Identification, evolution, and expression of GDSL-type Esterase/Lipase (GELP) gene family in three cotton species: a bioinformatic analysis

Abstract

Background: GDSL esterase/lipases (GELPs) play important roles in plant growth, development, and response to biotic and abiotic stresses. Presently, an extensive and in-depth analysis of GELP family genes in cotton is still not clear enough, which greatly limits the further understanding of cotton GELP function and regulatory mechanism.

Results: A total of 389 GELP family genes were identified in three cotton species of Gossypium hirsutum (193), G. arboreum (97), and G. raimondii (99). These GELPs could be classified into three groups and eight subgroups, with the GELPs in same group to have similar gene structures and conserved motifs. Evolutionary event analysis showed that the GELP family genes tend to be diversified at the spatial dimension and certain conservative at the time dimension, with a trend of potential continuous expansion in the future. The orthologous or paralogous GELPs among different genomes/subgenomes indicated the inheritance from genome-wide duplication during polyploidization, and the paralogous GELPs were derived from chromosomal segment duplication or tandem replication. GELP genes in the A/D subgenome underwent at least three large-scale replication events in the evolutionary process during the period of 0.6-3.2 MYA, with two large-scale evolutionary events between 0.6-1.8 MYA that were associated with tetraploidization, and the large-scale duplication between 2.6-9.1 MYA that occurred during diploidization. The cotton GELPs indicated diverse expression patterns in tissue development, ovule and fiber growth, and in response to biotic and abiotic stresses, combining the existing cis-elements in the promoter regions, suggesting the GELPs involvements of functions to be diversification and of the mechanisms to be a hormone-mediated manner.

Conclusions: Our results provide a systematic and comprehensive understanding the function and regulatory mechanism of cotton GELP family, and offer an effective reference for in-depth genetic improvement utilization of cotton GELPs.

Keywords: Biotic and abiotic stress; Cotton GDSL esterase/lipase; Evolution; Fiber growth; Tissue development; Transcriptomic expression; Whole genome duplication.

Fig. 1

Chromosomal localization of GELP genes in three cotton species of G. hirsutum, G. arboreum, and G. raimondii. The green lines show the GELP homologous genes between G. arboreum and G. hirsutum A subgenome; The orange lines represent the GELP homologous genes between G. hirsutum A subgenome and D subgenome; The purple lines indicate the GELP homologous genes between G. hirsutum D subgenome and G. arboreum; The blue lines denote the GELP homologous genes between G. hirsutum D subgenome and G. raimondii; The red lines indicate the GELP homologous genes between G. hirsutum A subgenome and G. raimondii; and thebrown lines display the GELP homologous genes between G. arboreum and G. raimondii

Fig. 2

The phylogenetic relationship among GELP families of Arabidopsis, G. hirsutum, G. arboreum, and G. raimondii. The GELPs from G. hirsutum, G. arboreum, G. raimondii and Arabidopsis were used for phylogenetic tree construction. Different colored lines denote the differnt clusterd groups of Group I—Group III. Diverse colored arc lines reprenent the clustered distrinct groups

Fig. 3

Sequence identity of the GELP genes in three cotton species G. hirsutum, G. arboreum, and G. raimondii. a Heat-map of sequence identity matrix between the nucleotide and amino acid levels. The color scale at the top of the heat map indicates the level of the sequence identities with light blue and red to represent low and high levels. The data at the diagonal lines are equal to 100%. b The identity of the GELP genes on the A and D subgenome among the three groups is compared at the nucleotide or amino acid level. c The correlation between the sequence identity of GELP gene and genetic distance

Fig. 4

Saturation of base substitutions between nucleotide sequences of orthologous or paralogous gene pairs. Kimura 2-parameter corrected genetic distance is estimated by MEGA-X. S: Transitions; V: Transversions

Fig. 5

WGD/segmental duplication event of GELP genes in G. arboreum, G. raimondii, and G. hirsutum. a Dotplot of GELP homologous gene pairs in subgenome. b The collinear relationship of GELP genes in the A subgenome of G. hirsutum. c The collinear relationship of GELP genes in the D subgenome of G. hirsutum. d The collinear relationship of GELP genes in G. arboreum. e The collinear relationship of GELP genes in G. raimondii. f The collinear relationship of GELP genes among different subgenomes of Gossypium spp. The GELP collinear gene pairs were presented by red line in b—e. The GELP collinear gene pairs of different subgenomes were indicated by different colored lines in f

Fig. 6

Evolutionary event analysis of GELP genes in G. arboreum, G. raimondii, and G. hirsutum. Evaluation of evolutionary events among orthologous GELPs a and paralogous GELPs b; Evolutionary selection pressure among orthologous GELPs c and paralogous GELPs d; The rate of non synonymous substitution (Ka) e and synonymous substitution (Ks) f among GELPs in G. arboreum, G. raimondii, and G. hirsutum

Fig. 7

Real-time quantitative PCR (RT-qPCR) detection analysis of GhGELPs expressions during fiber development stages. The ovules and fibers of different developmental periods of −3, −1, 0, 3, 5, 10, 15, 20, and 25 dpa were collected for RNA extraction and cDNA synthesis that were then used as templates for RT-qPCR with GhUBQ7 (DQ116441.1) as inter control for normalization. Error bars were calculated by three independent experiments. Significant difference was calculated by Student’s t-test using the data of −3 dpa as control, with *, **, and *** to represent p < 0.05, 0.01, and 0.001 respectively

Fig. 8

Co-expression analysis of differentially expressed GELP genes. Co-expression analysis of differentially expressed GELP genes during the processes of fiber development a, seed germination b, diverse abiotic stresses c, and different growth, development, and stress d

Fig. 9

Redundancy analysis of the putative regulatory cis-elements of the promoters of GELP genes in different cotton genomes/subgenomes. The green dots denote the GELPs, the pink arrows indicate the environmental factor varibale, and the blue arrows represent the species factor variable

Fig. 10

RT-qPCR-based heat-map of GhGELPs expression levels under treatments of plant hormone. Cotton leaf materials were treated by the plant hormones IAA, GA, ABA, JA, and SA for 0, 3, 6, and 9 h, which were collected for RNA extraction and cDNA synthesis that were then used as templates. GhUBQ7 (DQ116441.1) was used as internal reference for normalization. Three independent experiments were performed. “Ele” denotes the statistics number of corresponding cis-elements that existed in the promoters of GhGELPs. The heat-maps were generated by TBtools