摘要
zf-BED(zinc-finger BED)转录因子家族广泛参与调控植物生长发育以及逆境响应,但紫菜(Porphyra sensu lato)中zf-BED的组成和进化模式尚未明确。基于条斑紫菜(Pyropia yezoensis)、坛紫菜(Pyropia haitanensis)和脐形紫菜(Porphyra umbilicalis)基因组数据,通过生物信息学方法鉴定到11个条斑紫菜、2个坛紫菜和1个脐形紫菜zf-BED基因。根据其结构域特征分为4个类别:陆地植物中常见的I类(zf-BED_DUFdomain_Dimer_Tnp_hAT)、II类(zf-BED)、IV类(zf-BED_DUFdomain)以及一个包含碳氮水解酶结构域,不同于陆地植物的新类别(zf-BED_C-N_Hydrolase)。基因同源性分析和系统发育分析的结果表明,条斑紫菜zf-BED基因与坛紫菜存在2个直系同源基因,与脐形紫菜存在1个直系同源基因,zf-BED基因在条斑紫菜中发生了特异性扩增。此外,紫菜与陆地植物zf-BED基因聚在一起,形成两个分支,推断其具有古老的起源。基于条斑紫菜和坛紫菜的营养藻丝、壳孢子囊枝及30日龄叶状体的转录组数据,发现zf-BED基因在不同发育阶段的表达模式存在差异。该研究系统分析了紫菜zf-BED的基因构成、系统发育关系和表达特征,揭示了该基因家族在紫菜中的进化特征及功能分化现象,为阐明紫菜zf-BED基因的生物学功能提供一定的理论依据。
The zinc-finger BED(zf-BED)transcription factor family is extensively involved in the regulation of plant growth,development,and stress responses;however,the genomic composition and evolutionary patterns of zf-BED in Porphyra sensu lato remain uncharacterized.Based on the genomic data of Pyropia yezoensis,Pyropia haitanensis,and Porphyra umbilicalis,11 zf-BED genes in Py.yezoensis,2 in Py.haitanensis,and 1 in Po.umbilicalis were identified through bioinformatics methods.These genes were classified into four categories based on domain architecture:Class I(zf-BED_DUFdomain_Dimer_Tnp_hAT),Class II(zf-BED),and Class IV(zf-BED_DUFdomain),which are commonly found in land plants,as well as a novel category,zf-BED_C-N_Hydrolase,containing a carbon-nitrogen hydrolase domain distinct from those in land plants.Results from gene homology analysis and phylogenetic analysis indicated the presence of two orthologs between Py.yezoensis and Py.haitanensis zf-BED genes,and one ortholog with Po.umbilicalis,with species-specific expansion observed in Py.yezoensis.Additionally,zf-BED genes from Porphyra sensu lato and land plants clustered together,forming two branches,suggesting an ancient origin.Based on transcriptome data from vegetative filaments,conchosporangia,and 30-day-old thalli,differences in expression patterns of zf-BED genes across distinct developmental stages were observed.A systematic analysis of the genomic architecture,phylogenetic relationships,and expression profiles of zf-BED in Porphyra sensu lato elucidated their evolutionary characteristics and functional diversification.These findings provide a theoretical foundation for elucidating the biological functions of zf-BED genes in Porphyra sensu lato.
作者
王若寒
高大海
WANG Ruo-Han;GAO Da-Hai(Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources,Ministry of Education,Shanghai Ocean University,Shanghai 201306,China;Shanghai Engineering Research Center of Aquaculture,Shanghai Ocean University,Shanghai 201306,China)
出处
《海洋与湖沼》
北大核心
2025年第5期1205-1214,共10页
Oceanologia Et Limnologia Sinica
基金
国家重点研发计划“海洋农业与淡水渔业科技创新”专项“海洋农业与淡水渔业科技创新”项目,2023YFD2400105号。
关键词
条斑紫菜
坛紫菜
脐形紫菜
zf-BED基因家族
生物信息学分析
表达分析
Pyropia yezoensis
Pyropia haitanensis
Porphyra umbilicalis
zf-BED gene family
bioinformatics analysis
expression analysis
