual species and sequences that require human intervention at the final interpretation step.…”