坛紫菜HSP20基因家族成员的全基因组鉴定及生物信息学分析

【目的】鉴定坛紫菜（Pyropia haitanensis） HSP20基因家族成员（PhHSP20s），并进行生物信息学及表达谱分析，为揭示PhHSP20s基因在坛紫菜生长发育和非生物胁迫下的调控机理提供理论依据。【方法】对坛紫菜基因组序列进行基因结构预测，利用隐马尔可夫模型在坛紫菜蛋白序列中搜索含有ACD结构域且分子量为12~43 kD的HSP20家族蛋白，并对其理化性质、系统进化及编码基因启动子顺式作用元件和表达特性进行分析。【结果】从坛紫菜全基因组鉴定出8个PhHSP20s基因，其不均匀地分布在5条Scaffolds上，均只含有1个外显子，无内含子，开放阅读框（ORF）长度为402~930 bp，其编码蛋白的氨基酸残基数量为133~309个，分子量为13.7~31.9 kD，理论等电点（pI）为5.50~10.49，多数蛋白呈酸性。系统发育进化树分析结果显示，陆生植物（拟南芥）、红藻（脐形紫菜和坛紫菜）和细菌（大肠杆菌） HSP20分别聚类为独立的一支，但绿藻（莱茵衣藻） HSP20聚类为2个分支，分别与陆生植物和红藻HSP20聚类在一起；红藻（脐形紫菜和坛紫菜） HSP20蛋白高度相似，亲缘关系近，可分为2个小分支，均与陆生植物HSP20的亲缘关系较远，不属于陆生植物中已报道过的任何HSP20亚族。PhHSP20s基因启动子上除了含有保守的通用元件外，还含有非生物胁迫响应元件。在PhHSP20s基因中，除PhHSP32基因几乎不在任何条件下表达外，其余PhHSP20s基因至少在1种条件下高表达，且部分PhHSP20s基因表现出相似的表达模式；部分PhHSP20s基因在不同生长阶段、光质培养条件、失水胁迫和盐胁迫下具有表达特异性，即在生殖细胞发育阶段和单性生殖孢子发育期高表达，在低盐胁迫下高表达。【结论】坛紫菜HSP20家族基因在基因数目、基因结构及系统进化上明显不同于陆生植物HSP20家族基因，推测HSP20基因复制事件在红藻和陆生植物分化之后独立发生，且在坛紫菜生长发育和非生物胁迫应答中发挥作用。

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.