Genome-wide comparative analysis of papain-like cysteine protease family genes in castor bean and physic nut

Zhi Zou,Guishui Xie,Qixing Huang,Lifu Yang

doi:10.1038/s41598-017-18760-6

Zhi Zou, Guishui Xie + Show 2 more

Open Access

https://doi.org/10.1038/s41598-017-18760-6

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Abstract

Papain-like cysteine proteases (PLCPs) are a class of proteolytic enzymes involved in many plant processes. Compared with the extensive research in Arabidopsis thaliana, little is known in castor bean (Ricinus communis) and physic nut (Jatropha curcas), two Euphorbiaceous plants without any recent whole-genome duplication. In this study, a total of 26 or 23 PLCP genes were identified from the genomes of castor bean and physic nut respectively, which can be divided into nine subfamilies based on the phylogenetic analysis: RD21, CEP, XCP, XBCP3, THI, SAG12, RD19, ALP and CTB. Although most of them harbor orthologs in Arabidopsis, several members in subfamilies RD21, CEP, XBCP3 and SAG12 form new groups or subgroups as observed in other species, suggesting specific gene loss occurred in Arabidopsis. Recent gene duplicates were also identified in these two species, but they are limited to the SAG12 subfamily and were all derived from local duplication. Expression profiling revealed diverse patterns of different family members over various tissues. Furthermore, the evolution characteristics of PLCP genes were also compared and discussed. Our findings provide a useful reference to characterize PLCP genes and investigate the family evolution in Euphorbiaceae and species beyond.

Highlights

Castor bean (Ricinus communis L., 2n = 20) and physic nut (Jatropha curcas L., 2n = 22) are two economically important species that belong to the spurge family, Euphorbiaceae[1,2]
Except for RcCEP1 (GenBank accession number AF050756)[26], homology analysis showed that no full-length cDNA sequences of the other 25 RcPLCP genes were reported in any public database
The first genome-wide analysis of Papain-like cysteine proteases (PLCPs) family genes in castor bean and physic nut was performed in the present study, resulting in 26 or 23 members respectively

Summary

Introduction

Except for the ancient so-called γ whole-genome duplication (WGD) event shared by core eudicots including Arabidopsis thaliana and poplar (Populus trichocarpa), comparative genomics analysis indicated that both castor bean and physic nut didn’t experience additional recent WGD6,8,9. From this perspective, analysis of certain gene families in castor bean and physic nut may provide insights into lineage-specific evolution in high plants especially in core eudicots. Genome-wide identification of castor bean and physic nut PLCP family genes was carried out Their gene structures were manually curated through aligning transcriptome data to the gene-encoding scaffolds. The sequence feature, evolutionary relationship and expression pattern were investigated and compared

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