Background Golden2-Like (GLK) transcription factors are a type of transcriptional regulator in plants. They play a pivotal role in the plant physiological activity process and abiotic stress response. Methods In this study, the potential function of GLK family genes in Gossypium hirsutum was studied based on genomic identification, phylogenetic analysis, chromosome mapping and cis-regulatory elements prediction. Gene expression of nine key genes were analyzed by qRT-PCR experiments. Results Herein, we identified a total of 146 GhGLK genes in Gossypium hirsutum, which were unevenly distributed on each of the chromosomes. There were significant differences in the number and location of genes between the At sub-genome and the Dt sub-genome. According to the phylogenetic analysis, they were divided into ten subgroups, each of which had very similar number and structure of exons and introns. Some cis-regulatory elements were identified through promoter analysis, including five types of elements related to abiotic stress response, five types of elements related to phytohormone and five types of elements involved in growth and development. Based on public transcriptome data analysis, we identified nine key GhGLKs involved in salt, cold, and drought stress. The qRT-PCR results showed that these genes had different expression patterns under these stress conditions, suggesting that GhGLK genes played an important role in abiotic stress response. This study laid a theoretical foundation for the screening and functional verification of genes related to stress resistance of GLK gene family in cotton.

Telomeres are structures enriched in repetitive sequences at the end of chromosomes. In this study, using the telomere primer AA(CCCTAAA)3CCC for the single primer PCR, two DNA sequences were obtained from Gossypium hirsutum (Linnaeus, 1753) accession (acc.) TM-1. Sequence analysis showed that the two obtained sequences were all rich in A/T base, which was consistent with the characteristic of the telomere-associated sequence (TAS). They were designated as GhTAS1 and GhTAS2 respectively. GhTAS1 is 489 bp long, with 57.6% of A/T, and GhTAS2 is 539 bp long, with 63.9% of A/T. Fluorescence in situ hybridization results showed that both of the cloned TASs were located at the ends of the partial chromosomes of G. hirsutum, with the strong signals, which further confirmed that GhTAS1 and GhTAS2 were telomere-associated sequences including highly tandemly repetitive sequences. Results of blast against the assembled genome of G. hirsutum showed that GhTAS sequences may be missed on some assembled chromosomes. The results provide important evidence for the evaluation of the integrity of assembled chromosome end sequences, and will also contribute to the further perfection of the draft genomes of cotton.