Genome-wide identification and characterization of members of the LEA gene family in Panax notoginseng and their transcriptional responses to dehydration of recalcitrant seeds

Abstract

Background: Late embryogenesis abundant (LEA) proteins play an important role in dehydration process of seed maturation. The seeds of Panax notoginseng (Burkill) F. H. Chen are typically characterized with the recalcitrance and are highly sensitive to dehydration. However, it is not very well known about the role of LEA proteins in response to dehydration stress in P. notoginseng seeds. We will perform a genome-wide analysis of the LEA gene family and their transcriptional responses to dehydration stress in recalcitrant P. notoginseng seeds.

Results: In this study, 61 LEA genes were identified from the P. notoginseng genome, and they were renamed as PnoLEA. The PnoLEA genes were classified into seven subfamilies based on the phylogenetic relationships, gene structure and conserved domains. The PnoLEA genes family showed relatively few introns and was highly conserved. Unexpectedly, the LEA_6 subfamily was not found, and the LEA_2 subfamily contained 46 (75.4%) members. Within 19 pairs of fragment duplication events, among them 17 pairs were LEA_2 subfamily. In addition, the expression of the PnoLEA genes was obviously induced under dehydration stress, but the germination rate of P. notoginseng seeds decreased as the dehydration time prolonged.

Conclusions: We found that the lack of the LEA_6 subfamily, the expansion of the LEA_2 subfamily and low transcriptional levels of most PnoLEA genes might be implicated in the recalcitrant formation of P. notoginseng seeds. LEA proteins are essential in the response to dehydration stress in recalcitrant seeds, but the protective effect of LEA protein is not efficient. These results could improve our understanding of the function of LEA proteins in the response of dehydration stress and their contributions to the formation of seed recalcitrance.

Keywords: Dehydration stress; Expression patterns; LEA; Panax notoginseng; Recalcitrant seeds.

Fig. 1

The structure of the PnoLEA genes in P. notoginseng. The green boxes represent untranslated regions, the yellow boxes represent coding regions, and the lines represent introns

Fig. 2

Conserved motifs in PnoLEA proteins. These motifs were identified using Multiple EM for Motif Elicitation (MEME) and different colors boxes represent different motifs. The maximum number of motifs in each sequence is set to 15

Fig. 3

Phylogenetic analysis of LEA proteins in P. notoginseng and Arabidopsis. Different colors represent different PnoLEA genes families. The tree was constructed using MEGA11 by the neighbor-joining (NJ) method based on alignment by MAFFT

Fig. 4

Distribution of the PnoLEA genes on chromosomes. The scale of the chromosome is in millions of bases (Mb)

Fig. 5

Fragment duplication of PnoLEA genes. Fragment duplication of the PnoLEA genes are connected by red lines

Fig. 6

Expression patterns of PnoLEA genes in different tissues. The TPM values are transformed using log₂(TPM + 1)

Fig. 7

Germination rate of P. notoginseng seeds under dehydration stress. a Changes of water content. b Germination rate of seeds in different water content. Values presented are the means ± SE (n = 3). Different letters indicate significant differences among treatments in the same period using Duncan’s test (P < 0.05)

Fig. 8

Expression patterns of PnoLEA genes in P. notoginseng seeds under different dehydration stress. The TPM values are transformed using log₂(TPM + 1)

Fig. 9

Relative expression of LEA genes in P. notoginseng seeds under dehydration stress. Values presented are the means ± SE (n = 3). Different letters indicate significant differences among treatments in the same period using Duncan’s test (P < 0.05)