Papain-like cysteine protease encoding genes in rubber (Hevea brasiliensis): comparative genomics, phylogenetic, and transcriptional profiling analysis

43 HbPLCPs representing nine subfamilies or 20 orthologous groups were found in rubber, where paralogs were resulted from the recent WGD and local duplication. Several senescence-associated genes were also identified. Papain-like cysteine proteases (PLCPs) comprise a large family of proteolytic enzymes involved in plant growth and development, seed germination, organ senescence, immunity, and stress response. Despite their importance and the extensive research in the model plant Arabidopsis thaliana, little information is available on rubber tree (Hevea brasiliensis), a rubber-producing plant of the Euphorbiaceae family. This study performed a genome-wide identification of PLCP family genes in rubber, resulting in a relatively high number of 43 members. The phylogenetic analysis assigned these genes into nine subfamilies, i.e., RD21 (6), CEP (4), XCP (4), XBCP3 (2), THI (1), SAG12 (18), RD19 (4), ALP (2), and CTB (2). Most of them were shown to have orthologs in Arabidopsis; however, several members in SAG12, CEP and XBCP3 subfamilies form new groups as observed in other core eudicots such as Manihot esculenta, Ricinus communis, Populus trichocarpa, and Vitis vinifera. Based on an expert sequence comparison, 20 orthologous groups (OGs) were proposed for core eudicots, and rubber paralogs were shown to be resulted from the recent whole-genome duplication (WGD) as well as local duplication. Transcriptional profiling showed distinct expression pattern of different members across various tissues, e.g., root, leaf, bark, laticifer, flower, and seed. By using the senescence-specific HbSAG12H1 as the indicator, the transcriptome of senescent rubber leaves was deeply sequenced and several senescence-associated PLCP genes were identified. Results obtained from this study provide valuable information for future functional analysis and utilization of PLCP genes in Hevea and other species.