Genome-wide identification and bioinformatics analysis of HSP20 gene family in Pyropia haitanensis

【Objective】This paper aimed to identify HSP20 family members of Pyropia haitanensis(PhHSP20 s), analyze their bioinformatic characteristics and expression profiles, and provide a theoretical basis for future exploring the function of PhHSP20 s gene in development and biotic stress of P. haitanensis.【Method】Gene structures of P. haitanensis genomic sequences were predicted. The HSP20 proteins containing ACD domain were scanned in the protein amino acid sequences of P. haitanensis and molecular weight was 12-43 kD with a hidden Markov model by HMMER. Their physicochemical properties, gene structures, phylogeny, cis-acting elements in promoter, and expression profiles were analyzed.【Result】A total of 8 PhHSP20 s genes were identified from the genome of P. haitanensis, which were unevenly distributed on 5 scaffolds. All 8 genes were composed of one exon and had no introns. The open reading frames(ORF) of PhHSP20 s were 402-930 bp, encoding 133-309 amino acid residues, molecular weight was 13.7-31.9 kD with theoretical isoelectric points of 5.50-10.49. Most proteins were acidic. The phylogenetic tree analysis showed that the land plant(Arabidopsis thaliana), red algae(Porphyra umbilicalis and P. haitanensis) and bacteria(Escherichia coli) HSP20 s were clustered as an independent branch, respectively, but the green algae(Chlamydomonas reinhardtii) HSP20 s were clustered as two branches, which were clustered with the land plant and red algae HSP20 s, respectively. The HSP20 proteins of red algae(P. umbilicalis and P. haitanensis) were highly similar and closely related, and could be divided into two small branches.The two branchesshowed a relatively distant relationship with terrestrial plants HSP20 s, and were distinct from the HSP20 subgroups previously reported in terrestrial plants. The promoters of PhHSP20 genes contained both general cis-elements and abiotic stress response elements. Except for PhHSP32 gene, other PhHSP20 s genes were highly expressed under at least one condition. Part of PhHSP20 s genes showed similar expression patterns, and some of them had specific expression in different growth stages, light culture conditions, water loss stress and salt stress, that was, some PhHSP20 s were highly expressed during reproductive cell development stage, parthenospore development stage, and under low salt stress.【Conclusion】P. haitanensis HSP20 family genes are distinct from terrestrial plants HSP20 family genes in gene number, gene structure and phylogeny, indicating the HSP20 gene duplication events take place independently in the branches of red alga and terrestrial plants, and PhHSP20 s are involved in both developmental regulation and abiotic stress response.