玉米FAD基因家族的全基因组鉴定与组织表达差异分析

Genome-wide Identification and Differential Tissue Expression Analysis of the FAD Gene Family in Zea mays L.

摘要:

为系统解析玉米FAD基因家族特征，以水稻20个FAD蛋白序列为查询探针，通过BLASTP比对结合隐马尔可夫模型(HMM)方法，从玉米基因组中筛选鉴定出24个ZmFAD基因家族成员。通过多维度生物信息学分析发现，24个ZmFAD基因不均匀分布于9条染色体上，其中，1、2、10号染色体上分布密度最高(各含4个成员)；蛋白质理化分析显示，成员氨基酸长度介于254~464 aa，理论等电点(pI)为6.09~9.71，且多数为亲水性蛋白；系统进化分析表明，ZmFAD与水稻同源基因亲缘关系最近，同一亚家族成员具有相似的保守基序组成；基因结构呈现显著异质性，外显子数目2～10个(以ZmFAD04的10个为最多)，所有成员均含脂肪酸去饱和酶结构域，其中ZmFAD16和ZmFAD07额外携带Cyt-b5结构域；亚细胞定位预测显示，多数成员定位于叶绿体，二级结构以α-螺旋和无规卷曲为主；基因组共线性分析揭示，大片段复制事件驱动家族扩增，且ZmFAD与高粱、水稻FAD保持高度同源；启动子分析发现，激素应答(ABRE、CGTCA-motif)、逆境胁迫(MBS、LTR)及生长发育相关顺式元件；表达谱分析显示，I组的11个成员在玉米全生育期及多组织中广泛表达。

Abstract:

To systematically characterize the features of the FAD gene family in Zea mays L., 20 FAD protein sequences from Oryza sativa were adopted as query probes. A total of 24 ZmFAD family members were identified from the maize genome via BLASTP alignment combined with the Hidden Markov Model(HMM) method, followed by comprehensive multi-dimensional bioinformatic analyses. The results showed that the 24 ZmFAD genes were unevenly distributed across 9 chromosomes, with chromosomes 1, 2 and 10 harboring the highest density(4 members each). Physicochemical analysis indicated that the encoded proteins were 254-464 amino acid residues in length, with theoretical isoelectric points(pI) ranging from 6.09 to 9.71, and most proteins were predicted to be hydrophilic. Phylogenetic analysis revealed that ZmFAD genes shared the closest phylogenetic relationship with rice FAD orthologs, and members within the same subfamily had similar conserved motif compositions. Significant heterogeneity was observed in gene structures, with exon numbers varying from 2 to 10; ZmFAD04 contained the maximum number of 10 exons. All members harbored the conserved fatty acid desaturase domain, while the proteins encoded by ZmFAD16 and ZmFAD07 carried an additional Cyt-b5 domain. Subcellular localization prediction demonstrated that most ZmFAD proteins were localized in chloroplasts, and their secondary structures were mainly composed of α-helices and random coils. Genomic collinearity analysis revealed that segmental duplication events drove the expansion of the ZmFAD family, and ZmFAD genes maintained high homology with FAD genes in sorghum and rice. Promoter analysis identified abundant cis-acting elements related to hormone responses(ABRE, CGTCA-motif), stress responses(MBS, LTR), and plant growth and development. Expression profiling showed that 11 members in Group I were broadly expressed in multiple tissues throughout the whole growth period of maize. This study systematically characterizes the ZmFAD gene family in maize, and provides an important theoretical basis for further exploring its molecular regulatory mechanisms in stress resistance.