Genome-wide characterization of aspartic protease (AP) gene family in Populus trichocarpa and identification of the potential PtAPs involved in wood formation

Abstract

Background Aspartic protease (AP) is one of four large proteolytic enzyme families that are involved in plant growth and development. Little is known about the AP gene family in tree species, although it has been characterized in Arabidopsis , rice and grape. The AP genes that are involved in tree wood formation remain to be determined. Results A total of 67 AP genes were identified in Populus trichocarpa (PtAP) and classified into three categories (A, B and C). Chromosome mapping analysis revealed that two-thirds of the PtAP genes were located in genome duplication blocks, indicating the expansion of the AP family by segmental duplications in Populus . The microarray data from the Populus eFP browser demonstrated that PtAP genes had diversified tissue expression patterns. Semi-qRT-PCR analysis further determined that more than 10 PtAPs were highly or preferentially expressed in the developing xylem. When the involvement of the PtAPs in wood formation became the focus, many SCW-related cis -elements were found in the promoters of these PtAPs . Based on PtAP promoter ::GUS techniques, the activities of PtAP66 promoters were observed only in fiber cells, not in the vessels of stems as the xylem and leaf veins developed in the transgenic Populus tree, and strong GUS signals were detected in interfascicular fiber cells, roots, anthers and sepals of PtAP17 promoter ::GUS transgenic plants. Intensive GUS activities in various secondary tissues implied that PtAP66 and PtAP17 could function in wood formation. In addition, most of the PtAP proteins were predicted to contain N- and (or) O-glycosylation sites, and the integration of PNGase F digestion and western blotting revealed that the PtAP17 and PtAP66 proteins were N-glycosylated in Populus . Conclusions Comprehensive characterization of the PtAP genes suggests their functional diversity during Populus growth and development. Our findings provide an overall understanding of the AP gene family in trees and establish a better foundation to further describe the roles of PtAPs in wood formation. Electronic supplementary material The online version of this article (10.1186/s12870-019-1865-0) contains supplementary material, which is available to authorized users.

Genome-wide identification, evolution and expression analysis of the aspartic protease gene family during rapid growth of moso bamboo (Phyllostachys edulis) shoots

“…1 , 2 and Table S 1 ). Category A was the smallest category, and category C revealed gene expansion had occurred for its members, which was similar to findings in Arabidopsis , rice, poplar and grape [ 9 , 12 , 21 , 22 ]. Perhaps the formation of these three categories occurred before the monocotyledon and dicotyledon divergence.…”

“…4 ). The number of exons in category C was at most five, which was different from the numbers in Populus and grape [ 21 , 22 ], and most of the closest homologs, such as PhAP57s , − 14 s , − 7 s , and -4 s , on exhibited different gene structures (Fig. 4 ).…”

“…To investigate the evolutionary relationship of the PhAP family, a phylogenetic tree was constructed using 129 PhAP and 92 OsAP full-length amino acid residue sequences (Table S 1 and Table S 2 ). Both PhAPs and OsAPs were classed into three categories, as previously reported in Arabidopsis [ 9 ], rice [ 12 ], grape [ 21 ] and poplar [ 22 ]. Category A contained 16 PhAPs together with seven OsAPs; these proteins could be classified into seven subclades based on their relationships with their rice homologous proteins (Fig.…”

“…Because SCW formation and PCD have been reported to occur during the moso bamboo rapid-growth stage, PhAP genes may be involved with key transcription factors that regulate SCW and PCD. We further scanned 10 cis -elements previously discovered to participate in SCW formation and PCD by MEME scanning [ 22 , 55 ]. The results are shown in Figure S 1 .…”

“…We found that 56.6% (73 PhAP s) of PhAP s were located in duplication blocks (Fig. 3 ), the percentage of which was greater than that in rice (24.7%, 23 OsAP s) [ 12 ] and grape (32.0%, 16 VvAP s) [ 21 ] but less than that in poplar (62.6%, 42 PtAP s) [ 22 ]. In addition, we also identified tandem duplication events in the PhAP family, such as PhAP8/21 s , PhAP57 and PhAP93 (Fig.…”