Genome-wide identification, evolutionary estimation and functional characterization of two cotton CKI gene types

Abstract

Background: Casein kinase I (CKI) is a kind of serine/threonine protein kinase highly conserved in plants and animals. Although molecular function of individual member of CKI family has been investigated in Arabidopsis, little is known about their evolution and functions in Gossypium.

Results: In this study, five cotton species were applied to study CKI gene family in cotton, twenty-two species were applied to trace the origin and divergence of CKI genes. Four important insights were gained: (i) the cotton CKI genes were classified into two types based on their structural characteristics; (ii) two types of CKI genes expanded with tetraploid event in cotton; (iii) two types of CKI genes likely diverged about 1.5 billion years ago when red and green algae diverged; (iv) two types of cotton CKI genes which highly expressed in leaves showed stronger response to photoperiod (circadian clock) and light signal, and most two types of CKI genes highly expressed in anther showed identical heat inducible expression during anther development in tetraploid cotton (Gossypium hirsutum).

Conclusion: This study provides genome-wide insights into the evolutionary history of cotton CKI genes and lays a foundation for further investigation of the functional differentiation of two types of CKI genes in specific developmental processes and environmental stress conditions.

Keywords: Casein kinase I; Cotton; Evolutionary history; Gene expression.

Fig. 1

Phylogenetic tree of the Casein Kinase I (CKI) in Gossypium and chromosomal distribution and gene duplication in Gossypium hirsutum. a The phylogenetic tree was constructed using 202 cotton CKI protein sequences from G.hirsutum (58), G.arboreum (30), G.raimondii (31), G.barbadense (57), G.herbaceum (28) with the maximum likelihood (ML) method in MEGA 6. The five different symbols represent the five cotton species: red for G.hirsutum, blue for G.barbadense, green for G.arboretum, purple for G.herbaceum, yellow for G.raimondii. The Gene ID of CKI genes from G. hirsutum, G. arboreum, G. raimondii, G.barbadense, G.herbaceum were listed in Table S1. b The scale is in megabases (Mb), the value on each chromosome represents chromosome length, and the paralogous GhCKIs were connected with a blue line

Fig. 2

Phylogenetic tree, protein motif and Exon/Intron organization of the Casein Kinase I (CKI) in G. hirsutum.a Phylogenetic tree of the Casein Kinase I (CKI) in G.hirsutum and b Exon/Intron organization of the CKI genes in G.hirsutum. Red boxes represent exons and black lines indicate introns. c Motif composition of GhCKI proteins. Conserved motifs in the GhCKI proteins are indicated by colored boxes

Fig. 3

Collinear analysis among G. hirsutum, G. arboreum, G. raimondii and the distribution of Ka/Ks values of two types CKI genes. a Collinear analysis of chromosome fragments containing 20 adjacent genes upstream and downstream of two types of CKI genes among G. hirsutum, G. arboreum, G. raimondii.b-c A case of collinearity for a type I paralogous gene pairs and type II paralogous gene pairs respectively. Red for type I, green for type II. d The Ka/Ks values of homologous gene pair between diploid (G. arboretum and G. raimondii) and tetraploid (G. hirsutum) of two types CKI genes. G. hirsutum genes as reference. The above was the result of type I CKI, the below was the result of type II CKI

Fig. 4

Collinear analysis among grape, cacao, G. raimondii and phylogenetic tree and number of the Casein Kinase I (CKI) in eighteen species. a Collinear analysis of chromosome fragments containing 20 adjacent genes upstream and downstream of two types CKI genes among grape, cacao, G.raimondii.b Phylogenetic tree of the Casein Kinase I (CKI) in eighteen species. Blue dot represent algae of Protista, Black triangle represent plants of Plantae. c The number of two types CKI genes in eighteen species

Fig. 5

Expression profiles of two types GhCKI genes under different diurnal conditions. a and b Expression profiles of the type I and type II CKI genes in G. hirsutum under different diurnal conditions, respectively. Diurnal changes in transcript levels of 36 G. hirsutum CKI genes under short-day (SD) and long-day (LD) conditions. SD, short day (8 h light); LD, long day (16 h light); Black boxes denote dark, while the solid red boxes show light. Values are means ± standard deviations. Asterisks indicate statistically significant differences (*P < 0.05, **P < 0.01) by Student’s t-test. The GhUB7 (Gh_A11G096) was used as the reference gene to normalize the total amount of cDNA in each reaction

Fig. 6

Expression profiles of two types GhCKI genes under dark and light conditions. a and b Expression profiles of the type I GhCKI genes (26 genes) and type II GhCKI genes (18 genes) in upland cotton cotyledons under dark and light conditions, respectively. Error bars indicate ± standard deviations of triplicate experiments. Asterisks indicate statistically significant differences (*P < 0.05, **P < 0.01) by Student’s t-test. The GhUB7 (Gh_A11G096) gene was used as the reference gene to normalize the total amount of cDNA in each reaction

Fig. 7

Expression profiles of two types G. hirsutum CKI genes in anthers at different development stages under NT and HT conditions. a-b Expression patterns of G. hirsutum CKI genes in 84,021 and H05 at different anther developmental stages under NT and HT conditions from RNAseq (a) and Quantitative RT-PCR experiment (b). 8 N and 8H refer to 84,021 (the HT-tolerant line) under NT and HT conditions, respectively; HN and HH refer to H05 (the HT-sensitive line) under NT and HT conditions, respectively; TS: tetrads stage; TDS: tapetal degradation stage; ADS, anther dehiscence stage; FPKM: fragments per kb of transcript per million fragments mapped. The RNAseq data of the expression profiles was cited from Min et al. [33]. Error bars indicate ± standard deviations of triplicate experiments. Asterisks indicate statistically significant differences (*P < 0.05, **P < 0.01) by Student’s t-test. The GhUB7 (Gh_A11G096) was used as the reference gene to normalize the total amount of cDNA in each reaction