Genome-Wide Identification and Functional Analysis of C2H2 Zinc Finger Transcription Factor Genes in the Intertidal Macroalga Pyropia haitanensis

The possible regulatory effects of C2H2 zinc finger proteins, which are important transcription factors, on intertidal seaweed responses to abiotic stress are unclear. This study was conducted to comprehensively analyze the <i>C2H2</i> gene family of a representative intertidal seaweed species (<i>Pyropia haitanensis</i>) and clarify its genomic characteristics and biological functions. A total of 107 <i>PhC2H2</i> zinc finger protein-encoding genes distributed on five <i>P. haitanensis</i> chromosomes were identified and divided into three subgroups. The expression levels of 85, 61, 58, 45, and 41 <i>PhC2H2</i> genes responded in the maturation of filaments, high-temperature, salt, low-irradiance, and dehydration stress, respectively. The <i>PhC2H2</i> gene family was conserved during <i>Porphyra</i> evolution, with no indications of large-scale genome-wide replication events. On average, <i>PhC2H2</i> genes had more transposable element (TE) insertions than <i>Pyropia yezoensis</i> and <i>Porphyra umbilicalis</i><i>C2H2</i> genes, suggesting that TE insertions may have been the main driver of <i>PhC2H2</i> gene family expansion. A key gene (<i>PhC2H2.94</i>) screened following a quantitative trait locus analysis was significantly responsive to high-temperature stress and was associated with photosynthesis, peroxisomes, the ubiquitin proteasome pathway, and the endoplasmic reticulum-related protein processing pathway, which contribute to the stress tolerance of <i>P. haitanensis</i>. Additionally, <i>PhC2H2.94</i> transgenic <i>Chlamydomonas reinhardtii</i> exhibited increased tolerance to heat stress. This study provides new insights and genetic resources for characterizing the molecular mechanism underlying intertidal seaweed responses to abiotic stresses and breeding stress-resistant macroalgae.