National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
BMC Genomics. 2022 Mar 24;23(1):231. doi: 10.1186/s12864-022-08440-9.
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.
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.
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.
隐花色素（CRY）是植物和动物特有的蓝光受体，在植物生长、发育和应激耐受的生理过程中发挥着关键作用。
本研究对 12 种棉花物种的 CRY 基因家族进行了系统分析，在 5 种异源四倍体棉花（陆地棉、海岛棉、亚洲棉、草棉和达尔文棉）中分别鉴定出 18、17、17、17 和 17 个 CRY，在 7 种二倍体棉花中鉴定出 5 到 9 个 CRY。蛋白编码序列的系统发育分析表明，棉花和拟南芥的 CRY 基因可分为 7 个分支。共线性分析表明，陆地棉 Gh_A02G0384 的同源物在其他 4 种异源四倍体棉花中经历了一个进化丢失事件。顺式作用元件分析预测了 CRY 基因在陆地棉中的可能功能。RNA-seq 数据表明，Gh_D09G2225、Gh_A09G2012 和 Gh_A11G1040 在不同发育状态的纤维细胞中高表达。此外，1 个（Gh_A03G0120）、15 个和 9 个 GhCRY 基因的表达水平在 PEG、NaCl 和高温处理后下调，而在低温处理时，有 5 个 GhCRY 基因被诱导，有 5 个被抑制。这些结果表明，大多数 GhCRY 基因对非生物胁迫处理呈负调控。
我们系统地报告了陆地棉 CRY 基因的结构、结构域、分化、共线性和顺式作用元件分析。预测了 GhCRY 基因在棉花植物生命周期不同组织中的可能生物学功能以及对非生物胁迫的反应。
