Genome-Wide Identification, Characterization, and Stress-Responsive Expression Profiling of Genes Encoding LEA (Late Embryogenesis Abundant) Proteins in Moso Bamboo (Phyllostachys edulis)

Abstract

Late embryogenesis abundant (LEA) proteins have been identified in a wide range of organisms and are believed to play a role in the adaptation of plants to stress conditions. In this study, we performed genome-wide identification of LEA proteins and their coding genes in Moso bamboo (Phyllostachys edulis) of Poaceae. A total of 23 genes encoding LEA proteins (PeLEAs) were found in P. edulis that could be classified to six groups based on Pfam protein family and homologous analysis. Further in silico analyses of the structures, gene amount, and biochemical characteristics were conducted and compared with those of O. sativa (OsLEAs), B. distachyon (BdLEAs), Z. mays (ZmLEAs), S. bicolor (SbLEAs), Arabidopsis, and Populus trichocarpa. The less number of PeLEAs was found. Evolutionary analysis revealed orthologous relationship and colinearity between P. edulis, O. sativa, B. distachyon, Z. mays, and S. bicolor. Analyses of the non-synonymous (Ka) and synonymous (Ks)substitution rates and their ratios indicated that the duplication of PeLEAs may have occurred around 18.8 million years ago (MYA), and divergence time of LEA family among the P. edulis-O. sativa and P. edulis–B. distachyon, P. edulis-S. bicolor, and P. edulis-Z. mays was approximately 30 MYA, 36 MYA, 48 MYA, and 53 MYA, respectively. Almost all PeLEAs contain ABA- and (or) stress-responsive regulatory elements. Further RNA-seq analysis revealed approximately 78% of PeLEAs could be up-regulated by dehydration and cold stresses. The present study makes insights into the LEA family in P. edulis and provides inventory of stress-responsive genes for further functional validation and transgenic research aiming to plant genetic improvement of abiotic stress tolerance.

The Late Embryogenesis Abundant Protein Family in Cassava (Manihot esculenta Crantz): Genome-Wide Characterization and Expression during Abiotic Stress

“…These results suggested that the identified MeLEAs have the typical motifs of LEA family [ 8 ]. Generally, the LEA proteins belonging to the same subfamily shared similar motif organization, further supporting the phylogenetic classification [ 2 , 8 , 27 ].…”

“…Due to the significant roles of LEA proteins in abiotic stress response and the typical feature of drought tolerance of cassava, it is requisite to systematically investigate the potential role of LEAs. In this study, we identified 26 MeLEAs from the cassava genome, which is shrunk in comparison to LEA members from Arabidopsis [ 3 ], rice [ 2 ], Brassica napus [ 8 ], Brachypodium distachyon [ 28 ], and Populus trichocarpa [ 29 ], but expanded compared with that from moso bamboo [ 27 ]. Previous phylogenetic analyses indicated that LEAs in most plant species contained eight subfamilies (LEA_1, LEA_2, LEA_3, LEA_4, LEA_5, PvLEA18, dehydrin, and SMP) [ 8 ].…”

“…Genome-wide expression analysis have demonstrated the significant response of LEA genes to drought or osmotic stress in various species, including Arabidopsis , rice, Moso bamboo , and sweet orange [ 2 , 3 , 27 , 43 ]. In this study, we found that some MeLEA genes, including MeLEA-2 , -5 , -6 , -13 , -26 , were induced (Log 2 FPKM > 1) by drought in different cassava accessions.…”

“…Previous studies demonstrated that LEAs could widely participate in plants response to abiotic stress and hormones [ 2 , 3 , 8 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 ]. Here, we examined the expression of nine genes ( MeLEA-2 , -4 , -5 , -6 , -7 , -15 , -16 , -20 , -26 ) under salt, osmotic, cold, and H 2 O 2 and ABA treatments.…”

“…To date, LEA genes have been genome-wide identified in various plant species, such as 51 LEAs in Arabidopsis [ 3 ], 39 LEAs in rice [ 2 ], 108 LEAs in Brassica napus [ 8 ], 23 LEAs in Moso Bamboo [ 27 ], 36 LEAs in Brachypodium distachyon [ 28 ], and 53 LEAs in Populus trichocarpa [ 29 ]. However, less is known about this family in the important tropical crop cassava.…”