Comprehensive identification and expression analysis of CRY gene family in Gossypium

Abstract

Background: The cryptochromes (CRY) are specific blue light receptors of plants and animals, which play crucial roles in physiological processes of plant growth, development, and stress tolerance.

Results: In the present work, a systematic analysis of the CRY gene family was performed on twelve cotton species, resulting in 18, 17, 17, 17, and 17 CRYs identified in five alloteraploid cottons (Gossypium hirsutum, G. barbadense, G. tomentosum, G. mustelinum and G. darwinii), respectively, and five to nine CRY genes in the seven diploid species. Phylogenetic analysis of protein-coding sequences revealed that CRY genes from cottons and Arabidopsis thaliana could be classified into seven clades. Synteny analysis suggested that the homoeolog of G. hirsutum Gh_A02G0384 has undergone an evolutionary loss event in the other four allotetraploid cotton species. Cis-element analysis predicated the possible functions of CRY genes in G. hirsutum. RNA-seq data revealed that Gh_D09G2225, Gh_A09G2012 and Gh_A11G1040 had high expressions in fiber cells of different developmental states. In addition, the expression levels of one (Gh_A03G0120), 15 and nine GhCRY genes were down-regulated following the PEG, NaCl and high-temperature treatments, respectively. For the low-temperature treatment, five GhCRY genes were induced, and five were repressed. These results indicated that most GhCRY genes negatively regulate the abiotic stress treatments.

Conclusion: We report the structures, domains, divergence, synteny, and cis-elements analyses systematically of G. hirsutum CRY genes. Possible biological functions of GhCRY genes in differential tissues as well as in response to abiotic stress during the cotton plant life cycle were predicted.

Keywords: Abiotic stress; Cotton; Cryptochrome; Organ-specific expression; Phylogenetics.

Fig. 1

Dispersed distribution of CRY genes in G. hirsutum (AD₁) chromosomes. 18 GhCRY genes are scattered over 14 of the 26 G. hirsutum chromosomes

Fig. 2

Phylogenetic tree and gene structure of CRY genes in G. hirsutum. Exons and introns are represented by yellow boxes and black lines, respectively

Fig. 3

Phylogenetic analysis of CRY genes from five Gossypium species and Arabidopsis thaliana. The phylogenetic tree was established with entire protein-coding sequences with NJ methods. The numbers on the branches indicate bootstrap support values from 1000 replications

Fig. 4

Distribution of Ka (A), Ks (B) and Ka/Ks (C) values of CRY genes between the A and D subgenomes versus their corresponding diploid progenitor homoeologs

Fig. 5

Dynamic evolution of the number of CRY family genes in 12 Gossypium species, Gossypium kirkii and Arabidopsis thaliana

Fig. 6

Syntenic analysis of the Gossypium CRY gene family. A G. arboreum vs G. raimondii; B G. hirsutum; C G. barbadense; D G. tomentosum; E G. mustelinum; F G. darwinii. The scale on the circle is in Megabases. The CRY gene IDs of each Gossypium species were on the chromosomes; the numbers of each chromosome of Gossypium species are shown inside the circle of each bar. The syntenic relationships of CRY gene are connected by red lines

Fig. 7

Expression patterns of GhCRY genes in different cotton tissues and fiber cells of different stages based on the RPKM values of RNA-seq data. A Expression profiles of GhCRY genes in eight cotton tissues. B Expression patterns of GhCRY genes in seed germination, cotyledons and roots after germination. C Expression patterns of GhCRY genes in ovules of different stages. D Expression patterns of GhCRY genes in fibers of different stages

Fig. 8

Expression patterns of GhCRY genes in response to different stresses from RNA-seq data. The RNA-seq data were downloaded from Zhang et al., 2015 and re-analyzed the RPKM values of five time points (0, 1, 3, 6 and 12 h) after stresses treatments. A Drought stress; B Salt stress; C Hot stress; D Cold stress