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

Abstract

Background Aspartic proteases (APs) are a class of aspartic peptidases belonging to nine proteolytic enzyme families whose members are widely distributed in biological organisms. APs play essential functions during plant development and environmental adaptation. However, there are few reports about APs in fast-growing moso bamboo. Result In this study, we identified a total of 129 AP proteins (PhAPs) encoded by the moso bamboo genome. Phylogenetic and gene structure analyses showed that these 129 PhAPs could be divided into three categories (categories A, B and C). The PhAP gene family in moso bamboo may have undergone gene expansion, especially the members of categories A and B, although homologs of some members in category C have been lost. The chromosomal location of PhAPs suggested that segmental and tandem duplication events were critical for PhAP gene expansion. Promoter analysis revealed that PhAPs in moso bamboo may be involved in plant development and responses to environmental stress. Furthermore, PhAPs showed tissue-specific expression patterns and may play important roles in rapid growth, including programmed cell death, cell division and elongation, by integrating environmental signals such as light and gibberellin signals. Conclusion Comprehensive analysis of the AP gene family in moso bamboo suggests that PhAPs have experienced gene expansion that is distinct from that in rice and may play an important role in moso bamboo organ development and rapid growth. Our results provide a direction and lay a foundation for further analysis of plant AP genes to clarify their function during rapid growth.

Genome-wide identification and analysis of the YABBY gene family in Moso Bamboo (Phyllostachys edulis (Carrière) J. Houz)

“…The complete P. edulis genome files was downloaded from GigaDB ( Wang et al 2021 ; Zhao et al, 2018b ) ( http://gigadb.org/dataset/100498 ) while additional sequences of YABBY were obtained from the Pseudomolecule Download Site webpage in the RGAP 7 database (Rice Genome Annotation Project, http://rice.plantbiology.msu.edu/ ) and The Arabidopsis Information Resource, version 10 (TAIR 10) ( https://www.arabidopsis.org/ ). BLAST analysis of YABBY proteins using Hidden Markov Models (HMMs) against the protein database.…”

Genome-Wide Identification and Characterization of the Cystatin Gene Family in Bread Wheat (Triticum aestivum L.)

“…Cis-acting regulatory elements located in the promoter region can regulate the expression levels of target genes by binding to transcription factors [51,52]. Cis-acting elements have been reported to be involved in various plant responses to abiotic or biotic stress [53][54][55][56].…”

Identification of the 14-3-3 Gene Family in Bamboo and Characterization of Pe14-3-3b Reveals Its Potential Role in Promoting Growth

“…Before bamboo shoots were excavated, the number of nodes of bamboo culm were determined, and the growth of bamboo was mainly demonstrated by the growth of internodes after the excavation [ 22 ]. Cell division and cell elongation played an important role in the rapid growth of bamboo shoots [ 23 ], which were regulated by a series of factors, including hormones [ 18 ], proteins [ 24 ], transcriptional factors [ 25 ] and so on. Although 14-3-3 proteins play an important role in cell division and cell elongation during plant growth and development as an important regulatory protein [ 5 , 26 ], the role of the 14-3-3 family in bamboo is still unclear.…”